diff --git a/ALLLoadBalancer_8cpp.html b/ALLLoadBalancer_8cpp.html index d3daf9bb84..78681ba244 100644 --- a/ALLLoadBalancer_8cpp.html +++ b/ALLLoadBalancer_8cpp.html @@ -77,7 +77,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ALLLoadBalancer_8h.html b/ALLLoadBalancer_8h.html index 84ab9b23ae..487c3e24b3 100644 --- a/ALLLoadBalancer_8h.html +++ b/ALLLoadBalancer_8h.html @@ -88,7 +88,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ALLLoadBalancer_8h_source.html b/ALLLoadBalancer_8h_source.html index 80e9075bff..80638d3417 100644 --- a/ALLLoadBalancer_8h_source.html +++ b/ALLLoadBalancer_8h_source.html @@ -107,7 +107,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ASCIIReader_8h_source.html b/ASCIIReader_8h_source.html index ed4e10be26..577102a145 100644 --- a/ASCIIReader_8h_source.html +++ b/ASCIIReader_8h_source.html @@ -104,11 +104,11 @@
85
86#endif // ASCIIREADER_H_
ASCIIReader
The ASCIIReader reads in phasespace information using ls1-MarDyn's (old) ASCII input file format.
Definition: ASCIIReader.h:10
-
ASCIIReader::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
reads in the data of all molecules
Definition: ASCIIReader.cpp:256
-
ASCIIReader::setPhaseSpaceFile
void setPhaseSpaceFile(std::string filename)
Set the phase space file to be read.
Definition: ASCIIReader.cpp:29
-
ASCIIReader::setPhaseSpaceHeaderFile
void setPhaseSpaceHeaderFile(std::string filename)
For this class, header and data are in the same file, so there is no separate header file.
Definition: ASCIIReader.cpp:33
-
ASCIIReader::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *domain, double timestep)
reads in header of the input file (including component description)
Definition: ASCIIReader.cpp:50
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
ASCIIReader::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
reads in the data of all molecules
Definition: ASCIIReader.cpp:254
+
ASCIIReader::setPhaseSpaceFile
void setPhaseSpaceFile(std::string filename)
Set the phase space file to be read.
Definition: ASCIIReader.cpp:27
+
ASCIIReader::setPhaseSpaceHeaderFile
void setPhaseSpaceHeaderFile(std::string filename)
For this class, header and data are in the same file, so there is no separate header file.
Definition: ASCIIReader.cpp:31
+
ASCIIReader::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *domain, double timestep)
reads in header of the input file (including component description)
Definition: ASCIIReader.cpp:48
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -117,7 +117,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Accumulator_8h_source.html b/Accumulator_8h_source.html index e7145c24c7..d0912d2b8c 100644 --- a/Accumulator_8h_source.html +++ b/Accumulator_8h_source.html @@ -181,7 +181,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AdaptivePseudoParticleContainer_8h_source.html b/AdaptivePseudoParticleContainer_8h_source.html index 98ab5fefe0..eab92f30c1 100644 --- a/AdaptivePseudoParticleContainer_8h_source.html +++ b/AdaptivePseudoParticleContainer_8h_source.html @@ -170,7 +170,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Adios2Reader_8h_source.html b/Adios2Reader_8h_source.html index 285f9600ad..fc67a3513a 100644 --- a/Adios2Reader_8h_source.html +++ b/Adios2Reader_8h_source.html @@ -204,7 +204,7 @@
157 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
158 doTheRead(var.first, rx, buffer, offset);
159 } else {
-
160 global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
+
160 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
161 << std::endl;
162 }
163 }
@@ -212,7 +212,7 @@
165 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
166 doTheRead(var.first, ry, buffer, offset);
167 } else {
-
168 global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
+
168 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
169 << std::endl;
170 }
171 }
@@ -220,7 +220,7 @@
173 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
174 doTheRead(var.first, rz, buffer, offset);
175 } else {
-
176 global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
+
176 Log::global_log->error() << "[Adios2Reader] Positions should be doubles or floats (for now)."
177 << std::endl;
178 }
179 }
@@ -228,7 +228,7 @@
181 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
182 doTheRead(var.first, vx, buffer, offset);
183 } else {
-
184 global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
+
184 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
185 << std::endl;
186 }
187 }
@@ -236,7 +236,7 @@
189 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
190 doTheRead(var.first, vy, buffer, offset);
191 } else {
-
192 global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
+
192 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
193 << std::endl;
194 }
195 }
@@ -244,7 +244,7 @@
197 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
198 doTheRead(var.first, vz, buffer, offset);
199 } else {
-
200 global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
+
200 Log::global_log->error() << "[Adios2Reader] Velocities should be doubles or floats (for now)."
201 << std::endl;
202 }
203 }
@@ -252,7 +252,7 @@
205 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
206 doTheRead(var.first, qw, buffer, offset);
207 } else {
-
208 global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
+
208 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
209 << std::endl;
210 }
211 }
@@ -260,7 +260,7 @@
213 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
214 doTheRead(var.first, qx, buffer, offset);
215 } else {
-
216 global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
+
216 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
217 << std::endl;
218 }
219 }
@@ -268,7 +268,7 @@
221 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
222 doTheRead(var.first, qy, buffer, offset);
223 } else {
-
224 global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
+
224 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
225 << std::endl;
226 }
227 }
@@ -276,7 +276,7 @@
229 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
230 doTheRead(var.first, qz, buffer, offset);
231 } else {
-
232 global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
+
232 Log::global_log->error() << "[Adios2Reader] Quaternions should be doubles or floats (for now)."
233 << std::endl;
234 }
235 }
@@ -284,7 +284,7 @@
237 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
238 doTheRead(var.first, Lx, buffer, offset);
239 } else {
-
240 global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
+
240 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
241 << std::endl;
242 }
243 }
@@ -292,7 +292,7 @@
245 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
246 doTheRead(var.first, Ly, buffer, offset);
247 } else {
-
248 global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
+
248 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
249 << std::endl;
250 }
251 }
@@ -300,7 +300,7 @@
253 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
254 doTheRead(var.first, Lz, buffer, offset);
255 } else {
-
256 global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
+
256 Log::global_log->error() << "[Adios2Reader] Angular momentum should be doubles or floats (for now)."
257 << std::endl;
258 }
259 }
@@ -308,21 +308,21 @@
261 if (var.second["Type"] == "uint64_t") {
262 doTheRead(var.first, comp_id, buffer, offset);
263 } else {
-
264 global_log->error() << "[Adios2Reader] Component ids should be uint64_t (for now)." << std::endl;
+
264 Log::global_log->error() << "[Adios2Reader] Component ids should be uint64_t (for now)." << std::endl;
265 }
266 }
267 if (var.first == "molecule_id") {
268 if (var.second["Type"] == "uint64_t") {
269 doTheRead(var.first, mol_id, buffer, offset);
270 } else {
-
271 global_log->error() << "[Adios2Reader] Molecule ids should be uint64_t (for now)." << std::endl;
+
271 Log::global_log->error() << "[Adios2Reader] Molecule ids should be uint64_t (for now)." << std::endl;
272 }
273 }
274 if (var.first == "simulationtime") {
275 if (var.second["Type"] == "double" || var.second["Type"] == "float") {
276 doTheRead(var.first, _simtime);
277 } else {
-
278 global_log->error() << "[Adios2Reader] Simulation time should be double or float (for now)."
+
278 Log::global_log->error() << "[Adios2Reader] Simulation time should be double or float (for now)."
279 << std::endl;
280 }
281 }
@@ -331,7 +331,7 @@
284};
285#endif // ENABLE_ADIOS2
286#endif /* ADIOS2_READER_H_*/
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
InputBase
interface for any kind of input class
Definition: InputBase.h:18
@@ -345,7 +345,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Adios2Writer_8h_source.html b/Adios2Writer_8h_source.html index 62dbd900e9..126e5796fb 100644 --- a/Adios2Writer_8h_source.html +++ b/Adios2Writer_8h_source.html @@ -162,7 +162,7 @@
106};
107#endif
108#endif /* ADIOS2_WRITER_H_*/
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -179,7 +179,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AlignedAllocator_8h_source.html b/AlignedAllocator_8h_source.html index a8818e2914..fae7d7c5d5 100644 --- a/AlignedAllocator_8h_source.html +++ b/AlignedAllocator_8h_source.html @@ -174,7 +174,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AlignedArrayTriplet_8h_source.html b/AlignedArrayTriplet_8h_source.html index 2926755069..3e33d1eef1 100644 --- a/AlignedArrayTriplet_8h_source.html +++ b/AlignedArrayTriplet_8h_source.html @@ -255,7 +255,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AlignedArray_8h.html b/AlignedArray_8h.html index 5a770c1bef..9792e6f6f7 100644 --- a/AlignedArray_8h.html +++ b/AlignedArray_8h.html @@ -102,7 +102,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AlignedArray_8h_source.html b/AlignedArray_8h_source.html index 91b90babb7..29970e2b3e 100644 --- a/AlignedArray_8h_source.html +++ b/AlignedArray_8h_source.html @@ -284,7 +284,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Array2D_8h_source.html b/Array2D_8h_source.html index f39d16159b..c4ded7236e 100644 --- a/Array2D_8h_source.html +++ b/Array2D_8h_source.html @@ -154,7 +154,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasClass_8cpp.html b/AutoPasClass_8cpp.html index 4973820734..5754b92bb4 100644 --- a/AutoPasClass_8cpp.html +++ b/AutoPasClass_8cpp.html @@ -78,7 +78,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasContainer_8cpp.html b/AutoPasContainer_8cpp.html index 7fb46914a8..6b98de6a20 100644 --- a/AutoPasContainer_8cpp.html +++ b/AutoPasContainer_8cpp.html @@ -149,7 +149,7 @@

-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasContainer_8h.html b/AutoPasContainer_8h.html index 238c467116..98408364ac 100644 --- a/AutoPasContainer_8h.html +++ b/AutoPasContainer_8h.html @@ -89,7 +89,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasContainer_8h_source.html b/AutoPasContainer_8h_source.html index b25aa28a43..1668537fab 100644 --- a/AutoPasContainer_8h_source.html +++ b/AutoPasContainer_8h_source.html @@ -237,11 +237,11 @@
RegionParticleIterator
Definition: RegionParticleIterator.h:67
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-
pos
Definition: FakedOptFFT.h:23
+
pos
Definition: FakedOptFFT.h:21
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/AutoPasSimpleMolecule_8h_source.html b/AutoPasSimpleMolecule_8h_source.html index e881cc94e8..663837194b 100644 --- a/AutoPasSimpleMolecule_8h_source.html +++ b/AutoPasSimpleMolecule_8h_source.html @@ -400,7 +400,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Basis_8h_source.html b/Basis_8h_source.html index f15139f146..dc4206f64c 100644 --- a/Basis_8h_source.html +++ b/Basis_8h_source.html @@ -107,17 +107,17 @@
59
60#endif /* BASIS_H */
Basis
Definition: Basis.h:20
-
Basis::getMolecule
Molecule getMolecule(int i)
Definition: Basis.cpp:49
-
Basis::addMolecule
void addMolecule(const Molecule &molecule)
Definition: Basis.cpp:45
-
Basis::numMolecules
size_t numMolecules()
Definition: Basis.cpp:54
-
Basis::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Basis and all its included objects.
Definition: Basis.cpp:21
+
Basis::getMolecule
Molecule getMolecule(int i)
Definition: Basis.cpp:47
+
Basis::addMolecule
void addMolecule(const Molecule &molecule)
Definition: Basis.cpp:43
+
Basis::numMolecules
size_t numMolecules()
Definition: Basis.cpp:52
+
Basis::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Basis and all its included objects.
Definition: Basis.cpp:19
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xmlfileUnits.h
XML input file with unit handling/conversion support.
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/BinaryReader_8h_source.html b/BinaryReader_8h_source.html index a8c6cd4f55..03e74af3d5 100644 --- a/BinaryReader_8h_source.html +++ b/BinaryReader_8h_source.html @@ -117,11 +117,11 @@
102
103#endif /* BINARYREADER_H_ */
BinaryReader
Definition: BinaryReader.h:17
-
BinaryReader::setPhaseSpaceHeaderFile
void setPhaseSpaceHeaderFile(std::string filename)
For this class, header and data are in the same file, so there is no separate header file.
Definition: BinaryReader.cpp:72
-
BinaryReader::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
reads in the data of all molecules
Definition: BinaryReader.cpp:123
-
BinaryReader::setPhaseSpaceFile
void setPhaseSpaceFile(std::string filename)
gets a filename and opens an ifstream associated with the given file
Definition: BinaryReader.cpp:68
-
BinaryReader::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *domain, double timestep)
reads in header of the input file (including component description)
Definition: BinaryReader.cpp:76
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
BinaryReader::setPhaseSpaceHeaderFile
void setPhaseSpaceHeaderFile(std::string filename)
For this class, header and data are in the same file, so there is no separate header file.
Definition: BinaryReader.cpp:70
+
BinaryReader::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
reads in the data of all molecules
Definition: BinaryReader.cpp:121
+
BinaryReader::setPhaseSpaceFile
void setPhaseSpaceFile(std::string filename)
gets a filename and opens an ifstream associated with the given file
Definition: BinaryReader.cpp:66
+
BinaryReader::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *domain, double timestep)
reads in header of the input file (including component description)
Definition: BinaryReader.cpp:74
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -131,7 +131,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/BoxDomain_8h_source.html b/BoxDomain_8h_source.html index 3ecc2b428a..a81549d6d4 100644 --- a/BoxDomain_8h_source.html +++ b/BoxDomain_8h_source.html @@ -93,14 +93,14 @@
33
34#endif /* BOX_DOMAIN_H_ */
BoxDomain
Definition: BoxDomain.h:8
-
BoxDomain::V
virtual double V()
Definition: BoxDomain.cpp:22
-
BoxDomain::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for BoxDomain and all its included objects.
Definition: BoxDomain.cpp:14
+
BoxDomain::V
virtual double V()
Definition: BoxDomain.cpp:21
+
BoxDomain::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for BoxDomain and all its included objects.
Definition: BoxDomain.cpp:13
DomainBase
Definition: DomainBase.h:7
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/C04CellPairTraversal_8h_source.html b/C04CellPairTraversal_8h_source.html index 1e4b3269dd..3f363b1fd0 100644 --- a/C04CellPairTraversal_8h_source.html +++ b/C04CellPairTraversal_8h_source.html @@ -322,7 +322,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/C08BasedTraversals_8h_source.html b/C08BasedTraversals_8h_source.html index 5646b3c2bc..28b9601750 100644 --- a/C08BasedTraversals_8h_source.html +++ b/C08BasedTraversals_8h_source.html @@ -137,7 +137,7 @@
65
66 const int num_pairs = _cellPairOffsets8Pack.size();
67 for(int j = 0; j < num_pairs; ++j) {
-
68 pair<long, long> current_pair = _cellPairOffsets8Pack[j];
+
68 std::pair<long, long> current_pair = _cellPairOffsets8Pack[j];
69
70 unsigned offset1 = current_pair.first;
71 unsigned cellIndex1 = baseIndex + offset1;
@@ -191,21 +191,21 @@
119
120 int i = 0;
121 // if incrementing along X, the following order will be more cache-efficient:
-
122 _cellPairOffsets8Pack[i++] = make_pair(o, o );
-
123 _cellPairOffsets8Pack[i++] = make_pair(o, y );
-
124 _cellPairOffsets8Pack[i++] = make_pair(y, z );
-
125 _cellPairOffsets8Pack[i++] = make_pair(o, z );
-
126 _cellPairOffsets8Pack[i++] = make_pair(o, yz );
+
122 _cellPairOffsets8Pack[i++] = std::make_pair(o, o );
+
123 _cellPairOffsets8Pack[i++] = std::make_pair(o, y );
+
124 _cellPairOffsets8Pack[i++] = std::make_pair(y, z );
+
125 _cellPairOffsets8Pack[i++] = std::make_pair(o, z );
+
126 _cellPairOffsets8Pack[i++] = std::make_pair(o, yz );
127
-
128 _cellPairOffsets8Pack[i++] = make_pair(x, yz );
-
129 _cellPairOffsets8Pack[i++] = make_pair(x, y );
-
130 _cellPairOffsets8Pack[i++] = make_pair(x, z );
-
131 _cellPairOffsets8Pack[i++] = make_pair(o, x );
-
132 _cellPairOffsets8Pack[i++] = make_pair(o, xy );
-
133 _cellPairOffsets8Pack[i++] = make_pair(xy, z );
-
134 _cellPairOffsets8Pack[i++] = make_pair(y, xz );
-
135 _cellPairOffsets8Pack[i++] = make_pair(o, xz );
-
136 _cellPairOffsets8Pack[i++] = make_pair(o, xyz);
+
128 _cellPairOffsets8Pack[i++] = std::make_pair(x, yz );
+
129 _cellPairOffsets8Pack[i++] = std::make_pair(x, y );
+
130 _cellPairOffsets8Pack[i++] = std::make_pair(x, z );
+
131 _cellPairOffsets8Pack[i++] = std::make_pair(o, x );
+
132 _cellPairOffsets8Pack[i++] = std::make_pair(o, xy );
+
133 _cellPairOffsets8Pack[i++] = std::make_pair(xy, z );
+
134 _cellPairOffsets8Pack[i++] = std::make_pair(y, xz );
+
135 _cellPairOffsets8Pack[i++] = std::make_pair(o, xz );
+
136 _cellPairOffsets8Pack[i++] = std::make_pair(o, xyz);
137
138 i = 0;
139 _cellOffsets8Pack[i++] = o;
@@ -233,7 +233,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/C08CellPairTraversal_8h_source.html b/C08CellPairTraversal_8h_source.html index d2b0a23a58..881fb940aa 100644 --- a/C08CellPairTraversal_8h_source.html +++ b/C08CellPairTraversal_8h_source.html @@ -119,8 +119,8 @@
47 CellProcessor& cellProcessor) {
48
49 using std::array;
-
50 const array<unsigned long, 3> strides = { 2, 2, 2 };
-
51 array<unsigned long, 3> end;
+
50 const std::array<unsigned long, 3> strides = { 2, 2, 2 };
+
51 std::array<unsigned long, 3> end;
52 for (int d = 0; d < 3; ++d) {
53 end[d] = this->_dims[d] - 1;
54 }
@@ -150,13 +150,13 @@
78void C08CellPairTraversal<CellTemplate, eighthShell>::traverseCellPairsOuter(
79 CellProcessor& cellProcessor) {
80 if(eighthShell){
-
81 global_log->error() << "eightshell + overlapping not yet supported." << std::endl;
+
81 Log::global_log->error() << "eightshell + overlapping not yet supported." << std::endl;
82 Simulation::exit(-2);
83 }
84 using std::array;
85
86 {
-
87 unsigned long minsize = min(this->_dims[0], min(this->_dims[1], this->_dims[2]));
+
87 unsigned long minsize = std::min(this->_dims[0], std::min(this->_dims[1], this->_dims[2]));
88
89 if (minsize <= 5) {
90 // iterating in the inner region didn't do anything. Iterate normally.
@@ -165,7 +165,7 @@
93 }
94 }
95
-
96 const array<unsigned long, 3> strides2 = { 2, 2, 2 };
+
96 const std::array<unsigned long, 3> strides2 = { 2, 2, 2 };
97
98 #if defined(_OPENMP)
99 #pragma omp parallel
@@ -173,26 +173,26 @@
101 {
102 for (unsigned long col = 0; col < 8; ++col) {
103 // halo & boundaries in z direction
-
104 const array< unsigned long, 3> begin = threeDimensionalMapping::oneToThreeD(col, strides2);
+
104 const std::array< unsigned long, 3> begin = threeDimensionalMapping::oneToThreeD(col, strides2);
105
106 // values, which are modified by 2 are actually modified by the respective stride, which is always 2
-
107 array<unsigned long, 3> startZ = { begin[0], begin[1], begin[2] }; // default
-
108 array<unsigned long, 3> endZ = { this->_dims[0] - 1, this->_dims[1] - 1, this->_dims[2] - 1 }; // default
-
109 array<unsigned long, 3> stridesZ = {strides2[0], strides2[1], this->_dims[2] - 3}; // mod z
+
107 std::array<unsigned long, 3> startZ = { begin[0], begin[1], begin[2] }; // default
+
108 std::array<unsigned long, 3> endZ = { this->_dims[0] - 1, this->_dims[1] - 1, this->_dims[2] - 1 }; // default
+
109 std::array<unsigned long, 3> stridesZ = {strides2[0], strides2[1], this->_dims[2] - 3}; // mod z
110 traverseCellPairsBackend(cellProcessor, startZ, endZ, stridesZ);
111
112 // halo & boundaries in y direction
113 // boundaries in z direction are excluded!
-
114 array<unsigned long, 3> startY = { begin[0], begin[1], begin[2] + 2 }; // mod z
-
115 array<unsigned long, 3> endY = { this->_dims[0] - 1, this->_dims[1] - 1, this->_dims[2] - 3 }; // mod z
-
116 array<unsigned long, 3> stridesY = {strides2[0], this->_dims[1] - 3, strides2[2]}; // mod y
+
114 std::array<unsigned long, 3> startY = { begin[0], begin[1], begin[2] + 2 }; // mod z
+
115 std::array<unsigned long, 3> endY = { this->_dims[0] - 1, this->_dims[1] - 1, this->_dims[2] - 3 }; // mod z
+
116 std::array<unsigned long, 3> stridesY = {strides2[0], this->_dims[1] - 3, strides2[2]}; // mod y
117 traverseCellPairsBackend(cellProcessor, startY, endY, stridesY);
118
119 // halo & boundaries in x direction
120 // boundaries in z and y direction are excluded!
-
121 array<unsigned long, 3> startX = { begin[0], begin[1] + 2, begin[2] + 2 }; // mod yz
-
122 array<unsigned long, 3> endX = { this->_dims[0] - 1, this->_dims[1] - 3, this->_dims[2] - 3 }; // mod yz
-
123 array<unsigned long, 3> stridesX = {this->_dims[0] - 3, strides2[1], strides2[2]}; // mod x
+
121 std::array<unsigned long, 3> startX = { begin[0], begin[1] + 2, begin[2] + 2 }; // mod yz
+
122 std::array<unsigned long, 3> endX = { this->_dims[0] - 1, this->_dims[1] - 3, this->_dims[2] - 3 }; // mod yz
+
123 std::array<unsigned long, 3> stridesX = {this->_dims[0] - 3, strides2[1], strides2[2]}; // mod x
124 traverseCellPairsBackend(cellProcessor, startX, endX, stridesX);
125
126 #if defined(_OPENMP)
@@ -221,7 +221,7 @@
149 }
150 }
151 unsigned long splitsize = maxcellsize - 5;
-
152 unsigned long minsize = min(this->_dims[0], min(this->_dims[1], this->_dims[2]));
+
152 unsigned long minsize = std::min(this->_dims[0], std::min(this->_dims[1], this->_dims[2]));
153
154 mardyn_assert(minsize >= 4); // there should be at least 4 cells in each dimension, otherwise we did something stupid!
155
@@ -229,8 +229,8 @@
157 return; // we can not iterate over any inner cells, that do not depend on boundary or halo cells
158 }
159
-
160 array<unsigned long, 3> lower;
-
161 array<unsigned long, 3> upper;
+
160 std::array<unsigned long, 3> lower;
+
161 std::array<unsigned long, 3> upper;
162 for (unsigned long i = 0; i < 3; i++) {
163 lower[i] = 2;
164 upper[i] = this->_dims[i] - 3;
@@ -243,10 +243,10 @@
171 #pragma omp parallel
172 #endif
173 {
-
174 array<unsigned long, 3> strides = {2, 2, 2};
+
174 std::array<unsigned long, 3> strides = {2, 2, 2};
175
176 for (unsigned long col = 0; col < 8; ++col) {
-
177 array<unsigned long, 3> startIndices = threeDimensionalMapping::oneToThreeD(col, strides);
+
177 std::array<unsigned long, 3> startIndices = threeDimensionalMapping::oneToThreeD(col, strides);
178 for (int i = 0; i < 3; i++) {
179 startIndices[i] = startIndices[i] + lower[i];
180 }
@@ -303,13 +303,13 @@
C08BasedTraversals
Definition: C08BasedTraversals.h:17
C08CellPairTraversal
Definition: C08CellPairTraversal.h:20
CellProcessor
Definition: CellProcessor.h:29
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
C08CellPairTraversalData
Definition: C08CellPairTraversal.h:16
CellPairTraversalData
Definition: CellPairTraversals.h:16
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/COMaligner_8h_source.html b/COMaligner_8h_source.html index 6ffe26060c..f0a09c6e40 100644 --- a/COMaligner_8h_source.html +++ b/COMaligner_8h_source.html @@ -123,7 +123,7 @@
71 ~COMaligner(){};
72
73 void init(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override {
-
74 global_log -> debug() << "COM Realignment enabled" << std::endl;
+
74 Log::global_log -> debug() << "COM Realignment enabled" << std::endl;
75
76 for(unsigned d = 0; d < 3; d++){
77 _boxLength[d] = domain->getGlobalLength(d);
@@ -160,7 +160,7 @@
COMaligner::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: COMaligner.h:93
COMaligner::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
called after Forces are applied applies the motion calculated earlier
Definition: COMaligner.cpp:185
COMaligner::readXML
void readXML(XMLfileUnits &xmlconfig) override
will be called to read configuration
Definition: COMaligner.cpp:20
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Domain::getGlobalLength
double getGlobalLength(int d) const
return the length of the domain
Definition: Domain.h:163
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -170,7 +170,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CanonicalEnsemble_8h_source.html b/CanonicalEnsemble_8h_source.html index 41f4773c07..58e5541f34 100644 --- a/CanonicalEnsemble_8h_source.html +++ b/CanonicalEnsemble_8h_source.html @@ -152,11 +152,11 @@
86#endif /* CANONICAL_ENSEMBLE_H_ */
CanonicalEnsemble
Definition: CanonicalEnsemble.h:20
CanonicalEnsemble::N
unsigned long N() override
Returns the global number of Molecules of the ensemble.
Definition: CanonicalEnsemble.h:34
-
CanonicalEnsemble::beforeThermostat
void beforeThermostat(unsigned long simstep, unsigned long initStatistics) override
Definition: CanonicalEnsemble.cpp:211
+
CanonicalEnsemble::beforeThermostat
void beforeThermostat(unsigned long simstep, unsigned long initStatistics) override
Definition: CanonicalEnsemble.cpp:208
CanonicalEnsemble::T
double T() override
Returns the global Temperature of the ensemble.
Definition: CanonicalEnsemble.h:42
CanonicalEnsemble::V
double V() override
Returns the global volume of the ensemble.
Definition: CanonicalEnsemble.h:38
CanonicalEnsemble::mu
double mu() override
Returns the global chemical potential of the ensemble.
Definition: CanonicalEnsemble.h:46
-
CanonicalEnsemble::updateGlobalVariable
void updateGlobalVariable(ParticleContainer *particleContainer, GlobalVariable variable) override
Calculate global variables.
Definition: CanonicalEnsemble.cpp:31
+
CanonicalEnsemble::updateGlobalVariable
void updateGlobalVariable(ParticleContainer *particleContainer, GlobalVariable variable) override
Calculate global variables.
Definition: CanonicalEnsemble.cpp:28
CanonicalEnsemble::E
double E() override
Returns the global energy of the ensemble.
Definition: CanonicalEnsemble.h:54
CanonicalEnsemble::p
double p() override
Returns the global presure of the ensemble.
Definition: CanonicalEnsemble.h:50
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
@@ -167,7 +167,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CavityEnsemble_8h_source.html b/CavityEnsemble_8h_source.html index d601f0d7f8..ec51dca0ab 100644 --- a/CavityEnsemble_8h_source.html +++ b/CavityEnsemble_8h_source.html @@ -79,101 +79,100 @@
7
8#include "utils/Random.h"
9
-
10using namespace std;
-
11
-
12class DomainDecompBase;
-
13
-
14class ParticleContainer;
-
15
-
16class Component;
-
17
-
18#include "molecules/MoleculeForwardDeclaration.h"
-
19
-
20class CavityEnsemble {
-
21public:
-
22 CavityEnsemble();
-
23
-
24 void setSystem(double x, double y, double z, int maxNeighbors, float radius);
-
25
-
26 double systemSize(int d) { return this->system[d]; }
-
27
-
28 void setSubdomain(int rank, double x0, double x1, double y0, double y1, double z0, double z1);
-
29
-
30 void submitTemperature(double T_in) { this->T = T_in; }
-
31
-
32 void setControlVolume(
-
33 double x0, double y0, double z0, double x1, double y1, double z1
-
34 );
-
35
-
36 void setMaxNeighbours(unsigned n, double rr) {
-
37 this->maxNeighbours = n;
-
38 this->r2n = rr;
-
39 }
-
40
-
41 double getRR() const { return this->r2n; }
-
42
-
43 void init(Component *component, unsigned Nx, unsigned Ny, unsigned Nz);
-
44
-
45 void preprocessStep();
-
46
-
47 bool decideActivity(unsigned neighbours, unsigned long tmid);
-
48
-
49 bool decideActivity(double uPotTilde, unsigned long tmid);
-
50
-
51 void setIdOffset(unsigned long offset) { this->idoffset = offset; }
-
52
-
53 unsigned long communicateNumCavities(DomainDecompBase *comm);
-
54
-
55 unsigned long numCavities() { return this->globalActive; }
-
56
-
57 map<unsigned long, Molecule *> *particleContainer() { return &(this->reservoir); }
-
58
-
59 map<unsigned long, Molecule *> activeParticleContainer();
-
60
-
61 void determineBoundary();
-
62
-
63 void processBoundary();
-
64
-
65 void cavityStep(ParticleContainer *globalMoleculeContainer);
-
66
-
67private:
-
72 unsigned countNeighbours(ParticleContainer *container, Molecule *m1) const;
-
73
-
74 int ownrank; // for debugging purposes (indicate rank in console output)
-
75 bool initialized;
-
76 bool rotated;
-
77
-
78 unsigned componentid;
-
79 double T;
-
80
-
81 double globalV;
-
82 double system[3]; // extent of the system
-
83 float minredco[3]; // minimal coordinates of the subdomain reduced w. r. t. the system size
-
84 float maxredco[3]; // maximal coordinates of the subdomain reduced w. r. t. the system size
-
85
-
86 bool restrictedControlVolume;
-
87 double control_bottom[3];
-
88 double control_top[3];
-
89
-
90 unsigned long idoffset;
-
91 set<unsigned long> active;
-
92 map<unsigned long, Molecule *> reservoir;
-
93 unsigned long globalActive;
-
94
-
95 bool boundarySpecified;
-
96 double init_bottom[3];
-
97 double init_top[3];
-
98
-
99 unsigned maxNeighbours;
-
100 double r2n;
-
101
-
102 Random async;
-
103};
-
104
-
105#endif
-
CavityEnsemble
Definition: CavityEnsemble.h:20
+
10
+
11class DomainDecompBase;
+
12
+
13class ParticleContainer;
+
14
+
15class Component;
+
16
+
17#include "molecules/MoleculeForwardDeclaration.h"
+
18
+
19class CavityEnsemble {
+
20public:
+
21 CavityEnsemble();
+
22
+
23 void setSystem(double x, double y, double z, int maxNeighbors, float radius);
+
24
+
25 double systemSize(int d) { return this->system[d]; }
+
26
+
27 void setSubdomain(int rank, double x0, double x1, double y0, double y1, double z0, double z1);
+
28
+
29 void submitTemperature(double T_in) { this->T = T_in; }
+
30
+
31 void setControlVolume(
+
32 double x0, double y0, double z0, double x1, double y1, double z1
+
33 );
+
34
+
35 void setMaxNeighbours(unsigned n, double rr) {
+
36 this->maxNeighbours = n;
+
37 this->r2n = rr;
+
38 }
+
39
+
40 double getRR() const { return this->r2n; }
+
41
+
42 void init(Component *component, unsigned Nx, unsigned Ny, unsigned Nz);
+
43
+
44 void preprocessStep();
+
45
+
46 bool decideActivity(unsigned neighbours, unsigned long tmid);
+
47
+
48 bool decideActivity(double uPotTilde, unsigned long tmid);
+
49
+
50 void setIdOffset(unsigned long offset) { this->idoffset = offset; }
+
51
+
52 unsigned long communicateNumCavities(DomainDecompBase *comm);
+
53
+
54 unsigned long numCavities() { return this->globalActive; }
+
55
+
56 std::map<unsigned long, Molecule *> *particleContainer() { return &(this->reservoir); }
+
57
+
58 std::map<unsigned long, Molecule *> activeParticleContainer();
+
59
+
60 void determineBoundary();
+
61
+
62 void processBoundary();
+
63
+
64 void cavityStep(ParticleContainer *globalMoleculeContainer);
+
65
+
66private:
+
71 unsigned countNeighbours(ParticleContainer *container, Molecule *m1) const;
+
72
+
73 int ownrank; // for debugging purposes (indicate rank in console output)
+
74 bool initialized;
+
75 bool rotated;
+
76
+
77 unsigned componentid;
+
78 double T;
+
79
+
80 double globalV;
+
81 double system[3]; // extent of the system
+
82 float minredco[3]; // minimal coordinates of the subdomain reduced w. r. t. the system size
+
83 float maxredco[3]; // maximal coordinates of the subdomain reduced w. r. t. the system size
+
84
+
85 bool restrictedControlVolume;
+
86 double control_bottom[3];
+
87 double control_top[3];
+
88
+
89 unsigned long idoffset;
+
90 std::set<unsigned long> active;
+
91 std::map<unsigned long, Molecule *> reservoir;
+
92 unsigned long globalActive;
+
93
+
94 bool boundarySpecified;
+
95 double init_bottom[3];
+
96 double init_top[3];
+
97
+
98 unsigned maxNeighbours;
+
99 double r2n;
+
100
+
101 Random async;
+
102};
+
103
+
104#endif
+
CavityEnsemble
Definition: CavityEnsemble.h:19
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
Random
Definition: Random.h:12
@@ -181,7 +180,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CavityWriter_8h_source.html b/CavityWriter_8h_source.html index dfddb8e9da..d75f139bf4 100644 --- a/CavityWriter_8h_source.html +++ b/CavityWriter_8h_source.html @@ -130,17 +130,17 @@
131};
132
133#endif /* CAVITYWRITER_H_ */
-
CavityEnsemble
Definition: CavityEnsemble.h:20
+
CavityEnsemble
Definition: CavityEnsemble.h:19
CavityWriter
IO-plugin: Used to create instances of CavityEnsemble and output the corresponding files containing t...
Definition: CavityWriter.h:13
-
CavityWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) final
Output the sampled cavity information from all ensembles to file.
Definition: CavityWriter.cpp:176
-
CavityWriter::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) final
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: CavityWriter.cpp:160
+
CavityWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) final
Output the sampled cavity information from all ensembles to file.
Definition: CavityWriter.cpp:173
+
CavityWriter::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) final
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: CavityWriter.cpp:157
CavityWriter::CavityWriter
CavityWriter()=default
Initialisation of all necessary field is done in readXML and init.
-
CavityWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Nothing done here. Necessary for inheritance from PluginBase.
Definition: CavityWriter.cpp:239
+
CavityWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Nothing done here. Necessary for inheritance from PluginBase.
Definition: CavityWriter.cpp:236
CavityWriter::getPluginName
std::string getPluginName() final
return the name of the plugin
Definition: CavityWriter.h:113
-
CavityWriter::readXML
void readXML(XMLfileUnits &xmlconfig) final
reads in parameters for CavityEnsemble and output writefrequency: output timestep frequency AFTER i...
Definition: CavityWriter.cpp:18
-
CavityWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) final
Set all necessary variables for each CavityEnsemble. One is used per Component. Ensembles are assigne...
Definition: CavityWriter.cpp:113
-
CavityWriter::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) final
Method will be called first thing in a new timestep. If the writeFrequency is reached and this is the...
Definition: CavityWriter.cpp:148
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
CavityWriter::readXML
void readXML(XMLfileUnits &xmlconfig) final
reads in parameters for CavityEnsemble and output writefrequency: output timestep frequency AFTER i...
Definition: CavityWriter.cpp:15
+
CavityWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) final
Set all necessary variables for each CavityEnsemble. One is used per Component. Ensembles are assigne...
Definition: CavityWriter.cpp:110
+
CavityWriter::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) final
Method will be called first thing in a new timestep. If the writeFrequency is reached and this is the...
Definition: CavityWriter.cpp:145
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -149,7 +149,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellBorderAndFlagManager_8h_source.html b/CellBorderAndFlagManager_8h_source.html index 62ae0e20df..b063dc353e 100644 --- a/CellBorderAndFlagManager_8h_source.html +++ b/CellBorderAndFlagManager_8h_source.html @@ -246,7 +246,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellDataSoABase_8h_source.html b/CellDataSoABase_8h_source.html index fe89e001fc..79af2774b1 100644 --- a/CellDataSoABase_8h_source.html +++ b/CellDataSoABase_8h_source.html @@ -100,7 +100,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellDataSoARMM_8h_source.html b/CellDataSoARMM_8h_source.html index 735b07e506..61be102dfb 100644 --- a/CellDataSoARMM_8h_source.html +++ b/CellDataSoARMM_8h_source.html @@ -244,7 +244,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellDataSoA_8h_source.html b/CellDataSoA_8h_source.html index 6ee9d9fb57..c4e96c5d12 100644 --- a/CellDataSoA_8h_source.html +++ b/CellDataSoA_8h_source.html @@ -426,7 +426,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellPairTraversals_8h_source.html b/CellPairTraversals_8h_source.html index b7710f7658..492d070552 100644 --- a/CellPairTraversals_8h_source.html +++ b/CellPairTraversals_8h_source.html @@ -130,7 +130,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CellProcessor_8h_source.html b/CellProcessor_8h_source.html index 440b1f3c04..d64e15c22c 100644 --- a/CellProcessor_8h_source.html +++ b/CellProcessor_8h_source.html @@ -86,8 +86,8 @@
32 double _LJCutoffRadiusSquare;
33
34public:
-
35 CellProcessor(const double cutoffRadius, const double LJCutoffRadius) :
-
36 _cutoffRadiusSquare(cutoffRadius * cutoffRadius),
+
35 CellProcessor(const double cutoffRadius, const double LJCutoffRadius) :
+
36 _cutoffRadiusSquare(cutoffRadius * cutoffRadius),
37 _LJCutoffRadiusSquare(LJCutoffRadius * LJCutoffRadius) {}
41 virtual ~CellProcessor() {}
42
@@ -133,7 +133,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Cell_8h_source.html b/Cell_8h_source.html index 1894219e2f..484a5d3ffe 100644 --- a/Cell_8h_source.html +++ b/Cell_8h_source.html @@ -76,7 +76,7 @@
4class Cell {
5public:
6 Cell() : _cellIndex(0) {}
-
7
+
7
8 virtual ~Cell() {}
9
10 virtual void assignCellToHaloRegion() = 0;
@@ -112,7 +112,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CheckpointWriter_8h_source.html b/CheckpointWriter_8h_source.html index eb7de0c54f..b7c35d5205 100644 --- a/CheckpointWriter_8h_source.html +++ b/CheckpointWriter_8h_source.html @@ -80,13 +80,13 @@
8
9class CheckpointWriter : public PluginBase {
10public:
-
11
+
11
12 CheckpointWriter() {}
13 ~CheckpointWriter() {}
-
14
+
14
15
29 void readXML(XMLfileUnits& xmlconfig);
-
30
+
30
31 void init(ParticleContainer *particleContainer,
32 DomainDecompBase *domainDecomp, Domain *domain);
33 void endStep(
@@ -96,7 +96,7 @@
37 );
38 void finish(ParticleContainer *particleContainer,
39 DomainDecompBase *domainDecomp, Domain *domain);
-
40
+
40
41 std::string getPluginName() {
42 return std::string("CheckpointWriter");
43 }
@@ -111,12 +111,12 @@
52
53#endif // SRC_IO_CHECKPOINTWRITER_H_
CheckpointWriter
Definition: CheckpointWriter.h:9
-
CheckpointWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: CheckpointWriter.cpp:62
-
CheckpointWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for CheckpointWriter.
Definition: CheckpointWriter.cpp:17
-
CheckpointWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: CheckpointWriter.cpp:59
+
CheckpointWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: CheckpointWriter.cpp:59
+
CheckpointWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for CheckpointWriter.
Definition: CheckpointWriter.cpp:14
+
CheckpointWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: CheckpointWriter.cpp:56
CheckpointWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: CheckpointWriter.h:41
-
CheckpointWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: CheckpointWriter.cpp:89
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
CheckpointWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: CheckpointWriter.cpp:86
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -125,7 +125,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ChemicalPotential_8h_source.html b/ChemicalPotential_8h_source.html index 57842cb8e3..e31ececf91 100644 --- a/ChemicalPotential_8h_source.html +++ b/ChemicalPotential_8h_source.html @@ -204,10 +204,10 @@
135};
CellProcessor
Definition: CellProcessor.h:29
ChemicalPotential
Definition: ChemicalPotential.h:16
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
-
FullMolecule::check
void check(unsigned long id) override
Definition: FullMolecule.cpp:636
+
FullMolecule::check
void check(unsigned long id) override
Definition: FullMolecule.cpp:633
FullMolecule::getID
unsigned long getID() const override
Definition: FullMolecule.h:41
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
ParticleIterator
Definition: ParticleIterator.h:60
@@ -216,7 +216,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommBaseInterface_8h_source.html b/CollectiveCommBaseInterface_8h_source.html index 489f1463b3..c0e753c2e1 100644 --- a/CollectiveCommBaseInterface_8h_source.html +++ b/CollectiveCommBaseInterface_8h_source.html @@ -139,7 +139,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommBase_8h_source.html b/CollectiveCommBase_8h_source.html index b4dd1896d2..8fb936d8be 100644 --- a/CollectiveCommBase_8h_source.html +++ b/CollectiveCommBase_8h_source.html @@ -199,7 +199,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommunicationInterface_8h_source.html b/CollectiveCommunicationInterface_8h_source.html index 5445312e39..e6d80d04af 100644 --- a/CollectiveCommunicationInterface_8h_source.html +++ b/CollectiveCommunicationInterface_8h_source.html @@ -103,7 +103,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommunicationNonBlocking_8h_source.html b/CollectiveCommunicationNonBlocking_8h_source.html index 1214e93b09..bd912e5d95 100644 --- a/CollectiveCommunicationNonBlocking_8h_source.html +++ b/CollectiveCommunicationNonBlocking_8h_source.html @@ -87,167 +87,166 @@
15
16#if MPI_VERSION >= 3
17
-
18using Log::global_log;
-
25class CollectiveCommunicationNonBlocking: public CollectiveCommunicationInterface {
-
26public:
-
28 CollectiveCommunicationNonBlocking() :
-
29 _currentKey(-1), _comms() {
-
30 }
-
31
-
35 ~CollectiveCommunicationNonBlocking() override = default;
-
36
-
41 void init(MPI_Comm communicator, int numValues, int key = 0) override {
-
42 if (_currentKey != -1) {
-
43 global_log->error() << "CollectiveCommunicationNonBlocking: previous communication with key " << _currentKey
-
44 << " not yet finalized" << std::endl;
-
45 Simulation::exit(234);
-
46 }
-
47
-
48 _currentKey = key;
-
49
-
50 // add the key, if it is not yet existent:
-
51 if (_comms.count(_currentKey) == 1) {
-
52 // this happens, if the key is already existent.
-
53 global_log->debug() << "CollectiveCommunicationNonBlocking: key " << _currentKey
-
54 << " already existent. Reusing information." << std::endl;
-
55 } else {
-
56 global_log->debug() << "CollectiveCommunicationNonBlocking: key " << _currentKey
-
57 << " not existent. Cannot reuse information." << std::endl;
-
58 // Creates the CollectiveCommunicationSingleNonBlocking object
-
59 auto [_, inserted] = _comms.try_emplace(_currentKey);
-
60 if (not inserted) {
-
61 global_log->error() << "CollectiveCommunicationNonBlocking: key " << _currentKey
-
62 << " could not be inserted. Aborting!" << std::endl;
-
63 Simulation::exit(498789);
-
64 }
-
65 }
-
66 _comms.at(_currentKey).init(communicator, numValues, _currentKey);
-
67 }
-
68
-
71 void finalize() override {
-
72 _comms.at(_currentKey).finalize();
-
73 if (_currentKey == 0) {
-
74 global_log->debug() << "CollectiveCommunicationNonBlocking: finalizing with key " << _currentKey
-
75 << ", thus the entry is removed." << std::endl;
-
76 _comms.erase(_currentKey);
-
77 }
-
78 _currentKey = -1;
-
79 }
-
80
-
83 void appendInt(int intValue) override {
-
84 _comms.at(_currentKey).appendInt(intValue);
-
85 }
-
86
-
89 void appendUnsLong(unsigned long unsLongValue) override {
-
90 _comms.at(_currentKey).appendUnsLong(unsLongValue);
-
91 }
-
92
-
95 void appendFloat(float floatValue) override {
-
96 _comms.at(_currentKey).appendFloat(floatValue);
-
97 }
-
98
-
101 void appendDouble(double doubleValue) override {
-
102 _comms.at(_currentKey).appendDouble(doubleValue);
-
103 }
-
104
-
107 void appendLongDouble(long double longDoubleValue) override {
-
108 _comms.at(_currentKey).appendLongDouble(longDoubleValue);
-
109 }
-
110
-
113 MPI_Comm getTopology() override {
-
114 return _comms.at(_currentKey).getTopology();
-
115 }
-
116
-
122 int getInt() override {
-
123 return _comms.at(_currentKey).getInt();
-
124 }
-
125
-
131 unsigned long getUnsLong() override {
-
132 return _comms.at(_currentKey).getUnsLong();
-
133 }
-
134
-
140 float getFloat() override {
-
141 return _comms.at(_currentKey).getFloat();
-
142 }
-
143
-
149 double getDouble() override {
-
150 return _comms.at(_currentKey).getDouble();
-
151 }
-
152
-
158 long double getLongDouble() override {
-
159 return _comms.at(_currentKey).getLongDouble();
-
160 }
-
161
-
164 void broadcast(int root = 0) override {
-
165 _comms.at(_currentKey).broadcast(root);
-
166 }
-
167
-
169 void allreduceSum() override {
-
170 Log::global_log->debug() << "CollectiveCommunicationNonBlocking: normal Allreduce" << std::endl;
-
171 _comms.at(_currentKey).allreduceSum();
-
172 }
-
173
-
177 virtual void allreduceSumAllowPrevious() override {
-
178 Log::global_log->debug() << "CollectiveCommunicationNonBlocking: nonblocking Allreduce with id "<< _currentKey << std::endl;
-
179 mardyn_assert(_currentKey > 0); // _currentKey has to be positive non-zero and should be unique for allreduceSumAllowPrevious
-
180 _comms.at(_currentKey).allreduceSumAllowPrevious();
-
181 }
-
182
-
183 void allreduceCustom(ReduceType type) override{
-
184 _comms.at(_currentKey).allreduceCustom(type);
-
185 }
-
186
-
187 void scanSum() override {
-
188 _comms.at(_currentKey).scanSum();
-
189 }
-
190
-
195 /*
-
196 void waitSpecific(int key) {
-
197 _comms[key].waitAndUpdateData();
-
198 }*/
-
199
-
200 size_t getTotalSize() override {
-
201 size_t tmp = 0;
-
202 for (auto& comm : _comms){
-
203 tmp += comm.second.getTotalSize();
-
204 }
-
205 return tmp;
-
206 }
-
207private:
-
208 int _currentKey;
-
209 std::map<int, CollectiveCommunicationSingleNonBlocking> _comms;
-
210};
-
211
-
212#endif // MPI_VERSION >= 3
+
24class CollectiveCommunicationNonBlocking: public CollectiveCommunicationInterface {
+
25public:
+
27 CollectiveCommunicationNonBlocking() :
+
28 _currentKey(-1), _comms() {
+
29 }
+
30
+
34 ~CollectiveCommunicationNonBlocking() override = default;
+
35
+
40 void init(MPI_Comm communicator, int numValues, int key = 0) override {
+
41 if (_currentKey != -1) {
+
42 Log::global_log->error() << "CollectiveCommunicationNonBlocking: previous communication with key " << _currentKey
+
43 << " not yet finalized" << std::endl;
+
44 Simulation::exit(234);
+
45 }
+
46
+
47 _currentKey = key;
+
48
+
49 // add the key, if it is not yet existent:
+
50 if (_comms.count(_currentKey) == 1) {
+
51 // this happens, if the key is already existent.
+
52 Log::global_log->debug() << "CollectiveCommunicationNonBlocking: key " << _currentKey
+
53 << " already existent. Reusing information." << std::endl;
+
54 } else {
+
55 Log::global_log->debug() << "CollectiveCommunicationNonBlocking: key " << _currentKey
+
56 << " not existent. Cannot reuse information." << std::endl;
+
57 // Creates the CollectiveCommunicationSingleNonBlocking object
+
58 auto [_, inserted] = _comms.try_emplace(_currentKey);
+
59 if (not inserted) {
+
60 Log::global_log->error() << "CollectiveCommunicationNonBlocking: key " << _currentKey
+
61 << " could not be inserted. Aborting!" << std::endl;
+
62 Simulation::exit(498789);
+
63 }
+
64 }
+
65 _comms.at(_currentKey).init(communicator, numValues, _currentKey);
+
66 }
+
67
+
70 void finalize() override {
+
71 _comms.at(_currentKey).finalize();
+
72 if (_currentKey == 0) {
+
73 Log::global_log->debug() << "CollectiveCommunicationNonBlocking: finalizing with key " << _currentKey
+
74 << ", thus the entry is removed." << std::endl;
+
75 _comms.erase(_currentKey);
+
76 }
+
77 _currentKey = -1;
+
78 }
+
79
+
82 void appendInt(int intValue) override {
+
83 _comms.at(_currentKey).appendInt(intValue);
+
84 }
+
85
+
88 void appendUnsLong(unsigned long unsLongValue) override {
+
89 _comms.at(_currentKey).appendUnsLong(unsLongValue);
+
90 }
+
91
+
94 void appendFloat(float floatValue) override {
+
95 _comms.at(_currentKey).appendFloat(floatValue);
+
96 }
+
97
+
100 void appendDouble(double doubleValue) override {
+
101 _comms.at(_currentKey).appendDouble(doubleValue);
+
102 }
+
103
+
106 void appendLongDouble(long double longDoubleValue) override {
+
107 _comms.at(_currentKey).appendLongDouble(longDoubleValue);
+
108 }
+
109
+
112 MPI_Comm getTopology() override {
+
113 return _comms.at(_currentKey).getTopology();
+
114 }
+
115
+
121 int getInt() override {
+
122 return _comms.at(_currentKey).getInt();
+
123 }
+
124
+
130 unsigned long getUnsLong() override {
+
131 return _comms.at(_currentKey).getUnsLong();
+
132 }
+
133
+
139 float getFloat() override {
+
140 return _comms.at(_currentKey).getFloat();
+
141 }
+
142
+
148 double getDouble() override {
+
149 return _comms.at(_currentKey).getDouble();
+
150 }
+
151
+
157 long double getLongDouble() override {
+
158 return _comms.at(_currentKey).getLongDouble();
+
159 }
+
160
+
163 void broadcast(int root = 0) override {
+
164 _comms.at(_currentKey).broadcast(root);
+
165 }
+
166
+
168 void allreduceSum() override {
+
169 Log::global_log->debug() << "CollectiveCommunicationNonBlocking: normal Allreduce" << std::endl;
+
170 _comms.at(_currentKey).allreduceSum();
+
171 }
+
172
+
176 virtual void allreduceSumAllowPrevious() override {
+
177 Log::global_log->debug() << "CollectiveCommunicationNonBlocking: nonblocking Allreduce with id "<< _currentKey << std::endl;
+
178 mardyn_assert(_currentKey > 0); // _currentKey has to be positive non-zero and should be unique for allreduceSumAllowPrevious
+
179 _comms.at(_currentKey).allreduceSumAllowPrevious();
+
180 }
+
181
+
182 void allreduceCustom(ReduceType type) override{
+
183 _comms.at(_currentKey).allreduceCustom(type);
+
184 }
+
185
+
186 void scanSum() override {
+
187 _comms.at(_currentKey).scanSum();
+
188 }
+
189
+
194 /*
+
195 void waitSpecific(int key) {
+
196 _comms[key].waitAndUpdateData();
+
197 }*/
+
198
+
199 size_t getTotalSize() override {
+
200 size_t tmp = 0;
+
201 for (auto& comm : _comms){
+
202 tmp += comm.second.getTotalSize();
+
203 }
+
204 return tmp;
+
205 }
+
206private:
+
207 int _currentKey;
+
208 std::map<int, CollectiveCommunicationSingleNonBlocking> _comms;
+
209};
+
210
+
211#endif // MPI_VERSION >= 3
CollectiveCommunicationInterface
This class provides an interface for the collective communication classes.
Definition: CollectiveCommunicationInterface.h:15
-
CollectiveCommunicationNonBlocking
Definition: CollectiveCommunicationNonBlocking.h:25
-
CollectiveCommunicationNonBlocking::appendUnsLong
void appendUnsLong(unsigned long unsLongValue) override
Definition: CollectiveCommunicationNonBlocking.h:89
-
CollectiveCommunicationNonBlocking::finalize
void finalize() override
delete memory and MPI_Type
Definition: CollectiveCommunicationNonBlocking.h:71
-
CollectiveCommunicationNonBlocking::allreduceCustom
void allreduceCustom(ReduceType type) override
Definition: CollectiveCommunicationNonBlocking.h:183
-
CollectiveCommunicationNonBlocking::getTopology
MPI_Comm getTopology() override
Definition: CollectiveCommunicationNonBlocking.h:113
-
CollectiveCommunicationNonBlocking::getDouble
double getDouble() override
Definition: CollectiveCommunicationNonBlocking.h:149
-
CollectiveCommunicationNonBlocking::allreduceSumAllowPrevious
virtual void allreduceSumAllowPrevious() override
Definition: CollectiveCommunicationNonBlocking.h:177
-
CollectiveCommunicationNonBlocking::getFloat
float getFloat() override
Definition: CollectiveCommunicationNonBlocking.h:140
-
CollectiveCommunicationNonBlocking::init
void init(MPI_Comm communicator, int numValues, int key=0) override
allocate memory for the values to be sent, initialize counters for specific
Definition: CollectiveCommunicationNonBlocking.h:41
-
CollectiveCommunicationNonBlocking::CollectiveCommunicationNonBlocking
CollectiveCommunicationNonBlocking()
Constructor, does nothing yet.
Definition: CollectiveCommunicationNonBlocking.h:28
-
CollectiveCommunicationNonBlocking::appendFloat
void appendFloat(float floatValue) override
Definition: CollectiveCommunicationNonBlocking.h:95
-
CollectiveCommunicationNonBlocking::scanSum
void scanSum() override
Performs a scan (sum)
Definition: CollectiveCommunicationNonBlocking.h:187
-
CollectiveCommunicationNonBlocking::getTotalSize
size_t getTotalSize() override
Definition: CollectiveCommunicationNonBlocking.h:200
-
CollectiveCommunicationNonBlocking::allreduceSum
void allreduceSum() override
Do Allreduce off all values with reduce operation add.
Definition: CollectiveCommunicationNonBlocking.h:169
+
CollectiveCommunicationNonBlocking
Definition: CollectiveCommunicationNonBlocking.h:24
+
CollectiveCommunicationNonBlocking::appendUnsLong
void appendUnsLong(unsigned long unsLongValue) override
Definition: CollectiveCommunicationNonBlocking.h:88
+
CollectiveCommunicationNonBlocking::finalize
void finalize() override
delete memory and MPI_Type
Definition: CollectiveCommunicationNonBlocking.h:70
+
CollectiveCommunicationNonBlocking::allreduceCustom
void allreduceCustom(ReduceType type) override
Definition: CollectiveCommunicationNonBlocking.h:182
+
CollectiveCommunicationNonBlocking::getTopology
MPI_Comm getTopology() override
Definition: CollectiveCommunicationNonBlocking.h:112
+
CollectiveCommunicationNonBlocking::getDouble
double getDouble() override
Definition: CollectiveCommunicationNonBlocking.h:148
+
CollectiveCommunicationNonBlocking::allreduceSumAllowPrevious
virtual void allreduceSumAllowPrevious() override
Definition: CollectiveCommunicationNonBlocking.h:176
+
CollectiveCommunicationNonBlocking::getFloat
float getFloat() override
Definition: CollectiveCommunicationNonBlocking.h:139
+
CollectiveCommunicationNonBlocking::init
void init(MPI_Comm communicator, int numValues, int key=0) override
allocate memory for the values to be sent, initialize counters for specific
Definition: CollectiveCommunicationNonBlocking.h:40
+
CollectiveCommunicationNonBlocking::CollectiveCommunicationNonBlocking
CollectiveCommunicationNonBlocking()
Constructor, does nothing yet.
Definition: CollectiveCommunicationNonBlocking.h:27
+
CollectiveCommunicationNonBlocking::appendFloat
void appendFloat(float floatValue) override
Definition: CollectiveCommunicationNonBlocking.h:94
+
CollectiveCommunicationNonBlocking::scanSum
void scanSum() override
Performs a scan (sum)
Definition: CollectiveCommunicationNonBlocking.h:186
+
CollectiveCommunicationNonBlocking::getTotalSize
size_t getTotalSize() override
Definition: CollectiveCommunicationNonBlocking.h:199
+
CollectiveCommunicationNonBlocking::allreduceSum
void allreduceSum() override
Do Allreduce off all values with reduce operation add.
Definition: CollectiveCommunicationNonBlocking.h:168
CollectiveCommunicationNonBlocking::~CollectiveCommunicationNonBlocking
~CollectiveCommunicationNonBlocking() override=default
-
CollectiveCommunicationNonBlocking::getInt
int getInt() override
Definition: CollectiveCommunicationNonBlocking.h:122
-
CollectiveCommunicationNonBlocking::getUnsLong
unsigned long getUnsLong() override
Definition: CollectiveCommunicationNonBlocking.h:131
-
CollectiveCommunicationNonBlocking::appendDouble
void appendDouble(double doubleValue) override
Definition: CollectiveCommunicationNonBlocking.h:101
-
CollectiveCommunicationNonBlocking::appendLongDouble
void appendLongDouble(long double longDoubleValue) override
Definition: CollectiveCommunicationNonBlocking.h:107
-
CollectiveCommunicationNonBlocking::getLongDouble
long double getLongDouble() override
Definition: CollectiveCommunicationNonBlocking.h:158
-
CollectiveCommunicationNonBlocking::broadcast
void broadcast(int root=0) override
Definition: CollectiveCommunicationNonBlocking.h:164
-
CollectiveCommunicationNonBlocking::appendInt
void appendInt(int intValue) override
Definition: CollectiveCommunicationNonBlocking.h:83
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
CollectiveCommunicationNonBlocking::getInt
int getInt() override
Definition: CollectiveCommunicationNonBlocking.h:121
+
CollectiveCommunicationNonBlocking::getUnsLong
unsigned long getUnsLong() override
Definition: CollectiveCommunicationNonBlocking.h:130
+
CollectiveCommunicationNonBlocking::appendDouble
void appendDouble(double doubleValue) override
Definition: CollectiveCommunicationNonBlocking.h:100
+
CollectiveCommunicationNonBlocking::appendLongDouble
void appendLongDouble(long double longDoubleValue) override
Definition: CollectiveCommunicationNonBlocking.h:106
+
CollectiveCommunicationNonBlocking::getLongDouble
long double getLongDouble() override
Definition: CollectiveCommunicationNonBlocking.h:157
+
CollectiveCommunicationNonBlocking::broadcast
void broadcast(int root=0) override
Definition: CollectiveCommunicationNonBlocking.h:163
+
CollectiveCommunicationNonBlocking::appendInt
void appendInt(int intValue) override
Definition: CollectiveCommunicationNonBlocking.h:82
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommunicationSingleNonBlocking_8h_source.html b/CollectiveCommunicationSingleNonBlocking_8h_source.html index 677bcc317c..dd8ec7569e 100644 --- a/CollectiveCommunicationSingleNonBlocking_8h_source.html +++ b/CollectiveCommunicationSingleNonBlocking_8h_source.html @@ -227,7 +227,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CollectiveCommunication_8h_source.html b/CollectiveCommunication_8h_source.html index 007e2eb3f9..74d9ca4a16 100644 --- a/CollectiveCommunication_8h_source.html +++ b/CollectiveCommunication_8h_source.html @@ -428,13 +428,13 @@
CollectiveCommunication::appendLongDouble
void appendLongDouble(long double longDoubleValue) override
Definition: CollectiveCommunication.h:118
CollectiveCommunication::add
static void add(valType *invec, valType *inoutvec, int *, MPI_Datatype *dtype)
method used by MPI to add variables of this type
Definition: CollectiveCommunication.h:277
CollectiveCommunication::getTopology
MPI_Comm getTopology() override
Definition: CollectiveCommunication.h:125
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
CollectiveCommBase::valType
Definition: CollectiveCommBase.h:29
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CommVar_8h_source.html b/CommVar_8h_source.html index 83dc229a4f..cf89b9c9e0 100644 --- a/CommVar_8h_source.html +++ b/CommVar_8h_source.html @@ -93,7 +93,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Common_8h_source.html b/Common_8h_source.html index 0493bde8e9..c297f4ee70 100644 --- a/Common_8h_source.html +++ b/Common_8h_source.html @@ -98,7 +98,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CommunicationBuffer_8h_source.html b/CommunicationBuffer_8h_source.html index 034c1ed117..ee8d8e46b2 100644 --- a/CommunicationBuffer_8h_source.html +++ b/CommunicationBuffer_8h_source.html @@ -80,8 +80,8 @@
8#ifndef SRC_PARALLEL_COMMUNICATIONBUFFER_H_
9#define SRC_PARALLEL_COMMUNICATIONBUFFER_H_
10
-
11#include "molecules/MoleculeForwardDeclaration.h"
-
12#include "utils/mardyn_assert.h"
+
11#include "molecules/MoleculeForwardDeclaration.h"
+
12#include "utils/mardyn_assert.h"
13
14#include <vector>
15#include <stddef.h>
@@ -123,7 +123,7 @@
64 void readHaloMolecule(size_t indexOfMolecule, Molecule& m) const;
65 void readForceMolecule(size_t indexOfMolecule, Molecule& m) const;
66
-
67 void resizeForReceivingMolecules(unsigned long& numLeaving, unsigned long& numHalo);
+
67 void resizeForReceivingMolecules(unsigned long& numLeaving, unsigned long& numHalo);
68 void resizeForReceivingMolecules(unsigned long& numForces);
69
70 size_t getNumHalo() const {
@@ -133,7 +133,7 @@
74 size_t getNumLeaving() const {
75 return _numLeaving;
76 }
-
77
+
77
78 size_t getNumForces() const {
79 return _numForces;
80 }
@@ -200,7 +200,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CommunicationPartnerWriter_8h_source.html b/CommunicationPartnerWriter_8h_source.html index 048f0b6ac9..7eb5c231d9 100644 --- a/CommunicationPartnerWriter_8h_source.html +++ b/CommunicationPartnerWriter_8h_source.html @@ -78,13 +78,13 @@
6
11class CommunicationPartnerWriter : public PluginBase {
12public:
-
13
+
13
14 CommunicationPartnerWriter() {}
15 ~CommunicationPartnerWriter() {}
-
16
+
16
17
30 void readXML(XMLfileUnits& xmlconfig) override;
-
31
+
31
32 void init(ParticleContainer *particleContainer,
33 DomainDecompBase *domainDecomp, Domain *domain) override;
34 void afterForces(ParticleContainer *particleContainer,
@@ -97,7 +97,7 @@
41
42 void finish(ParticleContainer *particleContainer,
43 DomainDecompBase *domainDecomp, Domain *domain) override;
-
44
+
44
45 std::string getPluginName() override {
46 return std::string("CommunicationPartnerWriter");
47 }
@@ -110,13 +110,13 @@
54};
55
CommunicationPartnerWriter
Definition: CommunicationPartnerWriter.h:11
-
CommunicationPartnerWriter::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for CommunicationPartnerWriter.
Definition: CommunicationPartnerWriter.cpp:15
+
CommunicationPartnerWriter::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for CommunicationPartnerWriter.
Definition: CommunicationPartnerWriter.cpp:12
CommunicationPartnerWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: CommunicationPartnerWriter.h:37
-
CommunicationPartnerWriter::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: CommunicationPartnerWriter.cpp:50
-
CommunicationPartnerWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: CommunicationPartnerWriter.cpp:75
+
CommunicationPartnerWriter::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: CommunicationPartnerWriter.cpp:47
+
CommunicationPartnerWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: CommunicationPartnerWriter.cpp:72
CommunicationPartnerWriter::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: CommunicationPartnerWriter.h:45
-
CommunicationPartnerWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: CommunicationPartnerWriter.cpp:47
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
CommunicationPartnerWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: CommunicationPartnerWriter.cpp:44
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -125,7 +125,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CommunicationPartner_8h_source.html b/CommunicationPartner_8h_source.html index 47bd934e7d..b2543a3131 100644 --- a/CommunicationPartner_8h_source.html +++ b/CommunicationPartner_8h_source.html @@ -198,7 +198,7 @@
134 // technical variables
135 MPI_Request *_sendRequest, *_recvRequest;
136 MPI_Status *_sendStatus, *_recvStatus;
-
137 CommunicationBuffer _sendBuf, _recvBuf; // used to be ParticleData and
+
137 CommunicationBuffer _sendBuf, _recvBuf; // used to be ParticleData and
138 bool _msgSent, _countReceived, _msgReceived, _isSending, _isReceiving;
139
140 void collectLeavingMoleculesFromInvalidParticles(std::vector<Molecule>& invalidParticles, double lowCorner [3], double highCorner [3], double shift [3]);
@@ -211,7 +211,7 @@
CommunicationPartner
Definition: CommunicationPartner.h:38
CommunicationPartner::isFaceCommunicator
bool isFaceCommunicator() const
Definition: CommunicationPartner.h:81
CommunicationPartner::getFaceCommunicationDirection
int getFaceCommunicationDirection() const
Definition: CommunicationPartner.h:85
-
CommunicationPartner::add
void add(CommunicationPartner partner)
Definition: CommunicationPartner.cpp:429
+
CommunicationPartner::add
void add(CommunicationPartner partner)
Definition: CommunicationPartner.cpp:427
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
PositionInfo
Definition: CommunicationPartner.h:25
@@ -219,7 +219,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Comp2Param_8h_source.html b/Comp2Param_8h_source.html index db055dc101..004edcc965 100644 --- a/Comp2Param_8h_source.html +++ b/Comp2Param_8h_source.html @@ -84,8 +84,8 @@
16 public:
18 Comp2Param() : m_numcomp(0), m_ssparatbl(0,0) {}
19
-
23 Comp2Param(const std::vector<Component>& components,
-
24 const std::vector<double>& mixcoeff,
+
23 Comp2Param(const std::vector<Component>& components,
+
24 const std::vector<double>& mixcoeff,
25 double epsRF, double rc, double rcLJ) :
26 m_numcomp(components.size()), m_ssparatbl(m_numcomp,m_numcomp)
27 {
@@ -105,7 +105,7 @@
57#endif /* COMP2PARAM_H_ */
Array2D
Definition: Array2D.h:15
Comp2Param
Definition: Comp2Param.h:15
-
Comp2Param::initialize
void initialize(const std::vector< Component > &components, const std::vector< double > &mixcoeff, double epsRF, double rc, double rcLJ)
Initialize the parameter streams for each component-component table entry.
Definition: Comp2Param.cpp:10
+
Comp2Param::initialize
void initialize(const std::vector< Component > &components, const std::vector< double > &mixcoeff, double epsRF, double rc, double rcLJ)
Initialize the parameter streams for each component-component table entry.
Definition: Comp2Param.cpp:8
Comp2Param::operator()
ParaStrm & operator()(unsigned int i, unsigned int j)
Definition: Comp2Param.h:32
Comp2Param::Comp2Param
Comp2Param(const std::vector< Component > &components, const std::vector< double > &mixcoeff, double epsRF, double rc, double rcLJ)
Definition: Comp2Param.h:23
Comp2Param::Comp2Param
Comp2Param()
Definition: Comp2Param.h:18
@@ -113,7 +113,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Component_8h_source.html b/Component_8h_source.html index ca76c896ba..2583d2e5d1 100644 --- a/Component_8h_source.html +++ b/Component_8h_source.html @@ -197,9 +197,9 @@
163 double _E_trans; // translational energy
164 double _E_rot; // rotational energy
165 double _T; // temperature
-
166
+
166
167 bool _isStockmayer; //Checks whether component is a Stockmayer fluid to determine moments of inertia
-
168
+
168
169 std::string _name;
182 unsigned _lookUpID;
183};
@@ -218,17 +218,17 @@
Component::numSites
unsigned int numSites() const
Definition: Component.h:36
Component::m
double m() const
Definition: Component.h:53
Component::setID
void setID(unsigned int id)
Definition: Component.h:31
-
Component::write
void write(std::ostream &ostrm) const
Definition: Component.cpp:218
+
Component::write
void write(std::ostream &ostrm) const
Definition: Component.cpp:216
Component::numDipoles
unsigned int numDipoles() const
Definition: Component.h:48
Component::incNumMolecules
void incNumMolecules(int N)
Definition: Component.h:79
Component::getNumMolecules
unsigned long getNumMolecules() const
Definition: Component.h:80
Component::getEps
double getEps(unsigned int i) const
Definition: Component.h:128
Component::deleteLJCenter
void deleteLJCenter()
Definition: Component.h:100
-
Component::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for a component and all its included objects.
Definition: Component.cpp:32
-
Component::updateMassInertia
void updateMassInertia()
Definition: Component.cpp:137
+
Component::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for a component and all its included objects.
Definition: Component.cpp:30
+
Component::updateMassInertia
void updateMassInertia()
Definition: Component.cpp:135
Component::ID
unsigned int ID() const
Definition: Component.h:33
Component::incNumMolecules
void incNumMolecules()
Definition: Component.h:78
-
Component::updateAllLJcentersShift
void updateAllLJcentersShift(double rc)
Definition: Component.cpp:129
+
Component::updateAllLJcentersShift
void updateAllLJcentersShift(double rc)
Definition: Component.cpp:127
Dipole
Dipole center.
Definition: Site.h:281
LJcenter
Lennard-Jones 12-6 center.
Definition: Site.h:97
Quadrupole
Quadrupole center.
Definition: Site.h:343
@@ -241,7 +241,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ConcatenatedAlignedArrayRMM_8h_source.html b/ConcatenatedAlignedArrayRMM_8h_source.html index 840c477c0c..4fbb126886 100644 --- a/ConcatenatedAlignedArrayRMM_8h_source.html +++ b/ConcatenatedAlignedArrayRMM_8h_source.html @@ -377,7 +377,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ConcatenatedSites_8h_source.html b/ConcatenatedSites_8h_source.html index d9990d53a6..e4fcb539e4 100644 --- a/ConcatenatedSites_8h_source.html +++ b/ConcatenatedSites_8h_source.html @@ -245,7 +245,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Coordinate3D_8h_source.html b/Coordinate3D_8h_source.html index 0756be146d..1769a0f500 100644 --- a/Coordinate3D_8h_source.html +++ b/Coordinate3D_8h_source.html @@ -107,7 +107,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CppUnitCookbook.html b/CppUnitCookbook.html index 7797f4c731..f72372a372 100644 --- a/CppUnitCookbook.html +++ b/CppUnitCookbook.html @@ -340,7 +340,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CtrlVar_8h_source.html b/CtrlVar_8h_source.html index b6434787de..8761605f78 100644 --- a/CtrlVar_8h_source.html +++ b/CtrlVar_8h_source.html @@ -94,7 +94,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CubicGridGeneratorInternal_8h_source.html b/CubicGridGeneratorInternal_8h_source.html index 0b6e2508b4..97edd3aaa2 100644 --- a/CubicGridGeneratorInternal_8h_source.html +++ b/CubicGridGeneratorInternal_8h_source.html @@ -113,7 +113,7 @@
CubicGridGeneratorInternal::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *, double)
read the phase space components and header information
Definition: CubicGridGeneratorInternal.h:30
CubicGridGeneratorInternal::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MkTcTSGenerator and all its included objects.
Definition: CubicGridGeneratorInternal.cpp:29
CubicGridGeneratorInternal::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: CubicGridGeneratorInternal.cpp:61
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -121,7 +121,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/CuboidPyramidalMatrix_8h_source.html b/CuboidPyramidalMatrix_8h_source.html index e5296fdbd9..c2db8680f9 100644 --- a/CuboidPyramidalMatrix_8h_source.html +++ b/CuboidPyramidalMatrix_8h_source.html @@ -156,7 +156,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DOFProfile_8h_source.html b/DOFProfile_8h_source.html index a4b20ce515..706921a409 100644 --- a/DOFProfile_8h_source.html +++ b/DOFProfile_8h_source.html @@ -93,7 +93,7 @@
24 void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final {
25 _globalProfile[uID] = domainDecomp->collCommGetInt();
26 }
-
27 void output(string prefix, long unsigned accumulatedDatasets) final;
+
27 void output(std::string prefix, long unsigned accumulatedDatasets) final;
28 void reset(unsigned long uID) final {
29 _localProfile[uID] = 0;
30 _globalProfile[uID] = 0;
@@ -110,25 +110,26 @@
41 // Global 1D Profile
42 std::map<unsigned, int> _globalProfile;
43
-
44 void writeDataEntry(unsigned long uID, ofstream &outfile) const final;
+
44 void writeDataEntry(unsigned long uID, std::ofstream &outfile) const final;
45};
46
47
48#endif //MARDYN_DOFPROFILE_H
DOFProfile
Records (NO OUTPUT) the DOF of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DOFProfile.h:15
+
DOFProfile::output
void output(std::string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: DOFProfile.cpp:7
DOFProfile::record
void record(Molecule &mol, unsigned long uID) final
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
Definition: DOFProfile.h:18
DOFProfile::comms
int comms() final
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
Definition: DOFProfile.h:32
DOFProfile::collectAppend
void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID) final
Append all necessary communication per bin to the DomainDecomposition. Append from e....
Definition: DOFProfile.h:21
DOFProfile::reset
void reset(unsigned long uID) final
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
Definition: DOFProfile.h:28
DOFProfile::collectRetrieve
void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
Definition: DOFProfile.h:24
-
DOFProfile::output
void output(string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: DOFProfile.cpp:7
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DecompWriter_8h_source.html b/DecompWriter_8h_source.html index 874b52628e..ac138c558f 100644 --- a/DecompWriter_8h_source.html +++ b/DecompWriter_8h_source.html @@ -95,7 +95,7 @@
42 );
44 void finish(ParticleContainer *particleContainer,
45 DomainDecompBase *domainDecomp, Domain *domain);
-
46
+
46
47 std::string getPluginName() {
48 return std::string("DecompWriter");
49 }
@@ -109,12 +109,12 @@
57
58#endif // SRC_IO_DECOMPWRITER_H_
DecompWriter
writes out information about decomposition of the simulation domain.
Definition: DecompWriter.h:14
-
DecompWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: DecompWriter.cpp:66
+
DecompWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: DecompWriter.cpp:63
DecompWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: DecompWriter.h:47
-
DecompWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for DecompWriter.
Definition: DecompWriter.cpp:23
-
DecompWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: DecompWriter.cpp:46
-
DecompWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: DecompWriter.cpp:43
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DecompWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for DecompWriter.
Definition: DecompWriter.cpp:20
+
DecompWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: DecompWriter.cpp:43
+
DecompWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: DecompWriter.cpp:40
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -123,7 +123,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DensityControl_8h_source.html b/DensityControl_8h_source.html index bdbde2eef0..ca91eb5a7e 100644 --- a/DensityControl_8h_source.html +++ b/DensityControl_8h_source.html @@ -174,7 +174,7 @@
DensityControl::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: DensityControl.h:100
DensityControl::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DensityControl and all its included objects.
Definition: DensityControl.cpp:51
DensityControl::beforeForces
void beforeForces(ParticleContainer *, DomainDecompBase *, unsigned long) override
Definition: DensityControl.cpp:131
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -184,7 +184,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DensityProfile_8h_source.html b/DensityProfile_8h_source.html index 6e57a15b6b..f5bb1fce99 100644 --- a/DensityProfile_8h_source.html +++ b/DensityProfile_8h_source.html @@ -92,7 +92,7 @@
23 void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final {
24 _globalProfile[uID] = domainDecomp->collCommGetInt();
25 }
-
26 void output(string prefix, long unsigned accumulatedDatasets) final;
+
26 void output(std::string prefix, long unsigned accumulatedDatasets) final;
27 void reset(unsigned long uID) final {
28 _localProfile[uID] = 0;
29 _globalProfile[uID] = 0;
@@ -109,7 +109,7 @@
40 // Global 1D Profile
41 std::map<unsigned, int> _globalProfile;
42
-
43 void writeDataEntry(unsigned long uID, ofstream &outfile) const final;
+
43 void writeDataEntry(unsigned long uID, std::ofstream &outfile) const final;
44};
45
46
@@ -118,16 +118,17 @@
DensityProfile::collectAppend
void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID) final
Append all necessary communication per bin to the DomainDecomposition. Append from e....
Definition: DensityProfile.h:20
DensityProfile::comms
int comms() final
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
Definition: DensityProfile.h:31
DensityProfile::reset
void reset(unsigned long uID) final
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
Definition: DensityProfile.h:27
-
DensityProfile::output
void output(string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: DensityProfile.cpp:8
+
DensityProfile::output
void output(std::string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: DensityProfile.cpp:8
DensityProfile::collectRetrieve
void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
Definition: DensityProfile.h:23
DensityProfile::record
void record(Molecule &mol, unsigned long uID) final
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
Definition: DensityProfile.h:17
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DirectedPM_8h_source.html b/DirectedPM_8h_source.html index dc7ae221a6..f168e4bd30 100644 --- a/DirectedPM_8h_source.html +++ b/DirectedPM_8h_source.html @@ -163,7 +163,7 @@
115
116public:
117 void init(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override {
-
118 global_log->debug() << "DirectPM enabled" << std::endl;
+
118 Log::global_log->debug() << "DirectPM enabled" << std::endl;
119 _firstTime = true;
120 for (unsigned d = 0; d < 3; d++) {
121 _boxLength[d] = domain->getGlobalLength(d);
@@ -219,12 +219,12 @@
171 _DPMGlobalStream.open("Global_output_DPM_MK.txt", std::ios::out);
172 _DPMGlobalStream << "Ausgabe der globalen Gr��en gerichtete Geschwindigkeit, dichteGas, dichteLiq, druckGas, "
173 "druckLiq, TGas, TLiq, EkinxyzGas, EkinxyzLiq, TGasXZ, TLiqXZ,EkinxzGas und EkinxzLiq,"
-
174 << endl;
-
175 _DPMGlobalStream << endl;
+
174 << std::endl;
+
175 _DPMGlobalStream << std::endl;
176 _DPMGlobalStream << "Timestept \t\t gerichtete Geschw. \t\t dichteGas \t\t dichteLiq \t\t druckGas \t\t "
177 "druckLiq \t\t TGas \t\t TLiq \t\t EkinxyzGas \t\t EkinxyzLiq\t\t TGasXZ\t\t "
178 "TLiqXZ\t\t EkinxzGas \t\t EkinxzLiq\t\t"
-
179 << endl;
+
179 << std::endl;
180 _DPMGlobalStream.close();
181 }
182 void readXML(XMLfileUnits& xmlconfig) override;
@@ -248,7 +248,7 @@
DirectedPM::readXML
void readXML(XMLfileUnits &xmlconfig) override
will be called to read configuration
Definition: DirectedPM.cpp:15
DirectedPM::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: DirectedPM.cpp:44
DirectedPM::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: DirectedPM.cpp:555
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Domain::getGlobalLength
double getGlobalLength(int d) const
return the length of the domain
Definition: Domain.h:163
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -258,7 +258,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DistControl_8h_source.html b/DistControl_8h_source.html index 55693d2aa2..416a46d953 100644 --- a/DistControl_8h_source.html +++ b/DistControl_8h_source.html @@ -91,186 +91,185 @@
19#include "utils/CommVar.h"
20#include "molecules/MoleculeForwardDeclaration.h"
21
-
22using namespace std;
-
23
-
24class XMLfileUnits;
-
25class Domain;
-
26class ParticleContainer;
-
27class DomainDecompBase;
-
28
-
29#define FORMAT_SCI_MAX_DIGITS std::setw(24) << std::scientific << std::setprecision(std::numeric_limits<double>::digits10)
-
30
-
31enum DistControlUpdateMethods
-
32{
-
33 DCUM_UNKNOWN = 0,
-
34 DCUM_DENSITY_PROFILE = 1,
-
35 DCUM_DENSITY_PROFILE_DERIVATION = 2,
-
36// DCUM_FORCE_PROFILE = 3,
-
37};
-
38
-
39enum DistControlInitMethods
-
40{
-
41 DCIM_UNKNOWN = 0,
-
42 DCIM_START_CONFIGURATION = 1,
-
43 DCIM_MIDPOINT_VALUES = 2,
-
44 DCIM_READ_FROM_FILE = 3,
-
45};
-
46
-
47class DistControl : public PluginBase, public ControlInstance, public SubjectBase
-
48{
-
49public:
-
50 DistControl();
-
51 virtual ~DistControl();
-
52
-
53 std::string getShortName() override {return "DiC";}
-
54
-
85 void readXML(XMLfileUnits& xmlconfig) override;
-
86
-
87 void init(ParticleContainer *particleContainer,
-
88 DomainDecompBase *domainDecomp, Domain *domain) override;
-
89
-
90 void beforeEventNewTimestep(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
-
91 unsigned long simstep) override {};
-
92
-
93 void beforeForces(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
-
94 unsigned long simstep) override;
-
95
-
96 void siteWiseForces(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
-
97 unsigned long simstep) override {};
-
98 void afterForces(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
-
99 unsigned long simstep) override {}
-
100
-
101 void endStep(ParticleContainer *particleContainer,
-
102 DomainDecompBase *domainDecomp, Domain *domain,
-
103 unsigned long simstep) override {};
-
104
-
105 void finish(ParticleContainer *particleContainer,
-
106 DomainDecompBase *domainDecomp, Domain *domain) override {}
-
107
-
108 std::string getPluginName() override {return std::string("DistControl");}
-
109 static PluginBase* createInstance() {return new DistControl();}
-
110
-
111 // set subdivision
-
112 void SetSubdivision(const uint32_t& numBins) {_binParams.count = numBins; _nSubdivisionOpt = SDOPT_BY_NUM_SLABS;}
-
113 void SetSubdivision(const double& dBinWidth) {_binParams.width = dBinWidth; _nSubdivisionOpt = SDOPT_BY_SLAB_WIDTH;}
-
114 void PrepareSubdivision(); // need to be called before PrepareDataStructures()
-
115
-
116 // data structures
-
117 void PrepareDataStructures();
-
118
-
119 // init
-
120 void InitPositions(const double& dInterfaceMidLeft, const double& dInterfaceMidRight);
-
121
-
122 double GetInterfaceMidLeft() {return _dInterfaceMidLeft;}
-
123 double GetInterfaceMidRight() {return _dInterfaceMidRight;}
-
124 unsigned int GetUpdateFreq() {return _controlFreqs.update;}
-
125 unsigned int GetWriteFreqProfiles() {return _controlFreqs.write.profiles;}
-
126
-
127 void Init(ParticleContainer* particleContainer);
-
128 void WriteHeader();
-
129 void WriteData(const uint64_t& simstep);
-
130 void WriteDataProfiles(const uint64_t& simstep);
-
131
-
132 // place method inside loop over molecule container
-
133 void SampleProfiles(Molecule* mol);
-
134
-
135 void UpdatePositionsInit(ParticleContainer* particleContainer); // call in Simulation::prepare_start()
-
136 void UpdatePositions(const uint64_t& simstep);
-
137
-
138 // SubjectBase methods
-
139 void registerObserver(ObserverBase* observer) override;
-
140 void unregisterObserver(ObserverBase* observer) override;
-
141 void informObserver() override;
-
142
-
143private:
-
144 // place methods after the loop
-
145 void CalcProfiles();
-
146 void EstimateInterfaceMidpoint(); // called by UpdatePositions
-
147 void EstimateInterfaceMidpointsByForce();
-
148 void ResetLocalValues();
-
149
-
150 // data structures
-
151 void InitDataStructures();
-
152
-
153 // processing profiles
-
154 void SmoothProfile(double* dData, double* dSmoothData, const uint64_t& nNumVals, const uint32_t& nNeighbourVals);
-
155 void SmoothProfiles(const uint32_t& nNeighbourVals);
-
156 void DerivateProfile(double* dDataX, double* dDataY, double* dDerivDataY, const uint64_t& nNumVals, const uint32_t& nNeighbourVals);
-
157 void DerivateProfiles(const uint32_t& nNeighbourVals);
+
22
+
23class XMLfileUnits;
+
24class Domain;
+
25class ParticleContainer;
+
26class DomainDecompBase;
+
27
+
28#define FORMAT_SCI_MAX_DIGITS std::setw(24) << std::scientific << std::setprecision(std::numeric_limits<double>::digits10)
+
29
+
30enum DistControlUpdateMethods
+
31{
+
32 DCUM_UNKNOWN = 0,
+
33 DCUM_DENSITY_PROFILE = 1,
+
34 DCUM_DENSITY_PROFILE_DERIVATION = 2,
+
35// DCUM_FORCE_PROFILE = 3,
+
36};
+
37
+
38enum DistControlInitMethods
+
39{
+
40 DCIM_UNKNOWN = 0,
+
41 DCIM_START_CONFIGURATION = 1,
+
42 DCIM_MIDPOINT_VALUES = 2,
+
43 DCIM_READ_FROM_FILE = 3,
+
44};
+
45
+
46class DistControl : public PluginBase, public ControlInstance, public SubjectBase
+
47{
+
48public:
+
49 DistControl();
+
50 virtual ~DistControl();
+
51
+
52 std::string getShortName() override {return "DiC";}
+
53
+
84 void readXML(XMLfileUnits& xmlconfig) override;
+
85
+
86 void init(ParticleContainer *particleContainer,
+
87 DomainDecompBase *domainDecomp, Domain *domain) override;
+
88
+
89 void beforeEventNewTimestep(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
+
90 unsigned long simstep) override {};
+
91
+
92 void beforeForces(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
+
93 unsigned long simstep) override;
+
94
+
95 void siteWiseForces(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
+
96 unsigned long simstep) override {};
+
97 void afterForces(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
+
98 unsigned long simstep) override {}
+
99
+
100 void endStep(ParticleContainer *particleContainer,
+
101 DomainDecompBase *domainDecomp, Domain *domain,
+
102 unsigned long simstep) override {};
+
103
+
104 void finish(ParticleContainer *particleContainer,
+
105 DomainDecompBase *domainDecomp, Domain *domain) override {}
+
106
+
107 std::string getPluginName() override {return std::string("DistControl");}
+
108 static PluginBase* createInstance() {return new DistControl();}
+
109
+
110 // set subdivision
+
111 void SetSubdivision(const uint32_t& numBins) {_binParams.count = numBins; _nSubdivisionOpt = SDOPT_BY_NUM_SLABS;}
+
112 void SetSubdivision(const double& dBinWidth) {_binParams.width = dBinWidth; _nSubdivisionOpt = SDOPT_BY_SLAB_WIDTH;}
+
113 void PrepareSubdivision(); // need to be called before PrepareDataStructures()
+
114
+
115 // data structures
+
116 void PrepareDataStructures();
+
117
+
118 // init
+
119 void InitPositions(const double& dInterfaceMidLeft, const double& dInterfaceMidRight);
+
120
+
121 double GetInterfaceMidLeft() {return _dInterfaceMidLeft;}
+
122 double GetInterfaceMidRight() {return _dInterfaceMidRight;}
+
123 unsigned int GetUpdateFreq() {return _controlFreqs.update;}
+
124 unsigned int GetWriteFreqProfiles() {return _controlFreqs.write.profiles;}
+
125
+
126 void Init(ParticleContainer* particleContainer);
+
127 void WriteHeader();
+
128 void WriteData(const uint64_t& simstep);
+
129 void WriteDataProfiles(const uint64_t& simstep);
+
130
+
131 // place method inside loop over molecule container
+
132 void SampleProfiles(Molecule* mol);
+
133
+
134 void UpdatePositionsInit(ParticleContainer* particleContainer); // call in Simulation::prepare_start()
+
135 void UpdatePositions(const uint64_t& simstep);
+
136
+
137 // SubjectBase methods
+
138 void registerObserver(ObserverBase* observer) override;
+
139 void unregisterObserver(ObserverBase* observer) override;
+
140 void informObserver() override;
+
141
+
142private:
+
143 // place methods after the loop
+
144 void CalcProfiles();
+
145 void EstimateInterfaceMidpoint(); // called by UpdatePositions
+
146 void EstimateInterfaceMidpointsByForce();
+
147 void ResetLocalValues();
+
148
+
149 // data structures
+
150 void InitDataStructures();
+
151
+
152 // processing profiles
+
153 void SmoothProfile(double* dData, double* dSmoothData, const uint64_t& nNumVals, const uint32_t& nNeighbourVals);
+
154 void SmoothProfiles(const uint32_t& nNeighbourVals);
+
155 void DerivateProfile(double* dDataX, double* dDataY, double* dDerivDataY, const uint64_t& nNumVals, const uint32_t& nNeighbourVals);
+
156 void DerivateProfiles(const uint32_t& nNeighbourVals);
+
157
158
-
159
-
160private:
-
161 double _dInterfaceMidLeft;
-
162 double _dInterfaceMidRight;
-
163
-
164 uint16_t _nNumComponents;
-
165 uint16_t _nTargetCompID;
-
166 uint64_t _nNumValuesScalar;
-
167 std::vector<uint64_t> _nOffsets;
-
168
-
169 CommVar<std::vector<uint64_t> > _nNumMolecules;
-
170 CommVar<std::vector<uint64_t> > _dForceSum;
-
171 std::vector<double> _dMidpointPositions;
-
172 std::vector<double> _dDensityProfile;
-
173 std::vector<double> _dDensityProfileSmoothed;
-
174 std::vector<double> _dDensityProfileSmoothedDerivation;
-
175 std::vector<double> _dForceProfile;
-
176 std::vector<double> _dForceProfileSmoothed;
-
177
-
178 // update method
-
179 int _nMethod;
-
180 double _dVaporDensity;
-
181 uint16_t _nNeighbourValsSmooth;
-
182 uint16_t _nNeighbourValsDerivate;
-
183
-
184 int _nMethodInit;
-
185 std::string _strFilenameInit;
-
186 uint64_t _nRestartTimestep;
-
187
-
188 // write data
-
189 std::string _strFilename;
-
190 std::string _strFilenameProfilesPrefix;
-
191
-
192 // observer
-
193 std::vector<ObserverBase*> _observer;
-
194
-
195 int _nSubdivisionOpt;
-
196
-
197 struct BinParamsType
-
198 {
-
199 uint32_t count;
-
200 double width;
-
201 double invWidth;
-
202 double volume;
-
203 } _binParams;
-
204
-
205 struct ControlFreqType
-
206 {
-
207 uint32_t update;
-
208 struct WriteFreqType
-
209 {
-
210 uint32_t data;
-
211 uint32_t profiles;
-
212 } write;
-
213 } _controlFreqs;
-
214
-
215}; // class DistControl
+
159private:
+
160 double _dInterfaceMidLeft;
+
161 double _dInterfaceMidRight;
+
162
+
163 uint16_t _nNumComponents;
+
164 uint16_t _nTargetCompID;
+
165 uint64_t _nNumValuesScalar;
+
166 std::vector<uint64_t> _nOffsets;
+
167
+
168 CommVar<std::vector<uint64_t> > _nNumMolecules;
+
169 CommVar<std::vector<uint64_t> > _dForceSum;
+
170 std::vector<double> _dMidpointPositions;
+
171 std::vector<double> _dDensityProfile;
+
172 std::vector<double> _dDensityProfileSmoothed;
+
173 std::vector<double> _dDensityProfileSmoothedDerivation;
+
174 std::vector<double> _dForceProfile;
+
175 std::vector<double> _dForceProfileSmoothed;
+
176
+
177 // update method
+
178 int _nMethod;
+
179 double _dVaporDensity;
+
180 uint16_t _nNeighbourValsSmooth;
+
181 uint16_t _nNeighbourValsDerivate;
+
182
+
183 int _nMethodInit;
+
184 std::string _strFilenameInit;
+
185 uint64_t _nRestartTimestep;
+
186
+
187 // write data
+
188 std::string _strFilename;
+
189 std::string _strFilenameProfilesPrefix;
+
190
+
191 // observer
+
192 std::vector<ObserverBase*> _observer;
+
193
+
194 int _nSubdivisionOpt;
+
195
+
196 struct BinParamsType
+
197 {
+
198 uint32_t count;
+
199 double width;
+
200 double invWidth;
+
201 double volume;
+
202 } _binParams;
+
203
+
204 struct ControlFreqType
+
205 {
+
206 uint32_t update;
+
207 struct WriteFreqType
+
208 {
+
209 uint32_t data;
+
210 uint32_t profiles;
+
211 } write;
+
212 } _controlFreqs;
+
213
+
214}; // class DistControl
+
215
216
-
217
-
218#endif /* DISTCONTROL_H_ */
+
217#endif /* DISTCONTROL_H_ */
CommVar
Definition: CommVar.h:17
ControlInstance
Definition: Region.h:29
-
DistControl
Definition: DistControl.h:48
-
DistControl::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: DistControl.h:98
-
DistControl::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: DistControl.h:108
-
DistControl::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: DistControl.h:105
-
DistControl::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DistControl and all its included objects.
Definition: DistControl.cpp:59
-
DistControl::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method will be called first thing in a new timestep.
Definition: DistControl.h:90
-
DistControl::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: DistControl.cpp:237
-
DistControl::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: DistControl.h:101
-
DistControl::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: DistControl.cpp:228
-
DistControl::siteWiseForces
void siteWiseForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method siteWiseForces will be called before forcefields have been applied alterations to sitewise for...
Definition: DistControl.h:96
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DistControl
Definition: DistControl.h:47
+
DistControl::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: DistControl.h:97
+
DistControl::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: DistControl.h:107
+
DistControl::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: DistControl.h:104
+
DistControl::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DistControl and all its included objects.
Definition: DistControl.cpp:58
+
DistControl::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method will be called first thing in a new timestep.
Definition: DistControl.h:89
+
DistControl::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: DistControl.cpp:236
+
DistControl::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: DistControl.h:100
+
DistControl::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: DistControl.cpp:227
+
DistControl::siteWiseForces
void siteWiseForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method siteWiseForces will be called before forcefields have been applied alterations to sitewise for...
Definition: DistControl.h:95
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ObserverBase
Definition: ObserverBase.h:13
@@ -279,11 +278,11 @@
SubjectBase
Definition: ObserverBase.h:20
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-
DistControl::ControlFreqType::WriteFreqType
Definition: DistControl.h:209
+
DistControl::ControlFreqType::WriteFreqType
Definition: DistControl.h:208
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DomainBase_8h_source.html b/DomainBase_8h_source.html index 52310ba3ef..2601a3be1e 100644 --- a/DomainBase_8h_source.html +++ b/DomainBase_8h_source.html @@ -108,7 +108,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DomainDecompBase_8h_source.html b/DomainDecompBase_8h_source.html index 7f9e673ac8..46ea81f66c 100644 --- a/DomainDecompBase_8h_source.html +++ b/DomainDecompBase_8h_source.html @@ -88,183 +88,184 @@
16#include "molecules/MoleculeForwardDeclaration.h"
17#include "utils/Logger.h" // is this used?
18
-
19class Component;
-
20class Domain;
-
21class ParticleContainer;
-
22class XMLfileUnits;
-
23
-
51class DomainDecompBase: public MemoryProfilable {
-
52 friend class NeighbourCommunicationScheme;
-
53 friend class IndirectNeighbourCommunicationScheme;
-
54 friend class DirectNeighbourCommunicationScheme;
-
55public:
-
57 DomainDecompBase();
-
58
-
60 ~DomainDecompBase() override;
-
61
-
62 virtual void readXML(XMLfileUnits& xmlconfig);
+
19
+
20
+
21class Component;
+
22class Domain;
+
23class ParticleContainer;
+
24class XMLfileUnits;
+
25
+
53class DomainDecompBase: public MemoryProfilable {
+
54 friend class NeighbourCommunicationScheme;
+
55 friend class IndirectNeighbourCommunicationScheme;
+
56 friend class DirectNeighbourCommunicationScheme;
+
57public:
+
59 DomainDecompBase();
+
60
+
62 ~DomainDecompBase() override;
63
-
72 void exchangeMolecules(ParticleContainer* moleculeContainer, Domain* domain);
-
73
-
79 virtual void exchangeForces(ParticleContainer* moleculeContainer, Domain* domain);
-
80
-
87 virtual int getNonBlockingStageCount();
-
88
-
97 virtual bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer* moleculeContainer, Domain* domain, double etime);
-
98
-
110 virtual void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer* moleculeContainer, Domain* domain);
-
111
-
121 virtual bool procOwnsPos(double x, double y, double z, Domain* domain) final;
-
122
-
127 void getBoundingBoxMinMax(Domain* domain, double* min, double* max);
-
128
-
132 virtual double getBoundingBoxMin(int dimension, Domain* domain);
-
133
-
137 virtual double getBoundingBoxMax(int dimension, Domain* domain);
-
138
-
143 virtual void printDecomp(const std::string &filename, Domain *domain, ParticleContainer *particleContainer);
-
144
-
145
-
148 virtual int getRank() const;
-
149
-
152 virtual int getNumProcs() const;
-
153
-
155 virtual void barrier() const;
-
156
-
158 virtual double getTime() const;
-
159
-
161 virtual unsigned Ndistribution(unsigned localN, float* minrnd, float* maxrnd);
-
162
-
164 virtual void assertIntIdentity(int IX);
-
165 virtual void assertDisjunctivity(ParticleContainer* moleculeContainer) const;
-
166
-
175 double getIOCutoffRadius(int dim, Domain* domain, ParticleContainer* moleculeContainer);
-
176
-
177
-
178#ifdef ENABLE_MPI
-
183 void writeMoleculesToMPIFileBinary(const std::string& filename, ParticleContainer* moleculeContainer) const;
-
184#endif // ENABLE_MPI
-
185
-
193 void writeMoleculesToFile(const std::string& filename, ParticleContainer* moleculeContainer, bool binary = false) const;
-
194
-
195
-
196 void updateSendLeavingWithCopies(bool sendTogether){
-
197 using Log::global_log;
-
198 // Count all processes that need to send separately
-
199 collCommInit(1);
-
200 collCommAppendInt(!sendTogether);
-
201 collCommAllreduceSum();
-
202 _sendLeavingAndCopiesSeparately = collCommGetInt();
-
203 collCommFinalize();
-
204
+
64 virtual void readXML(XMLfileUnits& xmlconfig);
+
65
+
74 void exchangeMolecules(ParticleContainer* moleculeContainer, Domain* domain);
+
75
+
81 virtual void exchangeForces(ParticleContainer* moleculeContainer, Domain* domain);
+
82
+
89 virtual int getNonBlockingStageCount();
+
90
+
99 virtual bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer* moleculeContainer, Domain* domain, double etime);
+
100
+
112 virtual void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer* moleculeContainer, Domain* domain);
+
113
+
123 virtual bool procOwnsPos(double x, double y, double z, Domain* domain) final;
+
124
+
129 void getBoundingBoxMinMax(Domain* domain, double* min, double* max);
+
130
+
134 virtual double getBoundingBoxMin(int dimension, Domain* domain);
+
135
+
139 virtual double getBoundingBoxMax(int dimension, Domain* domain);
+
140
+
145 virtual void printDecomp(const std::string &filename, Domain *domain, ParticleContainer *particleContainer);
+
146
+
147
+
150 virtual int getRank() const;
+
151
+
154 virtual int getNumProcs() const;
+
155
+
157 virtual void barrier() const;
+
158
+
160 virtual double getTime() const;
+
161
+
163 virtual unsigned Ndistribution(unsigned localN, float* minrnd, float* maxrnd);
+
164
+
166 virtual void assertIntIdentity(int IX);
+
167 virtual void assertDisjunctivity(ParticleContainer* moleculeContainer) const;
+
168
+
177 double getIOCutoffRadius(int dim, Domain* domain, ParticleContainer* moleculeContainer);
+
178
+
179
+
180#ifdef ENABLE_MPI
+
185 void writeMoleculesToMPIFileBinary(const std::string& filename, ParticleContainer* moleculeContainer) const;
+
186#endif // ENABLE_MPI
+
187
+
195 void writeMoleculesToFile(const std::string& filename, ParticleContainer* moleculeContainer, bool binary = false) const;
+
196
+
197
+
198 void updateSendLeavingWithCopies(bool sendTogether){
+
199 // Count all processes that need to send separately
+
200 collCommInit(1);
+
201 collCommAppendInt(!sendTogether);
+
202 collCommAllreduceSum();
+
203 _sendLeavingAndCopiesSeparately = collCommGetInt();
+
204 collCommFinalize();
205
-
206 global_log->info() << "Sending leaving particles and halo copies "
-
207 << (sendLeavingWithCopies() ? "together" : "separately") << std::endl;
-
208 }
-
209
-
210 bool sendLeavingWithCopies() const{
-
211 // No process needs to send separately => send together
-
212 return _sendLeavingAndCopiesSeparately == 0;
-
213 }
-
214
+
206
+
207 Log::global_log->info() << "Sending leaving particles and halo copies "
+
208 << (sendLeavingWithCopies() ? "together" : "separately") << std::endl;
+
209 }
+
210
+
211 bool sendLeavingWithCopies() const{
+
212 // No process needs to send separately => send together
+
213 return _sendLeavingAndCopiesSeparately == 0;
+
214 }
215
-
216 //##################################################################
-
217 // The following methods with prefix "collComm" are all used
-
218 // in the context of collective communication. Each of the methods
-
219 // basically has to call the corresponding method from the class
-
220 // CollectiveCommunication (or CollectiveCommDummy in the sequential
-
221 // case). To get information about how to use this methods, read
-
222 // the documentation of the class CollectiveCommunication.
-
223 //##################################################################
-
225 virtual void collCommInit(int numValues, int key=0);
-
227 virtual void collCommFinalize();
-
229 virtual void collCommAppendInt(int intValue);
-
231 virtual void collCommAppendUnsLong(unsigned long unsLongValue);
-
233 virtual void collCommAppendFloat(float floatValue);
-
235 virtual void collCommAppendDouble(double doubleValue);
-
237 virtual void collCommAppendLongDouble(long double longDoubleValue);
-
239 virtual int collCommGetInt();
-
241 virtual unsigned long collCommGetUnsLong();
-
243 virtual float collCommGetFloat();
-
245 virtual double collCommGetDouble();
-
247 virtual long double collCommGetLongDouble();
-
249 virtual void collCommAllreduceSum();
-
251 virtual void collCommAllreduceSumAllowPrevious();
-
253 virtual void collCommAllreduceCustom(ReduceType type);
-
255 virtual void collCommScanSum();
-
257 virtual void collCommBroadcast(int root = 0);
-
258 //returns the ranks of the neighbours
-
259 virtual std::vector<int> getNeighbourRanks(){
-
260 return std::vector<int>(0);
-
261 }
-
262 //returns the ranks of the neighbours
-
263 virtual std::vector<int> getNeighbourRanksFullShell(){
-
264 std::cout << "Not yet implemented";
-
265 return std::vector<int>(0);
-
266 }
-
267
-
268 //returns the ranks of all ranks
-
269 virtual std::vector<std::vector<std::vector<int>>> getAllRanks(){
-
270 std::cout << "Not yet implemented";
-
271 return std::vector<std::vector<std::vector<int>>>(0);
-
272 }
-
273#if defined(ENABLE_MPI)
-
274 virtual MPI_Comm getCommunicator(){
-
275 return MPI_COMM_WORLD;
-
276 }
-
277#endif
-
278
-
279 virtual size_t getTotalSize() override {
-
280 return _collCommBase.getTotalSize();
-
281 }
-
282 virtual void printSubInfo(int offset) override {
-
283 return;
-
284 }
-
285 virtual std::string getName() override {
-
286 return "DomainDecompBase";
-
287 }
-
288
-
289 virtual void printCommunicationPartners(std::string filename) const {};
-
290
-
291protected:
-
292 void addLeavingMolecules(std::vector<Molecule>& invalidMolecules, ParticleContainer* moleculeContainer);
-
293
-
300 void handleDomainLeavingParticles(unsigned dim, ParticleContainer* moleculeContainer) const;
-
301
-
312 void handleDomainLeavingParticlesDirect(const HaloRegion& haloRegion, ParticleContainer* moleculeContainer,
-
313 std::vector<Molecule>& invalidParticles) const;
-
314
-
320 void handleForceExchange(unsigned dim, ParticleContainer* moleculeContainer) const;
-
321
-
327 virtual void handleForceExchangeDirect(const HaloRegion& haloRegion, ParticleContainer* moleculeContainer) const;
-
328
-
329 void populateHaloLayerWithCopies(unsigned dim, ParticleContainer* moleculeContainer) const;
-
330
-
331 void populateHaloLayerWithCopiesDirect(const HaloRegion& haloRegion, ParticleContainer* moleculeContainer,
-
332 bool positionCheck = true) const;
-
333
-
335 int _rank;
-
336
-
338 int _numProcs;
-
339
-
340private:
-
341 CollectiveCommBase _collCommBase;
-
342 int _sendLeavingAndCopiesSeparately = 0;
-
343};
-
344
-
345#endif /* DOMAINDECOMPBASE_H_ */
+
216
+
217 //##################################################################
+
218 // The following methods with prefix "collComm" are all used
+
219 // in the context of collective communication. Each of the methods
+
220 // basically has to call the corresponding method from the class
+
221 // CollectiveCommunication (or CollectiveCommDummy in the sequential
+
222 // case). To get information about how to use this methods, read
+
223 // the documentation of the class CollectiveCommunication.
+
224 //##################################################################
+
226 virtual void collCommInit(int numValues, int key=0);
+
228 virtual void collCommFinalize();
+
230 virtual void collCommAppendInt(int intValue);
+
232 virtual void collCommAppendUnsLong(unsigned long unsLongValue);
+
234 virtual void collCommAppendFloat(float floatValue);
+
236 virtual void collCommAppendDouble(double doubleValue);
+
238 virtual void collCommAppendLongDouble(long double longDoubleValue);
+
240 virtual int collCommGetInt();
+
242 virtual unsigned long collCommGetUnsLong();
+
244 virtual float collCommGetFloat();
+
246 virtual double collCommGetDouble();
+
248 virtual long double collCommGetLongDouble();
+
250 virtual void collCommAllreduceSum();
+
252 virtual void collCommAllreduceSumAllowPrevious();
+
254 virtual void collCommAllreduceCustom(ReduceType type);
+
256 virtual void collCommScanSum();
+
258 virtual void collCommBroadcast(int root = 0);
+
259 //returns the ranks of the neighbours
+
260 virtual std::vector<int> getNeighbourRanks(){
+
261 return std::vector<int>(0);
+
262 }
+
263 //returns the ranks of the neighbours
+
264 virtual std::vector<int> getNeighbourRanksFullShell(){
+
265 std::cout << "Not yet implemented";
+
266 return std::vector<int>(0);
+
267 }
+
268
+
269 //returns the ranks of all ranks
+
270 virtual std::vector<std::vector<std::vector<int>>> getAllRanks(){
+
271 std::cout << "Not yet implemented";
+
272 return std::vector<std::vector<std::vector<int>>>(0);
+
273 }
+
274#if defined(ENABLE_MPI)
+
275 virtual MPI_Comm getCommunicator(){
+
276 return MPI_COMM_WORLD;
+
277 }
+
278#endif
+
279
+
280 virtual size_t getTotalSize() override {
+
281 return _collCommBase.getTotalSize();
+
282 }
+
283 virtual void printSubInfo(int offset) override {
+
284 return;
+
285 }
+
286 virtual std::string getName() override {
+
287 return "DomainDecompBase";
+
288 }
+
289
+
290 virtual void printCommunicationPartners(std::string filename) const {};
+
291
+
292protected:
+
293 void addLeavingMolecules(std::vector<Molecule>& invalidMolecules, ParticleContainer* moleculeContainer);
+
294
+
301 void handleDomainLeavingParticles(unsigned dim, ParticleContainer* moleculeContainer) const;
+
302
+
313 void handleDomainLeavingParticlesDirect(const HaloRegion& haloRegion, ParticleContainer* moleculeContainer,
+
314 std::vector<Molecule>& invalidParticles) const;
+
315
+
321 void handleForceExchange(unsigned dim, ParticleContainer* moleculeContainer) const;
+
322
+
328 virtual void handleForceExchangeDirect(const HaloRegion& haloRegion, ParticleContainer* moleculeContainer) const;
+
329
+
330 void populateHaloLayerWithCopies(unsigned dim, ParticleContainer* moleculeContainer) const;
+
331
+
332 void populateHaloLayerWithCopiesDirect(const HaloRegion& haloRegion, ParticleContainer* moleculeContainer,
+
333 bool positionCheck = true) const;
+
334
+
336 int _rank;
+
337
+
339 int _numProcs;
+
340
+
341private:
+
342 CollectiveCommBase _collCommBase;
+
343 int _sendLeavingAndCopiesSeparately = 0;
+
344};
+
345
+
346#endif /* DOMAINDECOMPBASE_H_ */
CollectiveCommBase
This class is a dummy class which ensures that the collective communication commands also work if the...
Definition: CollectiveCommBase.h:21
CollectiveCommBase::getTotalSize
virtual size_t getTotalSize() override
Definition: CollectiveCommBase.h:156
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
DirectNeighbourCommunicationScheme
Definition: NeighbourCommunicationScheme.h:128
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
DomainDecompBase::collCommAppendFloat
virtual void collCommAppendFloat(float floatValue)
has to call appendFloat method of a CollComm class
Definition: DomainDecompBase.cpp:560
DomainDecompBase::handleDomainLeavingParticlesDirect
void handleDomainLeavingParticlesDirect(const HaloRegion &haloRegion, ParticleContainer *moleculeContainer, std::vector< Molecule > &invalidParticles) const
Definition: DomainDecompBase.cpp:223
DomainDecompBase::collCommGetDouble
virtual double collCommGetDouble()
has to call getDouble method of a CollComm class
Definition: DomainDecompBase.cpp:584
DomainDecompBase::collCommAppendInt
virtual void collCommAppendInt(int intValue)
has to call appendInt method of a CollComm class
Definition: DomainDecompBase.cpp:552
-
DomainDecompBase::_numProcs
int _numProcs
total number of processes in the simulation
Definition: DomainDecompBase.h:338
+
DomainDecompBase::_numProcs
int _numProcs
total number of processes in the simulation
Definition: DomainDecompBase.h:339
DomainDecompBase::writeMoleculesToMPIFileBinary
void writeMoleculesToMPIFileBinary(const std::string &filename, ParticleContainer *moleculeContainer) const
appends molecule data to the file. The format is the same as that of the input file This version uses...
Definition: DomainDecompBase.cpp:448
-
DomainDecompBase::_rank
int _rank
the id of the current process
Definition: DomainDecompBase.h:335
+
DomainDecompBase::_rank
int _rank
the id of the current process
Definition: DomainDecompBase.h:336
DomainDecompBase::balanceAndExchange
virtual void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain)
balance the load (and optimize communication) and exchange boundary particles
Definition: DomainDecompBase.cpp:399
DomainDecompBase::collCommInit
virtual void collCommInit(int numValues, int key=0)
has to call init method of a CollComm class
Definition: DomainDecompBase.cpp:544
DomainDecompBase::queryBalanceAndExchangeNonBlocking
virtual bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, double etime)
Checks whether the balance and exchange step can be performed non-blocking.
Definition: DomainDecompBase.cpp:395
@@ -314,7 +315,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DomainDecompMPIBase_8h_source.html b/DomainDecompMPIBase_8h_source.html index 524ec22124..3cda4f5a27 100644 --- a/DomainDecompMPIBase_8h_source.html +++ b/DomainDecompMPIBase_8h_source.html @@ -262,37 +262,37 @@
275};
276
277#endif /* DOMAINDECOMPMPIBASE_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
DomainDecompMPIBase
Definition: DomainDecompMPIBase.h:30
DomainDecompMPIBase::barrier
void barrier() const override
synchronizes all processes
Definition: DomainDecompMPIBase.h:37
DomainDecompMPIBase::collCommGetDouble
double collCommGetDouble() override
has to call getDouble method of a CollComm class
Definition: DomainDecompMPIBase.h:97
-
DomainDecompMPIBase::assertIntIdentity
void assertIntIdentity(int IX) override
checks identity of random number generators
Definition: DomainDecompMPIBase.cpp:191
+
DomainDecompMPIBase::assertIntIdentity
void assertIntIdentity(int IX) override
checks identity of random number generators
Definition: DomainDecompMPIBase.cpp:189
DomainDecompMPIBase::prepareNonBlockingStage
virtual void prepareNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber)=0
DomainDecompMPIBase::collCommInit
void collCommInit(int numValues, int key=0) override
has to call init method of a CollComm class
Definition: DomainDecompMPIBase.h:57
DomainDecompMPIBase::collCommFinalize
void collCommFinalize() override
has to call finalize method of a CollComm class
Definition: DomainDecompMPIBase.h:61
-
DomainDecompMPIBase::assertDisjunctivity
void assertDisjunctivity(ParticleContainer *moleculeContainer) const override
Definition: DomainDecompMPIBase.cpp:208
+
DomainDecompMPIBase::assertDisjunctivity
void assertDisjunctivity(ParticleContainer *moleculeContainer) const override
Definition: DomainDecompMPIBase.cpp:206
DomainDecompMPIBase::collCommGetFloat
float collCommGetFloat() override
has to call getFloat method of a CollComm class
Definition: DomainDecompMPIBase.h:93
-
DomainDecompMPIBase::balanceAndExchangeInitNonBlocking
virtual void balanceAndExchangeInitNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain)
Definition: DomainDecompMPIBase.cpp:261
+
DomainDecompMPIBase::balanceAndExchangeInitNonBlocking
virtual void balanceAndExchangeInitNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain)
Definition: DomainDecompMPIBase.cpp:259
DomainDecompMPIBase::collCommGetLongDouble
long double collCommGetLongDouble() override
has to call getLongDouble method of a CollComm class
Definition: DomainDecompMPIBase.h:101
DomainDecompMPIBase::collCommGetInt
int collCommGetInt() override
has to call getInt method of a CollComm class
Definition: DomainDecompMPIBase.h:85
-
DomainDecompMPIBase::prepareNonBlockingStageImpl
virtual void prepareNonBlockingStageImpl(ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber, MessageType msgType, bool removeRecvDuplicates=false)
Definition: DomainDecompMPIBase.cpp:267
-
DomainDecompMPIBase::readXML
virtual void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DomainDecompMPIBase.
Definition: DomainDecompMPIBase.cpp:60
+
DomainDecompMPIBase::prepareNonBlockingStageImpl
virtual void prepareNonBlockingStageImpl(ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber, MessageType msgType, bool removeRecvDuplicates=false)
Definition: DomainDecompMPIBase.cpp:265
+
DomainDecompMPIBase::readXML
virtual void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DomainDecompMPIBase.
Definition: DomainDecompMPIBase.cpp:58
DomainDecompMPIBase::collCommScanSum
void collCommScanSum() override
has to call scanSum method of a CollComm class (none in sequential version)
Definition: DomainDecompMPIBase.h:115
-
DomainDecompMPIBase::getNonBlockingStageCount
virtual int getNonBlockingStageCount() override
Definition: DomainDecompMPIBase.cpp:133
+
DomainDecompMPIBase::getNonBlockingStageCount
virtual int getNonBlockingStageCount() override
Definition: DomainDecompMPIBase.cpp:131
DomainDecompMPIBase::collCommAllreduceSum
void collCommAllreduceSum() override
has to call allreduceSum method of a CollComm class (none in sequential version)
Definition: DomainDecompMPIBase.h:105
DomainDecompMPIBase::collCommAppendDouble
void collCommAppendDouble(double doubleValue) override
has to call appendDouble method of a CollComm class
Definition: DomainDecompMPIBase.h:77
DomainDecompMPIBase::collCommBroadcast
void collCommBroadcast(int root=0) override
has to call broadcast method of a CollComm class (none in sequential version)
Definition: DomainDecompMPIBase.h:119
DomainDecompMPIBase::finishNonBlockingStage
virtual void finishNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber)=0
-
DomainDecompMPIBase::Ndistribution
unsigned Ndistribution(unsigned localN, float *minrnd, float *maxrnd) override
returns total number of molecules
Definition: DomainDecompMPIBase.cpp:175
-
DomainDecompMPIBase::collCommAllreduceSumAllowPrevious
void collCommAllreduceSumAllowPrevious() override
has to call allreduceSum method of a CollComm class (none in sequential version), allows for values o...
Definition: DomainDecompMPIBase.cpp:362
-
DomainDecompMPIBase::finishNonBlockingStageImpl
virtual void finishNonBlockingStageImpl(ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber, MessageType msgType, bool removeRecvDuplicates=false)
Definition: DomainDecompMPIBase.cpp:274
+
DomainDecompMPIBase::Ndistribution
unsigned Ndistribution(unsigned localN, float *minrnd, float *maxrnd) override
returns total number of molecules
Definition: DomainDecompMPIBase.cpp:173
+
DomainDecompMPIBase::collCommAllreduceSumAllowPrevious
void collCommAllreduceSumAllowPrevious() override
has to call allreduceSum method of a CollComm class (none in sequential version), allows for values o...
Definition: DomainDecompMPIBase.cpp:360
+
DomainDecompMPIBase::finishNonBlockingStageImpl
virtual void finishNonBlockingStageImpl(ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber, MessageType msgType, bool removeRecvDuplicates=false)
Definition: DomainDecompMPIBase.cpp:272
DomainDecompMPIBase::collCommAppendLongDouble
void collCommAppendLongDouble(long double longDoubleValue) override
has to call appendLongDouble method of a CollComm class
Definition: DomainDecompMPIBase.h:81
-
DomainDecompMPIBase::printDecomp
virtual void printDecomp(const std::string &filename, Domain *domain, ParticleContainer *particleContainer) override
writes information about the current decomposition into the given file
Definition: DomainDecompMPIBase.cpp:307
+
DomainDecompMPIBase::printDecomp
virtual void printDecomp(const std::string &filename, Domain *domain, ParticleContainer *particleContainer) override
writes information about the current decomposition into the given file
Definition: DomainDecompMPIBase.cpp:305
DomainDecompMPIBase::collCommAppendInt
void collCommAppendInt(int intValue) override
has to call appendInt method of a CollComm class
Definition: DomainDecompMPIBase.h:65
DomainDecompMPIBase::collCommAppendUnsLong
void collCommAppendUnsLong(unsigned long unsLongValue) override
has to call appendUnsLong method of a CollComm class
Definition: DomainDecompMPIBase.h:69
-
DomainDecompMPIBase::exchangeForces
void exchangeForces(ParticleContainer *moleculeContainer, Domain *domain) override
Exchanges forces at the domain boundaries if it's required by the cell container.
Definition: DomainDecompMPIBase.cpp:293
-
DomainDecompMPIBase::setCommunicationScheme
virtual void setCommunicationScheme(const std::string &scheme, const std::string &comScheme)
Definition: DomainDecompMPIBase.cpp:137
-
DomainDecompMPIBase::exchangeMoleculesMPI
void exchangeMoleculesMPI(ParticleContainer *moleculeContainer, Domain *domain, MessageType msgType, bool doHaloPositionCheck=true, bool removeRecvDuplicates=false)
exchange molecules between processes
Definition: DomainDecompMPIBase.cpp:280
+
DomainDecompMPIBase::exchangeForces
void exchangeForces(ParticleContainer *moleculeContainer, Domain *domain) override
Exchanges forces at the domain boundaries if it's required by the cell container.
Definition: DomainDecompMPIBase.cpp:291
+
DomainDecompMPIBase::setCommunicationScheme
virtual void setCommunicationScheme(const std::string &scheme, const std::string &comScheme)
Definition: DomainDecompMPIBase.cpp:135
+
DomainDecompMPIBase::exchangeMoleculesMPI
void exchangeMoleculesMPI(ParticleContainer *moleculeContainer, Domain *domain, MessageType msgType, bool doHaloPositionCheck=true, bool removeRecvDuplicates=false)
exchange molecules between processes
Definition: DomainDecompMPIBase.cpp:278
DomainDecompMPIBase::collCommAppendFloat
void collCommAppendFloat(float floatValue) override
has to call appendFloat method of a CollComm class
Definition: DomainDecompMPIBase.h:73
DomainDecompMPIBase::collCommAllreduceCustom
void collCommAllreduceCustom(ReduceType type) override
has to call allreduceCustom method of a CollComm class (none in sequential version)
Definition: DomainDecompMPIBase.h:111
DomainDecompMPIBase::_forceDirectPP
bool _forceDirectPP
Definition: DomainDecompMPIBase.h:267
@@ -307,7 +307,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DomainDecomposition_8h_source.html b/DomainDecomposition_8h_source.html index cb280576d2..c006837fb1 100644 --- a/DomainDecomposition_8h_source.html +++ b/DomainDecomposition_8h_source.html @@ -98,7 +98,7 @@
51
52 //returns a vector of the neighbour ranks in x y and z direction (only neighbours connected by an area to local area)
53 std::vector<int> getNeighbourRanks() override;
-
54
+
54
55 //returns a vector of all 26 neighbour ranks in x y and z direction
56 std::vector<int> getNeighbourRanksFullShell() override;
57
@@ -131,17 +131,17 @@
84#endif /* DOMAINDECOMPOSITION_H_ */
DomainDecompMPIBase
Definition: DomainDecompMPIBase.h:30
DomainDecomposition
Basic domain decomposition based parallelisation, dividing the domain into #procs equal sized cuboids...
Definition: DomainDecomposition.h:20
-
DomainDecomposition::finishNonBlockingStage
void finishNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: DomainDecomposition.cpp:71
+
DomainDecomposition::finishNonBlockingStage
void finishNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: DomainDecomposition.cpp:69
DomainDecomposition::_gridSize
std::array< int, DIMgeom > _gridSize
Number of processes in each dimension of the MPI process grid.
Definition: DomainDecomposition.h:80
-
DomainDecomposition::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DomainDecomposition and all its included objects.
Definition: DomainDecomposition.cpp:105
+
DomainDecomposition::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DomainDecomposition and all its included objects.
Definition: DomainDecomposition.cpp:103
DomainDecomposition::_coords
int _coords[DIMgeom]
Coordinate of the process in the MPI process grid.
Definition: DomainDecomposition.h:81
-
DomainDecomposition::DomainDecomposition
DomainDecomposition()
The constructor has to determine the own rank and the number of neighbours and sets up the topology.
Definition: DomainDecomposition.cpp:15
-
DomainDecomposition::queryBalanceAndExchangeNonBlocking
bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, double etime) override
Checks whether the balance and exchange step can be performed non-blocking.
Definition: DomainDecomposition.cpp:84
-
DomainDecomposition::getNeighbourRanksFullShell
std::vector< int > getNeighbourRanksFullShell() override
Definition: DomainDecomposition.cpp:147
-
DomainDecomposition::balanceAndExchange
void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain) override
balance the load (and optimize communication) and exchange boundary particles
Definition: DomainDecomposition.cpp:89
-
DomainDecomposition::getBoundingBoxMin
double getBoundingBoxMin(int dimension, Domain *domain) override
get the minimum of the bounding box of this process' domain in the given dimension (0,...
Definition: DomainDecomposition.cpp:117
-
DomainDecomposition::prepareNonBlockingStage
void prepareNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: DomainDecomposition.cpp:57
-
DomainDecomposition::getBoundingBoxMax
double getBoundingBoxMax(int dimension, Domain *domain) override
get the maximum of the bounding box of this process' domain in the given dimension (0,...
Definition: DomainDecomposition.cpp:121
+
DomainDecomposition::DomainDecomposition
DomainDecomposition()
The constructor has to determine the own rank and the number of neighbours and sets up the topology.
Definition: DomainDecomposition.cpp:13
+
DomainDecomposition::queryBalanceAndExchangeNonBlocking
bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, double etime) override
Checks whether the balance and exchange step can be performed non-blocking.
Definition: DomainDecomposition.cpp:82
+
DomainDecomposition::getNeighbourRanksFullShell
std::vector< int > getNeighbourRanksFullShell() override
Definition: DomainDecomposition.cpp:145
+
DomainDecomposition::balanceAndExchange
void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain) override
balance the load (and optimize communication) and exchange boundary particles
Definition: DomainDecomposition.cpp:87
+
DomainDecomposition::getBoundingBoxMin
double getBoundingBoxMin(int dimension, Domain *domain) override
get the minimum of the bounding box of this process' domain in the given dimension (0,...
Definition: DomainDecomposition.cpp:115
+
DomainDecomposition::prepareNonBlockingStage
void prepareNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: DomainDecomposition.cpp:55
+
DomainDecomposition::getBoundingBoxMax
double getBoundingBoxMax(int dimension, Domain *domain) override
get the maximum of the bounding box of this process' domain in the given dimension (0,...
Definition: DomainDecomposition.cpp:119
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
@@ -149,7 +149,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Domain_8h_source.html b/Domain_8h_source.html index ab9b67578f..29bbe4d396 100644 --- a/Domain_8h_source.html +++ b/Domain_8h_source.html @@ -84,8 +84,8 @@
12#include "ensemble/EnsembleBase.h"
13#include "Simulation.h"
14#include "utils/CommVar.h"
-
15/*
-
16 * TODO add comments for variables
+
15/*
+
16 * TODO add comments for variables
17 */
18#define CHECKPOINT_FILE_VERSION 20160512
20#define MIN_BETA 0.9
@@ -103,7 +103,7 @@
51 Domain(Domain &domain);
52
53 Domain& operator=(Domain &domain);
-
54
+
54
55public:
57 Domain(int rank);
58
@@ -126,19 +126,19 @@
129 void setLocalUpot(double Upot);
130
132 double getLocalUpot() const;
-
133
+
133
135 void setLocalUpotCompSpecific(double UpotCspec);
136
138 void setNumFluidComponents(unsigned nc);
-
139
+
139
141 unsigned getNumFluidComponents();
-
142
+
142
144 double getLocalUpotCompSpecific();
145
147 void setLocalVirial(double Virial);
148
150 double getLocalVirial() const;
-
151
+
151
153 double getGlobalBetaTrans();
154 double getGlobalBetaTrans(int thermostat);
155
@@ -156,7 +156,7 @@
177 void setGlobalTemperature(double T) { setTargetTemperature(0, T); }
178 void setTargetTemperature(int thermostatID, double T);
179
-
181 std::vector<double> & getmixcoeff();
+
181 std::vector<double> & getmixcoeff();
182
184 double getepsilonRF() const;
185
@@ -165,7 +165,7 @@
199 unsigned long getglobalNumMolecules(bool bUpdate = true, ParticleContainer* particleContainer = nullptr, DomainDecompBase* domainDecomp = nullptr);
200
202 void setglobalNumMolecules(unsigned long glnummol);
-
203
+
203
206 void updateglobalNumMolecules(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp);
207
209 CommVar<uint64_t> getMaxMoleculeID() const;
@@ -191,7 +191,7 @@
245 this->_localThermostatN[thermostat] = N;
246 this->_localRotationalDOF[thermostat] = rotDOF;
247 }
-
248
+
248
250 double getglobalRho();
251
253 void setglobalRho(double grho);
@@ -258,12 +258,12 @@
384 double cv();
385
386 // by Stefan Becker <stefan.becker@mv.uni-kl.de>
-
387 /* method returning the sigma parameter of a component
+
387 /* method returning the sigma parameter of a component
388 => needed in the output of the MmspdWriter (specifying the particles' radii in a movie) */
389 double getSigma(unsigned cid, unsigned nthSigma);
390 // needed for the MmspdWriter (MegaMol)
391 unsigned getNumberOfComponents();
-
392
+
392
393 void setUpotCorr(double upotcorr){ _UpotCorr = upotcorr; }
394 void setVirialCorr(double virialcorr){ _VirialCorr = virialcorr; }
395
@@ -318,8 +318,8 @@
471 int _universalSelectiveThermostatError;
472
474 std::map<int, double> _local2KETrans;
-
477 std::map<int, double> _local2KERot;
-
478
+
477 std::map<int, double> _local2KERot;
+
478
485 double _epsilonRF;
486
488 double _UpotCorr;
@@ -337,69 +337,69 @@
504#endif /*DOMAIN_H_*/
CommVar
Definition: CommVar.h:17
Comp2Param
Definition: Comp2Param.h:15
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Domain::getThermostat
int getThermostat(int cid)
thermostat to be applied to component cid
Definition: Domain.h:335
-
Domain::getGlobalBetaTrans
double getGlobalBetaTrans()
get thermostat scaling for translations
Definition: Domain.cpp:122
-
Domain::getmixcoeff
std::vector< double > & getmixcoeff()
get the mixcoeff
Definition: Domain.cpp:718
-
Domain::getLocalUpotCompSpecific
double getLocalUpotCompSpecific()
get the fluid and fluid-solid potential of the local process
Definition: Domain.cpp:854
+
Domain::getmixcoeff
std::vector< double > & getmixcoeff()
get the mixcoeff
Definition: Domain.cpp:716
+
Domain::getGlobalBetaTrans
double getGlobalBetaTrans()
get thermostat scaling for translations
Definition: Domain.cpp:120
+
Domain::getLocalUpotCompSpecific
double getLocalUpotCompSpecific()
get the fluid and fluid-solid potential of the local process
Definition: Domain.cpp:852
Domain::maxThermostat
unsigned maxThermostat()
returns the ID of the "last" thermostat in the system
Definition: Domain.h:346
-
Domain::getLocalUpot
double getLocalUpot() const
get the potential of the local process
Definition: Domain.cpp:115
-
Domain::getAverageGlobalVirial
double getAverageGlobalVirial()
get the global average virial per particle
Definition: Domain.cpp:146
+
Domain::getLocalUpot
double getLocalUpot() const
get the potential of the local process
Definition: Domain.cpp:113
+
Domain::getAverageGlobalVirial
double getAverageGlobalVirial()
get the global average virial per particle
Definition: Domain.cpp:144
Domain::setComponentThermostat
void setComponentThermostat(int cid, int thermostat)
associates a component with a thermostat
Definition: Domain.h:352
-
Domain::setLocalUpotCompSpecific
void setLocalUpotCompSpecific(double UpotCspec)
set the fluid and fluid-solid potential of the local process
Definition: Domain.cpp:852
-
Domain::getAverageGlobalUpot
double getAverageGlobalUpot()
get the global average potential per particle
Definition: Domain.cpp:148
-
Domain::getNumFluidComponents
unsigned getNumFluidComponents()
get the numbr of fluid molecules as specified in the config file (*_1R.cfg)
Definition: Domain.cpp:865
+
Domain::setLocalUpotCompSpecific
void setLocalUpotCompSpecific(double UpotCspec)
set the fluid and fluid-solid potential of the local process
Definition: Domain.cpp:850
+
Domain::getAverageGlobalUpot
double getAverageGlobalUpot()
get the global average potential per particle
Definition: Domain.cpp:146
+
Domain::getNumFluidComponents
unsigned getNumFluidComponents()
get the numbr of fluid molecules as specified in the config file (*_1R.cfg)
Definition: Domain.cpp:863
Domain::severalThermostats
bool severalThermostats()
returns whether there are several distinct thermostats in the system
Definition: Domain.h:332
Domain::calculateGlobalValues
void calculateGlobalValues(DomainDecompBase *domainDecomp, ParticleContainer *particleContainer)
calls this->calculateGlobalValues with Tfactor = 1 and without velocity collection
Definition: Domain.h:299
Domain::getGlobalCurrentTemperature
double getGlobalCurrentTemperature()
get the global temperature for the whole system (i.e. thermostat ID 0)
Definition: Domain.h:172
Domain::getThermostatDirectedVelocity
double getThermostatDirectedVelocity(int thermostat, int d)
returns the directed velocity associated with a thermostat
Definition: Domain.h:329
Domain::setLocalNrotDOF
void setLocalNrotDOF(int thermostat, unsigned long N, unsigned long rotDOF)
sets _localThermostatN and _localRotationalDOF for thermostat
Definition: Domain.h:244
-
Domain::setglobalRotDOF
void setglobalRotDOF(unsigned long grotdof)
set globalRotDOF
Definition: Domain.cpp:791
-
Domain::getglobalRotDOF
unsigned long getglobalRotDOF()
get globalRotDOF
Definition: Domain.cpp:786
-
Domain::calculateVelocitySums
void calculateVelocitySums(ParticleContainer *partCont)
calculate _localSummv2 and _localSumIw2
Definition: Domain.cpp:430
-
Domain::updateMaxMoleculeID
void updateMaxMoleculeID(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp)
update max. moleculeID
Definition: Domain.cpp:767
+
Domain::setglobalRotDOF
void setglobalRotDOF(unsigned long grotdof)
set globalRotDOF
Definition: Domain.cpp:789
+
Domain::getglobalRotDOF
unsigned long getglobalRotDOF()
get globalRotDOF
Definition: Domain.cpp:784
+
Domain::calculateVelocitySums
void calculateVelocitySums(ParticleContainer *partCont)
calculate _localSummv2 and _localSumIw2
Definition: Domain.cpp:428
+
Domain::updateMaxMoleculeID
void updateMaxMoleculeID(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp)
update max. moleculeID
Definition: Domain.cpp:765
Domain::getGlobalLength
double getGlobalLength(int d) const
return the length of the domain
Definition: Domain.h:163
-
Domain::setLocalSummv2
void setLocalSummv2(double summv2, int thermostat)
sets _localSummv2 to the given value
Definition: Domain.cpp:127
-
Domain::setLocalVirial
void setLocalVirial(double Virial)
set the virial of the local process
Definition: Domain.cpp:117
+
Domain::setLocalSummv2
void setLocalSummv2(double summv2, int thermostat)
sets _localSummv2 to the given value
Definition: Domain.cpp:125
+
Domain::setLocalVirial
void setLocalVirial(double Virial)
set the virial of the local process
Definition: Domain.cpp:115
Domain::thermostatIsUndirected
bool thermostatIsUndirected(int thermostat)
Definition: Domain.h:321
-
Domain::writeCheckpointHeader
void writeCheckpointHeader(std::string filename, ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, double currentTime)
writes a checkpoint file that can be used to continue the simulation
Definition: Domain.cpp:489
-
Domain::setLocalUpot
void setLocalUpot(double Upot)
set the potential of the local process
Definition: Domain.cpp:113
-
Domain::getNumFluidMolecules
unsigned long getNumFluidMolecules()
Definition: Domain.cpp:867
-
Domain::getSigma
double getSigma(unsigned cid, unsigned nthSigma)
methods implemented by Stefan Becker stefan.becker@mv.uni-kl.de
Definition: Domain.cpp:823
-
Domain::getGlobalPressure
double getGlobalPressure()
get the global pressure
Definition: Domain.cpp:140
-
Domain::writeCheckpoint
void writeCheckpoint(std::string filename, ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, double currentTime, bool useBinaryFormat=false)
writes a checkpoint file that can be used to continue the simulation
Definition: Domain.cpp:603
-
Domain::updateglobalNumMolecules
void updateglobalNumMolecules(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp)
update globalNumMolecules This method must be called by all processes and not just by root!
Definition: Domain.cpp:746
-
Domain::setNumFluidComponents
void setNumFluidComponents(unsigned nc)
set the number of fluid phase components (specified in the config-file)
Definition: Domain.cpp:863
-
Domain::getLocalVirial
double getLocalVirial() const
get the virial of the local process
Definition: Domain.cpp:119
-
Domain::setepsilonRF
void setepsilonRF(double erf)
set the epsilonRF
Definition: Domain.cpp:722
-
Domain::getepsilonRF
double getepsilonRF() const
get the epsilonRF
Definition: Domain.cpp:720
-
Domain::getComp2Params
Comp2Param & getComp2Params()
get the parameter streams
Definition: Domain.cpp:151
-
Domain::initParameterStreams
void initParameterStreams(double cutoffRadius, double cutoffRadiusLJ)
initialize far field correction parameters
Definition: Domain.cpp:625
-
Domain::setglobalRho
void setglobalRho(double grho)
set globalRho
Definition: Domain.cpp:784
-
Domain::getglobalNumMolecules
unsigned long getglobalNumMolecules(bool bUpdate=true, ParticleContainer *particleContainer=nullptr, DomainDecompBase *domainDecomp=nullptr)
get globalNumMolecules This method must be called by all processes and not just by root!
Definition: Domain.cpp:724
-
Domain::enableUndirectedThermostat
void enableUndirectedThermostat(int thermostat)
enables the "undirected" flag for the specified thermostat
Definition: Domain.cpp:711
-
Domain::getglobalRho
double getglobalRho()
get globalRho
Definition: Domain.cpp:782
-
Domain::enableComponentwiseThermostat
void enableComponentwiseThermostat()
enables the componentwise thermostat
Definition: Domain.cpp:697
-
Domain::setGlobalLength
void setGlobalLength(int index, double length)
set the length of the domain
Definition: Domain.cpp:796
+
Domain::writeCheckpointHeader
void writeCheckpointHeader(std::string filename, ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, double currentTime)
writes a checkpoint file that can be used to continue the simulation
Definition: Domain.cpp:487
+
Domain::setLocalUpot
void setLocalUpot(double Upot)
set the potential of the local process
Definition: Domain.cpp:111
+
Domain::getNumFluidMolecules
unsigned long getNumFluidMolecules()
Definition: Domain.cpp:865
+
Domain::getSigma
double getSigma(unsigned cid, unsigned nthSigma)
methods implemented by Stefan Becker stefan.becker@mv.uni-kl.de
Definition: Domain.cpp:821
+
Domain::getGlobalPressure
double getGlobalPressure()
get the global pressure
Definition: Domain.cpp:138
+
Domain::writeCheckpoint
void writeCheckpoint(std::string filename, ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, double currentTime, bool useBinaryFormat=false)
writes a checkpoint file that can be used to continue the simulation
Definition: Domain.cpp:601
+
Domain::updateglobalNumMolecules
void updateglobalNumMolecules(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp)
update globalNumMolecules This method must be called by all processes and not just by root!
Definition: Domain.cpp:744
+
Domain::setNumFluidComponents
void setNumFluidComponents(unsigned nc)
set the number of fluid phase components (specified in the config-file)
Definition: Domain.cpp:861
+
Domain::getLocalVirial
double getLocalVirial() const
get the virial of the local process
Definition: Domain.cpp:117
+
Domain::setepsilonRF
void setepsilonRF(double erf)
set the epsilonRF
Definition: Domain.cpp:720
+
Domain::getepsilonRF
double getepsilonRF() const
get the epsilonRF
Definition: Domain.cpp:718
+
Domain::getComp2Params
Comp2Param & getComp2Params()
get the parameter streams
Definition: Domain.cpp:149
+
Domain::initParameterStreams
void initParameterStreams(double cutoffRadius, double cutoffRadiusLJ)
initialize far field correction parameters
Definition: Domain.cpp:623
+
Domain::setglobalRho
void setglobalRho(double grho)
set globalRho
Definition: Domain.cpp:782
+
Domain::getglobalNumMolecules
unsigned long getglobalNumMolecules(bool bUpdate=true, ParticleContainer *particleContainer=nullptr, DomainDecompBase *domainDecomp=nullptr)
get globalNumMolecules This method must be called by all processes and not just by root!
Definition: Domain.cpp:722
+
Domain::enableUndirectedThermostat
void enableUndirectedThermostat(int thermostat)
enables the "undirected" flag for the specified thermostat
Definition: Domain.cpp:709
+
Domain::getglobalRho
double getglobalRho()
get globalRho
Definition: Domain.cpp:780
+
Domain::enableComponentwiseThermostat
void enableComponentwiseThermostat()
enables the componentwise thermostat
Definition: Domain.cpp:695
+
Domain::setGlobalLength
void setGlobalLength(int index, double length)
set the length of the domain
Definition: Domain.cpp:794
Domain::disableComponentwiseThermostat
void disableComponentwiseThermostat()
disables the componentwise thermostat (so that a single thermostat is applied to all DOF)
Definition: Domain.h:337
-
Domain::getMaxMoleculeID
CommVar< uint64_t > getMaxMoleculeID() const
get local/global max. moleculeID
Definition: Domain.cpp:763
-
Domain::getGlobalBetaRot
double getGlobalBetaRot()
get thermostat scaling for rotations
Definition: Domain.cpp:124
-
Domain::getAverageGlobalUpotCSpec
double getAverageGlobalUpotCSpec()
by Stefan Becker: return the average global potential of the fluid-fluid and fluid-solid interaction ...
Definition: Domain.cpp:857
-
Domain::calculateGlobalValues
void calculateGlobalValues(DomainDecompBase *domainDecomp, ParticleContainer *particleContainer, bool collectThermostatVelocities, double Tfactor)
calculate the global macroscopic values
Definition: Domain.cpp:155
-
Domain::calculateThermostatDirectedVelocity
void calculateThermostatDirectedVelocity(ParticleContainer *partCont)
Definition: Domain.cpp:372
-
Domain::setglobalNumMolecules
void setglobalNumMolecules(unsigned long glnummol)
set globalNumMolecules
Definition: Domain.cpp:744
+
Domain::getMaxMoleculeID
CommVar< uint64_t > getMaxMoleculeID() const
get local/global max. moleculeID
Definition: Domain.cpp:761
+
Domain::getGlobalBetaRot
double getGlobalBetaRot()
get thermostat scaling for rotations
Definition: Domain.cpp:122
+
Domain::getAverageGlobalUpotCSpec
double getAverageGlobalUpotCSpec()
by Stefan Becker: return the average global potential of the fluid-fluid and fluid-solid interaction ...
Definition: Domain.cpp:855
+
Domain::calculateGlobalValues
void calculateGlobalValues(DomainDecompBase *domainDecomp, ParticleContainer *particleContainer, bool collectThermostatVelocities, double Tfactor)
calculate the global macroscopic values
Definition: Domain.cpp:153
+
Domain::calculateThermostatDirectedVelocity
void calculateThermostatDirectedVelocity(ParticleContainer *partCont)
Definition: Domain.cpp:370
+
Domain::setglobalNumMolecules
void setglobalNumMolecules(unsigned long glnummol)
set globalNumMolecules
Definition: Domain.cpp:742
Domain::setGlobalTemperature
void setGlobalTemperature(double T)
set the global temperature
Definition: Domain.h:177
-
Domain::setLocalSumIw2
void setLocalSumIw2(double sumIw2, int thermostat)
sets _localSumIw2 to the given value
Definition: Domain.cpp:135
-
Domain::readXML
void readXML(XMLfileUnits &xmlconfig)
Definition: Domain.cpp:82
+
Domain::setLocalSumIw2
void setLocalSumIw2(double sumIw2, int thermostat)
sets _localSumIw2 to the given value
Definition: Domain.cpp:133
+
Domain::readXML
void readXML(XMLfileUnits &xmlconfig)
Definition: Domain.cpp:80
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DriftCtrl_8h_source.html b/DriftCtrl_8h_source.html index a424bb6b6a..e1d9fa386d 100644 --- a/DriftCtrl_8h_source.html +++ b/DriftCtrl_8h_source.html @@ -124,12 +124,12 @@
78 } binWidth;
79 } subdivision;
80 } _range;
-
81
+
81
82 struct Target {
83 std::array<double,3> drift;
84 uint32_t cid;
85 } _target;
-
86
+
86
87 std::vector<BinVectors> _sampling;
88
89 std::vector<short> _directions;
@@ -137,15 +137,15 @@
91
92#endif /*DRIFTCTRL_H_*/
CommVar
Definition: CommVar.h:17
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
DriftCtrl
Definition: DriftCtrl.h:20
-
DriftCtrl::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: DriftCtrl.cpp:153
+
DriftCtrl::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: DriftCtrl.cpp:151
DriftCtrl::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: DriftCtrl.h:60
DriftCtrl::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: DriftCtrl.h:59
-
DriftCtrl::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: DriftCtrl.cpp:24
+
DriftCtrl::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: DriftCtrl.cpp:22
DriftCtrl::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: DriftCtrl.h:58
-
DriftCtrl::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DriftCtrl and all its included objects.
Definition: DriftCtrl.cpp:81
+
DriftCtrl::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DriftCtrl and all its included objects.
Definition: DriftCtrl.cpp:79
DriftCtrl::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: DriftCtrl.h:61
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -158,7 +158,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Dropaccelerator_8h_source.html b/Dropaccelerator_8h_source.html index 6765755d5b..547bbbd752 100644 --- a/Dropaccelerator_8h_source.html +++ b/Dropaccelerator_8h_source.html @@ -108,7 +108,7 @@
55
56public:
57 void init(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override {
-
58 global_log->debug() << "DropletAccelerator enabled" << std::endl;
+
58 Log::global_log->debug() << "DropletAccelerator enabled" << std::endl;
59
60 for (unsigned d = 0; d < 3; d++) {
61 _boxLength[d] = domain->getGlobalLength(d);
@@ -130,7 +130,7 @@
77 static PluginBase* createInstance() { return new Dropaccelerator(); }
78};
79
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Domain::getGlobalLength
double getGlobalLength(int d) const
return the length of the domain
Definition: Domain.h:163
Dropaccelerator
Plugin: can be enabled via config.xml
Definition: Dropaccelerator.h:35
@@ -147,7 +147,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Dropaligner_8h_source.html b/Dropaligner_8h_source.html index 497976b107..5312df5a1e 100644 --- a/Dropaligner_8h_source.html +++ b/Dropaligner_8h_source.html @@ -103,7 +103,7 @@
52
53public:
54 void init(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override {
-
55 global_log->debug() << "DropletRealignment enabled" << std::endl;
+
55 Log::global_log->debug() << "DropletRealignment enabled" << std::endl;
56
57 for (unsigned d = 0; d < 3; d++) {
58 _boxLength[d] = domain->getGlobalLength(d);
@@ -124,7 +124,7 @@
73
74 static PluginBase* createInstance() { return new Dropaligner(); }
75};
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Domain::getGlobalLength
double getGlobalLength(int d) const
return the length of the domain
Definition: Domain.h:163
Dropaligner
Plugin: can be enabled via config.xml
Definition: Dropaligner.h:37
@@ -141,7 +141,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DttNode_8h_source.html b/DttNode_8h_source.html index e9c0ee646c..748ec5b4ac 100644 --- a/DttNode_8h_source.html +++ b/DttNode_8h_source.html @@ -172,7 +172,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DummyExpansion_8h_source.html b/DummyExpansion_8h_source.html index 6ed050c2a0..a30a522a20 100644 --- a/DummyExpansion_8h_source.html +++ b/DummyExpansion_8h_source.html @@ -84,7 +84,7 @@
12
13/*
14 * Dummy SH_Expansion used to compute the transfer function from the vector
-
15 *
+
15 *
16 * Use a DummyStorage (truncated version of SH_Storage)
17 */
18
@@ -174,7 +174,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/DynAlloc_8h_source.html b/DynAlloc_8h_source.html index b52fc49538..336341586c 100644 --- a/DynAlloc_8h_source.html +++ b/DynAlloc_8h_source.html @@ -82,57 +82,56 @@
10
11#include <iostream>
12#include <cstdint>
-
13using namespace std;
-
14
-
15// leak save dynamic memory allocation
-
16inline void AllocateUnsLongArray(unsigned long* &ptr, const unsigned int& nSize)
-
17{
-
18 if(NULL != ptr)
-
19 delete[] ptr;
-
20 ptr = new unsigned long[nSize];
-
21}
-
22
-
23inline void AllocateDoubleArray(double* &ptr, const unsigned int& nSize)
-
24{
-
25 if(NULL != ptr)
-
26 delete[] ptr;
-
27 ptr = new double[nSize];
-
28}
-
29
-
30inline void AllocateUint8Array(uint8_t* &ptr, const uint32_t& nSize)
-
31{
-
32 if(NULL != ptr)
-
33 delete[] ptr;
-
34 ptr = new uint8_t[nSize];
-
35}
-
36
-
37inline void AllocateUint16Array(uint16_t* &ptr, const uint32_t& nSize)
-
38{
-
39 if(NULL != ptr)
-
40 delete[] ptr;
-
41 ptr = new uint16_t[nSize];
-
42}
-
43
-
44inline void AllocateUint32Array(uint32_t* &ptr, const uint32_t& nSize)
-
45{
-
46 if(NULL != ptr)
-
47 delete[] ptr;
-
48 ptr = new uint32_t[nSize];
-
49}
-
50
-
51inline void AllocateUint64Array(uint64_t* &ptr, const uint32_t& nSize)
-
52{
-
53 if(NULL != ptr)
-
54 delete[] ptr;
-
55 ptr = new uint64_t[nSize];
-
56}
+
13
+
14// leak save dynamic memory allocation
+
15inline void AllocateUnsLongArray(unsigned long* &ptr, const unsigned int& nSize)
+
16{
+
17 if(NULL != ptr)
+
18 delete[] ptr;
+
19 ptr = new unsigned long[nSize];
+
20}
+
21
+
22inline void AllocateDoubleArray(double* &ptr, const unsigned int& nSize)
+
23{
+
24 if(NULL != ptr)
+
25 delete[] ptr;
+
26 ptr = new double[nSize];
+
27}
+
28
+
29inline void AllocateUint8Array(uint8_t* &ptr, const uint32_t& nSize)
+
30{
+
31 if(NULL != ptr)
+
32 delete[] ptr;
+
33 ptr = new uint8_t[nSize];
+
34}
+
35
+
36inline void AllocateUint16Array(uint16_t* &ptr, const uint32_t& nSize)
+
37{
+
38 if(NULL != ptr)
+
39 delete[] ptr;
+
40 ptr = new uint16_t[nSize];
+
41}
+
42
+
43inline void AllocateUint32Array(uint32_t* &ptr, const uint32_t& nSize)
+
44{
+
45 if(NULL != ptr)
+
46 delete[] ptr;
+
47 ptr = new uint32_t[nSize];
+
48}
+
49
+
50inline void AllocateUint64Array(uint64_t* &ptr, const uint32_t& nSize)
+
51{
+
52 if(NULL != ptr)
+
53 delete[] ptr;
+
54 ptr = new uint64_t[nSize];
+
55}
+
56
57
-
58
-
59#endif /* DYNALLOC_H_ */
+
58#endif /* DYNALLOC_H_ */
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/EighthShell_8h_source.html b/EighthShell_8h_source.html index c5b2ddd958..baeb788d10 100644 --- a/EighthShell_8h_source.html +++ b/EighthShell_8h_source.html @@ -121,7 +121,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/EnergyLogWriter_8h_source.html b/EnergyLogWriter_8h_source.html index dc9c4fcc65..99f4d73a81 100644 --- a/EnergyLogWriter_8h_source.html +++ b/EnergyLogWriter_8h_source.html @@ -94,7 +94,7 @@
43 );
44 void finish(ParticleContainer *particleContainer,
45 DomainDecompBase *domainDecomp, Domain *domain);
-
46
+
46
47 std::string getPluginName() {
48 return std::string("EnergyLogWriter");
49 }
@@ -105,13 +105,13 @@
54};
55
56#endif // SRC_IO_ENERGYLOGWRITER_H_
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
EnergyLogWriter
This writer creates a global energy log file.
Definition: EnergyLogWriter.h:20
-
EnergyLogWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: EnergyLogWriter.cpp:12
-
EnergyLogWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: EnergyLogWriter.cpp:39
-
EnergyLogWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for EnergyLogWriter and all its included objects.
Definition: EnergyLogWriter.cpp:30
-
EnergyLogWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: EnergyLogWriter.cpp:100
+
EnergyLogWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: EnergyLogWriter.cpp:11
+
EnergyLogWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: EnergyLogWriter.cpp:38
+
EnergyLogWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for EnergyLogWriter and all its included objects.
Definition: EnergyLogWriter.cpp:29
+
EnergyLogWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: EnergyLogWriter.cpp:99
EnergyLogWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: EnergyLogWriter.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -120,7 +120,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/EnsembleBase_8h_source.html b/EnsembleBase_8h_source.html index 948caa2be2..44ce71213d 100644 --- a/EnsembleBase_8h_source.html +++ b/EnsembleBase_8h_source.html @@ -189,7 +189,7 @@
ChemicalPotential
Definition: ChemicalPotential.h:16
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
DomainBase
Definition: DomainBase.h:7
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Ensemble
Base class for ensembles.
Definition: EnsembleBase.h:47
Ensemble::updateGlobalVariable
virtual void updateGlobalVariable(ParticleContainer *particleContainer, GlobalVariable variable)=0
Calculate global variables.
@@ -202,7 +202,7 @@
Ensemble::getLmu
virtual std::list< ChemicalPotential > * getLmu()
Definition: EnsembleBase.h:99
Ensemble::N
virtual unsigned long N()=0
Returns the global number of Molecules of the ensemble.
Ensemble::afterForces
virtual void afterForces(ParticleContainer *, DomainDecompBase *, CellProcessor *, unsigned long)
Definition: EnsembleBase.h:114
-
Ensemble::setComponentLookUpIDs
void setComponentLookUpIDs()
prepare the _compIDs used by the Vectorized*CellProcessors
Definition: EnsembleBase.cpp:91
+
Ensemble::setComponentLookUpIDs
void setComponentLookUpIDs()
prepare the _compIDs used by the Vectorized*CellProcessors
Definition: EnsembleBase.cpp:89
Ensemble::storeSample
virtual void storeSample(Molecule *m, uint32_t componentid)
Definition: EnsembleBase.h:122
Ensemble::T
virtual double T()=0
Returns the global Temperature of the ensemble.
Ensemble::getType
int getType()
Definition: EnsembleBase.h:96
@@ -217,7 +217,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/EqualVelocityAssigner_8h_source.html b/EqualVelocityAssigner_8h_source.html index 7679d0e9d9..d15b2b36ea 100644 --- a/EqualVelocityAssigner_8h_source.html +++ b/EqualVelocityAssigner_8h_source.html @@ -112,7 +112,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ExamplePlugin_8h_source.html b/ExamplePlugin_8h_source.html index eb1ecb2d1f..7a6b0b8ef9 100644 --- a/ExamplePlugin_8h_source.html +++ b/ExamplePlugin_8h_source.html @@ -138,17 +138,17 @@
71};
72
73#endif /* SRC_PLUGINS_EXAMPLEPLUGIN_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ExamplePlugin
Definition: ExamplePlugin.h:18
-
ExamplePlugin::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: ExamplePlugin.cpp:102
-
ExamplePlugin::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: ExamplePlugin.cpp:16
+
ExamplePlugin::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: ExamplePlugin.cpp:101
+
ExamplePlugin::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: ExamplePlugin.cpp:15
ExamplePlugin::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: ExamplePlugin.h:61
-
ExamplePlugin::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: ExamplePlugin.cpp:111
-
ExamplePlugin::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: ExamplePlugin.cpp:93
-
ExamplePlugin::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: ExamplePlugin.cpp:84
-
ExamplePlugin::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: ExamplePlugin.cpp:66
-
ExamplePlugin::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method will be called first thing in a new timestep.
Definition: ExamplePlugin.cpp:74
+
ExamplePlugin::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: ExamplePlugin.cpp:110
+
ExamplePlugin::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: ExamplePlugin.cpp:92
+
ExamplePlugin::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: ExamplePlugin.cpp:83
+
ExamplePlugin::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: ExamplePlugin.cpp:65
+
ExamplePlugin::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method will be called first thing in a new timestep.
Definition: ExamplePlugin.cpp:73
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
@@ -156,7 +156,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Expression_8cpp.html b/Expression_8cpp.html index 75da4d346e..96f363418c 100644 --- a/Expression_8cpp.html +++ b/Expression_8cpp.html @@ -82,7 +82,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Expression_8h.html b/Expression_8h.html index 48bcef998a..d24bb260a2 100644 --- a/Expression_8h.html +++ b/Expression_8h.html @@ -136,7 +136,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Expression_8h_source.html b/Expression_8h_source.html index ecfa6603b9..0dbe062e2e 100644 --- a/Expression_8h_source.html +++ b/Expression_8h_source.html @@ -91,12 +91,12 @@
23 public:
24 typedef long Tint;
25 typedef double Tfloat;
-
26
+
26
27 enum Evaltype {valtypeNONE, valtypeINT, valtypeFLOAT};
28 typedef enum Evaltype Tvaltype;
29 enum Etraversetype { traversetypePREFIX, traversetypeINFIX, traversetypePOSTFIX };
30 typedef enum Etraversetype Ttraversetype;
-
31
+
31
32 // Value -----------------------------------------------------------------------------------
33 class Value
34 {
@@ -107,7 +107,7 @@
39 Tfloat valFloat;
40 };
41 typedef union TUvalue Tvalue;
-
42
+
42
44 Value() : _type(valtypeNONE) { _value.valInt=0; }
46
50 Value(enum Evaltype type, Tvalue value)
@@ -120,7 +120,7 @@
63 //Value(Tfloat valFloat) { _type=valtypeFLOAT; _value.valFloat=valFloat; }
64 Value(float valFloat) { _type=valtypeFLOAT; _value.valFloat=Tfloat(valFloat); }
65 Value(double valFloat) { _type=valtypeFLOAT; _value.valFloat=Tfloat(valFloat); }
-
66
+
66
68
72 Tvaltype getType() const { return _type; }
74
@@ -139,7 +139,7 @@
98 default: return 0.;
99 }
100 }
-
101 operator Tfloat() const { return getValueFloat(); }
+
101 operator Tfloat() const { return getValueFloat(); }
103
106 Tint getValueInt() const
107 {
@@ -150,7 +150,7 @@
112 default: return 0.;
113 }
114 }
-
115 operator Tint() const { return getValueInt(); }
+
115 operator Tint() const { return getValueInt(); }
117
120 void write(std::ostream& ostrm=std::cout) const
121 {
@@ -174,13 +174,13 @@
139 const Value operator-(Value const& v) const;
140 const Value operator*(Value const& v) const;
141 const Value operator/(Value const& v) const;
-
142
+
142
143 private:
144 Tvaltype _type;
145 Tvalue _value;
146 };
147 // ----------------------------------------------------------------------------------- Value
-
148
+
148
149 class Variable;
150 // VariableGroup ---------------------------------------------------------------------------
157 class VariableGroup
@@ -193,13 +193,13 @@
164 bool removeVariable(const Variable* var)
165 { if(_variables.count(var)) { _variables.erase(var); return true; } else return false; }
166 unsigned int countVariables() const { return _variables.size(); }
-
167 operator unsigned int() const { return countVariables(); }
+
167 operator unsigned int() const { return countVariables(); }
168 private:
169 std::string _name;
170 std::set<const Variable*> _variables;
171 };
172 // --------------------------------------------------------------------------- VariableGroup
-
173
+
173
174 // Variable --------------------------------------------------------------------------------
175 class Variable
176 {
@@ -223,9 +223,9 @@
200 Tvaltype getType() const { return _value.getType(); }
201 Value getValue() const { return _value; }
202 Tfloat getValueFloat() const { return _value.getValueFloat(); }
-
203 operator Tfloat() const { return getValueFloat(); }
+
203 operator Tfloat() const { return getValueFloat(); }
204 Tint getValueInt() const { return _value.getValueInt(); }
-
205 operator Tint() const { return getValueInt(); }
+
205 operator Tint() const { return getValueInt(); }
206 bool isInt() const { return _value.isInt(); }
207 bool isFloat() const { return _value.isFloat(); }
208 const VariableGroup* getVariableGroup() const { return _vargrp; }
@@ -247,20 +247,20 @@
227 write(oss);
228 return oss.str();
229 }
-
230
+
230
231 private:
232 std::string _name;
233 Value _value;
234 VariableGroup* _vargrp;
235 };
236 // -------------------------------------------------------------------------------- Variable
-
237
+
237
238 // VariableSet -----------------------------------------------------------------------------
239 class VariableSet
240 {
241 public:
242 VariableSet() {};
-
243
+
243
244 const std::set<const VariableGroup*> getVariableGroupNames() const
245 {
246 std::set<const VariableGroup*> vargroups;
@@ -279,7 +279,7 @@
259 return (_vargroups.find(name)->second).countVariables();
260 else
261 return 0;
-
262
+
262
263 }
264 unsigned int VariablesCount() const { return _variables.size(); }
265 bool existVariable(const std::string& name) const { return _variables.count(name)>0; }
@@ -318,15 +318,15 @@
298 { return setVariable(std::string(vgrpname+":"+varname),val); }
299 //template <class T> bool setVariable(const char* vgrpname, const char* varname, T val=0) { return setVariable(std::string(vgrpname),std::string(varname),val); }
300 bool removeVariable(const std::string& name);
-
301
+
301
302 private:
303 std::map<std::string,Variable> _variables;
304 std::map<std::string,VariableGroup> _vargroups;
305 };
306 // ----------------------------------------------------------------------------- VariableSet
-
307
+
307
308 // Node and derivatives --------------------------------------------------------------------
-
309
+
309
310 // Node ------------------------------------------------------------------------------------
311 class Node
312 {
@@ -364,14 +364,14 @@
344 void write() const { write(std::cout); }
345 void traverse(std::list<const Node*>& nodelist, enum Etraversetype traversetype=traversetypePOSTFIX) const;
346 void writeSubExpr(std::ostream& ostrm=std::cout, enum Etraversetype traversetype=traversetypePOSTFIX, char sep=' ') const;
-
347
+
347
348 protected:
349 Node* _children[2];
350 Node* _parent;
351 short _priority;
352 };
353 // ------------------------------------------------------------------------------------ Node
-
354
+
354
355 // NodeConstant ----------------------------------------------------------------------------
356 class NodeConstant : public Node
357 {
@@ -387,7 +387,7 @@
367 Value _value;
368 };
369 // ---------------------------------------------------------------------------- NodeConstant
-
370
+
370
371 // NodeVariable ----------------------------------------------------------------------------
372 class NodeVariable : public Node
373 {
@@ -402,7 +402,7 @@
382 Variable* _var;
383 };
384 // ---------------------------------------------------------------------------- NodeVariable
-
385
+
385
386 // NodeOperation2 --------------------------------------------------------------------------
387 class NodeOperation2 : public Node
388 {
@@ -427,7 +427,7 @@
407 char _operator;
408 };
409 // -------------------------------------------------------------------------- NodeOperation2
-
410
+
410
411 // NodeFunction ----------------------------------------------------------------------------
412 class NodeFunction : public Node
413 {
@@ -463,9 +463,9 @@
443 , functypeMarkerVarSet2Arg // marker for functions using the VariableSet with 2 arguments ---
444 , functypeSTO // store value to <id>
445 };
-
446
+
446
447 static Efunctype functype(const std::string& name);
-
448
+
448
449 NodeFunction(Efunctype func
450 ,Node* child1, Node* child0=NULL, Node* parent=NULL)
451 : Node(child0,child1,parent,0), _functype(func) {}
@@ -475,12 +475,12 @@
455 Tvaltype valueType() const;
456 Value evaluate() const;
457 void write(std::ostream& ostrm) const;
-
458
+
458
459 protected:
460 enum Efunctype _functype;
461 };
462 // ---------------------------------------------------------------------------- NodeFunction
-
463
+
463
464 // NodeFunctionVarSet ----------------------------------------------------------------------
465 /*
466 Functions with the capability to store and load values from the given VariableSet
@@ -489,7 +489,7 @@
469 {
470 public:
471 // use enum Efunctype defined in NodeFunction
-
472
+
472
473 NodeFunctionVarSet(Efunctype func, VariableSet *variableset
474 ,Node* child1, Node* child0=NULL, Node* parent=NULL)
475 : NodeFunction(func,child1,child0,parent), _variableset(variableset) {}
@@ -497,14 +497,14 @@
477 Tvaltype valueType() const;
478 Value evaluate() const;
479 void write(std::ostream& ostrm) const;
-
480
+
480
481 protected:
482 VariableSet* _variableset;
483 };
484 // ---------------------------------------------------------------------- NodeFunctionVarSet
-
485
+
485
486 // -------------------------------------------------------------------- Node and derivatives
-
487
+
487
488 Expression(const std::string& label=std::string(), VariableSet* varset=NULL)
489 : _rootnode(NULL), _label(label), _variableset(varset), _variablesetcreated(false)
490 {
@@ -520,13 +520,13 @@
500 clear();
501 if(_variablesetcreated) delete _variableset;
502 }
-
503
+
503
504 void clear() { if(_rootnode) { delete(_rootnode); _rootnode=NULL; } }
505 void setLabel(const std::string& label) { _label=label; }
506 const std::string& getLabel() const { return _label; }
-
507
+
507
508 void initializeRPN(const std::string& exprstr, bool genlabel=true);
-
509
+
509
510 Expression& operator=(const Expression& rhs )
511 {
512 _label=rhs._label;
@@ -538,7 +538,7 @@
518 initializeRPN(oss.str());
519 return *this;
520 }
-
521
+
521
522 bool isEmpty() const { return _rootnode==NULL; }
523 bool isInt() const { if(_rootnode) return _rootnode->isInt(); else return false; }
524 bool isFloat() const { if(_rootnode) return _rootnode->isFloat(); else return false; }
@@ -556,14 +556,14 @@
536 else
537 return 0;
538 }
-
539
-
540 VariableSet* getVariableSet() { return _variableset; }
+
539
+
540 VariableSet* getVariableSet() { return _variableset; }
541 Variable* getVariable(const std::string& name) { return _variableset->getVariable(name); }
542 unsigned int VariablesCount() const { return _variableset->VariablesCount(); }
543 bool existVariable(const std::string& name) const { return _variableset->existVariable(name); }
544 unsigned int VariableGroupsCount() const { return _variableset->VariableGroupsCount(); }
545 bool existVariableGroup(const std::string& name) const { return _variableset->existVariableGroup(name); }
-
546
+
546
547 void writeExpr(std::ostream& ostrm=std::cout, enum Etraversetype traversetype=traversetypePOSTFIX, char sep=' ') const
548 {
549 if(_rootnode) _rootnode->writeSubExpr(ostrm,traversetype,sep);
@@ -579,7 +579,7 @@
559 _label=operator std::string();
560 //_label=static_cast<std::string>(*this);
561 }
-
562
+
562
563 protected:
564 Node* _rootnode;
565 std::string _label;
@@ -647,7 +647,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ExtractPhase_8h_source.html b/ExtractPhase_8h_source.html index cfcb155f74..159812eeee 100644 --- a/ExtractPhase_8h_source.html +++ b/ExtractPhase_8h_source.html @@ -155,9 +155,9 @@
115};
116
117#endif /* EXTRACT_PHASE_H_ */
-
CavityEnsemble
Definition: CavityEnsemble.h:20
+
CavityEnsemble
Definition: CavityEnsemble.h:19
ChemicalPotential
Definition: ChemicalPotential.h:16
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ExtractPhase
Definition: ExtractPhase.h:20
ExtractPhase::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: ExtractPhase.h:81
@@ -177,7 +177,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAccelerableExpansion_8h_source.html b/FFTAccelerableExpansion_8h_source.html index dcafec34f0..ff52156b65 100644 --- a/FFTAccelerableExpansion_8h_source.html +++ b/FFTAccelerableExpansion_8h_source.html @@ -118,7 +118,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAccelerationAPI_8h_source.html b/FFTAccelerationAPI_8h_source.html index f505ef63ae..62e1c1f84d 100644 --- a/FFTAccelerationAPI_8h_source.html +++ b/FFTAccelerationAPI_8h_source.html @@ -136,7 +136,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAccelerationAPI__extensions_8h_source.html b/FFTAccelerationAPI__extensions_8h_source.html index 35b27da577..09750635f5 100644 --- a/FFTAccelerationAPI__extensions_8h_source.html +++ b/FFTAccelerationAPI__extensions_8h_source.html @@ -145,7 +145,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__2wayM2L_8h_source.html b/FFTAcceleration__2wayM2L_8h_source.html index 68bcf2ce61..ef60fa70c8 100644 --- a/FFTAcceleration__2wayM2L_8h_source.html +++ b/FFTAcceleration__2wayM2L_8h_source.html @@ -136,7 +136,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__2wayM2L__fftw_8h_source.html b/FFTAcceleration__2wayM2L__fftw_8h_source.html index 125b40bd67..1608ccdd5d 100644 --- a/FFTAcceleration__2wayM2L__fftw_8h_source.html +++ b/FFTAcceleration__2wayM2L__fftw_8h_source.html @@ -86,7 +86,7 @@
14
15/*
16 * Basic implemtation using the FFTW library
-
17 *
+
17 *
18 * Use FFTDataContainer_arrays as Data container (2 arrays, here aligned)
19 * initialize_target, M2L and protected function to get the DataContainer defined in abstract FFTAcceleration_2wayM2L
20 */
@@ -122,7 +122,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__2wayM2L__optFFT_8h_source.html b/FFTAcceleration__2wayM2L__optFFT_8h_source.html index 79809efa3b..72f7da7818 100644 --- a/FFTAcceleration__2wayM2L__optFFT_8h_source.html +++ b/FFTAcceleration__2wayM2L__optFFT_8h_source.html @@ -86,7 +86,7 @@
14
15/*
16 * Basic implemtation using optimized FFT
-
17 *
+
17 *
18 * Use FFTDataContainer_matrices as Data container (2 matrices)
19 * initialize_target, M2L and protected function to get the DataContainer
20 * defined in parent class
@@ -132,7 +132,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__blocks_8h_source.html b/FFTAcceleration__blocks_8h_source.html index fb393a48f4..225fb6c589 100644 --- a/FFTAcceleration__blocks_8h_source.html +++ b/FFTAcceleration__blocks_8h_source.html @@ -86,7 +86,7 @@
14
15/*
16 * Abstract class with common code for basic fft and fftw implementation
-
17 *
+
17 *
18 * Use FFTDataContainer_blocks as Data container (2 arrays of matrices)
19 */
20class FFTAcceleration_blocks: public FFTAccelerationAPI_full {
@@ -172,7 +172,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__blocks__fftw_8h_source.html b/FFTAcceleration__blocks__fftw_8h_source.html index cfdd936c3c..35666763b2 100644 --- a/FFTAcceleration__blocks__fftw_8h_source.html +++ b/FFTAcceleration__blocks__fftw_8h_source.html @@ -86,7 +86,7 @@
14
15/*
16 * Basic implementation using the FFTW library
-
17 *
+
17 *
18 * Use FFTDataContainer_blocks as Data container (2 matrices)
19 * initialize_target, M2L and protected function to get the DataContainer defined in abstract FFTAcceleration_blocks
20 */
@@ -122,7 +122,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__blocks__optFFT_8h_source.html b/FFTAcceleration__blocks__optFFT_8h_source.html index 8bbd3c753a..e2aa1cc7e9 100644 --- a/FFTAcceleration__blocks__optFFT_8h_source.html +++ b/FFTAcceleration__blocks__optFFT_8h_source.html @@ -87,7 +87,7 @@
15
16/*
17 * Basic implementation using the optFFT
-
18 *
+
18 *
19 * Use FFTDataContainer_blocks as Data container (2 matrices)
20 * initialize_target, M2L and protected function to get the DataContainer defined in abstract FFTAcceleration_blocks
21 */
@@ -123,7 +123,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__matrices_8h_source.html b/FFTAcceleration__matrices_8h_source.html index 39b1108e30..eca99fa007 100644 --- a/FFTAcceleration__matrices_8h_source.html +++ b/FFTAcceleration__matrices_8h_source.html @@ -117,7 +117,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__matrices__fftw_8h_source.html b/FFTAcceleration__matrices__fftw_8h_source.html index 7e9c163c78..ff3903ac1f 100644 --- a/FFTAcceleration__matrices__fftw_8h_source.html +++ b/FFTAcceleration__matrices__fftw_8h_source.html @@ -85,7 +85,7 @@
13
14/*
15 * Basic implemtation using the FFTW library
-
16 *
+
16 *
17 * Use FFTDataContainer_matrices as Data container (2 matrices)
18 * initialize_target, M2L and protected function to get the DataContainer defined in abstract FFTAcceleration_matrices
19 */
@@ -121,7 +121,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__matrices__optFFT_8h_source.html b/FFTAcceleration__matrices__optFFT_8h_source.html index 6194cfd15b..21a04912a6 100644 --- a/FFTAcceleration__matrices__optFFT_8h_source.html +++ b/FFTAcceleration__matrices__optFFT_8h_source.html @@ -85,7 +85,7 @@
13
14/*
15 * Basic implemtation using Kurzak's optimized FFT
-
16 *
+
16 *
17 * Use FFTDataContainer_matrices as Data container (2 matrices)
18 * initialize_target, M2L and protected function to get the DataContainer defined in abstract FFTAcceleration_matrices
19 */
@@ -120,7 +120,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__scalBlocks__optFFT_8h_source.html b/FFTAcceleration__scalBlocks__optFFT_8h_source.html index 47348739bf..3a4481c5fa 100644 --- a/FFTAcceleration__scalBlocks__optFFT_8h_source.html +++ b/FFTAcceleration__scalBlocks__optFFT_8h_source.html @@ -85,7 +85,7 @@
13#include "bhfmm/fft/FFTSettings.h"
14#include "bhfmm/fft/tools/optimizedFFT/optFFT_API_Factory.h"
15
-
16/*
+
16/*
17 * Use FFTDataContainer_scalBlocks as Data container (2 arrays of matrices)
18 */
19class FFTAcceleration_scalBlocks_optFFT: public FFTAccelerationAPI_full {
@@ -193,7 +193,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTAcceleration__scalBlocks__v0_8h_source.html b/FFTAcceleration__scalBlocks__v0_8h_source.html index 340dba6d81..2cc07913eb 100644 --- a/FFTAcceleration__scalBlocks__v0_8h_source.html +++ b/FFTAcceleration__scalBlocks__v0_8h_source.html @@ -87,7 +87,7 @@
15
16/*
17 * v0 version of scaling block
-
18 *
+
18 *
19 * Use FFTDataContainer_scalBlocks_v0 as Data container (2 arrays of matrices)
20 */
21class FFTAcceleration_scalBlocks_v0: public FFTAccelerationAPI {
@@ -144,7 +144,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTDataContainer_8h_source.html b/FFTDataContainer_8h_source.html index 28f49ff718..5f9e09a43f 100644 --- a/FFTDataContainer_8h_source.html +++ b/FFTDataContainer_8h_source.html @@ -95,7 +95,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTDataContainer__arrays_8h_source.html b/FFTDataContainer__arrays_8h_source.html index ab5924c692..7d13d901a3 100644 --- a/FFTDataContainer__arrays_8h_source.html +++ b/FFTDataContainer__arrays_8h_source.html @@ -115,7 +115,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTDataContainer__blocks_8h_source.html b/FFTDataContainer__blocks_8h_source.html index 80cbf4717f..31ea5eab36 100644 --- a/FFTDataContainer__blocks_8h_source.html +++ b/FFTDataContainer__blocks_8h_source.html @@ -82,14 +82,14 @@
10#include "bhfmm/fft/FFTSettings_preprocessor.h" //tmp include for the typedef FFT_precision
11#include "bhfmm/fft/FFTDataContainer.h"
12#include "bhfmm/fft/tools/fft_utils.h"
-
13#include <stdlib.h>
+
13#include <stdlib.h>
14
15/*
16 * Storage for blocks, can be used with scaling Blocks (scalBlock)
-
17 *
+
17 *
18 * blocks[i] is a matrix reprensenting the ith block
19 * Convention: block 0 contain the terms of lowest order
-
20 * => source matrix in ascending block (block 0 is the top of the matrix),
+
20 * => source matrix in ascending block (block 0 is the top of the matrix),
21 * tf and target matrices in descending blocks (block 0 is the lower part of the matrix)
22 */
23class FFTDataContainer_blocks: public FFTDataContainer {
@@ -127,7 +127,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTDataContainer__matrices_8h_source.html b/FFTDataContainer__matrices_8h_source.html index 978023a3d6..cb7867bcd0 100644 --- a/FFTDataContainer__matrices_8h_source.html +++ b/FFTDataContainer__matrices_8h_source.html @@ -116,7 +116,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTDataContainer__scalBlocks_8h_source.html b/FFTDataContainer__scalBlocks_8h_source.html index 7d019c5915..bc2f68efde 100644 --- a/FFTDataContainer__scalBlocks_8h_source.html +++ b/FFTDataContainer__scalBlocks_8h_source.html @@ -82,14 +82,14 @@
10#include "bhfmm/fft/FFTSettings_preprocessor.h" //tmp include for the typedef FFT_precision
11#include "bhfmm/fft/FFTDataContainer.h"
12#include "bhfmm/fft/tools/fft_utils.h"
-
13#include <stdlib.h>
+
13#include <stdlib.h>
14
15/*
16 * Storage for blocks, can be used with scaling Blocks (scalBlock)
-
17 *
+
17 *
18 * blocks[i] is an array reprensenting the ith block
19 * Convention: block 0 contain the terms of lowest order
-
20 * => source matrix in ascending block (block 0 is the top of the matrix),
+
20 * => source matrix in ascending block (block 0 is the top of the matrix),
21 * tf and target matrices in descending blocks (block 0 is the lower part of the matrix)
22 */
23class FFTDataContainer_scalBlocks: public FFTDataContainer {
@@ -136,7 +136,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTDataContainer__scalBlocks__v0_8h_source.html b/FFTDataContainer__scalBlocks__v0_8h_source.html index cba941dd96..7964fb35dc 100644 --- a/FFTDataContainer__scalBlocks__v0_8h_source.html +++ b/FFTDataContainer__scalBlocks__v0_8h_source.html @@ -82,14 +82,14 @@
10#include "bhfmm/fft/FFTSettings_preprocessor.h" //tmp include for the typedef FFT_precision
11#include "bhfmm/fft/FFTDataContainer.h"
12#include "bhfmm/fft/tools/fft_utils.h"
-
13#include <stdlib.h>
+
13#include <stdlib.h>
14
15/*
16 * Storage for blocks, can be used with scaling Blocks (scalBlock)
-
17 *
+
17 *
18 * blocks[i] is a matrix reprensenting the ith block
19 * Convention: block 0 contain the terms of lowest order
-
20 * => source matrix in ascending block (block 0 is the top of the matrix),
+
20 * => source matrix in ascending block (block 0 is the top of the matrix),
21 * tf and target matrices in descending blocks (block 0 is the lower part of the matrix)
22 */
23class FFTDataContainer_scalBlocks_v0: public FFTDataContainer {
@@ -137,7 +137,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTFactory_8h_source.html b/FFTFactory_8h_source.html index 7f061b36b0..4617fde7db 100644 --- a/FFTFactory_8h_source.html +++ b/FFTFactory_8h_source.html @@ -155,7 +155,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTOrderReduction_8h_source.html b/FFTOrderReduction_8h_source.html index 36121e7309..3b9031052b 100644 --- a/FFTOrderReduction_8h_source.html +++ b/FFTOrderReduction_8h_source.html @@ -79,7 +79,7 @@
7#ifndef FFTORDERRED_H_
8#define FFTORDERRED_H_
9
-
10#include <stdlib.h>
+
10#include <stdlib.h>
11#include <stdio.h>
12#include <math.h>
13
@@ -103,7 +103,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTSettings_8h_source.html b/FFTSettings_8h_source.html index 60004d5436..ddb6756ac0 100644 --- a/FFTSettings_8h_source.html +++ b/FFTSettings_8h_source.html @@ -84,51 +84,50 @@
12#include <string>
13#include "bhfmm/fft/FFTSettings_preprocessor.h"
14
-
15using namespace std;
-
16
-
25class FFTSettings {
-
26public:
+
23class FFTSettings {
+
24public:
+
25
27
-
29
-
30 //FFT or FFTW (if none use the no FFT acceleration)
-
31 static bool USE_FFT; // set to use any FFT acceleration (default optFFT)
-
32 static bool USE_FFTW; //set to use fftw instead of optFFT
-
33
-
34 //TransferFunctionManager settings
-
35 static bool USE_TFMANAGER_UNIFORMGRID; //set to use memoized transfer function (require uniform grid)
-
36 //WARNING: if USE_TFMANAGER_UNIFORMGRID is set the tf should not be freed after an M2L, else it should be freed to avoid memory leaks
+
28 //FFT or FFTW (if none use the no FFT acceleration)
+
29 static bool USE_FFT; // set to use any FFT acceleration (default optFFT)
+
30 static bool USE_FFTW; //set to use fftw instead of optFFT
+
31
+
32 //TransferFunctionManager settings
+
33 static bool USE_TFMANAGER_UNIFORMGRID; //set to use memoized transfer function (require uniform grid)
+
34 //WARNING: if USE_TFMANAGER_UNIFORMGRID is set the tf should not be freed after an M2L, else it should be freed to avoid memory leaks
+
35
+
36 static bool TFMANAGER_VERBOSE; //set to print the TFManager stats at its destruct
37
-
38 static bool TFMANAGER_VERBOSE; //set to print the TFManager stats at its destruct
-
39
-
40 static bool USE_VECTORIZATION; //set to use vectorized FFT (/!\ can be faked, see FFTSettings_preprocessor.h)
-
41 static bool USE_2WAY_M2L; //set to use a 2way M2L (best on non uniform grid, requires vectorization)
-
42
-
43 static bool USE_BLOCK; //set to use a block decomposition
-
44 static bool USE_ADVBLOCK; //set to use a scaling block decomposition (requires USE_BLOCK)
+
38 static bool USE_VECTORIZATION; //set to use vectorized FFT (/!\ can be faked, see FFTSettings_preprocessor.h)
+
39 static bool USE_2WAY_M2L; //set to use a 2way M2L (best on non uniform grid, requires vectorization)
+
40
+
41 static bool USE_BLOCK; //set to use a block decomposition
+
42 static bool USE_ADVBLOCK; //set to use a scaling block decomposition (requires USE_BLOCK)
+
43
+
44 static bool USE_ORDER_REDUCTION; //Order Reduction scheme, only with blocks
45
-
46 static bool USE_ORDER_REDUCTION; //Order Reduction scheme, only with blocks
-
47
-
48 //sets Settings to the best default value for a given order
-
49 static void autoSetting(int order);
-
50
-
51 static bool issetFFTAcceleration() {
-
52 return USE_FFT;
-
53 }
-
54
-
55 //Used in the bhfmm code for command line interface
-
56 static void setOptions(string option);
-
57 static vector<string> getAvailableOptions();
-
58 static void printCurrentOptions();
+
46 //sets Settings to the best default value for a given order
+
47 static void autoSetting(int order);
+
48
+
49 static bool issetFFTAcceleration() {
+
50 return USE_FFT;
+
51 }
+
52
+
53 //Used in the bhfmm code for command line interface
+
54 static void setOptions(std::string option);
+
55 static std::vector<std::string> getAvailableOptions();
+
56 static void printCurrentOptions();
+
57
+
58};
59
-
60};
-
61
-
62#endif
-
FFTSettings
Definition: FFTSettings.h:25
-
FFTSettings::USE_FFT
static bool USE_FFT
Seetings, default values in FFTSettings.cpp.
Definition: FFTSettings.h:31
+
60#endif
+
FFTSettings
Definition: FFTSettings.h:23
+
FFTSettings::USE_FFT
static bool USE_FFT
Seetings, default values in FFTSettings.cpp.
Definition: FFTSettings.h:29
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTSettings__preprocessor_8h_source.html b/FFTSettings__preprocessor_8h_source.html index 81db5c6ce1..62354f1bb2 100644 --- a/FFTSettings__preprocessor_8h_source.html +++ b/FFTSettings__preprocessor_8h_source.html @@ -84,13 +84,13 @@
13
14//#define __TEST_FAKE_VECTORIZATION__ //To fake vectorization on a computer not supporting it (replace _mm_malloc with malloc and _mm_free with free)
16//Intel SSE = 16, AVX = 32, AVX-512 = 64 (https://software.intel.com/en-us/articles/fdiag15126)
-
17#define __FFT_MATRIX_ALIGNMENT__ 32
+
17#define __FFT_MATRIX_ALIGNMENT__ 32
18
19#endif
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTW__API_8h_source.html b/FFTW__API_8h_source.html index f4d4acd5ff..095d8eb7bd 100644 --- a/FFTW__API_8h_source.html +++ b/FFTW__API_8h_source.html @@ -136,7 +136,7 @@
81#endif
82 }
83
-
84#if defined(__SINGLE_PRECISION_FFT__)
+
84#if defined(__SINGLE_PRECISION_FFT__)
85 fftwf_complex* getIn_Forward() {return _f_in;}
86 fftwf_complex* getIn_Backward() {return _b_in;}
87
@@ -158,13 +158,13 @@
103 fftw_execute(_backward);
104 return _b_out;
105 }
-
106#endif
+
106#endif
107
108private:
109 int _nx;
110 int _ny;
111
-
112#if defined(__SINGLE_PRECISION_FFT__)
+
112#if defined(__SINGLE_PRECISION_FFT__)
113 fftwf_plan _forward;
114 fftwf_complex* _f_in;
115 fftwf_complex* _f_out;
@@ -188,7 +188,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FFTW__Helper_8h_source.html b/FFTW__Helper_8h_source.html index 67fd55e920..7c177a19b8 100644 --- a/FFTW__Helper_8h_source.html +++ b/FFTW__Helper_8h_source.html @@ -93,7 +93,7 @@
24 void FFT2Local(FFTAccelerableExpansion & Expansion, double radius);
25
26 inline void execute_S2FFT() {
-
27#if defined(__SINGLE_PRECISION_FFT__)
+
27#if defined(__SINGLE_PRECISION_FFT__)
28 fftwf_execute(S2FFT);
29#else
30 fftw_execute(S2FFT);
@@ -101,7 +101,7 @@
32 }
33
34 inline void execute_T2FFT() {
-
35#if defined(__SINGLE_PRECISION_FFT__)
+
35#if defined(__SINGLE_PRECISION_FFT__)
36 fftwf_execute(T2FFT);
37#else
38 fftw_execute(T2FFT);
@@ -109,14 +109,14 @@
40 }
41
42 inline void execute_FFT2L() {
-
43#if defined(__SINGLE_PRECISION_FFT__)
+
43#if defined(__SINGLE_PRECISION_FFT__)
44 fftwf_execute(FFT2L);
45#else
46 fftw_execute(FFT2L);
47#endif
48 }
49
-
50#if defined(__SINGLE_PRECISION_FFT__)
+
50#if defined(__SINGLE_PRECISION_FFT__)
51
52 fftwf_complex* Source2FFT(FFTAccelerableExpansion & Expansion, double radius);
53 fftwf_complex* TransferFunction2FFT(FFTAccelerableExpansion & Expansion);
@@ -169,7 +169,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FakedOptFFT_8h_source.html b/FakedOptFFT_8h_source.html index 0a15410019..7347e6d2d0 100644 --- a/FakedOptFFT_8h_source.html +++ b/FakedOptFFT_8h_source.html @@ -89,61 +89,59 @@
17#include <map>
18#include <iostream>
19
-
20using namespace std;
-
21
-
22//struct storing a int[2] for the map
-
23struct pos {
-
24 int x, y;
-
25};
-
26
-
27//comparator of pos (=int[2])
-
28struct pos_comp {
-
29 bool operator()(const pos &l, const pos &r) const {
-
30 return (l.x < r.x || (l.x == r.x && l.y < r.y));
-
31 }
-
32};
-
33
-
39class FakedOptFFT: public optFFT_API {
+
20//struct storing a int[2] for the map
+
21struct pos {
+
22 int x, y;
+
23};
+
24
+
25//comparator of pos (=int[2])
+
26struct pos_comp {
+
27 bool operator()(const pos &l, const pos &r) const {
+
28 return (l.x < r.x || (l.x == r.x && l.y < r.y));
+
29 }
+
30};
+
31
+
37class FakedOptFFT: public optFFT_API {
+
38
+
39public:
40
-
41public:
-
42
-
43 FakedOptFFT() {
-
44 } //cout << "Using faked opt FFT (see bhfmm/fft/tools/optimizedFFT)" << endl;}
-
45 ~FakedOptFFT() { //free all entry of the map and the map
-
46 auto itr = _fftw_api_map.begin();
-
47 while (itr != _fftw_api_map.end()) {
-
48 for (int i = 0; i < mardyn_get_max_threads(); ++i) {
-
49 delete ((*itr).second[i]);
-
50 }
-
51 delete ((*itr).second);
-
52 _fftw_api_map.erase(itr++);
-
53 }
-
54 _fftw_api_map.clear();
-
55 }
-
56
-
57 void optimizedFFT(FFT_precision** & Real, FFT_precision** & Imag,
+
41 FakedOptFFT() {
+
42 } //cout << "Using faked opt FFT (see bhfmm/fft/tools/optimizedFFT)" << endl;}
+
43 ~FakedOptFFT() { //free all entry of the map and the map
+
44 auto itr = _fftw_api_map.begin();
+
45 while (itr != _fftw_api_map.end()) {
+
46 for (int i = 0; i < mardyn_get_max_threads(); ++i) {
+
47 delete ((*itr).second[i]);
+
48 }
+
49 delete ((*itr).second);
+
50 _fftw_api_map.erase(itr++);
+
51 }
+
52 _fftw_api_map.clear();
+
53 }
+
54
+
55 void optimizedFFT(FFT_precision** & Real, FFT_precision** & Imag,
+
56 const int size_x, const int size_y);
+
57 void optimizedIFFT(FFT_precision** & Real, FFT_precision** & Imag,
58 const int size_x, const int size_y);
-
59 void optimizedIFFT(FFT_precision** & Real, FFT_precision** & Imag,
-
60 const int size_x, const int size_y);
-
61
-
62private:
-
63 map<pos, FFTW_API**, pos_comp> _fftw_api_map; //storage of the various FFTW_API required
-
64
-
65 FFTW_API* getFFTW_API(const int size_x, const int size_y); //memoized function using the map
-
66};
-
67
-
68#endif
+
59
+
60private:
+
61 std::map<pos, FFTW_API**, pos_comp> _fftw_api_map; //storage of the various FFTW_API required
+
62
+
63 FFTW_API* getFFTW_API(const int size_x, const int size_y); //memoized function using the map
+
64};
+
65
+
66#endif
FFTW_API
Definition: FFTW_API.h:25
-
FakedOptFFT
Definition: FakedOptFFT.h:39
+
FakedOptFFT
Definition: FakedOptFFT.h:37
FakedOptFFT::optimizedIFFT
void optimizedIFFT(FFT_precision **&Real, FFT_precision **&Imag, const int size_x, const int size_y)
Definition: FakedOptFFT.cpp:135
FakedOptFFT::optimizedFFT
void optimizedFFT(FFT_precision **&Real, FFT_precision **&Imag, const int size_x, const int size_y)
Definition: FakedOptFFT.cpp:72
optFFT_API
Definition: optFFT_API.h:18
-
pos_comp
Definition: FakedOptFFT.h:28
-
pos
Definition: FakedOptFFT.h:23
+
pos_comp
Definition: FakedOptFFT.h:26
+
pos
Definition: FakedOptFFT.h:21
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FastMultipoleMethod_8h_source.html b/FastMultipoleMethod_8h_source.html index d9a5a76a4f..dca4563337 100644 --- a/FastMultipoleMethod_8h_source.html +++ b/FastMultipoleMethod_8h_source.html @@ -177,7 +177,7 @@
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
bhfmm::FastMultipoleMethod
Definition: FastMultipoleMethod.h:45
-
bhfmm::FastMultipoleMethod::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for FastMultipoleMethod and all its included objects.
Definition: FastMultipoleMethod.cpp:33
+
bhfmm::FastMultipoleMethod::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for FastMultipoleMethod and all its included objects.
Definition: FastMultipoleMethod.cpp:30
bhfmm::L2PCellProcessor
Definition: L2PCellProcessor.h:17
bhfmm::P2MCellProcessor
Definition: P2MCellProcessor.h:18
bhfmm::PseudoParticleContainer
Definition: PseudoParticleContainer.h:46
@@ -187,7 +187,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FileUtils_8h_source.html b/FileUtils_8h_source.html index 1301886806..d2917fed1c 100644 --- a/FileUtils_8h_source.html +++ b/FileUtils_8h_source.html @@ -118,7 +118,7 @@
65 *
66 * call e.g. like this:
67 *
-
68 * std::vector<string> fields;
+
68 * std::vector<std::string> fields;
69 * std::string str = "split:this:string";
70 * fields = split( fields, str, ":", split_type::no_empties );
71 *
@@ -162,7 +162,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FixRegion_8h_source.html b/FixRegion_8h_source.html index fcea4af4da..4ca154a237 100644 --- a/FixRegion_8h_source.html +++ b/FixRegion_8h_source.html @@ -122,7 +122,7 @@
67 callbackMap["FixRegion::getMoleculesInRegion"] = [this] { return _molCount; };
68 }
69};
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FixRegion
Plugin: can be enabled via config.xml
Definition: FixRegion.h:35
FixRegion::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: FixRegion.cpp:78
@@ -140,7 +140,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FixedSizeQueue_8h_source.html b/FixedSizeQueue_8h_source.html index 8914b7fba2..0f804290eb 100644 --- a/FixedSizeQueue_8h_source.html +++ b/FixedSizeQueue_8h_source.html @@ -123,7 +123,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FlopCounter_8cpp.html b/FlopCounter_8cpp.html index a82aacd419..81abe9f8e0 100644 --- a/FlopCounter_8cpp.html +++ b/FlopCounter_8cpp.html @@ -98,7 +98,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FlopCounter_8h.html b/FlopCounter_8h.html index c570157ef6..c2e33fa2b1 100644 --- a/FlopCounter_8h.html +++ b/FlopCounter_8h.html @@ -106,7 +106,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FlopCounter_8h_source.html b/FlopCounter_8h_source.html index 5b798bb6af..ae2bcc1ea9 100644 --- a/FlopCounter_8h_source.html +++ b/FlopCounter_8h_source.html @@ -95,14 +95,14 @@
80 void initTraversal();
81
85 void preprocessCell(ParticleCell& cell) {}
-
86
+
86
87
88 double processSingleMolecule(Molecule* /*m1*/, ParticleCell& /*cell2*/) { return 0.0; } // why 0.0 flops???
89
93 void processCell(ParticleCell& cell);
94
95 void processCellPair(ParticleCell& c1, ParticleCell& c2, bool sumAll = false);
-
96
+
96
100 void postprocessCell(ParticleCell& cell) {}
101
105 void endTraversal();
@@ -299,12 +299,12 @@
CellDataSoA
Structure of Arrays for vectorized force calculation.
Definition: CellDataSoA.h:22
CellProcessor
Definition: CellProcessor.h:29
FlopCounter
Definition: FlopCounter.h:60
-
FlopCounter::~FlopCounter
~FlopCounter()
Definition: FlopCounter.cpp:143
-
FlopCounter::initTraversal
void initTraversal()
Initializes the internal counters.
Definition: FlopCounter.cpp:154
-
FlopCounter::processCell
void processCell(ParticleCell &cell)
Count flops for this cell.
Definition: FlopCounter.cpp:207
-
FlopCounter::FlopCounter
FlopCounter(double cutoffRadius, double LJcutoffRadius)
Set up the counter.
Definition: FlopCounter.cpp:124
-
FlopCounter::endTraversal
void endTraversal()
Print results.
Definition: FlopCounter.cpp:163
-
FlopCounter::processCellPair
void processCellPair(ParticleCell &c1, ParticleCell &c2, bool sumAll=false)
Definition: FlopCounter.cpp:227
+
FlopCounter::~FlopCounter
~FlopCounter()
Definition: FlopCounter.cpp:142
+
FlopCounter::initTraversal
void initTraversal()
Initializes the internal counters.
Definition: FlopCounter.cpp:153
+
FlopCounter::processCell
void processCell(ParticleCell &cell)
Count flops for this cell.
Definition: FlopCounter.cpp:206
+
FlopCounter::FlopCounter
FlopCounter(double cutoffRadius, double LJcutoffRadius)
Set up the counter.
Definition: FlopCounter.cpp:123
+
FlopCounter::endTraversal
void endTraversal()
Print results.
Definition: FlopCounter.cpp:162
+
FlopCounter::processCellPair
void processCellPair(ParticleCell &c1, ParticleCell &c2, bool sumAll=false)
Definition: FlopCounter.cpp:226
FlopCounter::preprocessCell
void preprocessCell(ParticleCell &cell)
Only pass through to child.
Definition: FlopCounter.h:85
FlopCounter::postprocessCell
void postprocessCell(ParticleCell &cell)
Only pass through to child.
Definition: FlopCounter.h:100
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
@@ -313,7 +313,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FlopRateWriter_8h_source.html b/FlopRateWriter_8h_source.html index 7d71c6e439..14e0c6c88b 100644 --- a/FlopRateWriter_8h_source.html +++ b/FlopRateWriter_8h_source.html @@ -127,7 +127,7 @@
72};
73
74#endif /* SRC_IO_FLOPRATEWRITER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FlopCounter
Definition: FlopCounter.h:60
FlopRateWriter
Definition: FlopRateWriter.h:17
@@ -145,7 +145,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ForceHelper_8h_source.html b/ForceHelper_8h_source.html index e3256fa208..5a0fb12408 100644 --- a/ForceHelper_8h_source.html +++ b/ForceHelper_8h_source.html @@ -84,7 +84,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FullMolecule_8h_source.html b/FullMolecule_8h_source.html index 1ab23b37fa..4c1f5ae045 100644 --- a/FullMolecule_8h_source.html +++ b/FullMolecule_8h_source.html @@ -118,7 +118,7 @@
55 double v(unsigned short d) const override { return _v[d]; }
57 void setv(unsigned short d, double v) override { _v[d] = v; }
59 double mass() const override { return _m; }
-
60
+
60
61 void setF(unsigned short d, double F) override { _F[d] = F; }
63 double F(unsigned short d) const override {return _F[d]; }
64
@@ -154,7 +154,7 @@
101 }
102
104 double v2() const override {return _v[0]*_v[0]+_v[1]*_v[1]+_v[2]*_v[2]; }
-
105
+
105
107 double L2() const override {return _L[0]*_L[0]+_L[1]*_L[1]+_L[2]*_L[2]; }
108
110 double F2() const override {return _F[0]*_F[0]+_F[1]*_F[1]+_F[2]*_F[2]; }
@@ -166,7 +166,7 @@
119 double U_rot() override ;
120 double U_rot_2() override ;
122 double U_kin() override { return U_trans() + U_rot(); }
-
123
+
123
124 void setupSoACache(CellDataSoABase * s, unsigned iLJ, unsigned iC, unsigned iD, unsigned iQ) override;
125
126 void setSoA(CellDataSoABase * s) override;
@@ -175,7 +175,7 @@
129 void setStartIndexSoA_D(unsigned i) override {_soa_index_d = i;}
130 void setStartIndexSoA_Q(unsigned i) override {_soa_index_q = i;}
131
-
132 /* TODO: Maybe we should better do this using the component directly?
+
132 /* TODO: Maybe we should better do this using the component directly?
133 * In the GNU STL vector.size() causes two memory accesses and one subtraction!
134 */
136 unsigned int numSites() const override { return _component->numSites(); }
@@ -297,7 +297,7 @@
261 }
262 return d2;
263 }
-
264
+
264
268 void setF(double F[3]) override { for(int d = 0; d < 3; d++ ) { _F[d] = F[d]; } }
269
273 void setM(double M[3]) override { for(int d = 0; d < 3; d++ ) { _M[d] = M[d]; } }
@@ -336,7 +336,7 @@
317
319 void clearFM() override;
321 void calcFM() override;
-
322
+
322
324 void check(unsigned long id) override;
325
331 void buildOwnSoA() override;
@@ -388,8 +388,8 @@
FullMolecule::_q
Quaternion _q
Definition: FullMolecule.h:344
FullMolecule::numSites
unsigned int numSites() const override
Definition: FullMolecule.h:136
FullMolecule::setF
void setF(double F[3]) override
Definition: FullMolecule.h:268
-
FullMolecule::clearFM
void clearFM() override
Definition: FullMolecule.cpp:479
-
FullMolecule::check
void check(unsigned long id) override
Definition: FullMolecule.cpp:636
+
FullMolecule::clearFM
void clearFM() override
Definition: FullMolecule.cpp:476
+
FullMolecule::check
void check(unsigned long id) override
Definition: FullMolecule.cpp:633
FullMolecule::Vi
double Vi(unsigned short d) const override
Definition: FullMolecule.h:79
FullMolecule::F2
double F2() const override
Definition: FullMolecule.h:110
FullMolecule::totalMemsize
unsigned long totalMemsize() const override
@@ -398,7 +398,7 @@
FullMolecule::F
double F(unsigned short d) const override
Definition: FullMolecule.h:63
FullMolecule::getID
unsigned long getID() const override
Definition: FullMolecule.h:41
FullMolecule::setv
void setv(unsigned short d, double v) override
Definition: FullMolecule.h:57
-
FullMolecule::U_rot
double U_rot() override
Definition: FullMolecule.cpp:392
+
FullMolecule::U_rot
double U_rot() override
Definition: FullMolecule.cpp:389
FullMolecule::_M
double _M[3]
Definition: FullMolecule.h:345
FullMolecule::buildOwnSoA
void buildOwnSoA() override
FullMolecule::updateMassInertia
void updateMassInertia() override
Definition: FullMolecule.h:88
@@ -414,21 +414,21 @@
FullMolecule::setM
void setM(double M[3]) override
Definition: FullMolecule.h:273
FullMolecule::U_kin
double U_kin() override
Definition: FullMolecule.h:122
FullMolecule::dist2
double dist2(const FullMolecule &molecule2, double dr[3]) const
Definition: FullMolecule.h:256
-
FullMolecule::upd_postF
void upd_postF(double dt_halve, double &summv2, double &sumIw2) override
Definition: FullMolecule.cpp:366
+
FullMolecule::upd_postF
void upd_postF(double dt_halve, double &summv2, double &sumIw2) override
Definition: FullMolecule.cpp:363
FullMolecule::U_trans
double U_trans() const override
Definition: FullMolecule.h:116
-
FullMolecule::writeBinary
void writeBinary(std::ostream &ostrm) const override
Definition: FullMolecule.cpp:451
-
FullMolecule::calcFM
void calcFM() override
Definition: FullMolecule.cpp:551
-
FullMolecule::upd_preF
void upd_preF(double dt) override
Definition: FullMolecule.cpp:334
+
FullMolecule::writeBinary
void writeBinary(std::ostream &ostrm) const override
Definition: FullMolecule.cpp:448
+
FullMolecule::calcFM
void calcFM() override
Definition: FullMolecule.cpp:548
+
FullMolecule::upd_preF
void upd_preF(double dt) override
Definition: FullMolecule.cpp:331
FullMolecule::component
Component * component() const override
Definition: FullMolecule.h:47
-
FullMolecule::calcFM_site
void calcFM_site(const std::array< double, 3 > &d, const std::array< double, 3 > &F)
Definition: FullMolecule.cpp:526
-
FullMolecule::calculate_mv2_Iw2
void calculate_mv2_Iw2(double &summv2, double &sumIw2) override
Calculate twice the translational and rotational kinetic energies.
Definition: FullMolecule.cpp:412
+
FullMolecule::calcFM_site
void calcFM_site(const std::array< double, 3 > &d, const std::array< double, 3 > &F)
Definition: FullMolecule.cpp:523
+
FullMolecule::calculate_mv2_Iw2
void calculate_mv2_Iw2(double &summv2, double &sumIw2) override
Calculate twice the translational and rotational kinetic energies.
Definition: FullMolecule.cpp:409
FullMolecule::D
double D(unsigned short d) const override
Definition: FullMolecule.h:73
-
FullMolecule::getWriteFormat
static std::string getWriteFormat()
Definition: FullMolecule.cpp:438
+
FullMolecule::getWriteFormat
static std::string getWriteFormat()
Definition: FullMolecule.cpp:435
FullMolecule::_component
Component * _component
Definition: FullMolecule.h:340
FullMolecule::setr
void setr(unsigned short d, double r) override
Definition: FullMolecule.h:53
FullMolecule::r
double r(unsigned short d) const override
Definition: FullMolecule.h:51
FullMolecule::getComponentLookUpID
unsigned getComponentLookUpID() const override
Definition: FullMolecule.h:49
-
FullMolecule::write
void write(std::ostream &ostrm) const override
Definition: FullMolecule.cpp:442
+
FullMolecule::write
void write(std::ostream &ostrm) const override
Definition: FullMolecule.cpp:439
FullMolecule::_r
double _r[3]
Definition: FullMolecule.h:341
FullMolecule::_m
double _m
Definition: FullMolecule.h:350
FullMolecule::releaseOwnSoA
void releaseOwnSoA() override
@@ -444,7 +444,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FullParticleCell_8h_source.html b/FullParticleCell_8h_source.html index 6e3c2bbece..3df9483384 100644 --- a/FullParticleCell_8h_source.html +++ b/FullParticleCell_8h_source.html @@ -156,20 +156,20 @@
CellDataSoA
Structure of Arrays for vectorized force calculation.
Definition: CellDataSoA.h:22
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
FullParticleCell
FullParticleCell data structure. Renamed from ParticleCell.
Definition: FullParticleCell.h:49
-
FullParticleCell::deallocateAllParticles
void deallocateAllParticles() override
removes and deallocates all elements
Definition: FullParticleCell.cpp:29
-
FullParticleCell::addParticle
bool addParticle(Molecule &particle, bool checkWhetherDuplicate=false) override
insert a single molecule into this cell
Definition: FullParticleCell.cpp:50
-
FullParticleCell::getMoleculeCount
int getMoleculeCount() const override
return the number of molecules contained in this cell
Definition: FullParticleCell.cpp:77
-
FullParticleCell::findMoleculeByID
bool findMoleculeByID(size_t &index, unsigned long molid) const override
Find the index of a molecule in a cell based on its molecule ID.
Definition: FullParticleCell.cpp:33
-
FullParticleCell::FullParticleCell
FullParticleCell()
Initialize data pointers to 0.
Definition: FullParticleCell.cpp:19
-
FullParticleCell::isEmpty
bool isEmpty() const override
Check if current cell contains no molecules.
Definition: FullParticleCell.cpp:73
-
FullParticleCell::~FullParticleCell
~FullParticleCell()
Destructor.
Definition: FullParticleCell.cpp:23
+
FullParticleCell::deallocateAllParticles
void deallocateAllParticles() override
removes and deallocates all elements
Definition: FullParticleCell.cpp:28
+
FullParticleCell::addParticle
bool addParticle(Molecule &particle, bool checkWhetherDuplicate=false) override
insert a single molecule into this cell
Definition: FullParticleCell.cpp:49
+
FullParticleCell::getMoleculeCount
int getMoleculeCount() const override
return the number of molecules contained in this cell
Definition: FullParticleCell.cpp:76
+
FullParticleCell::findMoleculeByID
bool findMoleculeByID(size_t &index, unsigned long molid) const override
Find the index of a molecule in a cell based on its molecule ID.
Definition: FullParticleCell.cpp:32
+
FullParticleCell::FullParticleCell
FullParticleCell()
Initialize data pointers to 0.
Definition: FullParticleCell.cpp:18
+
FullParticleCell::isEmpty
bool isEmpty() const override
Check if current cell contains no molecules.
Definition: FullParticleCell.cpp:72
+
FullParticleCell::~FullParticleCell
~FullParticleCell()
Destructor.
Definition: FullParticleCell.cpp:22
FullParticleCell::getCellDataSoA
CellDataSoA & getCellDataSoA()
Get the structure of arrays for VectorizedCellProcessor.
Definition: FullParticleCell.h:85
ParticleCellBase
ParticleCellBase defines the interface for cells used by the LinkedCells data structure to store mole...
Definition: ParticleCellBase.h:23
SingleCellIterator
Definition: SingleCellIterator.h:14
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FullShell_8h_source.html b/FullShell_8h_source.html index d3b1b3d948..706702f09e 100644 --- a/FullShell_8h_source.html +++ b/FullShell_8h_source.html @@ -116,7 +116,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/FunctionWrapper_8h_source.html b/FunctionWrapper_8h_source.html index 4faaa7c2c1..a505091395 100644 --- a/FunctionWrapper_8h_source.html +++ b/FunctionWrapper_8h_source.html @@ -109,7 +109,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/GammaWriter_8h_source.html b/GammaWriter_8h_source.html index 9c17f1afc9..f3dfeb066a 100644 --- a/GammaWriter_8h_source.html +++ b/GammaWriter_8h_source.html @@ -78,7 +78,7 @@
6#include <fstream>
7
8class ParticleContainer;
-
9class DomainDecompBase;
+
9class DomainDecompBase;
10class Domain;
11
16class XMLfileUnits;
@@ -112,7 +112,7 @@
59
60 void finish(ParticleContainer *particleContainer,
61 DomainDecompBase *domainDecomp, Domain *domain) override {}
-
62
+
62
63 std::string getPluginName() override { return "GammaWriter"; }
64 static PluginBase* createInstance() { return new GammaWriter(); }
65
@@ -136,7 +136,7 @@
83};
84
85#endif // SRC_IO_GAMMAWRITER_H_
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
GammaWriter
Definition: GammaWriter.h:17
GammaWriter::init
void init(ParticleContainer *, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: GammaWriter.cpp:28
@@ -151,7 +151,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/GeneralDomainDecomposition_8cpp.html b/GeneralDomainDecomposition_8cpp.html index 5bb23a1a67..ef8bb97c76 100644 --- a/GeneralDomainDecomposition_8cpp.html +++ b/GeneralDomainDecomposition_8cpp.html @@ -78,6 +78,11 @@ #include "NeighborAcquirer.h"
#include "NeighbourCommunicationScheme.h"
#include <numeric>
+#include <memory>
+#include <string>
+#include <vector>
+#include <algorithm>
+#include <tuple>
@@ -125,7 +130,7 @@

-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/GeneralDomainDecomposition_8h.html b/GeneralDomainDecomposition_8h.html index 6776a6fc24..18a486d7b7 100644 --- a/GeneralDomainDecomposition_8h.html +++ b/GeneralDomainDecomposition_8h.html @@ -89,7 +89,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/GeneralDomainDecomposition_8h_source.html b/GeneralDomainDecomposition_8h_source.html index 727a8983ec..d4fa34c1d8 100644 --- a/GeneralDomainDecomposition_8h_source.html +++ b/GeneralDomainDecomposition_8h_source.html @@ -189,13 +189,13 @@
DomainDecompMPIBase
Definition: DomainDecompMPIBase.h:30
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
GeneralDomainDecomposition
Definition: GeneralDomainDecomposition.h:17
-
GeneralDomainDecomposition::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DomainDecomposition and all its included objects.
Definition: GeneralDomainDecomposition.cpp:254
+
GeneralDomainDecomposition::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DomainDecomposition and all its included objects.
Definition: GeneralDomainDecomposition.cpp:259
GeneralDomainDecomposition::finishNonBlockingStage
void finishNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: GeneralDomainDecomposition.h:77
-
GeneralDomainDecomposition::getBoundingBoxMin
double getBoundingBoxMin(int dimension, Domain *domain) override
get the minimum of the bounding box of this process' domain in the given dimension (0,...
Definition: GeneralDomainDecomposition.cpp:61
+
GeneralDomainDecomposition::getBoundingBoxMin
double getBoundingBoxMin(int dimension, Domain *domain) override
get the minimum of the bounding box of this process' domain in the given dimension (0,...
Definition: GeneralDomainDecomposition.cpp:66
GeneralDomainDecomposition::queryBalanceAndExchangeNonBlocking
bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, double etime) override
Checks whether the balance and exchange step can be performed non-blocking.
Definition: GeneralDomainDecomposition.h:83
-
GeneralDomainDecomposition::GeneralDomainDecomposition
GeneralDomainDecomposition(double interactionLength, Domain *domain, bool forceGrid)
Definition: GeneralDomainDecomposition.cpp:17
-
GeneralDomainDecomposition::getBoundingBoxMax
double getBoundingBoxMax(int dimension, Domain *domain) override
get the maximum of the bounding box of this process' domain in the given dimension (0,...
Definition: GeneralDomainDecomposition.cpp:65
-
GeneralDomainDecomposition::balanceAndExchange
void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain) override
balance the load (and optimize communication) and exchange boundary particles
Definition: GeneralDomainDecomposition.cpp:72
+
GeneralDomainDecomposition::GeneralDomainDecomposition
GeneralDomainDecomposition(double interactionLength, Domain *domain, bool forceGrid)
Definition: GeneralDomainDecomposition.cpp:22
+
GeneralDomainDecomposition::getBoundingBoxMax
double getBoundingBoxMax(int dimension, Domain *domain) override
get the maximum of the bounding box of this process' domain in the given dimension (0,...
Definition: GeneralDomainDecomposition.cpp:70
+
GeneralDomainDecomposition::balanceAndExchange
void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain) override
balance the load (and optimize communication) and exchange boundary particles
Definition: GeneralDomainDecomposition.cpp:77
GeneralDomainDecomposition::prepareNonBlockingStage
void prepareNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: GeneralDomainDecomposition.h:71
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
@@ -203,7 +203,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/GetChunkSize_8h_source.html b/GetChunkSize_8h_source.html index 54a39efc7f..7d905aa355 100644 --- a/GetChunkSize_8h_source.html +++ b/GetChunkSize_8h_source.html @@ -82,7 +82,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/GrandCanonicalEnsemble_8h_source.html b/GrandCanonicalEnsemble_8h_source.html index 860393ee83..7f46ed46c1 100644 --- a/GrandCanonicalEnsemble_8h_source.html +++ b/GrandCanonicalEnsemble_8h_source.html @@ -96,7 +96,7 @@
40
41 // TODO: Implement STUB
42 void readXML(XMLfileUnits& xmlconfig) override {
-
43 global_log->info() << "[GrandCanonicalEnsemble] readXML not implemented!" << std::endl;
+
43 Log::global_log->info() << "[GrandCanonicalEnsemble] readXML not implemented!" << std::endl;
44 Simulation::exit(-1);
45 };
46
@@ -126,7 +126,7 @@
70
71 // TODO: Implement
72 void updateGlobalVariable(ParticleContainer* particleContainer, GlobalVariable variable) override {
-
73 global_log->info() << "[GrandCanonicalEnsemble] updateGlobalVariable not implemented!" << std::endl;
+
73 Log::global_log->info() << "[GrandCanonicalEnsemble] updateGlobalVariable not implemented!" << std::endl;
74 Simulation::exit(-1);
75 };
76
@@ -166,7 +166,7 @@
128
129};
CellProcessor
Definition: CellProcessor.h:29
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Ensemble
Base class for ensembles.
Definition: EnsembleBase.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
@@ -185,12 +185,12 @@
GrandCanonicalEnsemble::storeSample
void storeSample(Molecule *m, uint32_t componentid) override
Definition: GrandCanonicalEnsemble.cpp:139
GrandCanonicalEnsemble::mu
double mu() override
Returns the global chemical potential of the ensemble.
Definition: GrandCanonicalEnsemble.h:59
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/GridFiller_8h_source.html b/GridFiller_8h_source.html index b9037e0dab..daa5a3f7ae 100644 --- a/GridFiller_8h_source.html +++ b/GridFiller_8h_source.html @@ -139,7 +139,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/HalfShellTraversal_8h_source.html b/HalfShellTraversal_8h_source.html index e8b74fe94d..8273939066 100644 --- a/HalfShellTraversal_8h_source.html +++ b/HalfShellTraversal_8h_source.html @@ -122,7 +122,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/HalfShell_8h_source.html b/HalfShell_8h_source.html index 3a089619e9..337fa22a03 100644 --- a/HalfShell_8h_source.html +++ b/HalfShell_8h_source.html @@ -117,7 +117,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/HaloBufferNoOverlap_8h_source.html b/HaloBufferNoOverlap_8h_source.html index d6f44e98fd..8fbc6145b6 100644 --- a/HaloBufferNoOverlap_8h_source.html +++ b/HaloBufferNoOverlap_8h_source.html @@ -165,7 +165,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/HaloBufferOverlap_8h_source.html b/HaloBufferOverlap_8h_source.html index 569867ad14..5f32aaae28 100644 --- a/HaloBufferOverlap_8h_source.html +++ b/HaloBufferOverlap_8h_source.html @@ -700,7 +700,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/HaloParticleWriter_8h_source.html b/HaloParticleWriter_8h_source.html index a0340d116a..23f0c9c30a 100644 --- a/HaloParticleWriter_8h_source.html +++ b/HaloParticleWriter_8h_source.html @@ -79,13 +79,13 @@
7
13class HaloParticleWriter : public PluginBase {
14public:
-
15
+
15
16 HaloParticleWriter() = default;
17 ~HaloParticleWriter() override = default;
-
18
+
18
19
32 void readXML(XMLfileUnits& xmlconfig) override;
-
33
+
33
34 void init(ParticleContainer *particleContainer,
35 DomainDecompBase *domainDecomp, Domain *domain) override;
36 void afterForces(ParticleContainer *particleContainer,
@@ -98,7 +98,7 @@
43
44 void finish(ParticleContainer *particleContainer,
45 DomainDecompBase *domainDecomp, Domain *domain) override;
-
46
+
46
47 std::string getPluginName() override {
48 return std::string("HaloParticleWriter");
49 }
@@ -111,14 +111,14 @@
56};
57
58#endif // SRC_IO_HALOPARTICLEWRITER_H_
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
HaloParticleWriter
Definition: HaloParticleWriter.h:13
-
HaloParticleWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: HaloParticleWriter.cpp:43
-
HaloParticleWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: HaloParticleWriter.cpp:92
-
HaloParticleWriter::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: HaloParticleWriter.cpp:46
+
HaloParticleWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: HaloParticleWriter.cpp:40
+
HaloParticleWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: HaloParticleWriter.cpp:89
+
HaloParticleWriter::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: HaloParticleWriter.cpp:43
HaloParticleWriter::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: HaloParticleWriter.h:47
-
HaloParticleWriter::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for HaloParticleWriter.
Definition: HaloParticleWriter.cpp:15
+
HaloParticleWriter::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for HaloParticleWriter.
Definition: HaloParticleWriter.cpp:12
HaloParticleWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: HaloParticleWriter.h:39
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -127,7 +127,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/HaloRegion_8h_source.html b/HaloRegion_8h_source.html index 9f24212f22..d9580ba5f4 100644 --- a/HaloRegion_8h_source.html +++ b/HaloRegion_8h_source.html @@ -89,7 +89,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Homogeneous_8h_source.html b/Homogeneous_8h_source.html index f125b0f43d..2385b9b5b4 100644 --- a/Homogeneous_8h_source.html +++ b/Homogeneous_8h_source.html @@ -105,10 +105,10 @@
33 double _TICCv(int n,double rc,double sigma2);
34 double _TICSv(int n,double rc,double sigma2,double tau);
35 double _TISSv(int n,double rc,double sigma2,double tau1,double tau2);
-
36
+
36
38 std::vector<Component>* _components{nullptr};
40 Comp2Param _comp2params;
-
41
+
41
42 Domain* _domain{nullptr};
43
44 double _cutoff{std::numeric_limits<double>::quiet_NaN()};
@@ -121,16 +121,16 @@
51
52#endif /* __HOMOGENEOUS_H__ */
Comp2Param
Definition: Comp2Param.h:15
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Homogeneous
Definition: Homogeneous.h:15
LongRangeCorrection
Definition: LongRangeCorrection.h:12
-
Simulation
Controls the simulation process.
Definition: Simulation.h:70
+
Simulation
Controls the simulation process.
Definition: Simulation.h:72
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/IOHelpers_8h_source.html b/IOHelpers_8h_source.html index 0fa6675668..adba3fc07e 100644 --- a/IOHelpers_8h_source.html +++ b/IOHelpers_8h_source.html @@ -91,13 +91,13 @@
48
58std::array<double, 3> getRandomVelocityAccordingToTemperature(double temperature, Random& RNG);
59} // namespace IOHelpers
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
Random
Definition: Random.h:12
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/InMemoryCheckpointing_8h_source.html b/InMemoryCheckpointing_8h_source.html index 77fa8aae18..01c7df1cb0 100644 --- a/InMemoryCheckpointing_8h_source.html +++ b/InMemoryCheckpointing_8h_source.html @@ -198,15 +198,15 @@
132};
133
134#endif /* SRC_PLUGINS_INMEMORYCHECKPOINTING_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
InMemoryCheckpointing::Snapshot
Definition: InMemoryCheckpointing.h:62
InMemoryCheckpointing
Definition: InMemoryCheckpointing.h:18
InMemoryCheckpointing::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: InMemoryCheckpointing.h:53
-
InMemoryCheckpointing::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: InMemoryCheckpointing.cpp:19
-
InMemoryCheckpointing::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
restarting takes place here
Definition: InMemoryCheckpointing.cpp:29
-
InMemoryCheckpointing::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: InMemoryCheckpointing.cpp:63
+
InMemoryCheckpointing::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: InMemoryCheckpointing.cpp:18
+
InMemoryCheckpointing::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
restarting takes place here
Definition: InMemoryCheckpointing.cpp:28
+
InMemoryCheckpointing::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: InMemoryCheckpointing.cpp:62
InMemoryCheckpointing::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: InMemoryCheckpointing.h:23
InMemoryCheckpointing::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: InMemoryCheckpointing.h:36
InMemoryCheckpointing::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: InMemoryCheckpointing.h:56
@@ -218,7 +218,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/InputBase_8h_source.html b/InputBase_8h_source.html index 5e4c8ec9cd..f0afe9d6bc 100644 --- a/InputBase_8h_source.html +++ b/InputBase_8h_source.html @@ -100,7 +100,7 @@
38};
39
40#endif /*INPUTBASE_H_*/
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
InputBase::readPhaseSpace
virtual unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)=0
read the actual phase space information
@@ -110,7 +110,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Integrator_8h_source.html b/Integrator_8h_source.html index 7455a8e312..b6e6291603 100644 --- a/Integrator_8h_source.html +++ b/Integrator_8h_source.html @@ -121,7 +121,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/KDDStaticValues_8h_source.html b/KDDStaticValues_8h_source.html index 8a6ac022b5..2f2eab2b02 100644 --- a/KDDStaticValues_8h_source.html +++ b/KDDStaticValues_8h_source.html @@ -82,7 +82,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/KDDecomposition_8h_source.html b/KDDecomposition_8h_source.html index 1fc3c716e9..57370dc5a6 100644 --- a/KDDecomposition_8h_source.html +++ b/KDDecomposition_8h_source.html @@ -173,7 +173,7 @@
283 bool heteroDecompose(KDNode* fatherNode, KDNode*& ownArea, MPI_Comm commGroup);
284
291 bool calculateAllPossibleSubdivisions(KDNode* node, std::list<KDNode*>& subdividedNodes, MPI_Comm commGroup);
-
292
+
292
299 bool calculateHeteroSubdivision(KDNode* node, KDNode*& subdivededNode, MPI_Comm commGroup);
300
301 void updateMeanProcessorSpeeds(std::vector<double>& processorSpeeds,
@@ -290,15 +290,15 @@
DomainDecompMPIBase
Definition: DomainDecompMPIBase.h:30
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
KDDecomposition
KD tree based domain decomposition for better load balancing.
Definition: KDDecomposition.h:37
-
KDDecomposition::getBoundingBoxMin
double getBoundingBoxMin(int dimension, Domain *domain) override
Definition: KDDecomposition.cpp:674
-
KDDecomposition::queryBalanceAndExchangeNonBlocking
bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, double etime) override
Checks whether the balance and exchange step can be performed non-blocking.
Definition: KDDecomposition.cpp:235
-
KDDecomposition::readXML
virtual void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for KDDecomposition and all its included objects.
Definition: KDDecomposition.cpp:101
-
KDDecomposition::balanceAndExchange
void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain) override
balance the load (and optimize communication) and exchange boundary particles
Definition: KDDecomposition.cpp:261
-
KDDecomposition::printTree
void printTree(std::ostream &ostream)
Definition: KDDecomposition.cpp:1860
-
KDDecomposition::getBoundingBoxMax
double getBoundingBoxMax(int dimension, Domain *domain) override
Definition: KDDecomposition.cpp:688
-
KDDecomposition::prepareNonBlockingStage
virtual void prepareNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: KDDecomposition.cpp:206
-
KDDecomposition::KDDecomposition
KDDecomposition(double cutoffRadius, int numParticleTypes, int updateFrequency=100, int fullSearchThreshold=2)
create an initial decomposition tree
Definition: KDDecomposition.cpp:34
-
KDDecomposition::finishNonBlockingStage
virtual void finishNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: KDDecomposition.cpp:218
+
KDDecomposition::getBoundingBoxMin
double getBoundingBoxMin(int dimension, Domain *domain) override
Definition: KDDecomposition.cpp:672
+
KDDecomposition::queryBalanceAndExchangeNonBlocking
bool queryBalanceAndExchangeNonBlocking(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, double etime) override
Checks whether the balance and exchange step can be performed non-blocking.
Definition: KDDecomposition.cpp:233
+
KDDecomposition::readXML
virtual void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for KDDecomposition and all its included objects.
Definition: KDDecomposition.cpp:99
+
KDDecomposition::balanceAndExchange
void balanceAndExchange(double lastTraversalTime, bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain) override
balance the load (and optimize communication) and exchange boundary particles
Definition: KDDecomposition.cpp:259
+
KDDecomposition::printTree
void printTree(std::ostream &ostream)
Definition: KDDecomposition.cpp:1858
+
KDDecomposition::getBoundingBoxMax
double getBoundingBoxMax(int dimension, Domain *domain) override
Definition: KDDecomposition.cpp:686
+
KDDecomposition::prepareNonBlockingStage
virtual void prepareNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: KDDecomposition.cpp:204
+
KDDecomposition::KDDecomposition
KDDecomposition(double cutoffRadius, int numParticleTypes, int updateFrequency=100, int fullSearchThreshold=2)
create an initial decomposition tree
Definition: KDDecomposition.cpp:32
+
KDDecomposition::finishNonBlockingStage
virtual void finishNonBlockingStage(bool forceRebalancing, ParticleContainer *moleculeContainer, Domain *domain, unsigned int stageNumber) override
Definition: KDDecomposition.cpp:216
KDNode
represents a node in the decomposition tree when using KDDecomposition
Definition: KDNode.h:28
LoadCalc
Definition: LoadCalc.h:24
MeasureLoad
Definition: LoadCalc.h:227
@@ -308,7 +308,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/KDNode_8h_source.html b/KDNode_8h_source.html index 4f07713835..1d483d914c 100644 --- a/KDNode_8h_source.html +++ b/KDNode_8h_source.html @@ -228,34 +228,34 @@
262#endif /* KDNODE_H_ */
KDNode
represents a node in the decomposition tree when using KDDecomposition
Definition: KDNode.h:28
KDNode::_deviation
double _deviation
Definition: KDNode.h:247
-
KDNode::equals
bool equals(KDNode &other)
Definition: KDNode.cpp:34
+
KDNode::equals
bool equals(KDNode &other)
Definition: KDNode.cpp:33
KDNode::_owningProc
int _owningProc
process which owns this KDNode (only possible for leaf nodes)
Definition: KDNode.h:230
KDNode::MPIKDNode
MPIKDNodePacked MPIKDNode
Definition: KDNode.h:37
KDNode::_lowCorner
int _lowCorner[3]
in cells relative to global domain
Definition: KDNode.h:221
KDNode::_child1
KDNode * _child1
"left" child of this KDNode (only used if the child is no leaf)
Definition: KDNode.h:233
-
KDNode::plotNode
void plotNode(const std::string &vtkFile, const std::vector< double > *processorSpeeds=nullptr) const
Definition: KDNode.cpp:281
+
KDNode::plotNode
void plotNode(const std::string &vtkFile, const std::vector< double > *processorSpeeds=nullptr) const
Definition: KDNode.cpp:280
KDNode::_deviationLowerBound
double _deviationLowerBound
Definition: KDNode.h:243
-
KDNode::getOwningProcs
void getOwningProcs(const int low[KDDIM], const int high[KDDIM], std::vector< int > &procIDs, std::vector< int > &neighbHaloAreas) const
Definition: KDNode.cpp:321
-
KDNode::serialize
void serialize(const std::string &fileName)
Definition: KDNode.cpp:206
+
KDNode::getOwningProcs
void getOwningProcs(const int low[KDDIM], const int high[KDDIM], std::vector< int > &procIDs, std::vector< int > &neighbHaloAreas) const
Definition: KDNode.cpp:320
+
KDNode::serialize
void serialize(const std::string &fileName)
Definition: KDNode.cpp:205
KDNode::_nodeID
int _nodeID
ID of this KDNode.
Definition: KDNode.h:228
KDNode::_child2
KDNode * _child2
"left" child of this KDNode (only used if the child is no leaf)
Definition: KDNode.h:235
-
KDNode::deserialize
void deserialize(const std::string &fileName)
Definition: KDNode.cpp:243
-
KDNode::isResolvable
bool isResolvable()
Definition: KDNode.cpp:142
+
KDNode::deserialize
void deserialize(const std::string &fileName)
Definition: KDNode.cpp:242
+
KDNode::isResolvable
bool isResolvable()
Definition: KDNode.cpp:141
KDNode::calculateDeviationLowerBound
void calculateDeviationLowerBound(std::vector< double > *accumulatedProcessorSpeeds=nullptr)
Definition: KDNode.h:118
-
KDNode::split
void split(int divDimension, int splitIndex, int numProcsLeft)
Definition: KDNode.cpp:160
+
KDNode::split
void split(int divDimension, int splitIndex, int numProcsLeft)
Definition: KDNode.cpp:159
KDNode::_highCorner
int _highCorner[3]
in cells relative to global domain
Definition: KDNode.h:223
KDNode::KDNode
KDNode(const KDNode &other)
Definition: KDNode.h:49
KDNode::~KDNode
~KDNode()
The destructor deletes the childs (recursive call of destructors)
Definition: KDNode.h:80
KDNode::_numProcs
int _numProcs
number of procs which share this area
Definition: KDNode.h:219
-
KDNode::findAreaForProcess
KDNode * findAreaForProcess(int rank)
Definition: KDNode.cpp:18
+
KDNode::findAreaForProcess
KDNode * findAreaForProcess(int rank)
Definition: KDNode.cpp:17
KDNode::initMPIDataType
static void initMPIDataType()
Definition: KDNode.h:202
KDNode::_level
int _level
level of this node (at root node, level = 0)
Definition: KDNode.h:250
-
KDNode::getMPIKDNode
MPIKDNode getMPIKDNode()
Definition: KDNode.cpp:118
-
KDNode::buildKDTree
void buildKDTree()
create an initial decomposition of the domain represented by this node.
Definition: KDNode.cpp:68
+
KDNode::getMPIKDNode
MPIKDNode getMPIKDNode()
Definition: KDNode.cpp:117
+
KDNode::buildKDTree
void buildKDTree()
create an initial decomposition of the domain represented by this node.
Definition: KDNode.cpp:67
KDNode::_coversWholeDomain
bool _coversWholeDomain[KDDIM]
true if the domain in the given dimension is not divided into more than one process
Definition: KDNode.h:225
KDNode::shutdownMPIDataType
static void shutdownMPIDataType()
Definition: KDNode.h:209
-
KDNode::printTree
void printTree(const std::string &prefix, std::ostream &ostream)
prints this (sub-) tree to stdout
Definition: KDNode.cpp:91
-
KDNode::getNumMaxProcs
unsigned int getNumMaxProcs()
Definition: KDNode.cpp:151
+
KDNode::printTree
void printTree(const std::string &prefix, std::ostream &ostream)
prints this (sub-) tree to stdout
Definition: KDNode.cpp:90
+
KDNode::getNumMaxProcs
unsigned int getNumMaxProcs()
Definition: KDNode.cpp:150
MPIKDNodePacked
Definition: MPIKDNode.h:19
MPIKDNodePacked::initDatatype
static void initDatatype()
Definition: MPIKDNode.cpp:305
VTKGridWriterImplementation
Definition: VTKGridWriterImplementation.h:23
@@ -264,7 +264,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/KDTreePrinter_8h_source.html b/KDTreePrinter_8h_source.html index a84fe62b85..5d894c1499 100644 --- a/KDTreePrinter_8h_source.html +++ b/KDTreePrinter_8h_source.html @@ -94,7 +94,7 @@
37 bool _appendTimestamp {false};
38
39};
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
KDTreePrinter
Definition: KDTreePrinter.h:6
KDTreePrinter::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: KDTreePrinter.cpp:80
@@ -109,7 +109,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/KineticProfile_8h_source.html b/KineticProfile_8h_source.html index a086d17210..246ae41ff3 100644 --- a/KineticProfile_8h_source.html +++ b/KineticProfile_8h_source.html @@ -95,7 +95,7 @@
26 void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final {
27 _globalProfile[uID] = domainDecomp->collCommGetDouble();
28 }
-
29 void output(string prefix, long unsigned accumulatedDatasets) final;
+
29 void output(std::string prefix, long unsigned accumulatedDatasets) final;
30 void reset(unsigned long uID) final {
31 _localProfile[uID] = 0.0;
32 _globalProfile[uID] = 0.0;
@@ -112,26 +112,27 @@
43 // Global 1D Profile
44 std::map<unsigned, double> _globalProfile;
45
-
46 void writeDataEntry(unsigned long uID, ofstream &outfile) const final;
+
46 void writeDataEntry(unsigned long uID, std::ofstream &outfile) const final;
47
48};
49
50
51#endif //MARDYN_KINETICPROFILE_H
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
KineticProfile
Records (NO OUTPUT) the 2xKinetic Profile of molecules per bin specified by Sampling grid in Kartesia...
Definition: KineticProfile.h:14
KineticProfile::collectRetrieve
void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
Definition: KineticProfile.h:26
-
KineticProfile::output
void output(string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: KineticProfile.cpp:7
+
KineticProfile::output
void output(std::string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: KineticProfile.cpp:7
KineticProfile::comms
int comms() final
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
Definition: KineticProfile.h:34
KineticProfile::collectAppend
void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID) final
Append all necessary communication per bin to the DomainDecomposition. Append from e....
Definition: KineticProfile.h:23
KineticProfile::record
void record(Molecule &mol, unsigned long uID) final
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
Definition: KineticProfile.h:17
KineticProfile::reset
void reset(unsigned long uID) final
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
Definition: KineticProfile.h:30
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/L2PCellProcessor_8h_source.html b/L2PCellProcessor_8h_source.html index 2b475eb32b..ec15b9a4ce 100644 --- a/L2PCellProcessor_8h_source.html +++ b/L2PCellProcessor_8h_source.html @@ -115,7 +115,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LA_8h_source.html b/LA_8h_source.html index 3640026eed..21649f5493 100644 --- a/LA_8h_source.html +++ b/LA_8h_source.html @@ -85,7 +85,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LU_8h_source.html b/LU_8h_source.html index 3064ba4181..b2586b0c38 100644 --- a/LU_8h_source.html +++ b/LU_8h_source.html @@ -80,7 +80,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Lattice_8h_source.html b/Lattice_8h_source.html index ddd14f99a0..5cec376012 100644 --- a/Lattice_8h_source.html +++ b/Lattice_8h_source.html @@ -163,19 +163,19 @@
138
139#endif /* LATTICE_H */
Lattice
Definition: Lattice.h:44
-
Lattice::setDimsMax
void setDimsMax(long dimsMax[3])
Definition: Lattice.cpp:226
+
Lattice::setDimsMax
void setDimsMax(long dimsMax[3])
Definition: Lattice.cpp:225
Lattice::a
const double * a()
Definition: Lattice.h:116
-
Lattice::getPoint
int getPoint(double *r)
Definition: Lattice.cpp:117
-
Lattice::init
void init(LatticeSystem system, LatticeCentering centering, double a[3], double b[3], double c[3])
Definition: Lattice.cpp:106
-
Lattice::centeringName
const char * centeringName()
Definition: Lattice.cpp:235
-
Lattice::setDimsMin
void setDimsMin(long dimsMin[3])
Definition: Lattice.cpp:219
+
Lattice::getPoint
int getPoint(double *r)
Definition: Lattice.cpp:116
+
Lattice::init
void init(LatticeSystem system, LatticeCentering centering, double a[3], double b[3], double c[3])
Definition: Lattice.cpp:105
+
Lattice::centeringName
const char * centeringName()
Definition: Lattice.cpp:234
+
Lattice::setDimsMin
void setDimsMin(long dimsMin[3])
Definition: Lattice.cpp:218
Lattice::Lattice
Lattice()
Definition: Lattice.h:47
Lattice::~Lattice
~Lattice()
Definition: Lattice.h:49
-
Lattice::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Lattice and all its included objects.
Definition: Lattice.cpp:78
+
Lattice::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Lattice and all its included objects.
Definition: Lattice.cpp:77
Lattice::c
const double * c()
Definition: Lattice.h:120
-
Lattice::checkValidity
bool checkValidity()
Definition: Lattice.cpp:153
+
Lattice::checkValidity
bool checkValidity()
Definition: Lattice.cpp:152
Lattice::b
const double * b()
Definition: Lattice.h:118
-
Lattice::systemName
const char * systemName()
Definition: Lattice.cpp:232
+
Lattice::systemName
const char * systemName()
Definition: Lattice.cpp:231
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::name
::xsd::cxx::tree::name< char, token > name
C++ type corresponding to the Name XML Schema built-in type.
Definition: xml-schema.h:286
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
@@ -183,7 +183,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LeafNodesContainer_8h_source.html b/LeafNodesContainer_8h_source.html index 222cf1eb42..8b3377ac95 100644 --- a/LeafNodesContainer_8h_source.html +++ b/LeafNodesContainer_8h_source.html @@ -171,7 +171,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LeapfrogRMM_8h_source.html b/LeapfrogRMM_8h_source.html index e783dc6df6..bde605a1f2 100644 --- a/LeapfrogRMM_8h_source.html +++ b/LeapfrogRMM_8h_source.html @@ -96,7 +96,7 @@
24 }
25
26private:
-
27
+
27
28 void computePositions(ParticleContainer* molCont, Domain* dom);
29 void computeVelocities(ParticleContainer* molCont, Domain* dom);
30
@@ -119,7 +119,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Leapfrog_8h_source.html b/Leapfrog_8h_source.html index eedb3087e0..70864f1452 100644 --- a/Leapfrog_8h_source.html +++ b/Leapfrog_8h_source.html @@ -112,17 +112,17 @@
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Integrator
Update velocities and positions.
Definition: Integrator.h:32
Leapfrog
Implementation of the rotational leapfrog integration scheme.
Definition: Leapfrog.h:36
-
Leapfrog::eventForcesCalculated
void eventForcesCalculated(ParticleContainer *molCont, Domain *domain)
steps between the force calculation and the end of the time step
Definition: Leapfrog.cpp:35
-
Leapfrog::init
virtual void init()
Definition: Leapfrog.cpp:21
-
Leapfrog::~Leapfrog
~Leapfrog()
The destructor.
Definition: Leapfrog.cpp:26
-
Leapfrog::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for leapfrog integrator and all its included objects.
Definition: Leapfrog.cpp:28
-
Leapfrog::eventNewTimestep
void eventNewTimestep(ParticleContainer *molCont, Domain *domain)
performs all steps that can be done before new forces are needed
Definition: Leapfrog.cpp:41
+
Leapfrog::eventForcesCalculated
void eventForcesCalculated(ParticleContainer *molCont, Domain *domain)
steps between the force calculation and the end of the time step
Definition: Leapfrog.cpp:32
+
Leapfrog::init
virtual void init()
Definition: Leapfrog.cpp:18
+
Leapfrog::~Leapfrog
~Leapfrog()
The destructor.
Definition: Leapfrog.cpp:23
+
Leapfrog::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for leapfrog integrator and all its included objects.
Definition: Leapfrog.cpp:25
+
Leapfrog::eventNewTimestep
void eventNewTimestep(ParticleContainer *molCont, Domain *domain)
performs all steps that can be done before new forces are needed
Definition: Leapfrog.cpp:38
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LegacyCellProcessor_8h_source.html b/LegacyCellProcessor_8h_source.html index a669304ab5..31c6027dd4 100644 --- a/LegacyCellProcessor_8h_source.html +++ b/LegacyCellProcessor_8h_source.html @@ -103,7 +103,7 @@
36 void initTraversal();
37
38 void preprocessCell(ParticleCell& /*cell*/) {}
-
39
+
39
40 void processCellPair(ParticleCell& cell1, ParticleCell& cell2, bool sumAll = false);
41
42 double processSingleMolecule(Molecule* m1, ParticleCell& cell2);
@@ -120,17 +120,17 @@
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
FullParticleCell
FullParticleCell data structure. Renamed from ParticleCell.
Definition: FullParticleCell.h:49
LegacyCellProcessor
Definition: LegacyCellProcessor.h:21
-
LegacyCellProcessor::initTraversal
void initTraversal()
Definition: LegacyCellProcessor.cpp:29
-
LegacyCellProcessor::endTraversal
void endTraversal()
Definition: LegacyCellProcessor.cpp:154
-
LegacyCellProcessor::processCell
void processCell(ParticleCell &cell)
Definition: LegacyCellProcessor.cpp:129
+
LegacyCellProcessor::initTraversal
void initTraversal()
Definition: LegacyCellProcessor.cpp:27
+
LegacyCellProcessor::endTraversal
void endTraversal()
Definition: LegacyCellProcessor.cpp:152
+
LegacyCellProcessor::processCell
void processCell(ParticleCell &cell)
Definition: LegacyCellProcessor.cpp:127
LegacyCellProcessor::preprocessCell
void preprocessCell(ParticleCell &)
Definition: LegacyCellProcessor.h:38
LegacyCellProcessor::postprocessCell
void postprocessCell(ParticleCell &)
Definition: LegacyCellProcessor.h:46
-
LegacyCellProcessor::processCellPair
void processCellPair(ParticleCell &cell1, ParticleCell &cell2, bool sumAll=false)
Definition: LegacyCellProcessor.cpp:56
+
LegacyCellProcessor::processCellPair
void processCellPair(ParticleCell &cell1, ParticleCell &cell2, bool sumAll=false)
Definition: LegacyCellProcessor.cpp:54
ParticlePairsHandler
interface for defining the action performed when processing a pair
Definition: ParticlePairsHandler.h:38
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LesSolver_8h_source.html b/LesSolver_8h_source.html index 0286bd1af0..15e9b34958 100644 --- a/LesSolver_8h_source.html +++ b/LesSolver_8h_source.html @@ -87,7 +87,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LinkedCells_8h_source.html b/LinkedCells_8h_source.html index 866cd7cf9b..fbeb9ab22b 100644 --- a/LinkedCells_8h_source.html +++ b/LinkedCells_8h_source.html @@ -160,7 +160,7 @@
206 double* getCellLength() override {
207 return _cellLength;
208 }
-
209
+
209
216 std::variant<ParticleIterator, SingleCellIterator<ParticleCell>> getMoleculeAtPosition(const double pos[3]) override;
217
225 unsigned long int getCellIndexOfMolecule(Molecule* molecule) const;
@@ -198,7 +198,7 @@
264
265 std::vector<unsigned long> getParticleCellStatistics() override;
266
-
267 std::string getConfigurationAsString() override;
+
267 std::string getConfigurationAsString() override;
268
269private:
270 //####################################
@@ -256,43 +256,43 @@
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
FullParticleCell
FullParticleCell data structure. Renamed from ParticleCell.
Definition: FullParticleCell.h:49
LinkedCells
Linked Cell Data Structure.
Definition: LinkedCells.h:51
-
LinkedCells::getNumberOfParticles
unsigned long getNumberOfParticles(ParticleIterator::Type t=ParticleIterator::ALL_CELLS) override
Gets number of particles stored in Linked Cells.
Definition: LinkedCells.cpp:576
-
LinkedCells::clear
void clear() override
Delete all molecules in container.
Definition: LinkedCells.cpp:591
-
LinkedCells::getCellIndexOfMolecule
unsigned long int getCellIndexOfMolecule(Molecule *molecule) const
Get the index in the cell vector to which this Molecule belongs.
Definition: LinkedCells.cpp:830
-
LinkedCells::rebuild
bool rebuild(double bBoxMin[3], double bBoxMax[3]) override
rebuild the datastructure
Definition: LinkedCells.cpp:135
-
LinkedCells::initCubicGrid
unsigned long initCubicGrid(std::array< unsigned long, 3 > numMoleculesPerDimension, std::array< double, 3 > simBoxLength, size_t seed_offset) override
Definition: LinkedCells.cpp:939
-
LinkedCells::~LinkedCells
~LinkedCells()
Destructor.
Definition: LinkedCells.cpp:110
-
LinkedCells::deleteOuterParticles
void deleteOuterParticles() override
delete all Particles which are not within the bounding box
Definition: LinkedCells.cpp:612
+
LinkedCells::getNumberOfParticles
unsigned long getNumberOfParticles(ParticleIterator::Type t=ParticleIterator::ALL_CELLS) override
Gets number of particles stored in Linked Cells.
Definition: LinkedCells.cpp:574
+
LinkedCells::getConfigurationAsString
std::string getConfigurationAsString() override
Definition: LinkedCells.cpp:1183
+
LinkedCells::clear
void clear() override
Delete all molecules in container.
Definition: LinkedCells.cpp:589
+
LinkedCells::getCellIndexOfMolecule
unsigned long int getCellIndexOfMolecule(Molecule *molecule) const
Get the index in the cell vector to which this Molecule belongs.
Definition: LinkedCells.cpp:828
+
LinkedCells::rebuild
bool rebuild(double bBoxMin[3], double bBoxMax[3]) override
rebuild the datastructure
Definition: LinkedCells.cpp:133
+
LinkedCells::initCubicGrid
unsigned long initCubicGrid(std::array< unsigned long, 3 > numMoleculesPerDimension, std::array< double, 3 > simBoxLength, size_t seed_offset) override
Definition: LinkedCells.cpp:937
+
LinkedCells::~LinkedCells
~LinkedCells()
Destructor.
Definition: LinkedCells.cpp:108
+
LinkedCells::deleteOuterParticles
void deleteOuterParticles() override
delete all Particles which are not within the bounding box
Definition: LinkedCells.cpp:610
LinkedCells::setCutoff
void setCutoff(double rc) override
Definition: LinkedCells.h:196
-
LinkedCells::updateMoleculeCaches
virtual void updateMoleculeCaches() override
Update the caches of the molecules.
Definition: LinkedCells.cpp:1098
-
LinkedCells::traverseCells
void traverseCells(CellProcessor &cellProcessor) override
calculate the forces between the molecules.
Definition: LinkedCells.cpp:563
-
LinkedCells::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for LinkedCells and all its included objects.
Definition: LinkedCells.cpp:127
-
LinkedCells::updateBoundaryAndHaloMoleculeCaches
virtual void updateBoundaryAndHaloMoleculeCaches() override
Update the caches of the molecules, that lie in the boundary or halo cells. The caches of boundary an...
Definition: LinkedCells.cpp:1087
-
LinkedCells::addParticle
bool addParticle(Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false) override
add a single Molecule to the ParticleContainer.
Definition: LinkedCells.cpp:444
-
LinkedCells::LinkedCells
LinkedCells()
Default constructor.
Definition: LinkedCells.cpp:38
-
LinkedCells::updateInnerMoleculeCaches
virtual void updateInnerMoleculeCaches() override
Update the caches of the molecules, that lie in inner cells. The caches of boundary and halo cells is...
Definition: LinkedCells.cpp:1076
-
LinkedCells::getCellIndexOfPoint
unsigned long int getCellIndexOfPoint(const double point[3]) const
Get the index in the cell vector to which the point belongs.
Definition: LinkedCells.cpp:869
-
LinkedCells::getMoleculeAtPosition
std::variant< ParticleIterator, SingleCellIterator< ParticleCell > > getMoleculeAtPosition(const double pos[3]) override
Gets a molecule by its position.
Definition: LinkedCells.cpp:1145
-
LinkedCells::update
void update() override
Definition: LinkedCells.cpp:242
-
LinkedCells::getParticleCellStatistics
std::vector< unsigned long > getParticleCellStatistics() override
Definition: LinkedCells.cpp:1168
-
LinkedCells::addParticles
void addParticles(std::vector< Molecule > &particles, bool checkWhetherDuplicate=false) override
adds a whole vector of particles
Definition: LinkedCells.cpp:457
-
LinkedCells::get_halo_L
double get_halo_L(int index) const override
gets the width of the halo region in dimension index
Definition: LinkedCells.cpp:631
-
LinkedCells::getConfigurationAsString
std::string getConfigurationAsString() override
Definition: LinkedCells.cpp:1185
+
LinkedCells::updateMoleculeCaches
virtual void updateMoleculeCaches() override
Update the caches of the molecules.
Definition: LinkedCells.cpp:1096
+
LinkedCells::traverseCells
void traverseCells(CellProcessor &cellProcessor) override
calculate the forces between the molecules.
Definition: LinkedCells.cpp:561
+
LinkedCells::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for LinkedCells and all its included objects.
Definition: LinkedCells.cpp:125
+
LinkedCells::updateBoundaryAndHaloMoleculeCaches
virtual void updateBoundaryAndHaloMoleculeCaches() override
Update the caches of the molecules, that lie in the boundary or halo cells. The caches of boundary an...
Definition: LinkedCells.cpp:1085
+
LinkedCells::addParticle
bool addParticle(Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false) override
add a single Molecule to the ParticleContainer.
Definition: LinkedCells.cpp:442
+
LinkedCells::LinkedCells
LinkedCells()
Default constructor.
Definition: LinkedCells.cpp:36
+
LinkedCells::updateInnerMoleculeCaches
virtual void updateInnerMoleculeCaches() override
Update the caches of the molecules, that lie in inner cells. The caches of boundary and halo cells is...
Definition: LinkedCells.cpp:1074
+
LinkedCells::getCellIndexOfPoint
unsigned long int getCellIndexOfPoint(const double point[3]) const
Get the index in the cell vector to which the point belongs.
Definition: LinkedCells.cpp:867
+
LinkedCells::getMoleculeAtPosition
std::variant< ParticleIterator, SingleCellIterator< ParticleCell > > getMoleculeAtPosition(const double pos[3]) override
Gets a molecule by its position.
Definition: LinkedCells.cpp:1143
+
LinkedCells::update
void update() override
Definition: LinkedCells.cpp:240
+
LinkedCells::getParticleCellStatistics
std::vector< unsigned long > getParticleCellStatistics() override
Definition: LinkedCells.cpp:1166
+
LinkedCells::addParticles
void addParticles(std::vector< Molecule > &particles, bool checkWhetherDuplicate=false) override
adds a whole vector of particles
Definition: LinkedCells.cpp:455
+
LinkedCells::get_halo_L
double get_halo_L(int index) const override
gets the width of the halo region in dimension index
Definition: LinkedCells.cpp:629
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
ParticleIterator
Definition: ParticleIterator.h:60
ParticlePairsHandler
interface for defining the action performed when processing a pair
Definition: ParticlePairsHandler.h:38
RegionParticleIterator
Definition: RegionParticleIterator.h:67
ResortCellProcessorSliced
Definition: ResortCellProcessorSliced.h:17
-
TraversalTuner
Definition: TraversalTuner.h:23
+
TraversalTuner
Definition: TraversalTuner.h:22
VTKGridWriter
Definition: VTKGridWriter.h:24
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-
pos
Definition: FakedOptFFT.h:23
+
pos
Definition: FakedOptFFT.h:21
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LoadBalanceWriter_8h_source.html b/LoadBalanceWriter_8h_source.html index 7fa0872fe6..966a81cddd 100644 --- a/LoadBalanceWriter_8h_source.html +++ b/LoadBalanceWriter_8h_source.html @@ -140,7 +140,7 @@
118};
119
120#endif // SRC_IO_LOADBALANCEWRITER_H_
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
LoadbalanceWriter
The LoadbalanceWriter writes out information about the programs load balance.
Definition: LoadBalanceWriter.h:39
LoadbalanceWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: LoadBalanceWriter.cpp:53
@@ -156,7 +156,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LoadBalancer_8h.html b/LoadBalancer_8h.html index d4567ad4d2..09576c7502 100644 --- a/LoadBalancer_8h.html +++ b/LoadBalancer_8h.html @@ -89,7 +89,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LoadBalancer_8h_source.html b/LoadBalancer_8h_source.html index 58bbdcb9a1..b96d0535cd 100644 --- a/LoadBalancer_8h_source.html +++ b/LoadBalancer_8h_source.html @@ -96,7 +96,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LoadCalc_8h_source.html b/LoadCalc_8h_source.html index 3e0b2a4d92..09af27ae5d 100644 --- a/LoadCalc_8h_source.html +++ b/LoadCalc_8h_source.html @@ -287,7 +287,7 @@
267 bool _timeValuesShouldBeIncreasing{true};
268 int _interpolationStartsAt{1};
269};
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
LoadCalc
Definition: LoadCalc.h:24
MeasureLoad
Definition: LoadCalc.h:227
TradLoad
Definition: LoadCalc.h:203
@@ -301,7 +301,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LoadImbalanceThroughSleepPlugin_8h_source.html b/LoadImbalanceThroughSleepPlugin_8h_source.html index 064cdc90e5..6961d13307 100644 --- a/LoadImbalanceThroughSleepPlugin_8h_source.html +++ b/LoadImbalanceThroughSleepPlugin_8h_source.html @@ -96,7 +96,7 @@
41 bool _varyingSteps{true};
42 int _varyingStepsSleepTime{200};
43};
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
LoadImbalanceThroughSleepPlugin
Definition: LoadImbalanceThroughSleepPlugin.h:13
LoadImbalanceThroughSleepPlugin::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: LoadImbalanceThroughSleepPlugin.cpp:23
@@ -112,7 +112,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LocalParticle_8h_source.html b/LocalParticle_8h_source.html index 17a07f8cd0..5cdbe13853 100644 --- a/LocalParticle_8h_source.html +++ b/LocalParticle_8h_source.html @@ -119,7 +119,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Logger_8h_source.html b/Logger_8h_source.html index fcff245d78..18b7b94f29 100644 --- a/Logger_8h_source.html +++ b/Logger_8h_source.html @@ -112,207 +112,206 @@
45
46class Logger;
47
-
54#ifndef LOGGER_SRC
-
55extern Log::Logger *global_log;
-
56#endif
-
57
-
62typedef enum {
-
63 None = 0, /* supress output */
-
64 Fatal = 1, /* program exit */
-
65 Error = 2, /* program corrected */
-
66 Warning = 4, /* perhaps wrong */
-
67 Info = 8, /* user info */
-
68 Debug = 16, /* detailed info for debugging */
-
69 All = 32,
-
70} logLevel;
-
71
-
90class Logger {
-
91private:
-
92 logLevel _log_level;
-
93 logLevel _msg_log_level;
-
94 bool _do_output;
-
95 std::string _filename;
-
96 std::ostream *_log_stream;
-
97 std::map<logLevel, std::string> logLevelNames;
-
98#ifdef USE_GETTIMEOFDAY
-
99 timeval _starttime;
-
100#else
-
101 time_t _starttime;
-
102#endif
-
103
-
104 int _rank;
-
105
-
107 void init_log_levels() {
-
108 logLevelNames.insert(std::pair<logLevel, std::string>(None, "NONE"));
-
109 logLevelNames.insert(std::pair<logLevel, std::string>(Fatal, "FATAL ERROR"));
-
110 logLevelNames.insert(std::pair<logLevel, std::string>(Error, "ERROR" ));
-
111 logLevelNames.insert(std::pair<logLevel, std::string>(Warning, "WARNING" ));
-
112 logLevelNames.insert(std::pair<logLevel, std::string>(Info, "INFO" ));
-
113 logLevelNames.insert(std::pair<logLevel, std::string>(Debug, "DEBUG" ));
-
114 logLevelNames.insert(std::pair<logLevel, std::string>(All, "ALL" ));
-
115 }
-
116
-
117 // don't allow copy-construction
-
118 Logger(const Logger&) : _log_level(Log::Error), _msg_log_level(Log::Error), _do_output(true),
-
119 _filename(""), _log_stream(0), logLevelNames(), _starttime(), _rank(0)
-
120 { }
-
121
-
122 // don't allow assignment
-
123 Logger& operator=(const Logger&) { return *this; }
-
124
-
125public:
-
128 Logger(logLevel level = Log::Error, std::ostream *os = &(std::cout));
-
129
-
130 Logger(logLevel level, std::string prefix);
-
131
-
133 ~Logger();
-
134
-
136 template<typename T>
-
137 Logger &operator<<(T const& t) {
-
138 if (_msg_log_level <= _log_level && _do_output)
-
139 *_log_stream << t;
-
140 return *this;
-
141 }
-
142
-
143 /* Specialized versions for manipulators. */
-
144 // e.g. endl
-
145 Logger &operator<<(std::ostream& (*f)(std::ostream&)) {
-
146 if (_msg_log_level <= _log_level && _do_output)
-
147 *_log_stream << f;
-
148 return *this;
-
149 }
-
150 // e.g. hex.
-
151 Logger &operator<<(std::ios_base& (*f)(std::ios_base&)) {
-
152 if (_msg_log_level <= _log_level && _do_output)
-
153 f(*_log_stream);
-
154 return *this;
-
155 }
-
156 template<class Ch, class Tr>
-
157 Logger &operator<<(std::basic_ios<Ch, Tr>& (*f)(std::basic_ios<Ch, Tr>&)) {
-
158 if (_msg_log_level <= _log_level && _do_output)
-
159 f(*_log_stream);
-
160 return *this;
-
161 }
-
162
-
164 Logger& msg_level(logLevel level) {
-
165 using namespace std;
-
166 _msg_log_level = level;
-
167 if (_msg_log_level <= _log_level && _do_output) {
-
168 // Include timestamp
-
169 const auto now = std::chrono::system_clock::to_time_t(std::chrono::system_clock::now());
-
170 tm unused{};
-
171 const auto* lt = localtime_r(&now, &unused);
-
172 //*_log_stream << ctime(&t) << " ";
-
173 stringstream timestampstream;
-
174 // maybe sprintf is easier here...
-
175 timestampstream << setfill('0') << setw(4) << (1900 + lt->tm_year) << setw(2) << (1 + lt->tm_mon) << setw(2) << lt->tm_mday << "T" << setw(2) << lt->tm_hour << setw(2) << lt->tm_min << setw(2) << lt->tm_sec;
-
176 *_log_stream << logLevelNames[level] << ":\t" << timestampstream.str() << " ";
-
177 //timestampstream.str(""); timestampstream.clear();
-
178#ifdef USE_GETTIMEOFDAY
-
179 timeval tod;
-
180 gettimeofday(&tod, 0);
-
181 *_log_stream << setw(8) << tod.tv_sec - _starttime.tv_sec + (tod.tv_usec - _starttime.tv_usec) / 1.E6 << " ";
-
182#else
-
183 *_log_stream << t-_starttime << "\t";
-
184#endif
-
185
-
186 *_log_stream << "[" << _rank << "]\t";
-
187 }
-
188 return *this;
-
189 }
-
190
-
192 Logger& fatal() {
-
193 return msg_level(Fatal);
-
194 }
-
195 Logger& error() {
-
196 return msg_level(Error);
-
197 }
-
198 Logger& error_always_output() {
-
199 _do_output = true;
-
200 return msg_level(Error);
-
201 }
-
202 Logger& warning() {
-
203 return msg_level(Warning);
-
204 }
-
205 Logger& info() {
-
206 return msg_level(Info);
-
207 }
-
208 Logger& debug() {
-
209 return msg_level(Debug);
-
210 }
-
211
-
213 logLevel set_log_level(logLevel l) {
-
214 _log_level = l;
-
215 return _log_level;
-
216 }
-
218 logLevel set_log_level(std::string l) {
-
219 // identify the loglevel by comparing the first char of the names
-
220 for (const auto& [lvl, name] : logLevelNames) {
-
221 // case-insensitive matching
-
222 if (std::toupper(name[0]) == std::toupper(l[0])) {
-
223 _log_level = lvl;
-
224 return _log_level;
-
225 }
-
226 }
-
227 error_always_output() << "Logger::set_log_level() unknown argument '" << l
-
228 << "'. Falling back to output everything!" << std::endl;
-
229 return Log::All;
-
230 }
-
231
-
233 logLevel get_log_level() {
-
234 return _log_level;
-
235 }
-
236
-
238 bool set_do_output(bool val) {
-
239 return _do_output = val;
-
240 }
-
241
-
242 bool get_do_output() {
-
243 return _do_output;
-
244 }
-
245
-
247 void init_starting_time() {
-
248#ifdef USE_GETTIMEOFDAY
-
249 gettimeofday(&_starttime, 0);
-
250#else
-
251 _starttime = time(NULL);
-
252#endif
-
253 }
+
53#ifndef LOGGER_SRC
+
54extern Log::Logger *global_log;
+
55#endif
+
56
+
61typedef enum {
+
62 None = 0, /* supress output */
+
63 Fatal = 1, /* program exit */
+
64 Error = 2, /* program corrected */
+
65 Warning = 4, /* perhaps wrong */
+
66 Info = 8, /* user info */
+
67 Debug = 16, /* detailed info for debugging */
+
68 All = 32,
+
69} logLevel;
+
70
+
89class Logger {
+
90private:
+
91 logLevel _log_level;
+
92 logLevel _msg_log_level;
+
93 bool _do_output;
+
94 std::string _filename;
+
95 std::ostream *_log_stream;
+
96 std::map<logLevel, std::string> logLevelNames;
+
97#ifdef USE_GETTIMEOFDAY
+
98 timeval _starttime;
+
99#else
+
100 time_t _starttime;
+
101#endif
+
102
+
103 int _rank;
+
104
+
106 void init_log_levels() {
+
107 logLevelNames.insert(std::pair<logLevel, std::string>(None, "NONE"));
+
108 logLevelNames.insert(std::pair<logLevel, std::string>(Fatal, "FATAL ERROR"));
+
109 logLevelNames.insert(std::pair<logLevel, std::string>(Error, "ERROR" ));
+
110 logLevelNames.insert(std::pair<logLevel, std::string>(Warning, "WARNING" ));
+
111 logLevelNames.insert(std::pair<logLevel, std::string>(Info, "INFO" ));
+
112 logLevelNames.insert(std::pair<logLevel, std::string>(Debug, "DEBUG" ));
+
113 logLevelNames.insert(std::pair<logLevel, std::string>(All, "ALL" ));
+
114 }
+
115
+
116 // don't allow copy-construction
+
117 Logger(const Logger&) : _log_level(Log::Error), _msg_log_level(Log::Error), _do_output(true),
+
118 _filename(""), _log_stream(0), logLevelNames(), _starttime(), _rank(0)
+
119 { }
+
120
+
121 // don't allow assignment
+
122 Logger& operator=(const Logger&) { return *this; }
+
123
+
124public:
+
127 Logger(logLevel level = Log::Error, std::ostream *os = &(std::cout));
+
128
+
129 Logger(logLevel level, std::string prefix);
+
130
+
132 ~Logger();
+
133
+
135 template<typename T>
+
136 Logger &operator<<(T const& t) {
+
137 if (_msg_log_level <= _log_level && _do_output)
+
138 *_log_stream << t;
+
139 return *this;
+
140 }
+
141
+
142 /* Specialized versions for manipulators. */
+
143 // e.g. endl
+
144 Logger &operator<<(std::ostream& (*f)(std::ostream&)) {
+
145 if (_msg_log_level <= _log_level && _do_output)
+
146 *_log_stream << f;
+
147 return *this;
+
148 }
+
149 // e.g. hex.
+
150 Logger &operator<<(std::ios_base& (*f)(std::ios_base&)) {
+
151 if (_msg_log_level <= _log_level && _do_output)
+
152 f(*_log_stream);
+
153 return *this;
+
154 }
+
155 template<class Ch, class Tr>
+
156 Logger &operator<<(std::basic_ios<Ch, Tr>& (*f)(std::basic_ios<Ch, Tr>&)) {
+
157 if (_msg_log_level <= _log_level && _do_output)
+
158 f(*_log_stream);
+
159 return *this;
+
160 }
+
161
+
163 Logger& msg_level(logLevel level) {
+
164 _msg_log_level = level;
+
165 if (_msg_log_level <= _log_level && _do_output) {
+
166 // Include timestamp
+
167 const auto now = std::chrono::system_clock::to_time_t(std::chrono::system_clock::now());
+
168 tm unused{};
+
169 const auto* lt = localtime_r(&now, &unused);
+
170 //*_log_stream << ctime(&t) << " ";
+
171 std::stringstream timestampstream;
+
172 // maybe sprintf is easier here...
+
173 timestampstream << std::setfill('0') << std::setw(4) << (1900 + lt->tm_year) << std::setw(2) << (1 + lt->tm_mon) << std::setw(2) << lt->tm_mday << "T" << std::setw(2) << lt->tm_hour << std::setw(2) << lt->tm_min << std::setw(2) << lt->tm_sec;
+
174 *_log_stream << logLevelNames[level] << ":\t" << timestampstream.str() << " ";
+
175 //timestampstream.str(""); timestampstream.clear();
+
176#ifdef USE_GETTIMEOFDAY
+
177 timeval tod;
+
178 gettimeofday(&tod, 0);
+
179 *_log_stream << std::setw(8) << tod.tv_sec - _starttime.tv_sec + (tod.tv_usec - _starttime.tv_usec) / 1.E6 << " ";
+
180#else
+
181 *_log_stream << t-_starttime << "\t";
+
182#endif
+
183
+
184 *_log_stream << "[" << _rank << "]\t";
+
185 }
+
186 return *this;
+
187 }
+
188
+
190 Logger& fatal() {
+
191 return msg_level(Fatal);
+
192 }
+
193 Logger& error() {
+
194 return msg_level(Error);
+
195 }
+
196 Logger& error_always_output() {
+
197 _do_output = true;
+
198 return msg_level(Error);
+
199 }
+
200 Logger& warning() {
+
201 return msg_level(Warning);
+
202 }
+
203 Logger& info() {
+
204 return msg_level(Info);
+
205 }
+
206 Logger& debug() {
+
207 return msg_level(Debug);
+
208 }
+
209
+
211 logLevel set_log_level(logLevel l) {
+
212 _log_level = l;
+
213 return _log_level;
+
214 }
+
216 logLevel set_log_level(std::string l) {
+
217 // identify the loglevel by comparing the first char of the names
+
218 for (const auto& [lvl, name] : logLevelNames) {
+
219 // case-insensitive matching
+
220 if (std::toupper(name[0]) == std::toupper(l[0])) {
+
221 _log_level = lvl;
+
222 return _log_level;
+
223 }
+
224 }
+
225 error_always_output() << "Logger::set_log_level() unknown argument '" << l
+
226 << "'. Falling back to output everything!" << std::endl;
+
227 return Log::All;
+
228 }
+
229
+
231 logLevel get_log_level() {
+
232 return _log_level;
+
233 }
+
234
+
236 bool set_do_output(bool val) {
+
237 return _do_output = val;
+
238 }
+
239
+
240 bool get_do_output() {
+
241 return _do_output;
+
242 }
+
243
+
245 void init_starting_time() {
+
246#ifdef USE_GETTIMEOFDAY
+
247 gettimeofday(&_starttime, 0);
+
248#else
+
249 _starttime = time(NULL);
+
250#endif
+
251 }
+
252
+
253 /* methods for easy handling of output processes */
254
-
255 /* methods for easy handling of output processes */
-
256
-
258 void set_mpi_output_root(int root = 0);
-
259
-
261 void set_mpi_output_all();
-
262
-
264 bool set_mpi_output_ranks(int num_nums, int* nums);
+
256 void set_mpi_output_root(int root = 0);
+
257
+
259 void set_mpi_output_all();
+
260
+
262 bool set_mpi_output_ranks(int num_nums, int* nums);
+
263
+
264
265
-
266
-
267
-
268}; /* end of class Logger */
-
269} /* end of namespace */
-
270
-
271#endif /*LOGGER_H_*/
-
Log::Logger
The Logger class provides a simple interface to handle log messages.
Definition: Logger.h:90
-
Log::Logger::operator<<
Logger & operator<<(T const &t)
General output template for variables, strings, etc.
Definition: Logger.h:137
+
266}; /* end of class Logger */
+
267} /* end of namespace */
+
268
+
269#endif /*LOGGER_H_*/
+
Log::Logger
The Logger class provides a simple interface to handle log messages.
Definition: Logger.h:89
+
Log::Logger::operator<<
Logger & operator<<(T const &t)
General output template for variables, strings, etc.
Definition: Logger.h:136
Log::Logger::set_mpi_output_ranks
bool set_mpi_output_ranks(int num_nums, int *nums)
allow a set of processes for logging
Definition: Logger.cpp:55
-
Log::Logger::set_do_output
bool set_do_output(bool val)
switch on / off output
Definition: Logger.h:238
+
Log::Logger::set_do_output
bool set_do_output(bool val)
switch on / off output
Definition: Logger.h:236
Log::Logger::~Logger
~Logger()
Destructor flushes stream.
Definition: Logger.cpp:34
-
Log::Logger::get_log_level
logLevel get_log_level()
return log level
Definition: Logger.h:233
-
Log::Logger::msg_level
Logger & msg_level(logLevel level)
Add log info in front of messages.
Definition: Logger.h:164
-
Log::Logger::fatal
Logger & fatal()
shorthand versions for easy usage of the different log levels
Definition: Logger.h:192
+
Log::Logger::get_log_level
logLevel get_log_level()
return log level
Definition: Logger.h:231
+
Log::Logger::msg_level
Logger & msg_level(logLevel level)
Add log info in front of messages.
Definition: Logger.h:163
+
Log::Logger::fatal
Logger & fatal()
shorthand versions for easy usage of the different log levels
Definition: Logger.h:190
Log::Logger::set_mpi_output_root
void set_mpi_output_root(int root=0)
allow logging only for a single process
Definition: Logger.cpp:42
-
Log::Logger::init_starting_time
void init_starting_time()
initialize starting time
Definition: Logger.h:247
+
Log::Logger::init_starting_time
void init_starting_time()
initialize starting time
Definition: Logger.h:245
Log::Logger::set_mpi_output_all
void set_mpi_output_all()
all processes shall perform logging
Definition: Logger.cpp:50
-
Log::Logger::set_log_level
logLevel set_log_level(std::string l)
set log level from string
Definition: Logger.h:218
-
Log::Logger::set_log_level
logLevel set_log_level(logLevel l)
set log level
Definition: Logger.h:213
+
Log::Logger::set_log_level
logLevel set_log_level(std::string l)
set log level from string
Definition: Logger.h:216
+
Log::Logger::set_log_level
logLevel set_log_level(logLevel l)
set log level
Definition: Logger.h:211
xml_schema::time
::xsd::cxx::tree::time< char, simple_type > time
C++ type corresponding to the time XML Schema built-in type.
Definition: xml-schema.h:436
xml_schema::name
::xsd::cxx::tree::name< char, token > name
C++ type corresponding to the Name XML Schema built-in type.
Definition: xml-schema.h:286
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LongRangeCorrection_8h_source.html b/LongRangeCorrection_8h_source.html index a392902c91..be284d9a71 100644 --- a/LongRangeCorrection_8h_source.html +++ b/LongRangeCorrection_8h_source.html @@ -96,18 +96,18 @@
24 Planar* _planar;
25 Homogeneous* _homogen;
26*/
-
27
+
27
28};
29
30#endif /* __LONGRANGECORRECTION_H__ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
LongRangeCorrection
Definition: LongRangeCorrection.h:12
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/LorentzBerthelot_8h_source.html b/LorentzBerthelot_8h_source.html index 4201628f12..f5b615b71e 100644 --- a/LorentzBerthelot_8h_source.html +++ b/LorentzBerthelot_8h_source.html @@ -95,7 +95,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MPICheckpointWriter_8cpp.html b/MPICheckpointWriter_8cpp.html index a19248ff0d..3f692e09f4 100644 --- a/MPICheckpointWriter_8cpp.html +++ b/MPICheckpointWriter_8cpp.html @@ -100,7 +100,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MPICheckpointWriter_8h.html b/MPICheckpointWriter_8h.html index d7052fcde9..c70d62c1b2 100644 --- a/MPICheckpointWriter_8h.html +++ b/MPICheckpointWriter_8h.html @@ -92,7 +92,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MPICheckpointWriter_8h_source.html b/MPICheckpointWriter_8h_source.html index 0a54caac3a..9d90d0d24d 100644 --- a/MPICheckpointWriter_8h_source.html +++ b/MPICheckpointWriter_8h_source.html @@ -83,15 +83,15 @@
15
16class MPICheckpointWriter : public PluginBase {
17public:
-
18
+
18
19 MPICheckpointWriter(){}
-
38 MPICheckpointWriter(unsigned long writeFrequency
+
38 MPICheckpointWriter(unsigned long writeFrequency
39 , std::string outputPrefix, bool incremental=true
40 , std::string datarep=std::string(""));
41 //~MPICheckpointWriter() {};
-
42
+
42
43 void readXML(XMLfileUnits& xmlconfig);
-
44
+
44
45 void init(ParticleContainer *particleContainer,
46 DomainDecompBase *domainDecomp, Domain *domain);
47 void endStep(
@@ -101,7 +101,7 @@
51 );
52 void finish(ParticleContainer *particleContainer,
53 DomainDecompBase *domainDecomp, Domain *domain);
-
54
+
54
55 std::string getPluginName() {
56 return std::string("MPICheckpointWriter");
57 }
@@ -109,7 +109,7 @@
59private:
60 static const char _magicVersion[56];
61 static const int _endiannesstest;
-
62
+
62
63 std::string _outputPrefix;
64 unsigned long _writeFrequency;
65 bool _incremental;
@@ -124,15 +124,14 @@
74
75#endif /*MPICHECKPOINTWRITER_H_*/
76
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MPICheckpointWriter
Definition: MPICheckpointWriter.h:16
MPICheckpointWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: MPICheckpointWriter.h:55
-
MPICheckpointWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MPICheckpointWriter.cpp:407
-
MPICheckpointWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MPICheckpointWriter.cpp:134
-
MPICheckpointWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MPICheckpointWriter.cpp:113
-
MPICheckpointWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MPICheckpointWriter.cpp:48
-
MPICheckpointWriter::MPICheckpointWriter
MPICheckpointWriter(unsigned long writeFrequency, std::string outputPrefix, bool incremental=true, std::string datarep=std::string(""))
writes a checkpoint file that can be used to continue the simulation using MPIIO
+
MPICheckpointWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MPICheckpointWriter.cpp:450
+
MPICheckpointWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MPICheckpointWriter.cpp:132
+
MPICheckpointWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MPICheckpointWriter.cpp:111
+
MPICheckpointWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MPICheckpointWriter.cpp:46
MPI_Info_object
MPI Info object implements functionalities to handle MPI Info objects, e.g. initialize from a XML fil...
Definition: MPI_Info_object.h:14
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -141,7 +140,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MPIKDNode_8h_source.html b/MPIKDNode_8h_source.html index 22397b496a..a29b1fe87c 100644 --- a/MPIKDNode_8h_source.html +++ b/MPIKDNode_8h_source.html @@ -217,7 +217,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MPI__IOCheckpointWriter_8h_source.html b/MPI__IOCheckpointWriter_8h_source.html index 5e4f8d0ce5..1883b5ed63 100644 --- a/MPI__IOCheckpointWriter_8h_source.html +++ b/MPI__IOCheckpointWriter_8h_source.html @@ -118,14 +118,14 @@
55};
56
57#endif /* MPI_IOCHECKPOINTWRITER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MPI_IOCheckpointWriter
Definition: MPI_IOCheckpointWriter.h:15
-
MPI_IOCheckpointWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MPI_IOCheckpointWriter.cpp:50
-
MPI_IOCheckpointWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MPI_IOCheckpointWriter.cpp:424
+
MPI_IOCheckpointWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MPI_IOCheckpointWriter.cpp:49
+
MPI_IOCheckpointWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MPI_IOCheckpointWriter.cpp:423
MPI_IOCheckpointWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: MPI_IOCheckpointWriter.h:45
-
MPI_IOCheckpointWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MPI_IOCheckpointWriter.cpp:72
-
MPI_IOCheckpointWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MPI_IOCheckpointWriter.cpp:77
+
MPI_IOCheckpointWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MPI_IOCheckpointWriter.cpp:71
+
MPI_IOCheckpointWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MPI_IOCheckpointWriter.cpp:76
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
@@ -133,7 +133,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MPI__IOReader_8h_source.html b/MPI__IOReader_8h_source.html index 5b44245afb..2ac1070dc6 100644 --- a/MPI__IOReader_8h_source.html +++ b/MPI__IOReader_8h_source.html @@ -113,20 +113,20 @@
98};
99
100#endif /* MPI_IOREADER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
MPI_IOReader
Definition: MPI_IOReader.h:15
-
MPI_IOReader::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *domain, double timestep)
reads in header of the input file (including component description)
Definition: MPI_IOReader.cpp:55
-
MPI_IOReader::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
reads in the data of all molecules
Definition: MPI_IOReader.cpp:282
-
MPI_IOReader::setPhaseSpaceFile
void setPhaseSpaceFile(std::string filename)
gets a filename and opens an ifstream associated with the given file
Definition: MPI_IOReader.cpp:47
-
MPI_IOReader::setPhaseSpaceHeaderFile
void setPhaseSpaceHeaderFile(std::string filename)
For this class, header and data are in the same file, so there is no separate header file.
Definition: MPI_IOReader.cpp:51
+
MPI_IOReader::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *domain, double timestep)
reads in header of the input file (including component description)
Definition: MPI_IOReader.cpp:53
+
MPI_IOReader::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
reads in the data of all molecules
Definition: MPI_IOReader.cpp:280
+
MPI_IOReader::setPhaseSpaceFile
void setPhaseSpaceFile(std::string filename)
gets a filename and opens an ifstream associated with the given file
Definition: MPI_IOReader.cpp:45
+
MPI_IOReader::setPhaseSpaceHeaderFile
void setPhaseSpaceHeaderFile(std::string filename)
For this class, header and data are in the same file, so there is no separate header file.
Definition: MPI_IOReader.cpp:49
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MPI__Info__object_8h_source.html b/MPI__Info__object_8h_source.html index b0bbd9d435..f9745895ed 100644 --- a/MPI__Info__object_8h_source.html +++ b/MPI__Info__object_8h_source.html @@ -114,7 +114,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MamicoCoupling_8h_source.html b/MamicoCoupling_8h_source.html index 5f1b536433..1c8409f6c7 100644 --- a/MamicoCoupling_8h_source.html +++ b/MamicoCoupling_8h_source.html @@ -138,7 +138,7 @@
113#endif
114 bool _couplingEnabled = false;
115};
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MamicoCoupling
Allows execution of MaMiCo code to enable coupling with MaMiCo.
Definition: MamicoCoupling.h:20
MamicoCoupling::getCouplingState
bool getCouplingState()
Getter method for the coupling state.
Definition: MamicoCoupling.h:107
@@ -159,7 +159,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MaskGatherChooser_8h_source.html b/MaskGatherChooser_8h_source.html index 1dc10978a8..c2cd5c5adc 100644 --- a/MaskGatherChooser_8h_source.html +++ b/MaskGatherChooser_8h_source.html @@ -297,7 +297,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MaskVecDouble_8h_source.html b/MaskVecDouble_8h_source.html index aacedd3bb3..0861f1ef2c 100644 --- a/MaskVecDouble_8h_source.html +++ b/MaskVecDouble_8h_source.html @@ -258,7 +258,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MaskVecFloat_8h_source.html b/MaskVecFloat_8h_source.html index 4b0e3f6e45..d045d627a7 100644 --- a/MaskVecFloat_8h_source.html +++ b/MaskVecFloat_8h_source.html @@ -259,7 +259,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MaskVec_8h_source.html b/MaskVec_8h_source.html index ccddada5b2..f75ec9ddaf 100644 --- a/MaskVec_8h_source.html +++ b/MaskVec_8h_source.html @@ -102,7 +102,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Math_8h_source.html b/Math_8h_source.html index 4474c51413..c611c813d8 100644 --- a/Math_8h_source.html +++ b/Math_8h_source.html @@ -128,7 +128,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MaxCheck_8h_source.html b/MaxCheck_8h_source.html index d10471473d..a67305e468 100644 --- a/MaxCheck_8h_source.html +++ b/MaxCheck_8h_source.html @@ -174,17 +174,17 @@
137};
138
139#endif /*MAXCHECK_H_*/
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MaxCheck
Definition: MaxCheck.h:24
-
MaxCheck::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for MaxCheck and all its included objects.
Definition: MaxCheck.cpp:30
+
MaxCheck::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for MaxCheck and all its included objects.
Definition: MaxCheck.cpp:28
MaxCheck::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: MaxCheck.h:124
-
MaxCheck::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method will be called first thing in a new timestep.
Definition: MaxCheck.cpp:126
-
MaxCheck::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied.
Definition: MaxCheck.cpp:137
+
MaxCheck::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method will be called first thing in a new timestep.
Definition: MaxCheck.cpp:124
+
MaxCheck::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied.
Definition: MaxCheck.cpp:135
MaxCheck::siteWiseForces
void siteWiseForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method siteWiseForces will be called before forcefields have been applied alterations to sitewise for...
Definition: MaxCheck.h:101
MaxCheck::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: MaxCheck.h:121
MaxCheck::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: MaxCheck.h:115
-
MaxCheck::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: MaxCheck.cpp:25
+
MaxCheck::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: MaxCheck.cpp:23
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
@@ -192,7 +192,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MaxWriter_8h_source.html b/MaxWriter_8h_source.html index 261dc93c23..2e64a4223e 100644 --- a/MaxWriter_8h_source.html +++ b/MaxWriter_8h_source.html @@ -102,7 +102,7 @@
37
38 void finish(ParticleContainer *particleContainer,
39 DomainDecompBase *domainDecomp, Domain *domain);
-
40
+
40
41 std::string getPluginName() {
42 return std::string("MaxWriter");
43 }
@@ -128,13 +128,13 @@
63};
64
65#endif /*MAXWRITER_H_*/
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MaxWriter
Writes max values of velocity angular momentum and force to a file.
Definition: MaxWriter.h:18
-
MaxWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MaxWriter.cpp:117
-
MaxWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MaxWriter.cpp:49
-
MaxWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MaxWriter.cpp:131
-
MaxWriter::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MaxWriter and all its included objects.
Definition: MaxWriter.cpp:33
+
MaxWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MaxWriter.cpp:115
+
MaxWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MaxWriter.cpp:47
+
MaxWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MaxWriter.cpp:129
+
MaxWriter::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MaxWriter and all its included objects.
Definition: MaxWriter.cpp:31
MaxWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: MaxWriter.h:41
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -143,7 +143,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MaxwellVelocityAssigner_8h_source.html b/MaxwellVelocityAssigner_8h_source.html index d868652bdd..cb8d128ab7 100644 --- a/MaxwellVelocityAssigner_8h_source.html +++ b/MaxwellVelocityAssigner_8h_source.html @@ -109,7 +109,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MemoryProfiler_8h_source.html b/MemoryProfiler_8h_source.html index 26868b7e8d..2b66d97407 100644 --- a/MemoryProfiler_8h_source.html +++ b/MemoryProfiler_8h_source.html @@ -117,7 +117,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MettDeamonFeedrateDirector_8h_source.html b/MettDeamonFeedrateDirector_8h_source.html index e5b85a0132..bfccc6bde0 100644 --- a/MettDeamonFeedrateDirector_8h_source.html +++ b/MettDeamonFeedrateDirector_8h_source.html @@ -155,16 +155,16 @@
105
106#endif /*METTDEAMON_FEEDRATE_DIRECTOR_H_*/
CommVar
Definition: CommVar.h:17
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MettDeamonFeedrateDirector
Definition: MettDeamonFeedrateDirector.h:23
-
MettDeamonFeedrateDirector::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for MettDeamonFeedrateDirector and all its included objects.
Definition: MettDeamonFeedrateDirector.cpp:64
-
MettDeamonFeedrateDirector::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: MettDeamonFeedrateDirector.cpp:117
+
MettDeamonFeedrateDirector::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for MettDeamonFeedrateDirector and all its included objects.
Definition: MettDeamonFeedrateDirector.cpp:62
+
MettDeamonFeedrateDirector::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: MettDeamonFeedrateDirector.cpp:115
MettDeamonFeedrateDirector::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: MettDeamonFeedrateDirector.h:74
-
MettDeamonFeedrateDirector::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied.
Definition: MettDeamonFeedrateDirector.cpp:163
+
MettDeamonFeedrateDirector::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied.
Definition: MettDeamonFeedrateDirector.cpp:161
MettDeamonFeedrateDirector::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: MettDeamonFeedrateDirector.h:71
MettDeamonFeedrateDirector::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: MettDeamonFeedrateDirector.h:66
-
MettDeamonFeedrateDirector::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: MettDeamonFeedrateDirector.cpp:41
+
MettDeamonFeedrateDirector::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: MettDeamonFeedrateDirector.cpp:39
MettDeamon
Definition: MettDeamon.h:140
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -173,7 +173,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MettDeamon_8h_source.html b/MettDeamon_8h_source.html index d335263234..5f5225c1ee 100644 --- a/MettDeamon_8h_source.html +++ b/MettDeamon_8h_source.html @@ -248,17 +248,17 @@
220 void setActualFeedrate(const double& feed_actual) {
221 if (FRM_DIRECTED == _nFeedRateMethod) {
222 _feedrate.feed.actual = feed_actual;
-
223 global_log->info() << "[MettDeamon]: Set new feed rate by MDFRD to vf= " << _feedrate.feed.actual << std::endl;
+
223 Log::global_log->info() << "[MettDeamon]: Set new feed rate by MDFRD to vf= " << _feedrate.feed.actual << std::endl;
224 } else {
-
225 global_log->warning() << "[MettDeamon]: Feed rate not set because current feed method ( " << _nFeedRateMethod << " ) is not set to communicate with MDFRD (method " << FRM_DIRECTED << ")" << std::endl;
+
225 Log::global_log->warning() << "[MettDeamon]: Feed rate not set because current feed method ( " << _nFeedRateMethod << " ) is not set to communicate with MDFRD (method " << FRM_DIRECTED << ")" << std::endl;
226 }
227 }
228 void setInitFeedrate(const double& feed_init) {
229 if (FRM_DIRECTED == _nFeedRateMethod) {
230 _feedrate.feed.init = feed_init;
-
231 global_log->info() << "[MettDeamon]: Set init feed rate by MDFRD to vf= " << _feedrate.feed.init << std::endl;
+
231 Log::global_log->info() << "[MettDeamon]: Set init feed rate by MDFRD to vf= " << _feedrate.feed.init << std::endl;
232 } else {
-
233 global_log->warning() << "[MettDeamon]: Feed rate not set because current feed method ( " << _nFeedRateMethod << " ) is not set to communicate with MDFRD (method " << FRM_DIRECTED << ")" << std::endl;
+
233 Log::global_log->warning() << "[MettDeamon]: Feed rate not set because current feed method ( " << _nFeedRateMethod << " ) is not set to communicate with MDFRD (method " << FRM_DIRECTED << ")" << std::endl;
234 }
235 }
236 double getInvDensityArea() {return _dInvDensityArea;}
@@ -289,7 +289,7 @@
261 void updateReservoir(DomainDecompBase* domainDecomp, ParticleContainer* particleContainer);
262 void InsertReservoirSlab(ParticleContainer* particleContainer);
263 void initRestart();
-
264
+
264
265 // stat. evap
266 void readNormDistr();
267
@@ -334,7 +334,7 @@
306 uint32_t cid_ub;
307 } _manipfree;
308 FeedRateStruct _feedrate;
-
309
+
309
310 // stat. evap.
311 struct{
312 bool enabled;
@@ -351,7 +351,7 @@
323 } right;
324 } cid;
325 } _vap_trans_plane;
-
326
+
326
327 struct NormMB{
328 struct NormFnames{
329 std::string vxz;
@@ -360,7 +360,7 @@
332 std::list<double> vxz;
333 std::list<double> vy;
334 } _norm;
-
335
+
335
336 struct{
337 CommVar<uint64_t> count;
338 CommVar<uint64_t> deleted;
@@ -584,7 +584,7 @@
556 _last->_next = _first; // connect tail to head
557 }
558 }
-
559
+
559
560 void clear()
561 {
562 while (!isEmpty()) {
@@ -603,7 +603,7 @@
575 void showActualBin() {
576 for(auto& p:_actual->_particles)
577 std::cout << p << ", ";
-
578 std::cout << endl;
+
578 std::cout << std::endl;
579 }
580
581 void connectTailToHead()
@@ -668,7 +668,7 @@
640
BinQueue
Definition: MettDeamon.h:437
CommVar
Definition: CommVar.h:17
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Ensemble
Base class for ensembles.
Definition: EnsembleBase.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
@@ -676,14 +676,14 @@
MettDeamon
Definition: MettDeamon.h:140
MettDeamon::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: MettDeamon.h:196
MettDeamon::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: MettDeamon.h:197
-
MettDeamon::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: MettDeamon.cpp:441
-
MettDeamon::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: MettDeamon.cpp:455
+
MettDeamon::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: MettDeamon.cpp:440
+
MettDeamon::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: MettDeamon.cpp:454
MettDeamon::siteWiseForces
void siteWiseForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method siteWiseForces will be called before forcefields have been applied alterations to sitewise for...
Definition: MettDeamon.h:193
-
MettDeamon::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for MettDeamon and all its included objects.
Definition: MettDeamon.cpp:259
+
MettDeamon::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for MettDeamon and all its included objects.
Definition: MettDeamon.cpp:258
MettDeamon::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: MettDeamon.h:195
-
MettDeamon::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: MettDeamon.cpp:450
-
MettDeamon::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method will be called first thing in a new timestep.
Definition: MettDeamon.cpp:446
-
MoleculeDataReader
Definition: ReplicaGenerator.h:84
+
MettDeamon::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: MettDeamon.cpp:449
+
MettDeamon::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method will be called first thing in a new timestep.
Definition: MettDeamon.cpp:445
+
MoleculeDataReader
Definition: ReplicaGenerator.h:83
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
Random
Definition: Random.h:12
@@ -701,11 +701,11 @@
MettDeamon::NormMB::NormFnames
Definition: MettDeamon.h:328
ParamsNormMB
Definition: MettDeamon.h:90
RestartInfoType
Definition: MettDeamon.h:84
-
pos
Definition: FakedOptFFT.h:23
+
pos
Definition: FakedOptFFT.h:21
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MidpointTraversal_8h_source.html b/MidpointTraversal_8h_source.html index 2ecabf4039..e9771de1fa 100644 --- a/MidpointTraversal_8h_source.html +++ b/MidpointTraversal_8h_source.html @@ -212,17 +212,17 @@
143 // process only half of the faces to get no pair twice
144 for(int i=0; i<3; ++i){ // faces
145 int j = (i+3)%6;
-
146 _offsets3D[index++] = make_pair(_faces[i], _faces[j]);
+
146 _offsets3D[index++] = std::make_pair(_faces[i], _faces[j]);
147 }
148 // process only half of the edges to get no pair twice
149 for(int i=0; i<6; ++i){ // edges
150 int j = (i+6)%12;
-
151 _offsets3D[index++] = make_pair(_edges[i], _edges[j]);
+
151 _offsets3D[index++] = std::make_pair(_edges[i], _edges[j]);
152 }
153 // process only half of the corners to get no pair twice
154 for(int i=0; i<4; ++i){ // corners
155 int j = (i+4)%8;
-
156 _offsets3D[index++] = make_pair(_corners[i], _corners[j]);
+
156 _offsets3D[index++] = std::make_pair(_corners[i], _corners[j]);
157 }
158
159 mardyn_assert(index == 13);
@@ -312,14 +312,14 @@
243
244 for(long y=-1; y<=1; ++y){ // 3 * 4
245 for(long x=-1; x<=1; ++x){ // 3
-
246 _offsets3D[index++] = make_pair(origin, std::array<long,3>{x, y, 1l});
+
246 _offsets3D[index++] = std::make_pair(origin, std::array<long,3>{x, y, 1l});
247 }
248 // 1st
-
249 _offsets3D[index++] = make_pair(origin, std::array<long,3>{1l, y, 0l});
+
249 _offsets3D[index++] = std::make_pair(origin, std::array<long,3>{1l, y, 0l});
250 }
251
252 // 13th
-
253 _offsets3D[index++] = make_pair(origin, std::array<long,3>{0l, 1l, 0l});
+
253 _offsets3D[index++] = std::make_pair(origin, std::array<long,3>{0l, 1l, 0l});
254
255}
256
@@ -447,7 +447,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Midpoint_8h_source.html b/Midpoint_8h_source.html index ef0c95e7b6..6b396abf0e 100644 --- a/Midpoint_8h_source.html +++ b/Midpoint_8h_source.html @@ -118,7 +118,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MirrorSystem_8h_source.html b/MirrorSystem_8h_source.html index 94b8811943..1473617dd6 100644 --- a/MirrorSystem_8h_source.html +++ b/MirrorSystem_8h_source.html @@ -140,17 +140,17 @@
84};
85
86#endif /*MIRROR_SYSTEM_H_*/
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MirrorSystem
Definition: MirrorSystem.h:25
MirrorSystem::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: MirrorSystem.h:75
-
MirrorSystem::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method will be called first thing in a new timestep.
Definition: MirrorSystem.cpp:29
-
MirrorSystem::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for MirrorSystem and all its included objects.
Definition: MirrorSystem.cpp:250
+
MirrorSystem::beforeEventNewTimestep
void beforeEventNewTimestep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method will be called first thing in a new timestep.
Definition: MirrorSystem.cpp:27
+
MirrorSystem::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for MirrorSystem and all its included objects.
Definition: MirrorSystem.cpp:248
MirrorSystem::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: MirrorSystem.h:67
MirrorSystem::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: MirrorSystem.h:72
-
MirrorSystem::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied.
Definition: MirrorSystem.cpp:278
-
MirrorSystem::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: MirrorSystem.cpp:272
-
MirrorSystem::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: MirrorSystem.cpp:25
+
MirrorSystem::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied.
Definition: MirrorSystem.cpp:276
+
MirrorSystem::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: MirrorSystem.cpp:270
+
MirrorSystem::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: MirrorSystem.cpp:23
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
@@ -158,7 +158,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Mirror_8h_source.html b/Mirror_8h_source.html index 47f520f754..97585e2cbd 100644 --- a/Mirror_8h_source.html +++ b/Mirror_8h_source.html @@ -179,7 +179,7 @@
141 double velo_target {0.4};
142 float fixed_probability_factor {-1};
143 } _melandParams;
-
144
+
144
145 struct RampingParams {
146 unsigned long startStep {1000};
147 unsigned long stopStep {2000};
@@ -190,13 +190,13 @@
152 CommVar<std::vector<uint64_t> > reflected;
153 CommVar<std::vector<uint64_t> > deleted;
154 } _particleManipCount;
-
155
+
155
156 struct DiffuseMirror {
157 bool enabled;
158 float width;
159 std::map<uint64_t,double> pos_map;
160 } _diffuse_mirror;
-
161
+
161
162 struct SwitchComp {
163 bool enabled;
164 uint32_t cid_ub; // component id unity based
@@ -206,15 +206,15 @@
168#endif /*MIRROR_H_*/
CommVar
Definition: CommVar.h:17
ControlInstance
Definition: Region.h:29
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Mirror
Definition: Mirror.h:41
-
Mirror::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: Mirror.cpp:49
-
Mirror::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: Mirror.cpp:196
+
Mirror::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: Mirror.cpp:47
+
Mirror::beforeForces
void beforeForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method beforeForces will be called before forcefields have been applied no alterations w....
Definition: Mirror.cpp:194
Mirror::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: Mirror.h:96
-
Mirror::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for Mirror and all its included objects.
Definition: Mirror.cpp:53
+
Mirror::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for Mirror and all its included objects.
Definition: Mirror.cpp:51
Mirror::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: Mirror.h:104
-
Mirror::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied.
Definition: Mirror.cpp:402
+
Mirror::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied.
Definition: Mirror.cpp:400
Mirror::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: Mirror.h:101
ObserverBase
Definition: ObserverBase.h:13
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -227,7 +227,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MixingRuleBase_8h_source.html b/MixingRuleBase_8h_source.html index 3e4f4302e0..c319de2200 100644 --- a/MixingRuleBase_8h_source.html +++ b/MixingRuleBase_8h_source.html @@ -95,7 +95,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Mkesfera_8h_source.html b/Mkesfera_8h_source.html index 9792ada930..d5c4fe5c45 100644 --- a/Mkesfera_8h_source.html +++ b/Mkesfera_8h_source.html @@ -96,19 +96,19 @@
49
50#endif /* MKESFERA_H */
51
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
MkesferaGenerator
Single droplet scenario generator.
Definition: Mkesfera.h:13
-
MkesferaGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: Mkesfera.cpp:55
-
MkesferaGenerator::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MkesferaGenerator and all its included objects.
Definition: Mkesfera.cpp:26
+
MkesferaGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: Mkesfera.cpp:53
+
MkesferaGenerator::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MkesferaGenerator and all its included objects.
Definition: Mkesfera.cpp:24
MkesferaGenerator::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *, double)
read the phase space components and header information
Definition: Mkesfera.h:20
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MmpldWriter_8h_source.html b/MmpldWriter_8h_source.html index bf07316a4e..5792a52166 100644 --- a/MmpldWriter_8h_source.html +++ b/MmpldWriter_8h_source.html @@ -134,7 +134,7 @@
75 );
76 void finish(ParticleContainer *particleContainer,
77 DomainDecompBase *domainDecomp, Domain *domain);
-
78
+
78
79 std::string getPluginName() {
80 return std::string("MmpldWriter");
81 }
@@ -230,18 +230,18 @@
174};
175
176#endif /* MMPLDWRITER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
MPI_Info_object
MPI Info object implements functionalities to handle MPI Info objects, e.g. initialize from a XML fil...
Definition: MPI_Info_object.h:14
MmpldWriterMultiSphere
Definition: MmpldWriter.h:160
MmpldWriterSimpleSphere
Definition: MmpldWriter.h:143
MmpldWriter
Output plugin to generate a MegaMol™ Particle List Data file (*.mmpld).
Definition: MmpldWriter.h:42
-
MmpldWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MmpldWriter.cpp:322
-
MmpldWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MmpldWriter.cpp:144
-
MmpldWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MmpldWriter.cpp:65
+
MmpldWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MmpldWriter.cpp:320
+
MmpldWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MmpldWriter.cpp:142
+
MmpldWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MmpldWriter.cpp:63
MmpldWriter::_startTimestep
std::uint64_t _startTimestep
Definition: MmpldWriter.h:105
-
MmpldWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MmpldWriter.cpp:306
+
MmpldWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MmpldWriter.cpp:304
MmpldWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: MmpldWriter.h:79
MmpldWriter::_stopTimestep
std::uint64_t _stopTimestep
Definition: MmpldWriter.h:109
MmpldWriter::MmpldWriter
MmpldWriter(std::uint64_t startTimestep, std::uint64_t writeFrequency, std::uint64_t stopTimestep, std::uint64_t numFramesPerFile, std::string outputPrefix)
: writes a mmspd file used by MegaMol
@@ -253,7 +253,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MmspdBinWriter_8h_source.html b/MmspdBinWriter_8h_source.html index d15da36192..3237abc66a 100644 --- a/MmspdBinWriter_8h_source.html +++ b/MmspdBinWriter_8h_source.html @@ -80,7 +80,7 @@
8class MmspdBinWriter : public PluginBase{
9 public:
10 MmspdBinWriter(){};
-
22 MmspdBinWriter(unsigned long writeFrequency, std::string outputPrefix);
+
22 MmspdBinWriter(unsigned long writeFrequency, std::string outputPrefix);
23 ~MmspdBinWriter();
24
25 void readXML(XMLfileUnits& xmlconfig);
@@ -94,7 +94,7 @@
33 );
34 void finish(ParticleContainer *particleContainer,
35 DomainDecompBase *domainDecomp, Domain *domain);
-
36
+
36
37 std::string getPluginName() {
38 return std::string("MmspdBinWriter");
39 }
@@ -106,15 +106,14 @@
45};
46
47#endif /* MMSPDBINWRITER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MmspdBinWriter
Definition: MmspdBinWriter.h:8
-
MmspdBinWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MmspdBinWriter.cpp:175
-
MmspdBinWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MmspdBinWriter.cpp:263
-
MmspdBinWriter::MmspdBinWriter
MmspdBinWriter(unsigned long writeFrequency, std::string outputPrefix)
: writes a mmspd file used by MegaMol
-
MmspdBinWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MmspdBinWriter.cpp:52
+
MmspdBinWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: MmspdBinWriter.cpp:173
+
MmspdBinWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: MmspdBinWriter.cpp:261
+
MmspdBinWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MmspdBinWriter.cpp:50
MmspdBinWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: MmspdBinWriter.h:37
-
MmspdBinWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MmspdBinWriter.cpp:35
+
MmspdBinWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MmspdBinWriter.cpp:33
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
@@ -122,7 +121,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MmspdWriter_8h_source.html b/MmspdWriter_8h_source.html index d5729c776a..72e877789d 100644 --- a/MmspdWriter_8h_source.html +++ b/MmspdWriter_8h_source.html @@ -80,9 +80,9 @@
8class MmspdWriter : public PluginBase{
9 public:
10 MmspdWriter(){};
-
22 MmspdWriter(unsigned long writeFrequency, std::string outputPrefix);
+
22 MmspdWriter(unsigned long writeFrequency, std::string outputPrefix);
23 ~MmspdWriter();
-
24
+
24
25 void readXML(XMLfileUnits& xmlconfig);
26
27 void init(ParticleContainer *particleContainer,
@@ -105,15 +105,14 @@
46};
47
48#endif /* MMSPDWRITER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
MmspdWriter
Definition: MmspdWriter.h:8
-
MmspdWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: MmspdWriter.cpp:193
-
MmspdWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MmspdWriter.cpp:36
-
MmspdWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: MmspdWriter.cpp:124
+
MmspdWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: MmspdWriter.cpp:191
+
MmspdWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: MmspdWriter.cpp:34
+
MmspdWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: MmspdWriter.cpp:122
MmspdWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: MmspdWriter.h:37
-
MmspdWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MmspdWriter.cpp:53
-
MmspdWriter::MmspdWriter
MmspdWriter(unsigned long writeFrequency, std::string outputPrefix)
: writes a mmspd file used by MegaMol
+
MmspdWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: MmspdWriter.cpp:51
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
@@ -121,7 +120,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MoleculeForwardDeclaration_8h_source.html b/MoleculeForwardDeclaration_8h_source.html index fb394b936b..d0546575c1 100644 --- a/MoleculeForwardDeclaration_8h_source.html +++ b/MoleculeForwardDeclaration_8h_source.html @@ -101,7 +101,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MoleculeIdPool_8h_source.html b/MoleculeIdPool_8h_source.html index 6e3c5a7468..d96f4a9e4d 100644 --- a/MoleculeIdPool_8h_source.html +++ b/MoleculeIdPool_8h_source.html @@ -115,7 +115,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MoleculeInterface_8h_source.html b/MoleculeInterface_8h_source.html index e33a9d914b..9c7af7c562 100644 --- a/MoleculeInterface_8h_source.html +++ b/MoleculeInterface_8h_source.html @@ -159,7 +159,7 @@
87 virtual void setD(unsigned short d, double D) = 0;
88
89 inline virtual void move(int d, double dr) = 0;
-
90
+
90
91 //by Stefan Becker
92 virtual double getI(unsigned short d) const = 0;
93
@@ -237,30 +237,30 @@
165
166 //calculates orientation angle for ARDF
167 double orientationAngle(const MoleculeInterface& molecule2, double dr[3], double d2) const {
-
168
+
168
169 double cosPhi = 0.;
170 double orientationVector[3];
171 double orientationVectorSquared = 0.;
172 double roundingThreshold = 0.0001;
-
173
+
173
174 orientationVector[0] = 2. * (q().qx() * q().qz() + q().qw() * q().qy());
175 orientationVector[1] = 2. * (q().qy() * q().qz() - q().qw() * q().qx());
176 orientationVector[2] = 1. - 2. * (q().qx() * q().qx() + q().qy() * q().qy());
177
-
178
-
179
+
178
+
179
180 for (unsigned short d = 0; d < 3; d++) {
181 dr[d] = molecule2.r(d) - r(d);
182 orientationVectorSquared += orientationVector[d] * orientationVector[d];
183 }
-
184
+
184
185 for (unsigned short d = 0; d < 3; d++) {
186 cosPhi += orientationVector[d] * dr[d] / sqrt(orientationVectorSquared) / sqrt(d2);
187 }
188 return cosPhi;
-
189
+
189
190 }
-
191
+
191
192 virtual void setF(double F[3]) = 0;
193 virtual void setM(double M[3]) = 0;
194 virtual void setVi(double Vi[3]) = 0;
@@ -400,13 +400,13 @@
MoleculeInterface::inBox
virtual bool inBox(const double l[3], const double u[3]) const
test whether molecule is inside a cuboid region
Definition: MoleculeInterface.h:300
MoleculeInterface::buildOwnSoA
virtual void buildOwnSoA()=0
MoleculeInterface::releaseOwnSoA
virtual void releaseOwnSoA()=0
-
MoleculeInterface::isLessThan
bool isLessThan(const MoleculeInterface &m2) const
find out whether m1 is before m2 (in some global ordering)
Definition: MoleculeInterface.cpp:21
+
MoleculeInterface::isLessThan
bool isLessThan(const MoleculeInterface &m2) const
find out whether m1 is before m2 (in some global ordering)
Definition: MoleculeInterface.cpp:18
Quaternion
Definition: Quaternion.h:10
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MoleculeRMM_8h_source.html b/MoleculeRMM_8h_source.html index 70a023fdcb..d9a07c9d07 100644 --- a/MoleculeRMM_8h_source.html +++ b/MoleculeRMM_8h_source.html @@ -287,7 +287,7 @@
215 mardyn_assert(false);
216 return sizeof(*this);
217 }
-
218
+
218
219 void setF(double /*F*/ [3]) override {}
220 void setM(double /*M*/[3]) override {}
221 void setVi(double /*Vi*/[3]) override {}
@@ -356,7 +356,7 @@
284 StorageState getStorageState() const {
285 return _state;
286 }
-
287
+
287
288
289 void buildOwnSoA() override {
290 mardyn_assert(_state == STORAGE_AOS);
@@ -409,7 +409,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Molecule_8h_source.html b/Molecule_8h_source.html index cfa6b944f7..52883f4fa4 100644 --- a/Molecule_8h_source.html +++ b/Molecule_8h_source.html @@ -122,7 +122,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MultiObjectGenerator_8h_source.html b/MultiObjectGenerator_8h_source.html index e538fd36ce..a4f0c7e419 100644 --- a/MultiObjectGenerator_8h_source.html +++ b/MultiObjectGenerator_8h_source.html @@ -101,13 +101,13 @@
41};
42
43#endif // SRC_IO_MULTIOBJECTGENERATOR_H_
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
MultiObjectGenerator
Definition: MultiObjectGenerator.h:13
-
MultiObjectGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: MultiObjectGenerator.cpp:51
+
MultiObjectGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: MultiObjectGenerator.cpp:48
MultiObjectGenerator::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *, double)
read the phase space components and header information
Definition: MultiObjectGenerator.h:33
-
MultiObjectGenerator::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Generator and all its included objects.
Definition: MultiObjectGenerator.cpp:36
+
MultiObjectGenerator::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Generator and all its included objects.
Definition: MultiObjectGenerator.cpp:33
ObjectGenerator
The ObjectGenerator sets up a phase space by filling volumetric objects.
Definition: ObjectGenerator.h:22
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
VelocityAssignerBase
Definition: VelocityAssignerBase.h:8
@@ -115,7 +115,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/MultipoleParticle_8h_source.html b/MultipoleParticle_8h_source.html index 208295f9de..747789aed8 100644 --- a/MultipoleParticle_8h_source.html +++ b/MultipoleParticle_8h_source.html @@ -120,7 +120,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NeighborAcquirer_8cpp.html b/NeighborAcquirer_8cpp.html index 35c19dd672..6aef1fe99f 100644 --- a/NeighborAcquirer_8cpp.html +++ b/NeighborAcquirer_8cpp.html @@ -80,7 +80,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NeighborAcquirer_8h.html b/NeighborAcquirer_8h.html index bdf1003424..4f001c35fd 100644 --- a/NeighborAcquirer_8h.html +++ b/NeighborAcquirer_8h.html @@ -89,7 +89,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NeighborAcquirer_8h_source.html b/NeighborAcquirer_8h_source.html index 558045747c..ec42ba0632 100644 --- a/NeighborAcquirer_8h_source.html +++ b/NeighborAcquirer_8h_source.html @@ -104,7 +104,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NeighbourCommunicationScheme_8h_source.html b/NeighbourCommunicationScheme_8h_source.html index 708d9101f2..5ccd2080df 100644 --- a/NeighbourCommunicationScheme_8h_source.html +++ b/NeighbourCommunicationScheme_8h_source.html @@ -89,7 +89,7 @@
17class HaloRegion;
18class NeighbourCommunicationScheme {
19 friend class NeighbourCommunicationSchemeTest;
-
20
+
20
21public:
27 unsigned int getCommDims() {
28 return _commDimms;
@@ -163,13 +163,13 @@
96protected:
97
99 std::vector<std::vector<CommunicationPartner>> *_neighbours;
-
100
+
100
101 // -------------------------------------------------------------------------
102 std::vector<std::vector<CommunicationPartner>> *_haloExportForceImportNeighbours;
103 std::vector<std::vector<CommunicationPartner>> *_haloImportForceExportNeighbours;
104 std::vector<std::vector<CommunicationPartner>> *_leavingExportNeighbours;
105 std::vector<std::vector<CommunicationPartner>> *_leavingImportNeighbours;
-
106
+
106
107 void selectNeighbours(MessageType msgType, bool import);
108 // -------------------------------------------------------------------------
109
@@ -292,7 +292,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NeutralTerritoryTraversal_8h_source.html b/NeutralTerritoryTraversal_8h_source.html index e3410233ef..f8e28b7451 100644 --- a/NeutralTerritoryTraversal_8h_source.html +++ b/NeutralTerritoryTraversal_8h_source.html @@ -184,14 +184,14 @@
124
125template <class CellTemplate>
126void NeutralTerritoryTraversal<CellTemplate>::traverseCellPairsOuter(CellProcessor& cellProcessor) {
-
127 global_log->error() << "NT: overlapping Comm not implemented." << std::endl;
+
127 Log::global_log->error() << "NT: overlapping Comm not implemented." << std::endl;
128 Simulation::exit(46);
129}
130
131template <class CellTemplate>
132void NeutralTerritoryTraversal<CellTemplate>::traverseCellPairsInner(CellProcessor& cellProcessor, unsigned stage,
133 unsigned stageCount) {
-
134 global_log->error() << "NT: overlapping Comm not implemented." << std::endl;
+
134 Log::global_log->error() << "NT: overlapping Comm not implemented." << std::endl;
135 Simulation::exit(47);
136}
137
@@ -224,13 +224,13 @@
CellProcessor::processCellPair
virtual void processCellPair(ParticleCell &cell1, ParticleCell &cell2, bool sumAll=false)=0
NeutralTerritoryTraversal
Definition: NeutralTerritoryTraversal.h:25
NeutralTerritoryTraversal::rebuild
void rebuild(std::vector< CellTemplate > &cells, const std::array< unsigned long, 3 > &dims, double cellLength[3], double cutoff, CellPairTraversalData *data) override
Definition: NeutralTerritoryTraversal.h:38
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
CellPairTraversalData
Definition: CellPairTraversals.h:16
NeutralTerritoryTraversalData
Definition: NeutralTerritoryTraversal.h:13
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NeutralTerritory_8h_source.html b/NeutralTerritory_8h_source.html index 02d5f8f7ea..bbc077d552 100644 --- a/NeutralTerritory_8h_source.html +++ b/NeutralTerritory_8h_source.html @@ -130,7 +130,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NoLRC_8h_source.html b/NoLRC_8h_source.html index 422302a316..13d490dc50 100644 --- a/NoLRC_8h_source.html +++ b/NoLRC_8h_source.html @@ -77,43 +77,42 @@
5#include "LongRangeCorrection.h"
6
7#include "utils/Logger.h"
-
8using Log::global_log;
-
9
-
10class Simulation;
-
11class Domain;
-
12class LongRangeCorrection;
-
13
-
17class NoLRC: public LongRangeCorrection{
-
18
-
19public:
-
20 NoLRC(double /* cutoffRadius */, double /* cutoffRadiusLJ */, Domain* domain, Simulation* /* simulation */) {
-
21 _domain = domain;
-
22 };
-
23 virtual ~NoLRC() {}
-
24
-
25 virtual void init() { global_log->info() << "No long range correction is used: UpotCorr = VirialCorr = 0" << std::endl; }
-
26 virtual void readXML(XMLfileUnits& /* xmlconfig */) {}
-
27 virtual void calculateLongRange() {
-
28 _domain->setUpotCorr(0.);
-
29 _domain->setVirialCorr(0.);
-
30 };
-
31 virtual void writeProfiles(DomainDecompBase* /* domainDecomp */, Domain* /* domain */, unsigned long /* simstep */) {}
-
32
-
33private:
-
34 Domain* _domain;
-
35};
-
36
-
37#endif /* __NOLRC_H__ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
8
+
9class Simulation;
+
10class Domain;
+
11class LongRangeCorrection;
+
12
+
16class NoLRC: public LongRangeCorrection{
+
17
+
18public:
+
19 NoLRC(double /* cutoffRadius */, double /* cutoffRadiusLJ */, Domain* domain, Simulation* /* simulation */) {
+
20 _domain = domain;
+
21 };
+
22 virtual ~NoLRC() {}
+
23
+
24 virtual void init() { Log::global_log->info() << "No long range correction is used: UpotCorr = VirialCorr = 0" << std::endl; }
+
25 virtual void readXML(XMLfileUnits& /* xmlconfig */) {}
+
26 virtual void calculateLongRange() {
+
27 _domain->setUpotCorr(0.);
+
28 _domain->setVirialCorr(0.);
+
29 };
+
30 virtual void writeProfiles(DomainDecompBase* /* domainDecomp */, Domain* /* domain */, unsigned long /* simstep */) {}
+
31
+
32private:
+
33 Domain* _domain;
+
34};
+
35
+
36#endif /* __NOLRC_H__ */
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
LongRangeCorrection
Definition: LongRangeCorrection.h:12
-
NoLRC
Definition: NoLRC.h:17
-
Simulation
Controls the simulation process.
Definition: Simulation.h:70
+
NoLRC
Definition: NoLRC.h:16
+
Simulation
Controls the simulation process.
Definition: Simulation.h:72
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NonBlockingMPIHandlerBase_8h_source.html b/NonBlockingMPIHandlerBase_8h_source.html index 5b07f4bb8e..5a914d3b11 100644 --- a/NonBlockingMPIHandlerBase_8h_source.html +++ b/NonBlockingMPIHandlerBase_8h_source.html @@ -106,16 +106,16 @@
DomainDecompMPIBase
Definition: DomainDecompMPIBase.h:30
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
NonBlockingMPIHandlerBase
Definition: NonBlockingMPIHandlerBase.h:20
-
NonBlockingMPIHandlerBase::performOverlappingTasks
virtual void performOverlappingTasks(bool forceRebalancing, double etime) final
Definition: NonBlockingMPIHandlerBase.cpp:28
-
NonBlockingMPIHandlerBase::~NonBlockingMPIHandlerBase
virtual ~NonBlockingMPIHandlerBase()
Definition: NonBlockingMPIHandlerBase.cpp:26
-
NonBlockingMPIHandlerBase::NonBlockingMPIHandlerBase
NonBlockingMPIHandlerBase(DomainDecompMPIBase *domainDecomposition, ParticleContainer *moleculeContainer, Domain *domain, CellProcessor *cellProcessor)
Definition: NonBlockingMPIHandlerBase.cpp:18
-
NonBlockingMPIHandlerBase::initBalanceAndExchange
virtual void initBalanceAndExchange(bool forceRebalancing, double etime)
Definition: NonBlockingMPIHandlerBase.cpp:63
-
NonBlockingMPIHandlerBase::performComputation
virtual void performComputation()
Definition: NonBlockingMPIHandlerBase.cpp:54
+
NonBlockingMPIHandlerBase::performOverlappingTasks
virtual void performOverlappingTasks(bool forceRebalancing, double etime) final
Definition: NonBlockingMPIHandlerBase.cpp:27
+
NonBlockingMPIHandlerBase::~NonBlockingMPIHandlerBase
virtual ~NonBlockingMPIHandlerBase()
Definition: NonBlockingMPIHandlerBase.cpp:25
+
NonBlockingMPIHandlerBase::NonBlockingMPIHandlerBase
NonBlockingMPIHandlerBase(DomainDecompMPIBase *domainDecomposition, ParticleContainer *moleculeContainer, Domain *domain, CellProcessor *cellProcessor)
Definition: NonBlockingMPIHandlerBase.cpp:17
+
NonBlockingMPIHandlerBase::initBalanceAndExchange
virtual void initBalanceAndExchange(bool forceRebalancing, double etime)
Definition: NonBlockingMPIHandlerBase.cpp:62
+
NonBlockingMPIHandlerBase::performComputation
virtual void performComputation()
Definition: NonBlockingMPIHandlerBase.cpp:53
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/NonBlockingMPIMultiStepHandler_8h_source.html b/NonBlockingMPIMultiStepHandler_8h_source.html index 0d1f1f2025..549c5a1a5e 100644 --- a/NonBlockingMPIMultiStepHandler_8h_source.html +++ b/NonBlockingMPIMultiStepHandler_8h_source.html @@ -100,15 +100,15 @@
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
NonBlockingMPIHandlerBase
Definition: NonBlockingMPIHandlerBase.h:20
NonBlockingMPIMultiStepHandler
Definition: NonBlockingMPIMultiStepHandler.h:12
-
NonBlockingMPIMultiStepHandler::performComputation
virtual void performComputation()
Definition: NonBlockingMPIMultiStepHandler.cpp:30
-
NonBlockingMPIMultiStepHandler::~NonBlockingMPIMultiStepHandler
virtual ~NonBlockingMPIMultiStepHandler()
Definition: NonBlockingMPIMultiStepHandler.cpp:26
-
NonBlockingMPIMultiStepHandler::initBalanceAndExchange
virtual void initBalanceAndExchange(bool forceRebalancing, double etime)
Definition: NonBlockingMPIMultiStepHandler.cpp:96
-
NonBlockingMPIMultiStepHandler::NonBlockingMPIMultiStepHandler
NonBlockingMPIMultiStepHandler(DomainDecompMPIBase *domainDecomposition, ParticleContainer *moleculeContainer, Domain *domain, CellProcessor *cellProcessor)
Definition: NonBlockingMPIMultiStepHandler.cpp:19
+
NonBlockingMPIMultiStepHandler::performComputation
virtual void performComputation()
Definition: NonBlockingMPIMultiStepHandler.cpp:28
+
NonBlockingMPIMultiStepHandler::~NonBlockingMPIMultiStepHandler
virtual ~NonBlockingMPIMultiStepHandler()
Definition: NonBlockingMPIMultiStepHandler.cpp:24
+
NonBlockingMPIMultiStepHandler::initBalanceAndExchange
virtual void initBalanceAndExchange(bool forceRebalancing, double etime)
Definition: NonBlockingMPIMultiStepHandler.cpp:94
+
NonBlockingMPIMultiStepHandler::NonBlockingMPIMultiStepHandler
NonBlockingMPIMultiStepHandler(DomainDecompMPIBase *domainDecomposition, ParticleContainer *moleculeContainer, Domain *domain, CellProcessor *cellProcessor)
Definition: NonBlockingMPIMultiStepHandler.cpp:17
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ODFCellProcessor_8cpp.html b/ODFCellProcessor_8cpp.html index 71e131d83a..f2fdfae531 100644 --- a/ODFCellProcessor_8cpp.html +++ b/ODFCellProcessor_8cpp.html @@ -79,7 +79,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ODFCellProcessor_8h.html b/ODFCellProcessor_8h.html index 98d4ebc3f5..be412e4e07 100644 --- a/ODFCellProcessor_8h.html +++ b/ODFCellProcessor_8h.html @@ -88,7 +88,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ODFCellProcessor_8h_source.html b/ODFCellProcessor_8h_source.html index 7eebb6213a..13f948d074 100644 --- a/ODFCellProcessor_8h_source.html +++ b/ODFCellProcessor_8h_source.html @@ -117,7 +117,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ODF_8h.html b/ODF_8h.html index 286d34ab97..1bffa64951 100644 --- a/ODF_8h.html +++ b/ODF_8h.html @@ -91,7 +91,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ODF_8h_source.html b/ODF_8h_source.html index ee020fad9b..5833ab06b7 100644 --- a/ODF_8h_source.html +++ b/ODF_8h_source.html @@ -89,10 +89,10 @@
34 unsigned long simstep) override;
35 void reset();
36 void collect(DomainDecompBase* domainDecomp);
-
37 void calculateOrientation(const array<double, 3> &simBoxSize,
+
37 void calculateOrientation(const std::array<double, 3> &simBoxSize,
38 const Molecule &mol1,
39 const Molecule &mol2,
-
40 const array<double, 3> &orientationVector1);
+
40 const std::array<double, 3> &orientationVector1);
41 void output(Domain* domain, long unsigned timestep);
42 void finish(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override{};
43 std::string getPluginName() override { return std::string("ODF"); }
@@ -126,7 +126,7 @@
71 std::unique_ptr<ODFCellProcessor> _cellProcessor;
72};
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ODF
Definition: ODF.h:27
@@ -143,7 +143,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ObjectFactory_8h_source.html b/ObjectFactory_8h_source.html index 707673b0a8..08f77d1776 100644 --- a/ObjectFactory_8h_source.html +++ b/ObjectFactory_8h_source.html @@ -87,7 +87,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ObjectFillerBase_8h_source.html b/ObjectFillerBase_8h_source.html index 4c74c6125d..ad959888e8 100644 --- a/ObjectFillerBase_8h_source.html +++ b/ObjectFillerBase_8h_source.html @@ -109,7 +109,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ObjectFillerFactory_8h_source.html b/ObjectFillerFactory_8h_source.html index 1ac010af3e..89ff3b9b1d 100644 --- a/ObjectFillerFactory_8h_source.html +++ b/ObjectFillerFactory_8h_source.html @@ -90,7 +90,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ObjectGenerator_8h_source.html b/ObjectGenerator_8h_source.html index 717c3a230f..d9c1795202 100644 --- a/ObjectGenerator_8h_source.html +++ b/ObjectGenerator_8h_source.html @@ -111,15 +111,15 @@
57};
58
59#endif // SRC_IO_OBJECTGENERATOR_H_
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
MoleculeIdPool
The MoleculeIdPool manages molecule ID handling.
Definition: MoleculeIdPool.h:14
ObjectFillerBase
Definition: ObjectFillerBase.h:11
ObjectGenerator
The ObjectGenerator sets up a phase space by filling volumetric objects.
Definition: ObjectGenerator.h:22
ObjectGenerator::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *, double)
read the phase space components and header information
Definition: ObjectGenerator.h:48
-
ObjectGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: ObjectGenerator.cpp:116
-
ObjectGenerator::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectGenerator and all its included objects.
Definition: ObjectGenerator.cpp:21
+
ObjectGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: ObjectGenerator.cpp:114
+
ObjectGenerator::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectGenerator and all its included objects.
Definition: ObjectGenerator.cpp:19
Object
Definition: Objects.h:25
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
VelocityAssignerBase
Definition: VelocityAssignerBase.h:8
@@ -127,7 +127,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Objects_8h_source.html b/Objects_8h_source.html index bb6c79886f..499f931eca 100644 --- a/Objects_8h_source.html +++ b/Objects_8h_source.html @@ -341,17 +341,17 @@
372#endif /* OBJECTS_H */
Cuboid
Definition: Objects.h:46
Cuboid::getName
std::string getName()
Definition: Objects.h:62
-
Cuboid::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Cuboid and all its included objects.
Definition: Objects.cpp:19
-
Cuboid::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.cpp:40
-
Cuboid::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.cpp:45
-
Cuboid::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.cpp:34
-
Cuboid::isInside
bool isInside(double r[3])
Definition: Objects.cpp:28
+
Cuboid::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Cuboid and all its included objects.
Definition: Objects.cpp:17
+
Cuboid::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.cpp:38
+
Cuboid::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.cpp:43
+
Cuboid::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.cpp:32
+
Cuboid::isInside
bool isInside(double r[3])
Definition: Objects.cpp:26
Cylinder
Definition: Objects.h:110
-
Cylinder::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Cylinder and all its included objects.
Definition: Objects.cpp:108
-
Cylinder::isInside
bool isInside(double r[3])
Definition: Objects.cpp:132
-
Cylinder::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.cpp:157
-
Cylinder::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.cpp:141
-
Cylinder::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.cpp:150
+
Cylinder::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Cylinder and all its included objects.
Definition: Objects.cpp:106
+
Cylinder::isInside
bool isInside(double r[3])
Definition: Objects.cpp:130
+
Cylinder::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.cpp:155
+
Cylinder::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.cpp:139
+
Cylinder::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.cpp:148
Cylinder::getName
std::string getName()
Definition: Objects.h:132
ObjectIntersection
Definition: Objects.h:256
ObjectIntersection::ObjectIntersection
ObjectIntersection(std::shared_ptr< Object > obj1, std::shared_ptr< Object > obj2)
Definition: Objects.h:263
@@ -360,11 +360,11 @@
ObjectIntersection::isInside
bool isInside(double r[3])
Definition: Objects.h:279
ObjectIntersection::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.h:287
ObjectIntersection::getName
std::string getName()
Definition: Objects.h:276
-
ObjectIntersection::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectIntersection and all its included objects.
Definition: Objects.cpp:210
+
ObjectIntersection::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectIntersection and all its included objects.
Definition: Objects.cpp:208
ObjectShifter
Definition: Objects.h:311
ObjectShifter::isInside
bool isInside(double r[3])
Definition: Objects.h:335
ObjectShifter::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.h:344
-
ObjectShifter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectIntersection and all its included objects.
Definition: Objects.cpp:235
+
ObjectShifter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectIntersection and all its included objects.
Definition: Objects.cpp:233
ObjectShifter::getName
std::string getName()
Definition: Objects.h:331
ObjectShifter::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.h:360
ObjectShifter::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.h:353
@@ -372,7 +372,7 @@
ObjectSubtractor::isInside
bool isInside(double r[3])
Definition: Objects.h:234
ObjectSubtractor::ObjectSubtractor
ObjectSubtractor(std::shared_ptr< Object > original_ob, std::shared_ptr< Object > subtract_ob)
Definition: Objects.h:218
ObjectSubtractor::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.h:238
-
ObjectSubtractor::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectSubtractor and all its included objects.
Definition: Objects.cpp:189
+
ObjectSubtractor::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectSubtractor and all its included objects.
Definition: Objects.cpp:187
ObjectSubtractor::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.h:242
ObjectSubtractor::getName
std::string getName()
Definition: Objects.h:231
ObjectSubtractor::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.h:246
@@ -380,7 +380,7 @@
ObjectUnification::ObjectUnification
ObjectUnification(std::shared_ptr< Object > obj1, std::shared_ptr< Object > obj2)
Definition: Objects.h:159
ObjectUnification::getName
std::string getName()
Definition: Objects.h:172
ObjectUnification::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.h:193
-
ObjectUnification::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectUnification and all its included objects.
Definition: Objects.cpp:168
+
ObjectUnification::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ObjectUnification and all its included objects.
Definition: Objects.cpp:166
ObjectUnification::isInside
bool isInside(double r[3])
Definition: Objects.h:175
ObjectUnification::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.h:184
ObjectUnification::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.h:179
@@ -392,19 +392,19 @@
Object::getBboxMax
virtual void getBboxMax(double rmax[3])=0
Sphere
Definition: Objects.h:79
Sphere::getName
std::string getName()
Definition: Objects.h:95
-
Sphere::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.cpp:95
-
Sphere::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.cpp:90
-
Sphere::Sphere
Sphere()
Definition: Objects.cpp:53
-
Sphere::isInside
bool isInside(double r[3])
Definition: Objects.cpp:70
-
Sphere::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Sphere and all its included objects.
Definition: Objects.cpp:60
-
Sphere::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.cpp:80
+
Sphere::getBboxMax
void getBboxMax(double rmax[3])
Definition: Objects.cpp:93
+
Sphere::getBboxMin
void getBboxMin(double rmin[3])
Definition: Objects.cpp:88
+
Sphere::Sphere
Sphere()
Definition: Objects.cpp:51
+
Sphere::isInside
bool isInside(double r[3])
Definition: Objects.cpp:68
+
Sphere::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for Sphere and all its included objects.
Definition: Objects.cpp:58
+
Sphere::isInsideNoBorder
bool isInsideNoBorder(double r[3])
Definition: Objects.cpp:78
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
xmlfileUnits.h
XML input file with unit handling/conversion support.
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ObserverBase_8h_source.html b/ObserverBase_8h_source.html index ba249f51a8..5a0c498f4e 100644 --- a/ObserverBase_8h_source.html +++ b/ObserverBase_8h_source.html @@ -103,7 +103,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/OptionParser_8h_source.html b/OptionParser_8h_source.html index c1f331f42e..083863c1f9 100644 --- a/OptionParser_8h_source.html +++ b/OptionParser_8h_source.html @@ -320,12 +320,12 @@
optparse::Value
Class for automatic conversion from string -> anytype.
Definition: OptionParser.h:88
optparse::Values
Definition: OptionParser.h:108
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
-
optparse
Definition: OptionParser.cpp:25
+
optparse
Definition: OptionParser.cpp:24
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/OriginalCellPairTraversal_8h_source.html b/OriginalCellPairTraversal_8h_source.html index 9dd08f1df7..cb44a27d7d 100644 --- a/OriginalCellPairTraversal_8h_source.html +++ b/OriginalCellPairTraversal_8h_source.html @@ -146,7 +146,7 @@
74 }
75 }
76 } else {
-
77 global_log->error() << "OriginalCellPairTraversalDat::rebuild was called with incompatible Traversal data!" << endl;
+
77 Log::global_log->error() << "OriginalCellPairTraversalDat::rebuild was called with incompatible Traversal data!" << std::endl;
78 Simulation::exit(-1);
79 }
80}
@@ -294,14 +294,14 @@
OriginalCellPairTraversal::_backwardNeighbourOffsets
std::array< long, 13 > _backwardNeighbourOffsets
Neighbours that come in the total ordering before a cell.
Definition: OriginalCellPairTraversal.h:53
OriginalCellPairTraversal::_forwardNeighbourOffsets
std::array< long, 13 > _forwardNeighbourOffsets
Neighbours that come in the total ordering after a cell.
Definition: OriginalCellPairTraversal.h:52
OriginalCellPairTraversal::_innerMostCellIndices
std::vector< unsigned long > _innerMostCellIndices
Vector containing the indices (for the cells vector) of all inner cells (without boundary)
Definition: OriginalCellPairTraversal.h:54
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
CellPairTraversalData
Definition: CellPairTraversals.h:16
OriginalCellPairTraversalData
Definition: OriginalCellPairTraversal.h:17
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/P2MCellProcessor_8h_source.html b/P2MCellProcessor_8h_source.html index 5338c89e74..0372faa220 100644 --- a/P2MCellProcessor_8h_source.html +++ b/P2MCellProcessor_8h_source.html @@ -116,7 +116,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParaStrm_8h_source.html b/ParaStrm_8h_source.html index ee7c2779cf..54ee406b4e 100644 --- a/ParaStrm_8h_source.html +++ b/ParaStrm_8h_source.html @@ -171,7 +171,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleCellBase_8h_source.html b/ParticleCellBase_8h_source.html index 5d03c3ca3d..8e2bef9f9a 100644 --- a/ParticleCellBase_8h_source.html +++ b/ParticleCellBase_8h_source.html @@ -247,7 +247,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleCellForwardDeclaration_8h_source.html b/ParticleCellForwardDeclaration_8h_source.html index 1bad19aa30..322a3a79dd 100644 --- a/ParticleCellForwardDeclaration_8h_source.html +++ b/ParticleCellForwardDeclaration_8h_source.html @@ -94,7 +94,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleCellPointers_8h_source.html b/ParticleCellPointers_8h_source.html index b11dcd7c6f..c1885dcf29 100644 --- a/ParticleCellPointers_8h_source.html +++ b/ParticleCellPointers_8h_source.html @@ -185,17 +185,17 @@
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
bhfmm::ParticleCellPointers
Definition: ParticleCellPointers.h:44
bhfmm::ParticleCellPointers::getCellDataSoA
CellDataSoA & getCellDataSoA()
Get the structure of arrays for VectorizedCellProcessor.
Definition: ParticleCellPointers.h:76
-
bhfmm::ParticleCellPointers::removeAllParticles
void removeAllParticles()
removes all elements from the list molecules without deallocating them
Definition: ParticleCellPointers.cpp:35
-
bhfmm::ParticleCellPointers::getMoleculeCount
int getMoleculeCount() const
return the number of molecules contained in this cell
Definition: ParticleCellPointers.cpp:55
-
bhfmm::ParticleCellPointers::ParticleCellPointers
ParticleCellPointers()
Initialize data pointers to 0.
Definition: ParticleCellPointers.cpp:19
-
bhfmm::ParticleCellPointers::~ParticleCellPointers
~ParticleCellPointers()
Destructor.
Definition: ParticleCellPointers.cpp:29
-
bhfmm::ParticleCellPointers::addParticle
bool addParticle(Molecule *particle_ptr)
insert a single molecule into this cell
Definition: ParticleCellPointers.cpp:39
+
bhfmm::ParticleCellPointers::removeAllParticles
void removeAllParticles()
removes all elements from the list molecules without deallocating them
Definition: ParticleCellPointers.cpp:33
+
bhfmm::ParticleCellPointers::getMoleculeCount
int getMoleculeCount() const
return the number of molecules contained in this cell
Definition: ParticleCellPointers.cpp:53
+
bhfmm::ParticleCellPointers::ParticleCellPointers
ParticleCellPointers()
Initialize data pointers to 0.
Definition: ParticleCellPointers.cpp:17
+
bhfmm::ParticleCellPointers::~ParticleCellPointers
~ParticleCellPointers()
Destructor.
Definition: ParticleCellPointers.cpp:27
+
bhfmm::ParticleCellPointers::addParticle
bool addParticle(Molecule *particle_ptr)
insert a single molecule into this cell
Definition: ParticleCellPointers.cpp:37
bhfmm
Definition: L2PCellProcessor.cpp:15
xml_schema::id
::xsd::cxx::tree::id< char, ncname > id
C++ type corresponding to the ID XML Schema built-in type.
Definition: xml-schema.h:320
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleCellRMM_8h_source.html b/ParticleCellRMM_8h_source.html index 189b95cd87..3cd0cfa0b7 100644 --- a/ParticleCellRMM_8h_source.html +++ b/ParticleCellRMM_8h_source.html @@ -149,7 +149,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleCell_8h_source.html b/ParticleCell_8h_source.html index 283d6924d1..3ff1fbac2e 100644 --- a/ParticleCell_8h_source.html +++ b/ParticleCell_8h_source.html @@ -109,7 +109,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleContainer_8h_source.html b/ParticleContainer_8h_source.html index 80ebc1acbb..8025f73140 100644 --- a/ParticleContainer_8h_source.html +++ b/ParticleContainer_8h_source.html @@ -216,7 +216,7 @@
ParticleContainer::setCutoff
virtual void setCutoff(double rc)
Definition: ParticleContainer.h:261
ParticleContainer::get_halo_L
virtual double get_halo_L(int index) const =0
returns the width of the halo stripe (for the given dimension index)
ParticleContainer::getNumberOfParticles
virtual unsigned long getNumberOfParticles(ParticleIterator::Type t=ParticleIterator::ALL_CELLS)=0
Gets number of particles stored in this container.
-
ParticleContainer::getBoundingBoxMin
virtual double getBoundingBoxMin(int dimension) const
returns one coordinate of the lower corner of the bounding box
Definition: ParticleContainer.cpp:29
+
ParticleContainer::getBoundingBoxMin
virtual double getBoundingBoxMin(int dimension) const
returns one coordinate of the lower corner of the bounding box
Definition: ParticleContainer.cpp:27
ParticleContainer::traverseCells
virtual void traverseCells(CellProcessor &cellProcessor)=0
traverse pairs which are close to each other
ParticleContainer::updateMoleculeCaches
virtual void updateMoleculeCaches()=0
Update the caches of the molecules.
ParticleContainer::_invalidParticles
std::vector< Molecule > _invalidParticles
Definition: ParticleContainer.h:288
@@ -226,29 +226,29 @@
ParticleContainer::_boundingBoxMin
double _boundingBoxMin[3]
coordinates of the left, lower, front corner of the bounding box
Definition: ParticleContainer.h:283
ParticleContainer::initCubicGrid
virtual unsigned long initCubicGrid(std::array< unsigned long, 3 > numMoleculesPerDimension, std::array< double, 3 > simBoxLength, size_t seed_offset)=0
ParticleContainer::deleteOuterParticles
virtual void deleteOuterParticles()=0
delete all Particles which are not within the bounding box
-
ParticleContainer::rebuild
virtual bool rebuild(double bBoxMin[3], double bBoxMax[3])
rebuild the datastructure
Definition: ParticleContainer.cpp:16
-
ParticleContainer::isInBoundingBox
virtual bool isInBoundingBox(double r[3]) const
checks, whether given coordinates are within the bounding box
Definition: ParticleContainer.cpp:37
+
ParticleContainer::rebuild
virtual bool rebuild(double bBoxMin[3], double bBoxMax[3])
rebuild the datastructure
Definition: ParticleContainer.cpp:14
+
ParticleContainer::isInBoundingBox
virtual bool isInBoundingBox(double r[3]) const
checks, whether given coordinates are within the bounding box
Definition: ParticleContainer.cpp:35
ParticleContainer::updateBoundaryAndHaloMoleculeCaches
virtual void updateBoundaryAndHaloMoleculeCaches()=0
Update the caches of the molecules, that lie in the boundary or halo cells. The caches of boundary an...
ParticleContainer::getParticleCellStatistics
virtual std::vector< unsigned long > getParticleCellStatistics()
Definition: ParticleContainer.h:255
ParticleContainer::update
virtual void update()=0
do necessary updates resulting from changed particle positions
ParticleContainer::getHaloSize
virtual double * getHaloSize()
Definition: ParticleContainer.h:247
ParticleContainer::addParticle
virtual bool addParticle(Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false)=0
add a single Molecule to the ParticleContainer.
ParticleContainer::clear
virtual void clear()=0
Delete all molecules in container.
-
ParticleContainer::getBoundingBoxMax
virtual double getBoundingBoxMax(int dimension) const
returns one coordinate of the higher corner of the bounding box
Definition: ParticleContainer.cpp:33
+
ParticleContainer::getBoundingBoxMax
virtual double getBoundingBoxMax(int dimension) const
returns one coordinate of the higher corner of the bounding box
Definition: ParticleContainer.cpp:31
ParticleContainer::getConfigurationAsString
virtual std::string getConfigurationAsString()=0
ParticleContainer::getMoleculeAtPosition
virtual std::variant< ParticleIterator, SingleCellIterator< ParticleCell > > getMoleculeAtPosition(const double pos[3])=0
Gets a molecule by its position.
-
ParticleContainer::addHaloParticle
virtual bool addHaloParticle(Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false)
add a single Molecule to the ParticleContainer, ensures that it is added in the halo.
Definition: ParticleContainer.cpp:50
+
ParticleContainer::addHaloParticle
virtual bool addHaloParticle(Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false)
add a single Molecule to the ParticleContainer, ensures that it is added in the halo.
Definition: ParticleContainer.cpp:48
ParticleContainer::_boundingBoxMax
double _boundingBoxMax[3]
coordinates of the right, upper, back corner of the bounding box
Definition: ParticleContainer.h:285
ParticleIterator
Definition: ParticleIterator.h:60
ParticlePairsHandler
interface for defining the action performed when processing a pair
Definition: ParticlePairsHandler.h:38
RegionParticleIterator
Definition: RegionParticleIterator.h:67
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-
pos
Definition: FakedOptFFT.h:23
+
pos
Definition: FakedOptFFT.h:21
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleDataForwardDeclaration_8h_source.html b/ParticleDataForwardDeclaration_8h_source.html index 77540f1596..00aed1ffbe 100644 --- a/ParticleDataForwardDeclaration_8h_source.html +++ b/ParticleDataForwardDeclaration_8h_source.html @@ -93,7 +93,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleDataFull_8h_source.html b/ParticleDataFull_8h_source.html index c5bb4614e2..51c2e375df 100644 --- a/ParticleDataFull_8h_source.html +++ b/ParticleDataFull_8h_source.html @@ -107,7 +107,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleDataRMM_8h_source.html b/ParticleDataRMM_8h_source.html index 03fff548e4..6c0d27210a 100644 --- a/ParticleDataRMM_8h_source.html +++ b/ParticleDataRMM_8h_source.html @@ -101,7 +101,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleData_8h_source.html b/ParticleData_8h_source.html index 2190e05cd3..afc8d295dc 100644 --- a/ParticleData_8h_source.html +++ b/ParticleData_8h_source.html @@ -84,7 +84,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleForceData_8h_source.html b/ParticleForceData_8h_source.html index a94e0d8ce3..ed46de921b 100644 --- a/ParticleForceData_8h_source.html +++ b/ParticleForceData_8h_source.html @@ -102,7 +102,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticleIterator_8h_source.html b/ParticleIterator_8h_source.html index 12871ceec9..266aabb5b3 100644 --- a/ParticleIterator_8h_source.html +++ b/ParticleIterator_8h_source.html @@ -279,7 +279,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticlePairs2LoadCalcAdapter_8h_source.html b/ParticlePairs2LoadCalcAdapter_8h_source.html index 59b93d13be..3ff90dd3f8 100644 --- a/ParticlePairs2LoadCalcAdapter_8h_source.html +++ b/ParticlePairs2LoadCalcAdapter_8h_source.html @@ -111,7 +111,7 @@
46 MPI_CHECK( MPI_Allreduce(_globalLoadPerCell, temp, _globalNumCells, MPI_FLOAT, MPI_SUM, MPI_COMM_WORLD) );
47 delete[] _globalLoadPerCell;
48 _globalLoadPerCell = temp;
-
49 //cout << "LocalLoad: " << _localLoad << endl;
+
49 //cout << "LocalLoad: " << _localLoad << std::endl;
50 }
51
57 double processPair(Molecule& particle1, Molecule& particle2, double distanceVector[3],
@@ -164,7 +164,7 @@
FullMolecule::r
double r(unsigned short d) const override
Definition: FullMolecule.h:51
KDDecomposition
KD tree based domain decomposition for better load balancing.
Definition: KDDecomposition.h:37
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
-
ParticleContainer::getBoundingBoxMin
virtual double getBoundingBoxMin(int dimension) const
returns one coordinate of the lower corner of the bounding box
Definition: ParticleContainer.cpp:29
+
ParticleContainer::getBoundingBoxMin
virtual double getBoundingBoxMin(int dimension) const
returns one coordinate of the lower corner of the bounding box
Definition: ParticleContainer.cpp:27
ParticlePairs2LoadCalcAdapter
used for guessing load
Definition: ParticlePairs2LoadCalcAdapter.h:10
ParticlePairs2LoadCalcAdapter::ParticlePairs2LoadCalcAdapter
ParticlePairs2LoadCalcAdapter()
Constructor.
Definition: ParticlePairs2LoadCalcAdapter.h:13
ParticlePairs2LoadCalcAdapter::~ParticlePairs2LoadCalcAdapter
~ParticlePairs2LoadCalcAdapter()
Destructor.
Definition: ParticlePairs2LoadCalcAdapter.h:35
@@ -176,7 +176,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticlePairs2PotForceAdapter_8h_source.html b/ParticlePairs2PotForceAdapter_8h_source.html index 535372d4f7..cee096a111 100644 --- a/ParticlePairs2PotForceAdapter_8h_source.html +++ b/ParticlePairs2PotForceAdapter_8h_source.html @@ -194,17 +194,17 @@
157 switch (pairType) {
158
159 double dummy1, dummy2, dummy3, dummy4[3], Virial3[3];
-
160
-
161 case MOLECULE_MOLECULE :
+
160
+
161 case MOLECULE_MOLECULE :
162// if ( _rdf != NULL ) _rdf->observeRDF(molecule1, molecule2, dd); // moved to RDFCellProcessor
163 PotForce(molecule1, molecule2, params, distanceVector, my_threadData._upot6LJ, my_threadData._upotXpoles, my_threadData._myRF, Virial3, calculateLJ );
164 my_threadData._virial += 2*(Virial3[0]+Virial3[1]+Virial3[2]);
165 return my_threadData._upot6LJ + my_threadData._upotXpoles;
-
166 case MOLECULE_HALOMOLECULE :
+
166 case MOLECULE_HALOMOLECULE :
167
168 PotForce(molecule1, molecule2, params, distanceVector, dummy1, dummy2, dummy3, dummy4, calculateLJ);
169 return 0.0;
-
170 case MOLECULE_MOLECULE_FLUID :
+
170 case MOLECULE_MOLECULE_FLUID :
171 dummy1 = 0.0; // 6*U_LJ
172 dummy2 = 0.0; // U_polarity
173 dummy3 = 0.0; // U_dipole_reaction_field
@@ -236,9 +236,9 @@
204#endif /*PARTICLEPAIRS2POTFORCEADAPTER_H_*/
Comp2Param
Definition: Comp2Param.h:15
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
-
Domain::setLocalVirial
void setLocalVirial(double Virial)
set the virial of the local process
Definition: Domain.cpp:117
-
Domain::setLocalUpot
void setLocalUpot(double Upot)
set the potential of the local process
Definition: Domain.cpp:113
-
Domain::getComp2Params
Comp2Param & getComp2Params()
get the parameter streams
Definition: Domain.cpp:151
+
Domain::setLocalVirial
void setLocalVirial(double Virial)
set the virial of the local process
Definition: Domain.cpp:115
+
Domain::setLocalUpot
void setLocalUpot(double Upot)
set the potential of the local process
Definition: Domain.cpp:111
+
Domain::getComp2Params
Comp2Param & getComp2Params()
get the parameter streams
Definition: Domain.cpp:149
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ParaStrm
Definition: ParaStrm.h:21
ParaStrm::reset_read
void reset_read()
reset reading "pointer" to the beginning of the stream
Definition: ParaStrm.h:51
@@ -249,12 +249,12 @@
ParticlePairs2PotForceAdapter::~ParticlePairs2PotForceAdapter
~ParticlePairs2PotForceAdapter()
Destructor.
Definition: ParticlePairs2PotForceAdapter.h:41
ParticlePairs2PotForceAdapter::ParticlePairs2PotForceAdapter
ParticlePairs2PotForceAdapter(Domain &domain)
Constructor.
Definition: ParticlePairs2PotForceAdapter.h:23
ParticlePairsHandler
interface for defining the action performed when processing a pair
Definition: ParticlePairsHandler.h:38
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
ParticlePairs2PotForceAdapter::PP2PFAThreadData
Definition: ParticlePairs2PotForceAdapter.h:102
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ParticlePairsHandler_8h_source.html b/ParticlePairsHandler_8h_source.html index 53467f813c..a430406296 100644 --- a/ParticlePairsHandler_8h_source.html +++ b/ParticlePairsHandler_8h_source.html @@ -110,7 +110,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PerCellGenerator_8h_source.html b/PerCellGenerator_8h_source.html index 060fa5f60b..2ac29b0443 100644 --- a/PerCellGenerator_8h_source.html +++ b/PerCellGenerator_8h_source.html @@ -103,7 +103,7 @@
62 double _initTemperature{0.};
63};
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -118,7 +118,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Permittivity_8h_source.html b/Permittivity_8h_source.html index 11da228b2a..768d70d9bf 100644 --- a/Permittivity_8h_source.html +++ b/Permittivity_8h_source.html @@ -103,9 +103,9 @@
31 void finish(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override{};
32 std::string getPluginName() override { return std::string("Permittivity"); }
33 static PluginBase* createInstance() { return new Permittivity();}
-
34
-
35
-
36
+
34
+
35
+
36
37private:
38 bool _readStartingStep; // Auxiliary bool variable to read the current time step during the first iteration of endStep
39 unsigned long _writeFrequency; // Write frequency for all profiles -> Length of recording frame before output
@@ -139,7 +139,7 @@
67};
68
69#endif /*SRC_PLUGINS_PERMITTIVITY_H_*/
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
Permittivity
Definition: Permittivity.h:19
@@ -154,7 +154,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Planar_8h_source.html b/Planar_8h_source.html index 5b5566ebfc..0fc014990b 100644 --- a/Planar_8h_source.html +++ b/Planar_8h_source.html @@ -119,7 +119,7 @@
68 v.resize(numElements);
69 }
70
-
71 void centerCenter(double sig,double eps,unsigned ci,unsigned cj,unsigned si, unsigned sj);
+
71 void centerCenter(double sig,double eps,unsigned ci,unsigned cj,unsigned si, unsigned sj);
72 void centerSite(double sig,double eps,unsigned ci,unsigned cj,unsigned si, unsigned sj);
73 void siteSite(double sig,double eps,unsigned ci,unsigned cj,unsigned si, unsigned sj);
74 void dipoleDipole(unsigned ci,unsigned cj,unsigned si,unsigned sj);
@@ -164,11 +164,11 @@
113 int sint;
114 double temp;
115 unsigned simstep;
-
116
+
116
117 ParticleContainer* _particleContainer;
118 Domain* _domain;
119 DomainDecompBase* _domainDecomposition;
-
120
+
120
121 // write control
122 uint64_t _nStartWritingProfiles;
123 uint64_t _nWriteFreqProfiles;
@@ -178,22 +178,22 @@
127
128#endif /*Planar_H_*/
ControlInstance
Definition: Region.h:29
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
LongRangeCorrection
Definition: LongRangeCorrection.h:12
ObserverBase
Definition: ObserverBase.h:13
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
Planar
Definition: Planar.h:24
-
Planar::init
void init() override
Read in XML configuration for Planar and all its included objects.
Definition: Planar.cpp:40
-
Simulation
Controls the simulation process.
Definition: Simulation.h:70
+
Planar::init
void init() override
Read in XML configuration for Planar and all its included objects.
Definition: Planar.cpp:38
+
Simulation
Controls the simulation process.
Definition: Simulation.h:72
SubjectBase
Definition: ObserverBase.h:20
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PluginBase_8h_source.html b/PluginBase_8h_source.html index df5fad8e78..096e2f3a11 100644 --- a/PluginBase_8h_source.html +++ b/PluginBase_8h_source.html @@ -140,7 +140,7 @@
186};
187
188#endif /* PLUGINBASE_H */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -161,7 +161,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PluginFactory_8h_source.html b/PluginFactory_8h_source.html index 359cf915c8..0cd3a7c068 100644 --- a/PluginFactory_8h_source.html +++ b/PluginFactory_8h_source.html @@ -147,7 +147,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PluginsSummary.html b/PluginsSummary.html index e553565897..d4174ed40b 100644 --- a/PluginsSummary.html +++ b/PluginsSummary.html @@ -192,7 +192,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PosNegComp_8h_source.html b/PosNegComp_8h_source.html index a32266f8ba..704313543d 100644 --- a/PosNegComp_8h_source.html +++ b/PosNegComp_8h_source.html @@ -138,9 +138,9 @@
80
81
82#endif /* POSNEGCOMP_H_ */
-
CavityEnsemble
Definition: CavityEnsemble.h:20
+
CavityEnsemble
Definition: CavityEnsemble.h:19
ChemicalPotential
Definition: ChemicalPotential.h:16
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -154,11 +154,11 @@
PosNegComp::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: PosNegComp.h:55
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-
pos
Definition: FakedOptFFT.h:23
+
pos
Definition: FakedOptFFT.h:21
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PositionCellProcessorRMM_8h_source.html b/PositionCellProcessorRMM_8h_source.html index 8d611ac130..e3048b860e 100644 --- a/PositionCellProcessorRMM_8h_source.html +++ b/PositionCellProcessorRMM_8h_source.html @@ -185,7 +185,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PovWriter_8h_source.html b/PovWriter_8h_source.html index af87cf5175..e475f04c23 100644 --- a/PovWriter_8h_source.html +++ b/PovWriter_8h_source.html @@ -107,22 +107,22 @@
51};
52
53#endif // SRC_IO_POVWRITER_H_
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
PovWriter
Definition: PovWriter.h:8
-
PovWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for PovWriter and all its included objects.
Definition: PovWriter.cpp:36
-
PovWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: PovWriter.cpp:64
+
PovWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for PovWriter and all its included objects.
Definition: PovWriter.cpp:32
+
PovWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: PovWriter.cpp:60
PovWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: PovWriter.h:41
-
PovWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: PovWriter.cpp:141
-
PovWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: PovWriter.cpp:60
+
PovWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: PovWriter.cpp:137
+
PovWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: PovWriter.cpp:56
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PressureGradient_8h_source.html b/PressureGradient_8h_source.html index 6804ad43b9..6536947278 100644 --- a/PressureGradient_8h_source.html +++ b/PressureGradient_8h_source.html @@ -149,17 +149,17 @@
119 ####### REMOVED PG FROM DOMAIN CONSTRUCTOR -> REMOVED UNIVERSALPG -> REMOVED FORWARD DECL IN .H AND INCLUDE IN .CPP
120
121 this->_universalPG = pg;
-
122 // after: checkpointfilestream << _epsilonRF << endl;
-
123 map<unsigned, unsigned> componentSets = this->_universalPG->getComponentSets();
-
124 for( map<unsigned, unsigned>::const_iterator uCSIDit = componentSets.begin();
+
122 // after: checkpointfilestream << _epsilonRF << std::endl;
+
123 std::map<unsigned, unsigned> componentSets = this->_universalPG->getComponentSets();
+
124 for( std::map<unsigned, unsigned>::const_iterator uCSIDit = componentSets.begin();
125 uCSIDit != componentSets.end();
126 uCSIDit++ )
127 {
128 if(uCSIDit->first > 100) continue;
129 checkpointfilestream << " S\t" << 1+uCSIDit->first << "\t" << uCSIDit->second << "\n";
130 }
-
131 map<unsigned, double> tau = this->_universalPG->getTau();
-
132 for( map<unsigned, double>::const_iterator gTit = tau.begin();
+
131 std::map<unsigned, double> tau = this->_universalPG->getTau();
+
132 for( std::map<unsigned, double>::const_iterator gTit = tau.begin();
133 gTit != tau.end();
134 gTit++ )
135 {
@@ -182,13 +182,13 @@
152 PressureGradient* _pressureGradient;
153 //after: _longRangeCorrection->calculateLongRange(); in #######
154 if (_pressureGradient->isAcceleratingUniformly()) {
-
155 global_log->info() << "Initialising uniform acceleration." << endl;
+
155 Log::global_log->info() << "Initialising uniform acceleration." << std::endl;
156 unsigned long uCAT = _pressureGradient->getUCAT();
-
157 global_log->info() << "uCAT: " << uCAT << " steps." << endl;
+
157 Log::global_log->info() << "uCAT: " << uCAT << " steps." << std::endl;
158 _pressureGradient->determineAdditionalAcceleration(
159 _domainDecomposition, _moleculeContainer, uCAT
160 * _integrator->getTimestepLength());
-
161 global_log->info() << "Uniform acceleration initialised." << endl;
+
161 Log::global_log->info() << "Uniform acceleration initialised." << std::endl;
162 }
163
164 // first in simulate()
@@ -198,18 +198,18 @@
168 // after: _domain->calculateThermostatDirectedVelocity(_moleculeContainer); in simulate()
169 if (_pressureGradient->isAcceleratingUniformly()) {
170 if (!(_simstep % uCAT)) {
-
171 global_log->debug() << "Determine the additional acceleration" << endl;
+
171 Log::global_log->debug() << "Determine the additional acceleration" << std::endl;
172 _pressureGradient->determineAdditionalAcceleration(
173 _domainDecomposition, _moleculeContainer, uCAT
174 * _integrator->getTimestepLength());
175 }
-
176 global_log->debug() << "Process the uniform acceleration" << endl;
+
176 Log::global_log->debug() << "Process the uniform acceleration" << std::endl;
177 _integrator->accelerateUniformly(_moleculeContainer, _domain);
178 _pressureGradient->adjustTau(this->_integrator->getTimestepLength());
179 }
180
181 // in initialize() before Domain()
-
182 global_log->info() << "Creating PressureGradient ... " << endl;
+
182 Log::global_log->info() << "Creating PressureGradient ... " << std::endl;
183 _pressureGradient = new PressureGradient(ownrank);
184
185 ####### REMOVED FUNCTION ONLY CALLED BY PG FROM INTEGRATOR, LEAPFROG AND LEAPFROGRMM
@@ -248,10 +248,10 @@
218 );
219
220 void Leapfrog::accelerateUniformly(ParticleContainer* molCont, Domain* domain) {
-
221 map<unsigned, double>* additionalAcceleration = domain->getPG()->getUAA();
-
222 vector<Component> comp = *(_simulation.getEnsemble()->getComponents());
-
223 vector<Component>::iterator compit;
-
224 map<unsigned, double> componentwiseVelocityDelta[3];
+
221 std::map<unsigned, double>* additionalAcceleration = domain->getPG()->getUAA();
+
222 std::vector<Component> comp = *(_simulation.getEnsemble()->getComponents());
+
223 std::vector<Component>::iterator compit;
+
224 std::map<unsigned, double> componentwiseVelocityDelta[3];
225 for (compit = comp.begin(); compit != comp.end(); compit++) {
226 unsigned cosetid = domain->getPG()->getComponentSet(compit->ID());
227 if (cosetid != 0)
@@ -277,9 +277,9 @@
247 }
248
249 void Leapfrog::accelerateInstantaneously(ParticleContainer* molCont, Domain* domain) {
-
250 vector<Component> comp = *(_simulation.getEnsemble()->getComponents());
-
251 vector<Component>::iterator compit;
-
252 map<unsigned, double> componentwiseVelocityDelta[3];
+
250 std::vector<Component> comp = *(_simulation.getEnsemble()->getComponents());
+
251 std::vector<Component>::iterator compit;
+
252 std::map<unsigned, double> componentwiseVelocityDelta[3];
253 for (compit = comp.begin(); compit != comp.end(); compit++) {
254 unsigned cosetid = domain->getPG()->getComponentSet(compit->ID());
255 if (cosetid != 0)
@@ -361,27 +361,27 @@
331 MDGenerator
332 - inhereting generators
333*/
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PressureGradient
DEPRECATED CLASS.
Definition: PressureGradient.h:19
PressureGradient::isAcceleratingUniformly
bool isAcceleratingUniformly()
are there any cosets?
Definition: PressureGradient.h:39
PressureGradient::setZetaFlow
void setZetaFlow(double zeta)
sets the zeta value for the flow controller
Definition: PressureGradient.h:32
PressureGradient::assignCoset
void assignCoset(unsigned int cid, unsigned int cosetid)
assigns a coset ID to a component (ID)
Definition: PressureGradient.h:24
-
PressureGradient::getDirectedVelocity
double getDirectedVelocity(unsigned int cosetid, unsigned short int d)
returns the directed velocity for a component set
Definition: PressureGradient.cpp:177
+
PressureGradient::getDirectedVelocity
double getDirectedVelocity(unsigned int cosetid, unsigned short int d)
returns the directed velocity for a component set
Definition: PressureGradient.cpp:175
PressureGradient::getComponentSets
std::map< unsigned int, unsigned int > getComponentSets()
returns the component -> set ID map
Definition: PressureGradient.h:75
PressureGradient::getUAA
std::map< unsigned int, double > * getUAA()
returns the acceleration map (necessary for passing data to the integrator)
Definition: PressureGradient.h:49
-
PressureGradient::specifyComponentSet
void specifyComponentSet(unsigned int cosetid, double v[3], double tau, double ainit[3], double timestep)
sets the information on the acceleration model for one coset
Definition: PressureGradient.cpp:26
+
PressureGradient::specifyComponentSet
void specifyComponentSet(unsigned int cosetid, double v[3], double tau, double ainit[3], double timestep)
sets the information on the acceleration model for one coset
Definition: PressureGradient.cpp:24
PressureGradient::getComponentSet
unsigned int getComponentSet(unsigned int cid)
returns the cosetid of a component (0 for unaccelerated components)
Definition: PressureGradient.h:51
-
PressureGradient::getUniformAcceleration
double getUniformAcceleration(unsigned int cosetid)
returns the absolute external acceleration for a component set
Definition: PressureGradient.cpp:184
-
PressureGradient::determineAdditionalAcceleration
void determineAdditionalAcceleration(DomainDecompBase *domainDecomp, ParticleContainer *molCont, double dtConstantAcc)
updates the intensity and direction of the uniform acceleration
Definition: PressureGradient.cpp:57
+
PressureGradient::getUniformAcceleration
double getUniformAcceleration(unsigned int cosetid)
returns the absolute external acceleration for a component set
Definition: PressureGradient.cpp:182
+
PressureGradient::determineAdditionalAcceleration
void determineAdditionalAcceleration(DomainDecompBase *domainDecomp, ParticleContainer *molCont, double dtConstantAcc)
updates the intensity and direction of the uniform acceleration
Definition: PressureGradient.cpp:55
PressureGradient::getCosetN
double getCosetN(unsigned int cosetid)
total number of particles that belong to the specified component set
Definition: PressureGradient.h:71
-
PressureGradient::getMissingVelocity
double getMissingVelocity(unsigned int cosetid, unsigned short int d)
returns the difference between the desired velocity and the global average velocity
Definition: PressureGradient.cpp:196
+
PressureGradient::getMissingVelocity
double getMissingVelocity(unsigned int cosetid, unsigned short int d)
returns the difference between the desired velocity and the global average velocity
Definition: PressureGradient.cpp:194
PressureGradient::setUCAT
void setUCAT(unsigned int uCAT)
sets the number of timesteps between two updates of the uniform acceleration
Definition: PressureGradient.h:28
PressureGradient::getUCAT
unsigned int getUCAT()
returns the number of timesteps between two updates of the uniform acceleration
Definition: PressureGradient.h:30
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PrintThreadPinningToCPU_8h_source.html b/PrintThreadPinningToCPU_8h_source.html index db57552b55..c76298d5d0 100644 --- a/PrintThreadPinningToCPU_8h_source.html +++ b/PrintThreadPinningToCPU_8h_source.html @@ -86,7 +86,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ProfileBase_8h_source.html b/ProfileBase_8h_source.html index 94ce97a014..243cfd6e61 100644 --- a/ProfileBase_8h_source.html +++ b/ProfileBase_8h_source.html @@ -107,7 +107,7 @@
59
65 virtual void collectRetrieve(DomainDecompBase* domainDecomp, unsigned long uID) = 0;
66
-
74 virtual void output(string prefix, long unsigned accumulatedDatasets) = 0;
+
74 virtual void output(std::string prefix, long unsigned accumulatedDatasets) = 0;
75
80 virtual void reset(unsigned long uID) = 0;
81
@@ -115,44 +115,45 @@
88
89protected:
90 // output file prefix
-
91 string _profilePrefix;
+
91 std::string _profilePrefix;
92
93 SamplingInformation _samplInfo;
94 long _accumulatedDatasets = -1; // Number of Datasets between output writes / profile resets // -1 if not set properly
95
-
101 virtual void writeDataEntry(unsigned long uID, ofstream& outfile) const = 0;
+
101 virtual void writeDataEntry(unsigned long uID, std::ofstream& outfile) const = 0;
102
-
107 void writeMatrix(ofstream& outfile);
+
107 void writeMatrix(std::ofstream& outfile);
108
-
109 void writeKartMatrix(ofstream& outfile);
+
109 void writeKartMatrix(std::ofstream& outfile);
110
115 // TODO: implement if needed
-
116 void writeSimpleMatrix(ofstream& outfile);
+
116 void writeSimpleMatrix(std::ofstream& outfile);
117
-
122 void writeCylMatrix(ofstream& outfile);
+
122 void writeCylMatrix(std::ofstream& outfile);
123};
124
125#endif //MARDYN_TRUNK_PROFILEBASE_H
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
-
ProfileBase::output
virtual void output(string prefix, long unsigned accumulatedDatasets)=0
Whatever is necessary to output for this profile.
-
ProfileBase::writeDataEntry
virtual void writeDataEntry(unsigned long uID, ofstream &outfile) const =0
Write Single Data Entry for Matrix with given uID to outfile.
+
ProfileBase::writeDataEntry
virtual void writeDataEntry(unsigned long uID, std::ofstream &outfile) const =0
Write Single Data Entry for Matrix with given uID to outfile.
+
ProfileBase::writeCylMatrix
void writeCylMatrix(std::ofstream &outfile)
cylinder Matrix output
Definition: ProfileBase.cpp:49
+
ProfileBase::writeMatrix
void writeMatrix(std::ofstream &outfile)
Matrix writing routine to avoid code duplication.
Definition: ProfileBase.cpp:8
ProfileBase::reset
virtual void reset(unsigned long uID)=0
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
+
ProfileBase::writeSimpleMatrix
void writeSimpleMatrix(std::ofstream &outfile)
STUB for simple Matrix output without headers.
Definition: ProfileBase.cpp:45
ProfileBase::collectAppend
virtual void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID)=0
Append all necessary communication per bin to the DomainDecomposition. Append from e....
-
ProfileBase::writeCylMatrix
void writeCylMatrix(ofstream &outfile)
cylinder Matrix output
Definition: ProfileBase.cpp:49
-
ProfileBase::writeMatrix
void writeMatrix(ofstream &outfile)
Matrix writing routine to avoid code duplication.
Definition: ProfileBase.cpp:8
+
ProfileBase::output
virtual void output(std::string prefix, long unsigned accumulatedDatasets)=0
Whatever is necessary to output for this profile.
ProfileBase::init
virtual void init(SamplingInformation &samplingInformation)
Init function is given a pointer to the KartesianProfile object handling this profile....
Definition: ProfileBase.h:44
ProfileBase::record
virtual void record(Molecule &mol, unsigned long uID)=0
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
ProfileBase::collectRetrieve
virtual void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID)=0
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
ProfileBase::comms
virtual int comms()=0
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
-
ProfileBase::writeSimpleMatrix
void writeSimpleMatrix(ofstream &outfile)
STUB for simple Matrix output without headers.
Definition: ProfileBase.cpp:45
SpatialProfile
SpatialProfile is a Plugin that is called like any other plugin derived from PluginBase....
Definition: SpatialProfile.h:73
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
SamplingInformation
Definition: ProfileBase.h:13
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PseudoParticleContainer_8h_source.html b/PseudoParticleContainer_8h_source.html index 587ee105cd..950d0ddf45 100644 --- a/PseudoParticleContainer_8h_source.html +++ b/PseudoParticleContainer_8h_source.html @@ -122,7 +122,7 @@
50 }
51 virtual ~PseudoParticleContainer() {
52 }
-
53
+
53
54 virtual void build(ParticleContainer* pc) = 0;
55 virtual void upwardPass(P2MCellProcessor * cp) = 0;
56 virtual void horizontalPass(VectorizedChargeP2PCellProcessor * cp) = 0;
@@ -161,7 +161,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/PseudoParticle_8h_source.html b/PseudoParticle_8h_source.html index 80d1a8c8e7..e6c5d37667 100644 --- a/PseudoParticle_8h_source.html +++ b/PseudoParticle_8h_source.html @@ -150,7 +150,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Quaternion_8h_source.html b/Quaternion_8h_source.html index 0b59e4d2bd..a215c73fea 100644 --- a/Quaternion_8h_source.html +++ b/Quaternion_8h_source.html @@ -165,7 +165,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/QuickschedTraversal_8h_source.html b/QuickschedTraversal_8h_source.html index fafe98f919..e8ccc14524 100644 --- a/QuickschedTraversal_8h_source.html +++ b/QuickschedTraversal_8h_source.html @@ -89,264 +89,263 @@
17#include "quicksched.h"
18#endif
19
-
20using Log::global_log;
-
21
-
22struct QuickschedTraversalData : CellPairTraversalData {
-
23 std::array<unsigned long, 3> taskBlockSize;
-
24};
-
25
-
26template<class CellTemplate>
-
27class QuickschedTraversal : public C08BasedTraversals<CellTemplate> {
-
28public:
-
29 QuickschedTraversal(std::vector<CellTemplate> &cells,
-
30 const std::array<unsigned long, 3> &dims,
-
31 const std::array<unsigned long, 3> &taskBlockSize);
-
32
-
33 ~QuickschedTraversal();
+
20
+
21struct QuickschedTraversalData : CellPairTraversalData {
+
22 std::array<unsigned long, 3> taskBlockSize;
+
23};
+
24
+
25template<class CellTemplate>
+
26class QuickschedTraversal : public C08BasedTraversals<CellTemplate> {
+
27public:
+
28 QuickschedTraversal(std::vector<CellTemplate> &cells,
+
29 const std::array<unsigned long, 3> &dims,
+
30 const std::array<unsigned long, 3> &taskBlockSize);
+
31
+
32 ~QuickschedTraversal();
+
33
34
-
35
-
36 virtual void rebuild(std::vector<CellTemplate> &cells,
-
37 const std::array<unsigned long, 3> &dims, double cellLength[3], double cutoff,
-
38 CellPairTraversalData *data);
-
39
-
40 void traverseCellPairs(CellProcessor &cellProcessor);
-
41
-
42 void traverseCellPairsOuter(CellProcessor &cellProcessor);
-
43
-
44 void traverseCellPairsInner(CellProcessor &cellProcessor, unsigned stage, unsigned stageCount);
-
45
-
46private:
-
47 enum taskType {
-
48 PackedAdjustable
-
49 };
-
50
-
51 void init();
-
52
-
53 static void runner(int type, void *data);
-
54
-
55 array<unsigned long, 3> _taskBlocksize;
-
56 CellProcessor *_contextCellProcessor;
-
57
-
58 struct qsched *_scheduler;
-
59 taskType _taskTypeSelector;
-
60};
-
61
-
62template<class CellTemplate>
-
63QuickschedTraversal<CellTemplate>::QuickschedTraversal(std::vector<CellTemplate> &cells,
-
64 const std::array<unsigned long, 3> &dims,
-
65 const std::array<unsigned long, 3> &taskBlockSize)
-
66#ifdef QUICKSCHED
-
67 : C08BasedTraversals<CellTemplate>(cells, dims),
-
68 _taskBlocksize(taskBlockSize),
-
69 _contextCellProcessor(nullptr),
-
70 _scheduler(new struct qsched),
-
71 _taskTypeSelector(PackedAdjustable) {
-
72 mardyn_assert((is_base_of<ParticleCellBase, CellTemplate>::value));
-
73 qsched_init(_scheduler, mardyn_get_max_threads(), qsched_flag_none);
-
74}
-
75
-
76#else
-
77 : C08BasedTraversals<CellTemplate>(cells, dims) {}
-
78#endif /* QUICKSCHED */
-
79
-
80template<class CellTemplate>
-
81void QuickschedTraversal<CellTemplate>::rebuild(std::vector<CellTemplate> &cells,
-
82 const std::array<unsigned long, 3> &dims, double cellLength[3], double cutoff,
-
83 CellPairTraversalData *data) {
-
84#ifdef QUICKSCHED
-
85 if (QuickschedTraversalData *qui_data = dynamic_cast<QuickschedTraversalData *>(data)) {
-
86 CellPairTraversals<CellTemplate>::rebuild(cells, dims, cellLength, cutoff, data);
-
87 qsched_reset(_scheduler);
-
88 _taskBlocksize = qui_data->taskBlockSize;
-
89 init();
-
90 } else {
-
91 global_log->error() << "QuickschedTraversal::rebuild was called with incompatible Traversal data!" << endl;
-
92 }
-
93#endif /* QUICKSCHED */
-
94}
-
95
-
96template<class CellTemplate>
-
97void QuickschedTraversal<CellTemplate>::init() {
-
98#ifdef QUICKSCHED
-
99 qsched_res_t resourceId;
-
100 qsched_task_t taskId;
-
101 unsigned long cellIndex;
-
102 // macro for easier access and to avoid aliasing
-
103//#define m_cells (*((vector<ParticleCellBase> *)(this->_cells)))
-
104// vector<ParticleCellBase> m_cells = *(dynamic_cast<vector<ParticleCellBase> *>(this->_cells));
-
105 vector<ParticleCell> m_cells = *((vector<ParticleCell> *)(this->_cells));
-
106
-
107 switch (_taskTypeSelector) {
-
108 case PackedAdjustable: {
-
109 // check that blocksize is within domain size
-
110 for (int i = 0; i < 3; ++i) {
-
111 if (_taskBlocksize[i] > this->_dims[i]) {
-
112 global_log->error() << "Blocksize is bigger than number of cells in dimension "
-
113 << (char) ('x' + i) << ". (" << _taskBlocksize[i] << " > "
-
114 << this->_dims[i] << ")" << std::endl;
-
115 Simulation::exit(1);
-
116 }
-
117 }
-
118
-
119 global_log->info() << "Generating resource and task ids" << std::endl;
-
120 for (unsigned long z = 0; z < this->_dims[2]; ++z) {
-
121 for (unsigned long y = 0; y < this->_dims[1]; ++y) {
-
122 for (unsigned long x = 0; x < this->_dims[0]; ++x) {
-
123 cellIndex = threeDimensionalMapping::threeToOneD(x, y, z, this->_dims);
-
124 resourceId = qsched_addres(_scheduler, qsched_owner_none, qsched_res_none);
-
125 m_cells[cellIndex].setResourceId(resourceId);
-
126 // only create tasks with offset blocksize-1.
-
127 // -1 because they need to overlap
-
128 // skip tasks for rear halo layer as they would only contain halo cells
-
129 if ((z % (_taskBlocksize[2] - 1) == 0
-
130 && y % (_taskBlocksize[1] - 1) == 0
-
131 && x % (_taskBlocksize[0] - 1) == 0)
-
132 &&
-
133 (x < this->_dims[0] - 1
-
134 && y < this->_dims[1] - 1
-
135 && z < this->_dims[2] - 1)) {
-
136 // also save the pointers as long
-
137 unsigned long payload[]{x, y, z, (unsigned long) this};
-
138 taskId = qsched_addtask(_scheduler,
-
139 PackedAdjustable,
-
140 task_flag_none,
-
141 payload,
-
142 sizeof(payload),
-
143 1);
-
144 m_cells[cellIndex].setTaskId(taskId);
-
145 }
-
146 } /* end for-x */
-
147 } /* end for-y*/
-
148 } /* end for-z */
-
149
-
150 // set dependencies
-
151 global_log->info() << "Setting task dependencies" << std::endl;
-
152 for (unsigned long z = 0; z < this->_dims[2] - 1; z += _taskBlocksize[2] - 1) {
-
153 for (unsigned long y = 0; y < this->_dims[1] - 1; y += _taskBlocksize[1] - 1) {
-
154 for (unsigned long x = 0; x < this->_dims[0] - 1; x += _taskBlocksize[0] - 1) {
-
155 cellIndex = threeDimensionalMapping::threeToOneD(x, y, z, this->_dims);
-
156
-
157 // create locks for all 8 corners of the block
-
158 for (unsigned long i = 0; i < _taskBlocksize[0]
-
159 && x + i < this->_dims[0]; i += _taskBlocksize[0] - 1) {
-
160 for (unsigned long j = 0; j < _taskBlocksize[1]
-
161 && y + j < this->_dims[1]; j += _taskBlocksize[1] - 1) {
-
162 for (unsigned long k = 0; k < _taskBlocksize[2]
-
163 && z + k < this->_dims[2]; k += _taskBlocksize[2] - 1) {
-
164 qsched_addlock(_scheduler,
-
165 m_cells[cellIndex].getTaskId(),
-
166 m_cells[threeDimensionalMapping::threeToOneD(x + i,
-
167 y + j,
-
168 z + k,
-
169 this->_dims)].getRescourceId());
-
170 }
-
171 }
-
172 }
-
173 } /* end for-x */
-
174 } /* end for-y*/
-
175 } /* end for-z */
-
176 break;
-
177 } /* end case PackedAdjustable */
-
178 default:
-
179 global_log->error() << "QuickschedHandler::init() received non existing task type!"
-
180 << std::endl;
-
181 }
-
182#endif // QUICKSCHED
-
183}
-
184
-
185template<class CellTemplate>
-
186QuickschedTraversal<CellTemplate>::~QuickschedTraversal() {
-
187#ifdef QUICKSCHED
-
188 qsched_free(_scheduler);
-
189 delete (_scheduler);
-
190#endif // QUICKSCHED
-
191}
-
192
-
193template<class CellTemplate>
-
194void QuickschedTraversal<CellTemplate>::runner(int type, void *data) {
-
195#ifdef QUICKSCHED
-
196
-
197 QuickschedTraversal *context = ((QuickschedTraversal **) data)[3];
-
198#ifdef PRINT_SCHEDULING_TIMINGS
-
199 struct VectorizedCellProcessor::Timings timing ;
-
200 if(_simulation.getSimStep() > 10){
-
201 timing.start = _rdtsc();
-
202 }
-
203#endif
-
204 switch (type) {
-
205 case PackedAdjustable: {
-
206 // TODO optimize calculation order (1. corners 2. edges 3. rest) and gradually release resources
-
207 unsigned long x = ((unsigned long *) data)[0];
-
208 unsigned long y = ((unsigned long *) data)[1];
-
209 unsigned long z = ((unsigned long *) data)[2];
-
210
-
211 // traverse over block
-
212 for (unsigned long i = 0; i < context->_taskBlocksize[0] - 1
-
213 && i < context->_dims[0] - 1; ++i) {
-
214 for (unsigned long j = 0; j < context->_taskBlocksize[1] - 1
-
215 && j < context->_dims[1] - 1; ++j) {
-
216 for (unsigned long k = 0; k < context->_taskBlocksize[2] - 1
-
217 && k < context->_dims[2] - 1; ++k) {
-
218
-
219 //process cell
-
220 unsigned long baseIndex = threeDimensionalMapping::threeToOneD(x + i,
-
221 y + j,
-
222 z + k,
-
223 context->_dims);
-
224 context->processBaseCell(
-
225 *(context->_contextCellProcessor),
-
226 baseIndex);
-
227 }
-
228 }
-
229 }
-
230 break;
-
231 } /* end case PackedAdjustable */
-
232 default:
-
233 global_log->error() << "Undefined Quicksched task type: " << type << std::endl;
-
234 }
-
235#ifdef PRINT_SCHEDULING_TIMINGS
-
236 if(_simulation.getSimStep() > 10){
-
237 timing.end = _rdtsc();
-
238 (dynamic_cast<VectorizedCellProcessor*>(_contextCellProcessor))->getThreadData()[omp_get_thread_num()]->_timings.push_back(timing);
-
239 }
-
240#endif
-
241#endif /* QUICKSCHED */
-
242}
-
243
-
244template<class CellTemplate>
-
245void QuickschedTraversal<CellTemplate>::traverseCellPairs(CellProcessor &cellProcessor) {
-
246 _contextCellProcessor = &cellProcessor;
-
247#ifdef QUICKSCHED
-
248 qsched_run(_scheduler, mardyn_get_max_threads(), runner);
-
249#endif /* QUICKSCHED */
-
250}
-
251
-
252template<class CellTemplate>
-
253void QuickschedTraversal<CellTemplate>::traverseCellPairsInner(CellProcessor &cellProcessor, unsigned stage,
-
254 unsigned stageCount) {
-
255 global_log->error() << "QuickschedTraversal::traverseCellPairsInner is not implemented!" << std::endl;
-
256}
-
257
-
258template<class CellTemplate>
-
259void QuickschedTraversal<CellTemplate>::traverseCellPairsOuter(CellProcessor &cellProcessor) {
-
260 global_log->error() << "QuickschedTraversal::traverseCellPairsOuter is not implemented!" << std::endl;
-
261}
-
262
-
263#endif //SRC_PARTICLECONTAINER_LINKEDCELLTRAVERSALS_QUICKSCHEDTRAVERSAL_H
+
35 virtual void rebuild(std::vector<CellTemplate> &cells,
+
36 const std::array<unsigned long, 3> &dims, double cellLength[3], double cutoff,
+
37 CellPairTraversalData *data);
+
38
+
39 void traverseCellPairs(CellProcessor &cellProcessor);
+
40
+
41 void traverseCellPairsOuter(CellProcessor &cellProcessor);
+
42
+
43 void traverseCellPairsInner(CellProcessor &cellProcessor, unsigned stage, unsigned stageCount);
+
44
+
45private:
+
46 enum taskType {
+
47 PackedAdjustable
+
48 };
+
49
+
50 void init();
+
51
+
52 static void runner(int type, void *data);
+
53
+
54 std::array<unsigned long, 3> _taskBlocksize;
+
55 CellProcessor *_contextCellProcessor;
+
56
+
57 struct qsched *_scheduler;
+
58 taskType _taskTypeSelector;
+
59};
+
60
+
61template<class CellTemplate>
+
62QuickschedTraversal<CellTemplate>::QuickschedTraversal(std::vector<CellTemplate> &cells,
+
63 const std::array<unsigned long, 3> &dims,
+
64 const std::array<unsigned long, 3> &taskBlockSize)
+
65#ifdef QUICKSCHED
+
66 : C08BasedTraversals<CellTemplate>(cells, dims),
+
67 _taskBlocksize(taskBlockSize),
+
68 _contextCellProcessor(nullptr),
+
69 _scheduler(new struct qsched),
+
70 _taskTypeSelector(PackedAdjustable) {
+
71 mardyn_assert((std::is_base_of<ParticleCellBase, CellTemplate>::value));
+
72 qsched_init(_scheduler, mardyn_get_max_threads(), qsched_flag_none);
+
73}
+
74
+
75#else
+
76 : C08BasedTraversals<CellTemplate>(cells, dims) {}
+
77#endif /* QUICKSCHED */
+
78
+
79template<class CellTemplate>
+
80void QuickschedTraversal<CellTemplate>::rebuild(std::vector<CellTemplate> &cells,
+
81 const std::array<unsigned long, 3> &dims, double cellLength[3], double cutoff,
+
82 CellPairTraversalData *data) {
+
83#ifdef QUICKSCHED
+
84 if (QuickschedTraversalData *qui_data = dynamic_cast<QuickschedTraversalData *>(data)) {
+
85 CellPairTraversals<CellTemplate>::rebuild(cells, dims, cellLength, cutoff, data);
+
86 qsched_reset(_scheduler);
+
87 _taskBlocksize = qui_data->taskBlockSize;
+
88 init();
+
89 } else {
+
90 Log::global_log->error() << "QuickschedTraversal::rebuild was called with incompatible Traversal data!" << std::endl;
+
91 }
+
92#endif /* QUICKSCHED */
+
93}
+
94
+
95template<class CellTemplate>
+
96void QuickschedTraversal<CellTemplate>::init() {
+
97#ifdef QUICKSCHED
+
98 qsched_res_t resourceId;
+
99 qsched_task_t taskId;
+
100 unsigned long cellIndex;
+
101 // macro for easier access and to avoid aliasing
+
102//#define m_cells (*((std::vector<ParticleCellBase> *)(this->_cells)))
+
103// std::vector<ParticleCellBase> m_cells = *(dynamic_cast<std::vector<ParticleCellBase> *>(this->_cells));
+
104 std::vector<ParticleCell> m_cells = *((std::vector<ParticleCell> *)(this->_cells));
+
105
+
106 switch (_taskTypeSelector) {
+
107 case PackedAdjustable: {
+
108 // check that blocksize is within domain size
+
109 for (int i = 0; i < 3; ++i) {
+
110 if (_taskBlocksize[i] > this->_dims[i]) {
+
111 Log::global_log->error() << "Blocksize is bigger than number of cells in dimension "
+
112 << (char) ('x' + i) << ". (" << _taskBlocksize[i] << " > "
+
113 << this->_dims[i] << ")" << std::endl;
+
114 Simulation::exit(1);
+
115 }
+
116 }
+
117
+
118 Log::global_log->info() << "Generating resource and task ids" << std::endl;
+
119 for (unsigned long z = 0; z < this->_dims[2]; ++z) {
+
120 for (unsigned long y = 0; y < this->_dims[1]; ++y) {
+
121 for (unsigned long x = 0; x < this->_dims[0]; ++x) {
+
122 cellIndex = threeDimensionalMapping::threeToOneD(x, y, z, this->_dims);
+
123 resourceId = qsched_addres(_scheduler, qsched_owner_none, qsched_res_none);
+
124 m_cells[cellIndex].setResourceId(resourceId);
+
125 // only create tasks with offset blocksize-1.
+
126 // -1 because they need to overlap
+
127 // skip tasks for rear halo layer as they would only contain halo cells
+
128 if ((z % (_taskBlocksize[2] - 1) == 0
+
129 && y % (_taskBlocksize[1] - 1) == 0
+
130 && x % (_taskBlocksize[0] - 1) == 0)
+
131 &&
+
132 (x < this->_dims[0] - 1
+
133 && y < this->_dims[1] - 1
+
134 && z < this->_dims[2] - 1)) {
+
135 // also save the pointers as long
+
136 unsigned long payload[]{x, y, z, (unsigned long) this};
+
137 taskId = qsched_addtask(_scheduler,
+
138 PackedAdjustable,
+
139 task_flag_none,
+
140 payload,
+
141 sizeof(payload),
+
142 1);
+
143 m_cells[cellIndex].setTaskId(taskId);
+
144 }
+
145 } /* end for-x */
+
146 } /* end for-y*/
+
147 } /* end for-z */
+
148
+
149 // set dependencies
+
150 Log::global_log->info() << "Setting task dependencies" << std::endl;
+
151 for (unsigned long z = 0; z < this->_dims[2] - 1; z += _taskBlocksize[2] - 1) {
+
152 for (unsigned long y = 0; y < this->_dims[1] - 1; y += _taskBlocksize[1] - 1) {
+
153 for (unsigned long x = 0; x < this->_dims[0] - 1; x += _taskBlocksize[0] - 1) {
+
154 cellIndex = threeDimensionalMapping::threeToOneD(x, y, z, this->_dims);
+
155
+
156 // create locks for all 8 corners of the block
+
157 for (unsigned long i = 0; i < _taskBlocksize[0]
+
158 && x + i < this->_dims[0]; i += _taskBlocksize[0] - 1) {
+
159 for (unsigned long j = 0; j < _taskBlocksize[1]
+
160 && y + j < this->_dims[1]; j += _taskBlocksize[1] - 1) {
+
161 for (unsigned long k = 0; k < _taskBlocksize[2]
+
162 && z + k < this->_dims[2]; k += _taskBlocksize[2] - 1) {
+
163 qsched_addlock(_scheduler,
+
164 m_cells[cellIndex].getTaskId(),
+
165 m_cells[threeDimensionalMapping::threeToOneD(x + i,
+
166 y + j,
+
167 z + k,
+
168 this->_dims)].getRescourceId());
+
169 }
+
170 }
+
171 }
+
172 } /* end for-x */
+
173 } /* end for-y*/
+
174 } /* end for-z */
+
175 break;
+
176 } /* end case PackedAdjustable */
+
177 default:
+
178 Log::global_log->error() << "QuickschedHandler::init() received non existing task type!"
+
179 << std::endl;
+
180 }
+
181#endif // QUICKSCHED
+
182}
+
183
+
184template<class CellTemplate>
+
185QuickschedTraversal<CellTemplate>::~QuickschedTraversal() {
+
186#ifdef QUICKSCHED
+
187 qsched_free(_scheduler);
+
188 delete (_scheduler);
+
189#endif // QUICKSCHED
+
190}
+
191
+
192template<class CellTemplate>
+
193void QuickschedTraversal<CellTemplate>::runner(int type, void *data) {
+
194#ifdef QUICKSCHED
+
195
+
196 QuickschedTraversal *context = ((QuickschedTraversal **) data)[3];
+
197#ifdef PRINT_SCHEDULING_TIMINGS
+
198 struct VectorizedCellProcessor::Timings timing ;
+
199 if(_simulation.getSimStep() > 10){
+
200 timing.start = _rdtsc();
+
201 }
+
202#endif
+
203 switch (type) {
+
204 case PackedAdjustable: {
+
205 // TODO optimize calculation order (1. corners 2. edges 3. rest) and gradually release resources
+
206 unsigned long x = ((unsigned long *) data)[0];
+
207 unsigned long y = ((unsigned long *) data)[1];
+
208 unsigned long z = ((unsigned long *) data)[2];
+
209
+
210 // traverse over block
+
211 for (unsigned long i = 0; i < context->_taskBlocksize[0] - 1
+
212 && i < context->_dims[0] - 1; ++i) {
+
213 for (unsigned long j = 0; j < context->_taskBlocksize[1] - 1
+
214 && j < context->_dims[1] - 1; ++j) {
+
215 for (unsigned long k = 0; k < context->_taskBlocksize[2] - 1
+
216 && k < context->_dims[2] - 1; ++k) {
+
217
+
218 //process cell
+
219 unsigned long baseIndex = threeDimensionalMapping::threeToOneD(x + i,
+
220 y + j,
+
221 z + k,
+
222 context->_dims);
+
223 context->processBaseCell(
+
224 *(context->_contextCellProcessor),
+
225 baseIndex);
+
226 }
+
227 }
+
228 }
+
229 break;
+
230 } /* end case PackedAdjustable */
+
231 default:
+
232 Log::global_log->error() << "Undefined Quicksched task type: " << type << std::endl;
+
233 }
+
234#ifdef PRINT_SCHEDULING_TIMINGS
+
235 if(_simulation.getSimStep() > 10){
+
236 timing.end = _rdtsc();
+
237 (dynamic_cast<VectorizedCellProcessor*>(_contextCellProcessor))->getThreadData()[omp_get_thread_num()]->_timings.push_back(timing);
+
238 }
+
239#endif
+
240#endif /* QUICKSCHED */
+
241}
+
242
+
243template<class CellTemplate>
+
244void QuickschedTraversal<CellTemplate>::traverseCellPairs(CellProcessor &cellProcessor) {
+
245 _contextCellProcessor = &cellProcessor;
+
246#ifdef QUICKSCHED
+
247 qsched_run(_scheduler, mardyn_get_max_threads(), runner);
+
248#endif /* QUICKSCHED */
+
249}
+
250
+
251template<class CellTemplate>
+
252void QuickschedTraversal<CellTemplate>::traverseCellPairsInner(CellProcessor &cellProcessor, unsigned stage,
+
253 unsigned stageCount) {
+
254 Log::global_log->error() << "QuickschedTraversal::traverseCellPairsInner is not implemented!" << std::endl;
+
255}
+
256
+
257template<class CellTemplate>
+
258void QuickschedTraversal<CellTemplate>::traverseCellPairsOuter(CellProcessor &cellProcessor) {
+
259 Log::global_log->error() << "QuickschedTraversal::traverseCellPairsOuter is not implemented!" << std::endl;
+
260}
+
261
+
262#endif //SRC_PARTICLECONTAINER_LINKEDCELLTRAVERSALS_QUICKSCHEDTRAVERSAL_H
C08BasedTraversals
Definition: C08BasedTraversals.h:17
CellPairTraversals::rebuild
virtual void rebuild(std::vector< CellTemplate > &cells, const std::array< unsigned long, 3 > &dims, double cellLength[3], double cutoff, CellPairTraversalData *data)
Definition: CellPairTraversals.h:32
CellProcessor
Definition: CellProcessor.h:29
-
QuickschedTraversal
Definition: QuickschedTraversal.h:27
-
QuickschedTraversal::rebuild
virtual void rebuild(std::vector< CellTemplate > &cells, const std::array< unsigned long, 3 > &dims, double cellLength[3], double cutoff, CellPairTraversalData *data)
Definition: QuickschedTraversal.h:81
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
QuickschedTraversal
Definition: QuickschedTraversal.h:26
+
QuickschedTraversal::rebuild
virtual void rebuild(std::vector< CellTemplate > &cells, const std::array< unsigned long, 3 > &dims, double cellLength[3], double cutoff, CellPairTraversalData *data)
Definition: QuickschedTraversal.h:80
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
VectorizedCellProcessor
Vectorized calculation of the force.
Definition: VectorizedCellProcessor.h:29
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
CellPairTraversalData
Definition: CellPairTraversals.h:16
-
QuickschedTraversalData
Definition: QuickschedTraversal.h:22
+
QuickschedTraversalData
Definition: QuickschedTraversal.h:21
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RDFCellProcessor_8h_source.html b/RDFCellProcessor_8h_source.html index 18aa6429cd..9af46f7fc7 100644 --- a/RDFCellProcessor_8h_source.html +++ b/RDFCellProcessor_8h_source.html @@ -122,14 +122,14 @@
RDFCellProcessor::initTraversal
void initTraversal()
Definition: RDFCellProcessor.h:30
RDFCellProcessor::postprocessCell
void postprocessCell(ParticleCell &)
Definition: RDFCellProcessor.h:40
RDFCellProcessor::preprocessCell
void preprocessCell(ParticleCell &)
Definition: RDFCellProcessor.h:32
-
RDFCellProcessor::processCellPair
void processCellPair(ParticleCell &cell1, ParticleCell &cell2, bool sumAll=false)
Definition: RDFCellProcessor.cpp:49
-
RDFCellProcessor::processCell
void processCell(ParticleCell &cell)
Definition: RDFCellProcessor.cpp:18
+
RDFCellProcessor::processCellPair
void processCellPair(ParticleCell &cell1, ParticleCell &cell2, bool sumAll=false)
Definition: RDFCellProcessor.cpp:47
+
RDFCellProcessor::processCell
void processCell(ParticleCell &cell)
Definition: RDFCellProcessor.cpp:16
RDFCellProcessor::endTraversal
void endTraversal()
Definition: RDFCellProcessor.h:42
RDF
This class calculates the Radial Distribution Function (RDF).
Definition: RDF.h:37
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RDF_8h_source.html b/RDF_8h_source.html index b4686a087f..408638709d 100644 --- a/RDF_8h_source.html +++ b/RDF_8h_source.html @@ -119,9 +119,9 @@
87 }
88
91 void accumulateNumberOfMolecules(std::vector<Component>& components);
-
92
+
92
93 void observeARDFMolecule(double dd, double cosPhi, double cosPhiReverse, unsigned cid1, unsigned cid2) {
-
94
+
94
95 if(dd > _maxDistanceSquare) { return; }
96 size_t distanceBinID = floor( sqrt(dd) / binwidth() );
97 size_t angularBinID = floor( (-cosPhi + 1.)/ angularbinwidth() );
@@ -217,13 +217,13 @@
196 void writeToFile(const Domain* domain, const std::string& filename, unsigned int i, unsigned int j) const;
197 void writeToFileARDF(const Domain* domain, const std::string& filename, unsigned int i, unsigned int j) const;
200 double _intervalLength;
-
201
+
201
204 double _angularIntervalLength;
205
208 unsigned long _bins;
-
209
+
209
212 unsigned long _angularBins {1};
-
213
+
213
216 unsigned long _ARDFBins;
217
219 unsigned int _numberOfComponents;
@@ -246,7 +246,7 @@
252 CommVar<std::vector<std::vector<std::vector<unsigned long>>>> _ARDFdistribution;
254 std::vector<std::vector<std::vector<unsigned long>>> _globalAccumulatedDistribution;
255 std::vector<std::vector<std::vector<unsigned long>>> _globalAccumulatedARDFDistribution;
-
256
+
256
257 bool _doCollectSiteRDF;
258 bool _doARDF;
259 // vector indices:
@@ -271,7 +271,7 @@
278#endif /* RDF_H */
CommVar
Definition: CommVar.h:17
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
FullMolecule::numSites
unsigned int numSites() const override
Definition: FullMolecule.h:136
@@ -279,25 +279,25 @@
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
RDFCellProcessor
Definition: RDFCellProcessor.h:16
RDF
This class calculates the Radial Distribution Function (RDF).
Definition: RDF.h:37
-
RDF::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomposition, Domain *domain, unsigned long simStep)
plot all the statistics calculated to one or several files
Definition: RDF.cpp:343
+
RDF::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomposition, Domain *domain, unsigned long simStep)
plot all the statistics calculated to one or several files
Definition: RDF.cpp:341
RDF::setOutputTimestep
void setOutputTimestep(unsigned int timestep)
Definition: RDF.h:73
RDF::observeRDFMolecule
void observeRDFMolecule(double dd, unsigned i, unsigned j)
Definition: RDF.h:138
-
RDF::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for RDFWriter.
Definition: RDF.cpp:154
+
RDF::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for RDFWriter.
Definition: RDF.cpp:152
RDF::observeRDFSite
void observeRDFSite(double dd, unsigned i, unsigned j, unsigned m, unsigned n)
Definition: RDF.h:152
-
RDF::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: RDF.cpp:185
-
RDF::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: RDF.cpp:573
-
RDF::accumulateNumberOfMolecules
void accumulateNumberOfMolecules(std::vector< Component > &components)
Definition: RDF.cpp:195
-
RDF::reset
void reset()
reset all values to 0, except the accumulated ones.
Definition: RDF.cpp:309
+
RDF::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: RDF.cpp:183
+
RDF::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep)
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: RDF.cpp:571
+
RDF::accumulateNumberOfMolecules
void accumulateNumberOfMolecules(std::vector< Component > &components)
Definition: RDF.cpp:193
+
RDF::reset
void reset()
reset all values to 0, except the accumulated ones.
Definition: RDF.cpp:307
RDF::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: RDF.h:66
RDF::tickRDF
void tickRDF()
Definition: RDF.h:85
RDF::setOutputPrefix
void setOutputPrefix(std::string prefix)
Definition: RDF.h:77
-
RDF::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: RDF.cpp:181
+
RDF::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: RDF.cpp:179
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Random_8h_source.html b/Random_8h_source.html index 8e886df4aa..1e55fcce62 100644 --- a/Random_8h_source.html +++ b/Random_8h_source.html @@ -107,7 +107,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RealAccumVecSPDP_8h_source.html b/RealAccumVecSPDP_8h_source.html index efd8f68523..14db2bbfaf 100644 --- a/RealAccumVecSPDP_8h_source.html +++ b/RealAccumVecSPDP_8h_source.html @@ -405,7 +405,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RealVecDouble_8h_source.html b/RealVecDouble_8h_source.html index 6a0bb1a720..4a2d558b3e 100644 --- a/RealVecDouble_8h_source.html +++ b/RealVecDouble_8h_source.html @@ -612,7 +612,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RealVecFloat_8h_source.html b/RealVecFloat_8h_source.html index 140a1e0928..179a184f2a 100644 --- a/RealVecFloat_8h_source.html +++ b/RealVecFloat_8h_source.html @@ -624,7 +624,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RealVec_8h_source.html b/RealVec_8h_source.html index e27a4811aa..8aa6611b32 100644 --- a/RealVec_8h_source.html +++ b/RealVec_8h_source.html @@ -108,7 +108,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RegionParticleIterator_8h_source.html b/RegionParticleIterator_8h_source.html index bc54e23552..e8cfe809f1 100644 --- a/RegionParticleIterator_8h_source.html +++ b/RegionParticleIterator_8h_source.html @@ -252,7 +252,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RegionSampling_8h_source.html b/RegionSampling_8h_source.html index 9c1f63b45e..f1ead03fb9 100644 --- a/RegionSampling_8h_source.html +++ b/RegionSampling_8h_source.html @@ -384,7 +384,7 @@
312 // output file
313 std::string _strFilePrefixFieldYR;
314 uint8_t _nFileTypeFieldYR;
-
315
+
315
316 bool _boolSingleComp;
317};
318
@@ -431,7 +431,7 @@
426
427private:
428 std::vector<SampleRegion*> _vecSampleRegions;
-
429
+
429
430 unsigned long _initSamplingProfiles;
431 unsigned long _writeFrequencyProfiles;
432 unsigned long _initSamplingVDF;
@@ -441,19 +441,19 @@
436#endif /* REGIONSAMPLING_H_ */
ControlInstance
Definition: Region.h:29
CuboidRegionObs
Definition: Region.h:109
-
DistControl
Definition: DistControl.h:48
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DistControl
Definition: DistControl.h:47
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
RegionSampling
Definition: RegionSampling.h:321
RegionSampling::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: RegionSampling.h:413
-
RegionSampling::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DistControl and all its included objects.
Definition: RegionSampling.cpp:2040
-
RegionSampling::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: RegionSampling.cpp:2096
+
RegionSampling::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DistControl and all its included objects.
Definition: RegionSampling.cpp:2039
+
RegionSampling::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: RegionSampling.cpp:2095
RegionSampling::afterForces
void afterForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
Method afterForces will be called after forcefields have been applied no sitewise Forces can be appli...
Definition: RegionSampling.h:400
RegionSampling::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: RegionSampling.h:410
-
RegionSampling::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: RegionSampling.cpp:2080
+
RegionSampling::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: RegionSampling.cpp:2079
SampleRegion
Definition: RegionSampling.h:52
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
@@ -461,7 +461,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Region_8h_source.html b/Region_8h_source.html index 186d2e9bca..cb53e70aa5 100644 --- a/Region_8h_source.html +++ b/Region_8h_source.html @@ -202,7 +202,7 @@
ControlInstance
Definition: Region.h:29
CuboidRegionObs
Definition: Region.h:109
CuboidRegion
Definition: Region.h:60
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ObserverBase
Definition: ObserverBase.h:13
Region
Definition: Region.h:37
@@ -211,7 +211,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ReplicaFiller_8h_source.html b/ReplicaFiller_8h_source.html index 476c4e2647..8b8997dde8 100644 --- a/ReplicaFiller_8h_source.html +++ b/ReplicaFiller_8h_source.html @@ -131,15 +131,15 @@
ObjectFillerBase
Definition: ObjectFillerBase.h:11
Object
Definition: Objects.h:25
ReplicaFiller
Definition: ReplicaFiller.h:24
-
ReplicaFiller::init
void init()
Definition: ReplicaFiller.cpp:194
-
ReplicaFiller::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ReplicaFiller and all its included objects.
Definition: ReplicaFiller.cpp:145
-
ReplicaFiller::getMolecule
int getMolecule(Molecule *molecule)
Definition: ReplicaFiller.cpp:225
+
ReplicaFiller::init
void init()
Definition: ReplicaFiller.cpp:192
+
ReplicaFiller::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ReplicaFiller and all its included objects.
Definition: ReplicaFiller.cpp:143
+
ReplicaFiller::getMolecule
int getMolecule(Molecule *molecule)
Definition: ReplicaFiller.cpp:223
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ReplicaGenerator_8h_source.html b/ReplicaGenerator_8h_source.html index 7ec1948572..a92904f6be 100644 --- a/ReplicaGenerator_8h_source.html +++ b/ReplicaGenerator_8h_source.html @@ -82,200 +82,199 @@
10#include <iostream>
11#include <cstdint>
12
-
13using namespace std;
-
14
-
15enum SystemTypes : uint8_t {
-
16 ST_UNKNOWN = 0,
-
17 ST_HOMOGENEOUS = 1,
-
18 ST_HETEROGENEOUS_VAPOR_LIQUID_VAPOR = 2,
-
19 ST_HETEROGENEOUS_LIQUID_VAPOR = 3,
-
20};
-
21
-
22struct SubDomain {
-
23 std::string strFilePathHeader;
-
24 std::string strFilePathData;
-
25 std::vector<Molecule> vecParticles;
-
26 uint64_t numParticles;
-
27 std::array<double, 3> arrBoxLength;
-
28 double dVolume;
-
29 double dDensity;
-
30};
-
31
-
36class DomainDecompBase;
-
37
-
38class MoleculeDataReader;
-
39
-
40class ReplicaGenerator : public InputBase {
-
41public:
-
42 ReplicaGenerator();
-
43
-
44 ~ReplicaGenerator();
-
45
-
46 void readPhaseSpaceHeader(Domain* /*domain*/, double /*timestep*/) {}
-
47
-
48 unsigned long readPhaseSpace(ParticleContainer* particleContainer, Domain* domain, DomainDecompBase* domainDecomp);
-
49
-
58 void readXML(XMLfileUnits& xmlconfig);
-
59
-
60private:
-
61 void init();
-
62
-
63 void readReplicaPhaseSpaceHeader(SubDomain& subDomain);
-
64
-
65 void readReplicaPhaseSpaceData(SubDomain& subDomain, DomainDecompBase* domainDecomp);
-
66
-
67private:
-
68 std::vector<SubDomain> _vecSubDomains;
-
69 uint64_t _numParticlesTotal;
-
70 uint32_t _numBlocksXZ;
-
71 uint32_t _numBlocksLiqY;
-
72 uint32_t _numBlocksVapY;
-
73 uint32_t _nIndexLiqBeginY;
-
74 uint32_t _nIndexLiqEndY;
-
75 uint32_t _nMoleculeFormat;
-
76 MoleculeDataReader* _moleculeDataReader;
-
77 double _dMoleculeDiameter;
-
78 double _fspY[6]; // free space positions
-
79 uint8_t _nSystemType;
-
80 std::vector<uint32_t> _vecChangeCompIDsVap;
-
81 std::vector<uint32_t> _vecChangeCompIDsLiq;
-
82};
-
83
-
84class MoleculeDataReader {
-
85protected:
-
86 MoleculeDataReader() {}
-
87
-
88public:
-
89 virtual ~MoleculeDataReader() {};
-
90
-
91 virtual void read(std::ifstream& ifs, Molecule& mol, std::vector<Component>& components) = 0;
-
92};
-
93
-
94class MoleculeDataReaderICRVQD : public MoleculeDataReader {
-
95public:
-
96 MoleculeDataReaderICRVQD() {}
-
97
-
98public:
-
99 virtual ~MoleculeDataReaderICRVQD() {};
-
100
-
101 virtual void read(std::ifstream& ifs, Molecule& mol, std::vector<Component>& components) {
-
102 double rx, ry, rz, vx, vy, vz, q0, q1, q2, q3, Dx, Dy, Dz;
-
103 rx = ry = rz = vx = vy = vz = q0 = q1 = q2 = q3 = Dx = Dy = Dz = 0.;
-
104 uint64_t id = 0;
-
105 uint32_t cid = 0;
-
106
-
107 ifs.read(reinterpret_cast<char*> (&id), 8);
-
108 ifs.read(reinterpret_cast<char*> (&cid), 4);
-
109 ifs.read(reinterpret_cast<char*> (&rx), 8);
-
110 ifs.read(reinterpret_cast<char*> (&ry), 8);
-
111 ifs.read(reinterpret_cast<char*> (&rz), 8);
-
112 ifs.read(reinterpret_cast<char*> (&vx), 8);
-
113 ifs.read(reinterpret_cast<char*> (&vy), 8);
-
114 ifs.read(reinterpret_cast<char*> (&vz), 8);
-
115 ifs.read(reinterpret_cast<char*> (&q0), 8);
-
116 ifs.read(reinterpret_cast<char*> (&q1), 8);
-
117 ifs.read(reinterpret_cast<char*> (&q2), 8);
-
118 ifs.read(reinterpret_cast<char*> (&q3), 8);
-
119 ifs.read(reinterpret_cast<char*> (&Dx), 8);
-
120 ifs.read(reinterpret_cast<char*> (&Dy), 8);
-
121 ifs.read(reinterpret_cast<char*> (&Dz), 8);
-
122
-
123 Component* component = &components.at(cid - 1);
-
124 Molecule tmp(id, component,
-
125 rx, ry, rz,
-
126 vx, vy, vz,
-
127 q0, q1, q2, q3,
-
128 Dx, Dy, Dz);
-
129 mol = tmp;
-
130 }
-
131};
-
132
-
133class MoleculeDataReaderICRV : public MoleculeDataReader {
-
134public:
-
135 MoleculeDataReaderICRV() {}
-
136
-
137public:
-
138 virtual ~MoleculeDataReaderICRV() {};
-
139
-
140 virtual void read(std::ifstream& ifs, Molecule& mol, std::vector<Component>& components) {
-
141 double rx, ry, rz, vx, vy, vz, q0, q1, q2, q3, Dx, Dy, Dz;
-
142 rx = ry = rz = vx = vy = vz = q0 = q1 = q2 = q3 = Dx = Dy = Dz = 0.;
-
143 uint64_t id = 0;
-
144 uint32_t cid = 0;
-
145
-
146 ifs.read(reinterpret_cast<char*> (&id), 8);
-
147 ifs.read(reinterpret_cast<char*> (&cid), 4);
-
148 ifs.read(reinterpret_cast<char*> (&rx), 8);
-
149 ifs.read(reinterpret_cast<char*> (&ry), 8);
-
150 ifs.read(reinterpret_cast<char*> (&rz), 8);
-
151 ifs.read(reinterpret_cast<char*> (&vx), 8);
-
152 ifs.read(reinterpret_cast<char*> (&vy), 8);
-
153 ifs.read(reinterpret_cast<char*> (&vz), 8);
-
154
-
155 Component* component = &components.at(cid - 1);
-
156 Molecule tmp(id, component,
-
157 rx, ry, rz,
-
158 vx, vy, vz,
-
159 q0, q1, q2, q3,
-
160 Dx, Dy, Dz);
-
161 mol = tmp;
-
162 }
-
163};
-
164
-
165class MoleculeDataReaderIRV : public MoleculeDataReader {
-
166public:
-
167 MoleculeDataReaderIRV() {}
-
168
-
169public:
-
170 virtual ~MoleculeDataReaderIRV() {};
-
171
-
172 virtual void read(std::ifstream& ifs, Molecule& mol, std::vector<Component>& components) {
-
173 double rx, ry, rz, vx, vy, vz, q0, q1, q2, q3, Dx, Dy, Dz;
-
174 rx = ry = rz = vx = vy = vz = q0 = q1 = q2 = q3 = Dx = Dy = Dz = 0.;
-
175 uint64_t id = 0;
-
176 uint32_t cid = 0;
-
177
-
178 ifs.read(reinterpret_cast<char*> (&id), 8);
-
179 ifs.read(reinterpret_cast<char*> (&rx), 8);
-
180 ifs.read(reinterpret_cast<char*> (&ry), 8);
-
181 ifs.read(reinterpret_cast<char*> (&rz), 8);
-
182 ifs.read(reinterpret_cast<char*> (&vx), 8);
-
183 ifs.read(reinterpret_cast<char*> (&vy), 8);
-
184 ifs.read(reinterpret_cast<char*> (&vz), 8);
-
185
-
186 Component* component = &components.at(0);
-
187 Molecule tmp(id, component,
-
188 rx, ry, rz,
-
189 vx, vy, vz,
-
190 q0, q1, q2, q3,
-
191 Dx, Dy, Dz);
-
192 mol = tmp;
-
193 }
-
194};
-
195
-
196#endif /* REPLICA_GENERATOR_H */
-
197
+
13
+
14enum SystemTypes : uint8_t {
+
15 ST_UNKNOWN = 0,
+
16 ST_HOMOGENEOUS = 1,
+
17 ST_HETEROGENEOUS_VAPOR_LIQUID_VAPOR = 2,
+
18 ST_HETEROGENEOUS_LIQUID_VAPOR = 3,
+
19};
+
20
+
21struct SubDomain {
+
22 std::string strFilePathHeader;
+
23 std::string strFilePathData;
+
24 std::vector<Molecule> vecParticles;
+
25 uint64_t numParticles;
+
26 std::array<double, 3> arrBoxLength;
+
27 double dVolume;
+
28 double dDensity;
+
29};
+
30
+
35class DomainDecompBase;
+
36
+
37class MoleculeDataReader;
+
38
+
39class ReplicaGenerator : public InputBase {
+
40public:
+
41 ReplicaGenerator();
+
42
+
43 ~ReplicaGenerator();
+
44
+
45 void readPhaseSpaceHeader(Domain* /*domain*/, double /*timestep*/) {}
+
46
+
47 unsigned long readPhaseSpace(ParticleContainer* particleContainer, Domain* domain, DomainDecompBase* domainDecomp);
+
48
+
57 void readXML(XMLfileUnits& xmlconfig);
+
58
+
59private:
+
60 void init();
+
61
+
62 void readReplicaPhaseSpaceHeader(SubDomain& subDomain);
+
63
+
64 void readReplicaPhaseSpaceData(SubDomain& subDomain, DomainDecompBase* domainDecomp);
+
65
+
66private:
+
67 std::vector<SubDomain> _vecSubDomains;
+
68 uint64_t _numParticlesTotal;
+
69 uint32_t _numBlocksXZ;
+
70 uint32_t _numBlocksLiqY;
+
71 uint32_t _numBlocksVapY;
+
72 uint32_t _nIndexLiqBeginY;
+
73 uint32_t _nIndexLiqEndY;
+
74 uint32_t _nMoleculeFormat;
+
75 MoleculeDataReader* _moleculeDataReader;
+
76 double _dMoleculeDiameter;
+
77 double _fspY[6]; // free space positions
+
78 uint8_t _nSystemType;
+
79 std::vector<uint32_t> _vecChangeCompIDsVap;
+
80 std::vector<uint32_t> _vecChangeCompIDsLiq;
+
81};
+
82
+
83class MoleculeDataReader {
+
84protected:
+
85 MoleculeDataReader() {}
+
86
+
87public:
+
88 virtual ~MoleculeDataReader() {};
+
89
+
90 virtual void read(std::ifstream& ifs, Molecule& mol, std::vector<Component>& components) = 0;
+
91};
+
92
+
93class MoleculeDataReaderICRVQD : public MoleculeDataReader {
+
94public:
+
95 MoleculeDataReaderICRVQD() {}
+
96
+
97public:
+
98 virtual ~MoleculeDataReaderICRVQD() {};
+
99
+
100 virtual void read(std::ifstream& ifs, Molecule& mol, std::vector<Component>& components) {
+
101 double rx, ry, rz, vx, vy, vz, q0, q1, q2, q3, Dx, Dy, Dz;
+
102 rx = ry = rz = vx = vy = vz = q0 = q1 = q2 = q3 = Dx = Dy = Dz = 0.;
+
103 uint64_t id = 0;
+
104 uint32_t cid = 0;
+
105
+
106 ifs.read(reinterpret_cast<char*> (&id), 8);
+
107 ifs.read(reinterpret_cast<char*> (&cid), 4);
+
108 ifs.read(reinterpret_cast<char*> (&rx), 8);
+
109 ifs.read(reinterpret_cast<char*> (&ry), 8);
+
110 ifs.read(reinterpret_cast<char*> (&rz), 8);
+
111 ifs.read(reinterpret_cast<char*> (&vx), 8);
+
112 ifs.read(reinterpret_cast<char*> (&vy), 8);
+
113 ifs.read(reinterpret_cast<char*> (&vz), 8);
+
114 ifs.read(reinterpret_cast<char*> (&q0), 8);
+
115 ifs.read(reinterpret_cast<char*> (&q1), 8);
+
116 ifs.read(reinterpret_cast<char*> (&q2), 8);
+
117 ifs.read(reinterpret_cast<char*> (&q3), 8);
+
118 ifs.read(reinterpret_cast<char*> (&Dx), 8);
+
119 ifs.read(reinterpret_cast<char*> (&Dy), 8);
+
120 ifs.read(reinterpret_cast<char*> (&Dz), 8);
+
121
+
122 Component* component = &components.at(cid - 1);
+
123 Molecule tmp(id, component,
+
124 rx, ry, rz,
+
125 vx, vy, vz,
+
126 q0, q1, q2, q3,
+
127 Dx, Dy, Dz);
+
128 mol = tmp;
+
129 }
+
130};
+
131
+
132class MoleculeDataReaderICRV : public MoleculeDataReader {
+
133public:
+
134 MoleculeDataReaderICRV() {}
+
135
+
136public:
+
137 virtual ~MoleculeDataReaderICRV() {};
+
138
+
139 virtual void read(std::ifstream& ifs, Molecule& mol, std::vector<Component>& components) {
+
140 double rx, ry, rz, vx, vy, vz, q0, q1, q2, q3, Dx, Dy, Dz;
+
141 rx = ry = rz = vx = vy = vz = q0 = q1 = q2 = q3 = Dx = Dy = Dz = 0.;
+
142 uint64_t id = 0;
+
143 uint32_t cid = 0;
+
144
+
145 ifs.read(reinterpret_cast<char*> (&id), 8);
+
146 ifs.read(reinterpret_cast<char*> (&cid), 4);
+
147 ifs.read(reinterpret_cast<char*> (&rx), 8);
+
148 ifs.read(reinterpret_cast<char*> (&ry), 8);
+
149 ifs.read(reinterpret_cast<char*> (&rz), 8);
+
150 ifs.read(reinterpret_cast<char*> (&vx), 8);
+
151 ifs.read(reinterpret_cast<char*> (&vy), 8);
+
152 ifs.read(reinterpret_cast<char*> (&vz), 8);
+
153
+
154 Component* component = &components.at(cid - 1);
+
155 Molecule tmp(id, component,
+
156 rx, ry, rz,
+
157 vx, vy, vz,
+
158 q0, q1, q2, q3,
+
159 Dx, Dy, Dz);
+
160 mol = tmp;
+
161 }
+
162};
+
163
+
164class MoleculeDataReaderIRV : public MoleculeDataReader {
+
165public:
+
166 MoleculeDataReaderIRV() {}
+
167
+
168public:
+
169 virtual ~MoleculeDataReaderIRV() {};
+
170
+
171 virtual void read(std::ifstream& ifs, Molecule& mol, std::vector<Component>& components) {
+
172 double rx, ry, rz, vx, vy, vz, q0, q1, q2, q3, Dx, Dy, Dz;
+
173 rx = ry = rz = vx = vy = vz = q0 = q1 = q2 = q3 = Dx = Dy = Dz = 0.;
+
174 uint64_t id = 0;
+
175 uint32_t cid = 0;
+
176
+
177 ifs.read(reinterpret_cast<char*> (&id), 8);
+
178 ifs.read(reinterpret_cast<char*> (&rx), 8);
+
179 ifs.read(reinterpret_cast<char*> (&ry), 8);
+
180 ifs.read(reinterpret_cast<char*> (&rz), 8);
+
181 ifs.read(reinterpret_cast<char*> (&vx), 8);
+
182 ifs.read(reinterpret_cast<char*> (&vy), 8);
+
183 ifs.read(reinterpret_cast<char*> (&vz), 8);
+
184
+
185 Component* component = &components.at(0);
+
186 Molecule tmp(id, component,
+
187 rx, ry, rz,
+
188 vx, vy, vz,
+
189 q0, q1, q2, q3,
+
190 Dx, Dy, Dz);
+
191 mol = tmp;
+
192 }
+
193};
+
194
+
195#endif /* REPLICA_GENERATOR_H */
+
196
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
InputBase
interface for any kind of input class
Definition: InputBase.h:18
-
MoleculeDataReaderICRVQD
Definition: ReplicaGenerator.h:94
-
MoleculeDataReaderICRV
Definition: ReplicaGenerator.h:133
-
MoleculeDataReaderIRV
Definition: ReplicaGenerator.h:165
-
MoleculeDataReader
Definition: ReplicaGenerator.h:84
+
MoleculeDataReaderICRVQD
Definition: ReplicaGenerator.h:93
+
MoleculeDataReaderICRV
Definition: ReplicaGenerator.h:132
+
MoleculeDataReaderIRV
Definition: ReplicaGenerator.h:164
+
MoleculeDataReader
Definition: ReplicaGenerator.h:83
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
-
ReplicaGenerator
Definition: ReplicaGenerator.h:40
-
ReplicaGenerator::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *, double)
read the phase space components and header information
Definition: ReplicaGenerator.h:46
-
ReplicaGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: ReplicaGenerator.cpp:380
-
ReplicaGenerator::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MkesferaGenerator and all its included objects.
Definition: ReplicaGenerator.cpp:178
+
ReplicaGenerator
Definition: ReplicaGenerator.h:39
+
ReplicaGenerator::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *, double)
read the phase space components and header information
Definition: ReplicaGenerator.h:45
+
ReplicaGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: ReplicaGenerator.cpp:379
+
ReplicaGenerator::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MkesferaGenerator and all its included objects.
Definition: ReplicaGenerator.cpp:177
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-
SubDomain
Definition: ReplicaGenerator.h:22
+
SubDomain
Definition: ReplicaGenerator.h:21
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ResilienceComm_8h_source.html b/ResilienceComm_8h_source.html index 31aa917316..01c5c92ba5 100644 --- a/ResilienceComm_8h_source.html +++ b/ResilienceComm_8h_source.html @@ -80,7 +80,7 @@
8#define SRC_PARALLEL_RESILIENCECOMM_H_
9
10#ifdef ENABLE_MPI
-
11#include "utils/mardyn_assert.h"
+
11#include "utils/mardyn_assert.h"
12
13#include <memory>
14#include <vector>
@@ -102,12 +102,12 @@
39 ResilienceComm(ResilienceComm const& rc); // copy constructor
40 ~ResilienceComm(); // destructor
55 int scatterBackupInfo(
-
56 std::vector<int>& backupInfo,
+
56 std::vector<int>& backupInfo,
57 int const numberOfBackups,
58 size_t const sizePerRank,
-
59 std::vector<int>& backing,
-
60 std::vector<int>& backedBy,
-
61 std::vector<int>& backingTags,
+
59 std::vector<int>& backing,
+
60 std::vector<int>& backedBy,
+
61 std::vector<int>& backingTags,
62 std::vector<int>& backedByTags
63 );
77 int exchangeSnapshotSizes(
@@ -115,7 +115,7 @@
79 std::vector<int>& backedBy,
80 std::vector<int>& backingTags,
81 std::vector<int>& backedByTags,
-
82 size_t const snapshotSize,
+
82 size_t const snapshotSize,
83 std::vector<int>& backupDataSizes
84 );
98 int exchangeSnapshots(
@@ -134,13 +134,13 @@
111#endif /* ENABLE_MPI */
112#endif /* SRC_PARALLEL_RESILIENCECOMM_H_ */
ResilienceComm
Definition: ResilienceComm.h:34
-
ResilienceComm::scatterBackupInfo
int scatterBackupInfo(std::vector< int > &backupInfo, int const numberOfBackups, size_t const sizePerRank, std::vector< int > &backing, std::vector< int > &backedBy, std::vector< int > &backingTags, std::vector< int > &backedByTags)
Definition: ResilienceComm.cpp:33
-
ResilienceComm::exchangeSnapshotSizes
int exchangeSnapshotSizes(std::vector< int > &backing, std::vector< int > &backedBy, std::vector< int > &backingTags, std::vector< int > &backedByTags, size_t const snapshotSize, std::vector< int > &backupDataSizes)
Definition: ResilienceComm.cpp:92
-
ResilienceComm::exchangeSnapshots
int exchangeSnapshots(std::vector< int > &backing, std::vector< int > &backedBy, std::vector< int > &backingTags, std::vector< int > &backedByTags, std::vector< int > &backupDataSizes, std::vector< char > &sendData, std::vector< char > &recvData)
Definition: ResilienceComm.cpp:127
+
ResilienceComm::scatterBackupInfo
int scatterBackupInfo(std::vector< int > &backupInfo, int const numberOfBackups, size_t const sizePerRank, std::vector< int > &backing, std::vector< int > &backedBy, std::vector< int > &backingTags, std::vector< int > &backedByTags)
Definition: ResilienceComm.cpp:32
+
ResilienceComm::exchangeSnapshotSizes
int exchangeSnapshotSizes(std::vector< int > &backing, std::vector< int > &backedBy, std::vector< int > &backingTags, std::vector< int > &backedByTags, size_t const snapshotSize, std::vector< int > &backupDataSizes)
Definition: ResilienceComm.cpp:91
+
ResilienceComm::exchangeSnapshots
int exchangeSnapshots(std::vector< int > &backing, std::vector< int > &backedBy, std::vector< int > &backingTags, std::vector< int > &backedByTags, std::vector< int > &backupDataSizes, std::vector< char > &sendData, std::vector< char > &recvData)
Definition: ResilienceComm.cpp:126
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ResortCellProcessorSliced_8h_source.html b/ResortCellProcessorSliced_8h_source.html index 1fdc5e00bf..92e37b0646 100644 --- a/ResortCellProcessorSliced_8h_source.html +++ b/ResortCellProcessorSliced_8h_source.html @@ -150,7 +150,7 @@
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
FullParticleCell
FullParticleCell data structure. Renamed from ParticleCell.
Definition: FullParticleCell.h:49
LinkedCells
Linked Cell Data Structure.
Definition: LinkedCells.h:51
-
LinkedCells::addParticle
bool addParticle(Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false) override
add a single Molecule to the ParticleContainer.
Definition: LinkedCells.cpp:444
+
LinkedCells::addParticle
bool addParticle(Molecule &particle, bool inBoxCheckedAlready=false, bool checkWhetherDuplicate=false, const bool &rebuildCaches=false) override
add a single Molecule to the ParticleContainer.
Definition: LinkedCells.cpp:442
ResortCellProcessorSliced
Definition: ResortCellProcessorSliced.h:17
ResortCellProcessorSliced::postprocessCell
void postprocessCell(ParticleCell &)
Definition: ResortCellProcessorSliced.h:59
ResortCellProcessorSliced::processCell
void processCell(ParticleCell &cell)
Definition: ResortCellProcessorSliced.h:46
@@ -162,7 +162,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ResultWriter_8h_source.html b/ResultWriter_8h_source.html index 1e29f48272..4ed87c32e2 100644 --- a/ResultWriter_8h_source.html +++ b/ResultWriter_8h_source.html @@ -101,7 +101,7 @@
53
54 void finish(ParticleContainer *particleContainer,
55 DomainDecompBase *domainDecomp, Domain *domain);
-
56
+
56
57 std::string getPluginName() {
58 return std::string("ResultWriter");
59 }
@@ -118,22 +118,22 @@
70
71#endif // SRC_IO_RESULTWRITER_H_
Accumulator
Definition: TemperatureControl.h:213
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
ResultWriter
Writes thermodynamic properties to a file.
Definition: ResultWriter.h:23
-
ResultWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: ResultWriter.cpp:31
+
ResultWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: ResultWriter.cpp:30
ResultWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: ResultWriter.h:57
-
ResultWriter::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ResultWriter and all its included objects.
Definition: ResultWriter.cpp:11
-
ResultWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: ResultWriter.cpp:79
-
ResultWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: ResultWriter.cpp:55
+
ResultWriter::readXML
virtual void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for ResultWriter and all its included objects.
Definition: ResultWriter.cpp:10
+
ResultWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: ResultWriter.cpp:78
+
ResultWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: ResultWriter.cpp:54
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/RotationParameter_8h_source.html b/RotationParameter_8h_source.html index 4454925e8a..6ce40a6588 100644 --- a/RotationParameter_8h_source.html +++ b/RotationParameter_8h_source.html @@ -102,7 +102,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SHLocalParticle_8h_source.html b/SHLocalParticle_8h_source.html index 98f94956f9..f1f1badeff 100644 --- a/SHLocalParticle_8h_source.html +++ b/SHLocalParticle_8h_source.html @@ -157,7 +157,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SHMultipoleParticle_8h_source.html b/SHMultipoleParticle_8h_source.html index 94a24be65d..68281924e7 100644 --- a/SHMultipoleParticle_8h_source.html +++ b/SHMultipoleParticle_8h_source.html @@ -149,7 +149,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SIMD__DEFINITIONS_8h.html b/SIMD__DEFINITIONS_8h.html index a2dcd4960c..8d4bd273cd 100644 --- a/SIMD__DEFINITIONS_8h.html +++ b/SIMD__DEFINITIONS_8h.html @@ -128,7 +128,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SIMD__DEFINITIONS_8h_source.html b/SIMD__DEFINITIONS_8h_source.html index 0c2e3c021e..5cfa37668a 100644 --- a/SIMD__DEFINITIONS_8h_source.html +++ b/SIMD__DEFINITIONS_8h_source.html @@ -257,7 +257,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SIMD__TYPES_8h.html b/SIMD__TYPES_8h.html index a036287617..03a1ce57eb 100644 --- a/SIMD__TYPES_8h.html +++ b/SIMD__TYPES_8h.html @@ -172,7 +172,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SIMD__TYPES_8h_source.html b/SIMD__TYPES_8h_source.html index 210774bc77..15d951eb6c 100644 --- a/SIMD__TYPES_8h_source.html +++ b/SIMD__TYPES_8h_source.html @@ -246,7 +246,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SIMD__VectorizedCellProcessorHelpers_8h_source.html b/SIMD__VectorizedCellProcessorHelpers_8h_source.html index 30702c6870..b9b75b3047 100644 --- a/SIMD__VectorizedCellProcessorHelpers_8h_source.html +++ b/SIMD__VectorizedCellProcessorHelpers_8h_source.html @@ -500,7 +500,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ScenarioGenerator.html b/ScenarioGenerator.html index 329b448d52..dcfdfaef55 100644 --- a/ScenarioGenerator.html +++ b/ScenarioGenerator.html @@ -102,7 +102,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SigsegvHandler_8h_source.html b/SigsegvHandler_8h_source.html index 9124dd9880..3bb7e00876 100644 --- a/SigsegvHandler_8h_source.html +++ b/SigsegvHandler_8h_source.html @@ -109,11 +109,11 @@
37
38#endif
39
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SimpleCellProcessor_8h_source.html b/SimpleCellProcessor_8h_source.html index fccd8c2a3c..d40339c919 100644 --- a/SimpleCellProcessor_8h_source.html +++ b/SimpleCellProcessor_8h_source.html @@ -112,7 +112,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Simulation_8h_source.html b/Simulation_8h_source.html index 69876a1eb2..2204d1774a 100644 --- a/Simulation_8h_source.html +++ b/Simulation_8h_source.html @@ -76,340 +76,342 @@
4#include <memory>
5#include <any>
6
-
7#include "ensemble/CavityEnsemble.h"
-
8#include "io/TimerProfiler.h"
-
9#include "thermostats/VelocityScalingThermostat.h"
-
10#include "utils/FixedSizeQueue.h"
-
11#include "utils/FunctionWrapper.h"
-
12#include "utils/SysMon.h"
+
7#include "io/TimerProfiler.h"
+
8#include "thermostats/VelocityScalingThermostat.h"
+
9#include "utils/FixedSizeQueue.h"
+
10#include "utils/FunctionWrapper.h"
+
11#include "utils/SysMon.h"
+
12#include "utils/Random.h"
13
-
14// plugins
-
15#include "plugins/PluginFactory.h"
-
16
-
17#if !defined (SIMULATION_SRC) or defined (IN_IDE_PARSER)
-
18class Simulation;
-
20extern Simulation* global_simulation;
-
21#endif
-
22
-
23class ParticleInsertion;
-
24class Ensemble;
-
25
-
26
+
14
+
15
+
16// plugins
+
17#include "plugins/PluginFactory.h"
+
18
+
19#if !defined (SIMULATION_SRC) or defined (IN_IDE_PARSER)
+
20class Simulation;
+
22extern Simulation* global_simulation;
+
23#endif
+
24
+
25class ParticleInsertion;
+
26class Ensemble;
27
-
29#define _simulation (*global_simulation)
-
30
-
31#include <list>
-
32#include <vector>
-
33#include <string>
-
34#include <io/TaskTimingProfiler.h>
-
35
-
36#ifdef STEEREO
-
37class SteereoSimSteering;
-
38class SteereoCouplingSim;
-
39#endif
-
40
-
41class Domain;
-
42class ParticleContainer;
-
43class ParticlePairsHandler;
-
44class CellProcessor;
-
45class Integrator;
-
46class PluginBase;
-
47class DomainDecompBase;
-
48class InputBase;
-
49class RDF;
-
50class FlopCounter;
-
51class LongRangeCorrection;
-
52class Homogeneous;
-
53class Planar;
-
54class TemperatureControl;
-
55class MemoryProfiler;
-
56
-
57// by Stefan Becker
-
58const int VELSCALE_THERMOSTAT = 1;
-
59
-
60namespace bhfmm {
-
61class FastMultipoleMethod;
-
62} // bhfmm
-
63
-
64
-
70class Simulation {
-
71private:
-
72 Simulation(Simulation &simulation);
-
73 Simulation& operator=(Simulation &simulation);
-
74 void updateForces();
-
75
-
76public:
-
78 Simulation();
-
79
-
81 ~Simulation();
-
82
-
124 void readXML(XMLfileUnits& xmlconfig);
-
125
-
132 static void exit(int exitcode);
-
133
-
139 void readConfigFile(std::string filename);
-
140
-
144 void initConfigXML(const std::string& inputfilename);
-
145
-
155 void prepare_start();
-
156
-
180 void simulate();
-
181
-
190 void pluginEndStepCall(unsigned long simstep);
-
191
-
193 void finalize();
-
194
-
200 void updateParticleContainerAndDecomposition(double lastTraversalTime, bool useTimers);
-
201
-
207 void performOverlappingDecompositionAndCellTraversalStep(double etime);
-
208
-
213 void setDomainDecomposition(DomainDecompBase* domainDecomposition);
-
214
-
216 DomainDecompBase& domainDecomposition() { return *_domainDecomposition; }
-
217
-
219 Domain* getDomain() { return _domain; }
-
220
-
222 Integrator* getIntegrator() {return _integrator; }
-
223
-
225 ParticleContainer* getMoleculeContainer() { return _moleculeContainer; }
-
226
-
228 void setNumTimesteps( unsigned long steps ) { _numberOfTimesteps = steps; }
-
230 unsigned long getNumTimesteps() { return _numberOfTimesteps; }
-
232 unsigned long getNumInitTimesteps() { return _initSimulation; }
-
234 unsigned long getSimulationStep() { return _simstep; }
-
236 void setLoopAbortTime(double time) {
-
237 global_log->info() << "Max loop-abort-time set: " << time << "\n";
-
238 _wallTimeEnabled = true;
-
239 _maxWallTime = time;
-
240 }
-
241
-
242 double getcutoffRadius() const { return _cutoffRadius; }
-
243 void setcutoffRadius(double cutoffRadius) { _cutoffRadius = cutoffRadius; }
-
244 double getLJCutoff() const { return _LJCutoffRadius; }
-
245 void setLJCutoff(double LJCutoffRadius) { _LJCutoffRadius = LJCutoffRadius; }
-
246 unsigned long getTotalNumberOfMolecules() const;
-
247
-
274 double Tfactor(unsigned long simstep);
-
275
-
276 void initCanonical(unsigned long t) { this->_initCanonical = t; }
-
277 void initGrandCanonical(unsigned long t) { this->_initGrandCanonical = t; }
-
278 void initStatistics(unsigned long t) { this->_initStatistics = t; }
-
279 unsigned long getInitStatistics() const { return this->_initStatistics; }
-
280
-
281 void setSimulationTime(double curtime) { _simulationTime = curtime; }
-
282 void advanceSimulationTime(double timestep) { _simulationTime += timestep; }
-
283 double getSimulationTime() { return _simulationTime; }
-
284
-
285 void setEnsemble(Ensemble *ensemble) { _ensemble = ensemble; }
-
286 Ensemble* getEnsemble() { return _ensemble; }
-
287
-
288 std::shared_ptr<MemoryProfiler> getMemoryProfiler() {
-
289 return _memoryProfiler;
-
290 }
-
291
-
292 TimerProfiler* timers() {
-
293 return &_timerProfiler;
-
294 }
-
295
-
297 double getH() {return h;}
-
299 void setH(double h_extern) {h = h_extern;}
-
300
-
301private:
+
28
+
29
+
31#define _simulation (*global_simulation)
+
32
+
33#include <list>
+
34#include <vector>
+
35#include <string>
+
36#include <io/TaskTimingProfiler.h>
+
37
+
38#ifdef STEEREO
+
39class SteereoSimSteering;
+
40class SteereoCouplingSim;
+
41#endif
+
42
+
43class Domain;
+
44class ParticleContainer;
+
45class ParticlePairsHandler;
+
46class CellProcessor;
+
47class Integrator;
+
48class PluginBase;
+
49class DomainDecompBase;
+
50class InputBase;
+
51class RDF;
+
52class FlopCounter;
+
53class LongRangeCorrection;
+
54class Homogeneous;
+
55class Planar;
+
56class TemperatureControl;
+
57class MemoryProfiler;
+
58
+
59// by Stefan Becker
+
60const int VELSCALE_THERMOSTAT = 1;
+
61
+
62namespace bhfmm {
+
63class FastMultipoleMethod;
+
64} // bhfmm
+
65
+
66
+
72class Simulation {
+
73private:
+
74 Simulation(Simulation &simulation);
+
75 Simulation& operator=(Simulation &simulation);
+
76 void updateForces();
+
77
+
78public:
+
80 Simulation();
+
81
+
83 ~Simulation();
+
84
+
126 void readXML(XMLfileUnits& xmlconfig);
+
127
+
134 static void exit(int exitcode);
+
135
+
141 void readConfigFile(std::string filename);
+
142
+
146 void initConfigXML(const std::string& inputfilename);
+
147
+
157 void prepare_start();
+
158
+
182 void simulate();
+
183
+
192 void pluginEndStepCall(unsigned long simstep);
+
193
+
195 void finalize();
+
196
+
202 void updateParticleContainerAndDecomposition(double lastTraversalTime, bool useTimers);
+
203
+
209 void performOverlappingDecompositionAndCellTraversalStep(double etime);
+
210
+
215 void setDomainDecomposition(DomainDecompBase* domainDecomposition);
+
216
+
218 DomainDecompBase& domainDecomposition() { return *_domainDecomposition; }
+
219
+
221 Domain* getDomain() { return _domain; }
+
222
+
224 Integrator* getIntegrator() {return _integrator; }
+
225
+
227 ParticleContainer* getMoleculeContainer() { return _moleculeContainer; }
+
228
+
230 void setNumTimesteps( unsigned long steps ) { _numberOfTimesteps = steps; }
+
232 unsigned long getNumTimesteps() { return _numberOfTimesteps; }
+
234 unsigned long getNumInitTimesteps() { return _initSimulation; }
+
236 unsigned long getSimulationStep() { return _simstep; }
+
238 void setLoopAbortTime(double time) {
+
239 Log::global_log->info() << "Max loop-abort-time set: " << time << "\n";
+
240 _wallTimeEnabled = true;
+
241 _maxWallTime = time;
+
242 }
+
243
+
244 double getcutoffRadius() const { return _cutoffRadius; }
+
245 void setcutoffRadius(double cutoffRadius) { _cutoffRadius = cutoffRadius; }
+
246 double getLJCutoff() const { return _LJCutoffRadius; }
+
247 void setLJCutoff(double LJCutoffRadius) { _LJCutoffRadius = LJCutoffRadius; }
+
248 unsigned long getTotalNumberOfMolecules() const;
+
249
+
276 double Tfactor(unsigned long simstep);
+
277
+
278 void initCanonical(unsigned long t) { this->_initCanonical = t; }
+
279 void initGrandCanonical(unsigned long t) { this->_initGrandCanonical = t; }
+
280 void initStatistics(unsigned long t) { this->_initStatistics = t; }
+
281 unsigned long getInitStatistics() const { return this->_initStatistics; }
+
282
+
283 void setSimulationTime(double curtime) { _simulationTime = curtime; }
+
284 void advanceSimulationTime(double timestep) { _simulationTime += timestep; }
+
285 double getSimulationTime() { return _simulationTime; }
+
286
+
287 void setEnsemble(Ensemble *ensemble) { _ensemble = ensemble; }
+
288 Ensemble* getEnsemble() { return _ensemble; }
+
289
+
290 std::shared_ptr<MemoryProfiler> getMemoryProfiler() {
+
291 return _memoryProfiler;
+
292 }
+
293
+
294 TimerProfiler* timers() {
+
295 return &_timerProfiler;
+
296 }
+
297
+
299 double getH() {return h;}
+
301 void setH(double h_extern) {h = h_extern;}
302
-
303
-
304 double _simulationTime;
-
309 unsigned long _maxMoleculeId;
-
310
-
312 double _cutoffRadius;
-
313
-
315 double _LJCutoffRadius;
-
316
-
330 unsigned _collectThermostatDirectedVelocity;
-
331
-
334 int _thermostatType;
-
335
-
336 unsigned long _numberOfTimesteps;
-
337public:
-
338 unsigned long getNumberOfTimesteps() const;
-
339
-
340private:
-
343 unsigned long _simstep;
-
346 unsigned long _initSimulation;
-
348 unsigned long _initCanonical;
-
350 unsigned long _initGrandCanonical;
-
352 unsigned long _initStatistics;
-
353
-
354 Ensemble* _ensemble;
+
303private:
+
304
+
305
+
306 double _simulationTime;
+
311 unsigned long _maxMoleculeId;
+
312
+
314 double _cutoffRadius;
+
315
+
317 double _LJCutoffRadius;
+
318
+
332 unsigned _collectThermostatDirectedVelocity;
+
333
+
336 int _thermostatType;
+
337
+
338 unsigned long _numberOfTimesteps;
+
339public:
+
340 unsigned long getNumberOfTimesteps() const;
+
341
+
342private:
+
345 unsigned long _simstep;
+
348 unsigned long _initSimulation;
+
350 unsigned long _initCanonical;
+
352 unsigned long _initGrandCanonical;
+
354 unsigned long _initStatistics;
355
-
357 ParticleContainer* _moleculeContainer;
-
358
-
360 ParticlePairsHandler* _particlePairsHandler;
-
361
-
363 CellProcessor* _cellProcessor;
-
364
-
366 DomainDecompBase* _domainDecomposition;
-
367
-
369 Integrator* _integrator;
-
370
-
372 Domain* _domain;
-
373
-
375 InputBase* _inputReader;
-
376
-
378 std::string _outputPrefix;
-
379
-
381 unsigned _momentumInterval;
-
382
-
384 Random _rand;
-
385
-
387 LongRangeCorrection* _longRangeCorrection;
-
388
-
390 TemperatureControl* _temperatureControl;
-
391
-
393 bhfmm::FastMultipoleMethod* _FMM;
-
394
-
396 TimerProfiler _timerProfiler;
-
397
-
399 std::shared_ptr<MemoryProfiler> _memoryProfiler;
-
400
-
401#ifdef TASKTIMINGPROFILE
-
403 TaskTimingProfiler* _taskTimingProfiler;
-
404#endif
-
405public:
-
406#ifdef TASKTIMINGPROFILE
-
407 TaskTimingProfiler* getTaskTimingProfiler(){
-
408 return _taskTimingProfiler;
-
409 }
-
410#endif
-
412 double getAndResetOneLoopCompTime() {
-
413 if(_loopCompTimeSteps==0){
-
414 return 1.;
-
415 }
-
416 double t = _loopCompTime/_loopCompTimeSteps;
-
417 _loopCompTime = 0.;
-
418 _loopCompTimeSteps = 0;
-
419 return t;
-
420 }
-
421 void setOutputPrefix( std::string prefix ) { _outputPrefix = prefix; }
-
422 void setOutputPrefix( char *prefix ) { _outputPrefix = std::string( prefix ); }
-
423 std::string getOutputPrefix() { return _outputPrefix; }
-
424
-
425 void enableFinalCheckpoint() { _finalCheckpoint = true; }
-
426 void disableFinalCheckpoint() { _finalCheckpoint = false; }
-
427
-
428 void useLegacyCellProcessor() { _legacyCellProcessor = true; }
+
356 Ensemble* _ensemble;
+
357
+
359 ParticleContainer* _moleculeContainer;
+
360
+
362 ParticlePairsHandler* _particlePairsHandler;
+
363
+
365 CellProcessor* _cellProcessor;
+
366
+
368 DomainDecompBase* _domainDecomposition;
+
369
+
371 Integrator* _integrator;
+
372
+
374 Domain* _domain;
+
375
+
377 InputBase* _inputReader;
+
378
+
380 std::string _outputPrefix;
+
381
+
383 unsigned _momentumInterval;
+
384
+
386 Random _rand;
+
387
+
389 LongRangeCorrection* _longRangeCorrection;
+
390
+
392 TemperatureControl* _temperatureControl;
+
393
+
395 bhfmm::FastMultipoleMethod* _FMM;
+
396
+
398 TimerProfiler _timerProfiler;
+
399
+
401 std::shared_ptr<MemoryProfiler> _memoryProfiler;
+
402
+
403#ifdef TASKTIMINGPROFILE
+
405 TaskTimingProfiler* _taskTimingProfiler;
+
406#endif
+
407public:
+
408#ifdef TASKTIMINGPROFILE
+
409 TaskTimingProfiler* getTaskTimingProfiler(){
+
410 return _taskTimingProfiler;
+
411 }
+
412#endif
+
414 double getAndResetOneLoopCompTime() {
+
415 if(_loopCompTimeSteps==0){
+
416 return 1.;
+
417 }
+
418 double t = _loopCompTime/_loopCompTimeSteps;
+
419 _loopCompTime = 0.;
+
420 _loopCompTimeSteps = 0;
+
421 return t;
+
422 }
+
423 void setOutputPrefix( std::string prefix ) { _outputPrefix = prefix; }
+
424 void setOutputPrefix( char *prefix ) { _outputPrefix = std::string( prefix ); }
+
425 std::string getOutputPrefix() { return _outputPrefix; }
+
426
+
427 void enableFinalCheckpoint() { _finalCheckpoint = true; }
+
428 void disableFinalCheckpoint() { _finalCheckpoint = false; }
429
-
430 void enableMemoryProfiler() {
-
431 _memoryProfiler = std::make_shared<MemoryProfiler>();
-
432 _memoryProfiler->registerObject(reinterpret_cast<MemoryProfilable**>(&_moleculeContainer));
-
433 _memoryProfiler->registerObject(reinterpret_cast<MemoryProfilable**>(&_domainDecomposition));
-
434 }
-
435
-
436 void setForcedCheckpointTime(double time) { _forced_checkpoint_time = time; }
+
430 void useLegacyCellProcessor() { _legacyCellProcessor = true; }
+
431
+
432 void enableMemoryProfiler() {
+
433 _memoryProfiler = std::make_shared<MemoryProfiler>();
+
434 _memoryProfiler->registerObject(reinterpret_cast<MemoryProfilable**>(&_moleculeContainer));
+
435 _memoryProfiler->registerObject(reinterpret_cast<MemoryProfilable**>(&_domainDecomposition));
+
436 }
437
-
439 void initialize();
-
440
-
444 PluginBase* getPlugin(const std::string& name);
-
445
-
446 std::list<PluginBase*>* getPluginList(){
-
447 return &_plugins;
-
448 }
-
449
-
451 void initGlobalEnergyLog();
-
452 void writeGlobalEnergyLog(const double& globalUpot, const double& globalT, const double& globalPressure);
-
453
-
454 CellProcessor *getCellProcessor() const;
+
438 void setForcedCheckpointTime(double time) { _forced_checkpoint_time = time; }
+
439
+
441 void initialize();
+
442
+
446 PluginBase* getPlugin(const std::string& name);
+
447
+
448 std::list<PluginBase*>* getPluginList(){
+
449 return &_plugins;
+
450 }
+
451
+
453 void initGlobalEnergyLog();
+
454 void writeGlobalEnergyLog(const double& globalUpot, const double& globalT, const double& globalPressure);
455
-
457 void refreshParticleIDs();
-
458
-
460 bool keepRunning();
-
461
-
462private:
+
456 CellProcessor *getCellProcessor() const;
+
457
+
459 void refreshParticleIDs();
+
460
+
462 bool keepRunning();
463
-
469 void parseMiscOptions(XMLfileUnits& xmlconfig);
-
470
-
472 Timer* _timerForLoad{nullptr};
-
473
-
474 Timer _timeFromStart;
-
475 double _maxWallTime = -1;
-
476 bool _wallTimeEnabled = false;
-
477
-
479 bool _finalCheckpoint;
-
480
-
482 bool _legacyCellProcessor = false;
-
483
-
489 bool _overlappingP2P {false};
-
490
-
492 std::list<PluginBase*> _plugins;
-
493
-
499 std::map<std::string, FunctionWrapper> _callbacks;
-
500
-
501 VelocityScalingThermostat _velocityScalingThermostat;
+
464private:
+
465
+
471 void parseMiscOptions(XMLfileUnits& xmlconfig);
+
472
+
474 Timer* _timerForLoad{nullptr};
+
475
+
476 Timer _timeFromStart;
+
477 double _maxWallTime = -1;
+
478 bool _wallTimeEnabled = false;
+
479
+
481 bool _finalCheckpoint;
+
482
+
484 bool _legacyCellProcessor = false;
+
485
+
491 bool _overlappingP2P {false};
+
492
+
494 std::list<PluginBase*> _plugins;
+
495
+
501 std::map<std::string, FunctionWrapper> _callbacks;
502
-
510 double h;
-
511
-
513 double _forced_checkpoint_time;
-
514
-
516 double _loopCompTime;
-
517
-
518 int _loopCompTimeSteps;
+
503 VelocityScalingThermostat _velocityScalingThermostat;
+
504
+
512 double h;
+
513
+
515 double _forced_checkpoint_time;
+
516
+
518 double _loopCompTime;
519
-
521 unsigned long _nWriteFreqGlobalEnergy;
-
522 std::string _globalEnergyLogFilename;
-
523
-
533 std::map<std::string, bool> _miscOptions;
-
534
-
535 FixedSizeQueue<double> _lastTraversalTimeHistory;
+
520 int _loopCompTimeSteps;
+
521
+
523 unsigned long _nWriteFreqGlobalEnergy;
+
524 std::string _globalEnergyLogFilename;
+
525
+
535 std::map<std::string, bool> _miscOptions;
536
-
537
-
538public:
-
539 /*** @brief Performs one time step. Is called as many times as timesteps are needed for the full simulation.
-
540 *
-
541 * In library mode, this function is used to externally control the simulation. In normal usage, this function is
-
542 * only called in the simulate() function, within the simulation loop.
-
543 * preSimLoopSteps() needs to be called before this function is called.
-
544 */
-
545 void simulateOneTimestep();
-
546
-
547 /*** @brief Performs necessary setup before the first timestep, which includes initializing all timers. */
-
548 void preSimLoopSteps();
-
549
-
550 /*** @brief Performs immediate cleanup after the simulation ends.
-
551 *
-
552 * The final checkpoint is written, the final plugin call is made, and all timers are stopped.
-
553 * Relevant timer information is printed.
-
554 */
-
555 void postSimLoopSteps();
-
556
-
557 /*** @brief Used to flag simulation as finished and to proceed to cleanup. Only used when ls1 is compiled and used
-
558 * as a library, and not in normal usage.
-
559 *
-
560 * Normally, the simulation is controlled entirely by the simulate() function, which determines whether the
-
561 * simulation is complete by checking the keepRunning() function.
-
562 * However in library mode, it is expected that the external code will manually control the simulation by calling
-
563 * simulateOneTimeStep(). As such, the keepRunning() function will never be called, and the exit conditions will
-
564 * never be checked on ls1's side. \n
-
565 * This function acts as a way for the external code to perform some cleanup steps, before ending the simulation
-
566 * on the ls1 side. For now, it only sets the simulationDone boolean to true, which is used as a check within
-
567 * the postSimLoopSteps() function.
-
568 * */
-
569 void markSimAsDone();
-
570
-
571private:
-
572 // stores the timing info for the previous load. This is used for the load calculation and the rebalancing.
-
573 double previousTimeForLoad = 0.;
-
574 /*** @brief Act as safeguards for the preSimLoopSteps(), simulateOneTimestep() and postSimLoopSteps() functions.
-
575 *
-
576 * These three functions are public, since they need to be reachable by external code when ls1 is compiled
-
577 * as a library. However it is possible to call them out of order, causing unexpected behaviour. As such,
-
578 * these bool values help keep track of the simulation and can be used to verify the state the simulation is in.
-
579 */
-
580 bool preSimLoopStepsDone = false, simulationDone = false, postSimLoopStepsDone = false;
-
581
-
582};
-
583#endif /*SIMULATION_H_*/
+
537 FixedSizeQueue<double> _lastTraversalTimeHistory;
+
538
+
539
+
540public:
+
541 /*** @brief Performs one time step. Is called as many times as timesteps are needed for the full simulation.
+
542 *
+
543 * In library mode, this function is used to externally control the simulation. In normal usage, this function is
+
544 * only called in the simulate() function, within the simulation loop.
+
545 * preSimLoopSteps() needs to be called before this function is called.
+
546 */
+
547 void simulateOneTimestep();
+
548
+
549 /*** @brief Performs necessary setup before the first timestep, which includes initializing all timers. */
+
550 void preSimLoopSteps();
+
551
+
552 /*** @brief Performs immediate cleanup after the simulation ends.
+
553 *
+
554 * The final checkpoint is written, the final plugin call is made, and all timers are stopped.
+
555 * Relevant timer information is printed.
+
556 */
+
557 void postSimLoopSteps();
+
558
+
559 /*** @brief Used to flag simulation as finished and to proceed to cleanup. Only used when ls1 is compiled and used
+
560 * as a library, and not in normal usage.
+
561 *
+
562 * Normally, the simulation is controlled entirely by the simulate() function, which determines whether the
+
563 * simulation is complete by checking the keepRunning() function.
+
564 * However in library mode, it is expected that the external code will manually control the simulation by calling
+
565 * simulateOneTimeStep(). As such, the keepRunning() function will never be called, and the exit conditions will
+
566 * never be checked on ls1's side. \n
+
567 * This function acts as a way for the external code to perform some cleanup steps, before ending the simulation
+
568 * on the ls1 side. For now, it only sets the simulationDone boolean to true, which is used as a check within
+
569 * the postSimLoopSteps() function.
+
570 * */
+
571 void markSimAsDone();
+
572
+
573private:
+
574 // stores the timing info for the previous load. This is used for the load calculation and the rebalancing.
+
575 double previousTimeForLoad = 0.;
+
576 /*** @brief Act as safeguards for the preSimLoopSteps(), simulateOneTimestep() and postSimLoopSteps() functions.
+
577 *
+
578 * These three functions are public, since they need to be reachable by external code when ls1 is compiled
+
579 * as a library. However it is possible to call them out of order, causing unexpected behaviour. As such,
+
580 * these bool values help keep track of the simulation and can be used to verify the state the simulation is in.
+
581 */
+
582 bool preSimLoopStepsDone = false, simulationDone = false, postSimLoopStepsDone = false;
+
583
+
584};
+
585#endif /*SIMULATION_H_*/
SysMon.h
System monitoring class.
CellProcessor
Definition: CellProcessor.h:29
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
Ensemble
Base class for ensembles.
Definition: EnsembleBase.h:47
FixedSizeQueue
Definition: FixedSizeQueue.h:15
@@ -426,39 +428,39 @@
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
RDF
This class calculates the Radial Distribution Function (RDF).
Definition: RDF.h:37
Random
Definition: Random.h:12
-
Simulation
Controls the simulation process.
Definition: Simulation.h:70
-
Simulation::pluginEndStepCall
void pluginEndStepCall(unsigned long simstep)
call plugins every nth-simstep
Definition: Simulation.cpp:1295
-
Simulation::setDomainDecomposition
void setDomainDecomposition(DomainDecompBase *domainDecomposition)
Definition: Simulation.cpp:1400
-
Simulation::domainDecomposition
DomainDecompBase & domainDecomposition()
Definition: Simulation.h:216
-
Simulation::getAndResetOneLoopCompTime
double getAndResetOneLoopCompTime()
computational time for one execution of traverseCell
Definition: Simulation.h:412
-
Simulation::simulateOneTimestep
void simulateOneTimestep()
Definition: Simulation.cpp:1013
-
Simulation::performOverlappingDecompositionAndCellTraversalStep
void performOverlappingDecompositionAndCellTraversalStep(double etime)
Definition: Simulation.cpp:1380
-
Simulation::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for simulation and all its included objects.
Definition: Simulation.cpp:167
-
Simulation::simulate
void simulate()
Controls the main loop of the simulation.
Definition: Simulation.cpp:942
-
Simulation::getMoleculeContainer
ParticleContainer * getMoleculeContainer()
Definition: Simulation.h:225
-
Simulation::initConfigXML
void initConfigXML(const std::string &inputfilename)
Opens given XML file and reads in parameters for the simulaion.
Definition: Simulation.cpp:696
-
Simulation::getH
double getH()
get Planck constant
Definition: Simulation.h:297
-
Simulation::refreshParticleIDs
void refreshParticleIDs()
Refresh particle IDs to continuous numbering starting at zero.
Definition: Simulation.cpp:1489
-
Simulation::readConfigFile
void readConfigFile(std::string filename)
process configuration file
Definition: Simulation.cpp:684
-
Simulation::getIntegrator
Integrator * getIntegrator()
Definition: Simulation.h:222
-
Simulation::Simulation
Simulation()
Definition: Simulation.cpp:92
-
Simulation::getPlugin
PluginBase * getPlugin(const std::string &name)
get plugin
Definition: Simulation.cpp:1472
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
-
Simulation::updateParticleContainerAndDecomposition
void updateParticleContainerAndDecomposition(double lastTraversalTime, bool useTimers)
Definition: Simulation.cpp:1344
-
Simulation::initialize
void initialize()
Definition: Simulation.cpp:1424
-
Simulation::setLoopAbortTime
void setLoopAbortTime(double time)
Definition: Simulation.h:236
-
Simulation::getSimulationStep
unsigned long getSimulationStep()
Definition: Simulation.h:234
-
Simulation::getDomain
Domain * getDomain()
Definition: Simulation.h:219
-
Simulation::setNumTimesteps
void setNumTimesteps(unsigned long steps)
Definition: Simulation.h:228
-
Simulation::~Simulation
~Simulation()
Definition: Simulation.cpp:134
-
Simulation::getNumInitTimesteps
unsigned long getNumInitTimesteps()
Definition: Simulation.h:232
-
Simulation::setH
void setH(double h_extern)
set Planck constant
Definition: Simulation.h:299
-
Simulation::prepare_start
void prepare_start()
calculate all values for the starting timepoint
Definition: Simulation.cpp:787
-
Simulation::keepRunning
bool keepRunning()
Checks if Simsteps or MaxWallTime are reached.
Definition: Simulation.cpp:1451
-
Simulation::finalize
void finalize()
clean up simulation
Definition: Simulation.cpp:1321
-
Simulation::Tfactor
double Tfactor(unsigned long simstep)
Temperature increase factor function during automatic equilibration.
Definition: Simulation.cpp:1410
+
Simulation
Controls the simulation process.
Definition: Simulation.h:72
+
Simulation::pluginEndStepCall
void pluginEndStepCall(unsigned long simstep)
call plugins every nth-simstep
Definition: Simulation.cpp:1292
+
Simulation::setDomainDecomposition
void setDomainDecomposition(DomainDecompBase *domainDecomposition)
Definition: Simulation.cpp:1396
+
Simulation::domainDecomposition
DomainDecompBase & domainDecomposition()
Definition: Simulation.h:218
+
Simulation::getAndResetOneLoopCompTime
double getAndResetOneLoopCompTime()
computational time for one execution of traverseCell
Definition: Simulation.h:414
+
Simulation::simulateOneTimestep
void simulateOneTimestep()
Definition: Simulation.cpp:1010
+
Simulation::performOverlappingDecompositionAndCellTraversalStep
void performOverlappingDecompositionAndCellTraversalStep(double etime)
Definition: Simulation.cpp:1376
+
Simulation::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for simulation and all its included objects.
Definition: Simulation.cpp:164
+
Simulation::simulate
void simulate()
Controls the main loop of the simulation.
Definition: Simulation.cpp:939
+
Simulation::getMoleculeContainer
ParticleContainer * getMoleculeContainer()
Definition: Simulation.h:227
+
Simulation::initConfigXML
void initConfigXML(const std::string &inputfilename)
Opens given XML file and reads in parameters for the simulaion.
Definition: Simulation.cpp:693
+
Simulation::getH
double getH()
get Planck constant
Definition: Simulation.h:299
+
Simulation::refreshParticleIDs
void refreshParticleIDs()
Refresh particle IDs to continuous numbering starting at zero.
Definition: Simulation.cpp:1485
+
Simulation::readConfigFile
void readConfigFile(std::string filename)
process configuration file
Definition: Simulation.cpp:681
+
Simulation::getIntegrator
Integrator * getIntegrator()
Definition: Simulation.h:224
+
Simulation::Simulation
Simulation()
Definition: Simulation.cpp:89
+
Simulation::getPlugin
PluginBase * getPlugin(const std::string &name)
get plugin
Definition: Simulation.cpp:1468
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
+
Simulation::updateParticleContainerAndDecomposition
void updateParticleContainerAndDecomposition(double lastTraversalTime, bool useTimers)
Definition: Simulation.cpp:1340
+
Simulation::initialize
void initialize()
Definition: Simulation.cpp:1420
+
Simulation::setLoopAbortTime
void setLoopAbortTime(double time)
Definition: Simulation.h:238
+
Simulation::getSimulationStep
unsigned long getSimulationStep()
Definition: Simulation.h:236
+
Simulation::getDomain
Domain * getDomain()
Definition: Simulation.h:221
+
Simulation::setNumTimesteps
void setNumTimesteps(unsigned long steps)
Definition: Simulation.h:230
+
Simulation::~Simulation
~Simulation()
Definition: Simulation.cpp:131
+
Simulation::getNumInitTimesteps
unsigned long getNumInitTimesteps()
Definition: Simulation.h:234
+
Simulation::setH
void setH(double h_extern)
set Planck constant
Definition: Simulation.h:301
+
Simulation::prepare_start
void prepare_start()
calculate all values for the starting timepoint
Definition: Simulation.cpp:784
+
Simulation::keepRunning
bool keepRunning()
Checks if Simsteps or MaxWallTime are reached.
Definition: Simulation.cpp:1447
+
Simulation::finalize
void finalize()
clean up simulation
Definition: Simulation.cpp:1317
+
Simulation::Tfactor
double Tfactor(unsigned long simstep)
Temperature increase factor function during automatic equilibration.
Definition: Simulation.cpp:1406
Simulation::initGlobalEnergyLog
void initGlobalEnergyLog()
-
Simulation::getNumTimesteps
unsigned long getNumTimesteps()
Definition: Simulation.h:230
+
Simulation::getNumTimesteps
unsigned long getNumTimesteps()
Definition: Simulation.h:232
TemperatureControl
Definition: TemperatureControl.h:167
TimerProfiler
Class for managing timers across the simulation.
Definition: TimerProfiler.h:28
Timer
This class is used to measure times in sequential and parallel versions.
Definition: Timer.h:59
@@ -472,7 +474,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SingleCellIterator_8h_source.html b/SingleCellIterator_8h_source.html index 472270d783..7b98dfe200 100644 --- a/SingleCellIterator_8h_source.html +++ b/SingleCellIterator_8h_source.html @@ -167,13 +167,13 @@
95#endif /* SRC_PARTICLECONTAINER_SINGLECELLITERATOR_H_ */
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
FullParticleCell
FullParticleCell data structure. Renamed from ParticleCell.
Definition: FullParticleCell.h:49
-
FullParticleCell::getMoleculeCount
int getMoleculeCount() const override
return the number of molecules contained in this cell
Definition: FullParticleCell.cpp:77
+
FullParticleCell::getMoleculeCount
int getMoleculeCount() const override
return the number of molecules contained in this cell
Definition: FullParticleCell.cpp:76
SingleCellIterator
Definition: SingleCellIterator.h:14
-
bhfmm::operator*
SolidHarmonicsExpansion operator*(double scalar, SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:67
+
bhfmm::operator*
SolidHarmonicsExpansion operator*(double scalar, SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:65
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Site_8h_source.html b/Site_8h_source.html index 46f9695838..988cea08d6 100644 --- a/Site_8h_source.html +++ b/Site_8h_source.html @@ -81,7 +81,7 @@
9#include <cmath>
10#include <cstdint>
11
-
12using Log::global_log;
+
12
13
20class Site {
21public:
@@ -106,9 +106,9 @@
55 xmlconfig.getNodeValueReduced("coords/y", _r[1]);
56 xmlconfig.getNodeValueReduced("coords/z", _r[2]);
57 xmlconfig.getNodeValueReduced("mass", _m);
-
58
+
58
59 if (!xmlconfig.getNodeValue("@name", _name)) {
-
60 global_log->error() << "Cannot find site name. Defaulting to type." << std::endl;
+
60 Log::global_log->error() << "Cannot find site name. Defaulting to type." << std::endl;
61 xmlconfig.getNodeValue("@type", _name);
62 }
63
@@ -142,7 +142,7 @@
128 xmlconfig.getNodeValueReduced("sigma", _sigma);
129 xmlconfig.getNodeValue("shifted", _shiftRequested);
130 }
-
131
+
131
133 void write(std::ostream& ostrm) const {
134 Site::write(ostrm);
135 ostrm << "\t" << eps() << " " << sigma() << " " << shift6();
@@ -345,7 +345,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SlicedCellPairTraversal_8h_source.html b/SlicedCellPairTraversal_8h_source.html index 317f255af0..ca0ccf5d7b 100644 --- a/SlicedCellPairTraversal_8h_source.html +++ b/SlicedCellPairTraversal_8h_source.html @@ -154,8 +154,8 @@
82inline void SlicedCellPairTraversal<CellTemplate>::traverseCellPairs(
83 CellProcessor& cellProcessor) {
84 using std::array;
-
85 const array<unsigned long, 3> start = { 0, 0, 0 };
-
86 array<unsigned long, 3> end;
+
85 const std::array<unsigned long, 3> start = { 0, 0, 0 };
+
86 std::array<unsigned long, 3> end;
87 for (int d = 0; d < 3; ++d) {
88 end[d] = this->_dims[d] - 1;
89 }
@@ -180,37 +180,37 @@
108
109 // values, which are modified by 2 are actually modified by the respective stride, which is always 2
110 // lower part
-
111 array<unsigned long, 3> startZlo = { 0, 0, 0 };
-
112 array<unsigned long, 3> endZlo = { this->_dims[0] - 1, this->_dims[1] - 1, 2 };
+
111 std::array<unsigned long, 3> startZlo = { 0, 0, 0 };
+
112 std::array<unsigned long, 3> endZlo = { this->_dims[0] - 1, this->_dims[1] - 1, 2 };
113 traverseCellPairsBackend(cellProcessor, startZlo, endZlo);
114
115 // upper part
-
116 array<unsigned long, 3> startZhi = { 0, 0, this->_dims[2] - 3 };
-
117 array<unsigned long, 3> endZhi = { this->_dims[0] - 1, this->_dims[1] - 1, this->_dims[2] - 1 };
+
116 std::array<unsigned long, 3> startZhi = { 0, 0, this->_dims[2] - 3 };
+
117 std::array<unsigned long, 3> endZhi = { this->_dims[0] - 1, this->_dims[1] - 1, this->_dims[2] - 1 };
118 traverseCellPairsBackend(cellProcessor, startZhi, endZhi);
119
120 // halo & boundaries in y direction
121 // boundaries in z direction are excluded!
122 // lower part
-
123 array<unsigned long, 3> startYlo = { 0, 0, 2 };
-
124 array<unsigned long, 3> endYlo = { this->_dims[0] - 1, 2, this->_dims[2] - 3 };
+
123 std::array<unsigned long, 3> startYlo = { 0, 0, 2 };
+
124 std::array<unsigned long, 3> endYlo = { this->_dims[0] - 1, 2, this->_dims[2] - 3 };
125 traverseCellPairsBackend(cellProcessor, startYlo, endYlo);
126
127 // upper part
-
128 array<unsigned long, 3> startYhi = { 0, this->_dims[1] - 3, 2 };
-
129 array<unsigned long, 3> endYhi = { this->_dims[0] - 1, this->_dims[1] - 1, this->_dims[2] - 3 };
+
128 std::array<unsigned long, 3> startYhi = { 0, this->_dims[1] - 3, 2 };
+
129 std::array<unsigned long, 3> endYhi = { this->_dims[0] - 1, this->_dims[1] - 1, this->_dims[2] - 3 };
130 traverseCellPairsBackend(cellProcessor, startYhi, endYhi);
131
132 // halo & boundaries in x direction
133 // boundaries in z and y direction are excluded!
134 // lower part
-
135 array<unsigned long, 3> startXlo = { 0, 2, 2 };
-
136 array<unsigned long, 3> endXlo = { 2, this->_dims[1] - 3, this->_dims[2] - 3 };
+
135 std::array<unsigned long, 3> startXlo = { 0, 2, 2 };
+
136 std::array<unsigned long, 3> endXlo = { 2, this->_dims[1] - 3, this->_dims[2] - 3 };
137 traverseCellPairsBackend(cellProcessor, startXlo, endXlo);
138
139 // upper part
-
140 array<unsigned long, 3> startXhi = { this->_dims[0] - 3, 2, 2 };
-
141 array<unsigned long, 3> endXhi = { this->_dims[0] - 1, this->_dims[1] - 3, this->_dims[2] - 3 };
+
140 std::array<unsigned long, 3> startXhi = { this->_dims[0] - 3, 2, 2 };
+
141 std::array<unsigned long, 3> endXhi = { this->_dims[0] - 1, this->_dims[1] - 3, this->_dims[2] - 3 };
142 traverseCellPairsBackend(cellProcessor, startXhi, endXhi);
143}
144
@@ -238,8 +238,8 @@
166 return; // we can not iterate over any inner cells, that do not depend on boundary or halo cells
167 }
168
-
169 array<unsigned long, 3> lower;
-
170 array<unsigned long, 3> upper;
+
169 std::array<unsigned long, 3> lower;
+
170 std::array<unsigned long, 3> upper;
171 for (unsigned long i = 0; i < 3; i++) {
172 lower[i] = 2;
173 upper[i] = this->_dims[i] - 3;
@@ -266,7 +266,7 @@
194 mardyn_exit(1);
195 }
196
-
197 array<unsigned long, 3> diff;
+
197 std::array<unsigned long, 3> diff;
198
199 unsigned long num_cells = 1;
200 for(int d = 0; d < 3; ++d) {
@@ -281,8 +281,8 @@
209 #endif
210 {
211 Permutation perm = getPermutationForIncreasingSorting(diff);
-
212 array<unsigned long, 3> diff_permuted = permuteForward(perm, diff);
-
213 array<unsigned long, 3> start_permuted = permuteForward(perm, start);
+
212 std::array<unsigned long, 3> diff_permuted = permuteForward(perm, diff);
+
213 std::array<unsigned long, 3> start_permuted = permuteForward(perm, start);
214
215 initLocks();
216
@@ -310,7 +310,7 @@
238 }
239
240 // unroll
-
241 array<unsigned long, 3> newInd_permuted = threeDimensionalMapping::oneToThreeD(i,diff_permuted);
+
241 std::array<unsigned long, 3> newInd_permuted = threeDimensionalMapping::oneToThreeD(i,diff_permuted);
242
243 // add inner-, middle- and outer-start
244 for(int d = 0; d < 3; ++d) {
@@ -318,7 +318,7 @@
246 }
247
248 // permute newInd backwards
-
249 array<unsigned long, 3> newInd = permuteBackward(perm, newInd_permuted);
+
249 std::array<unsigned long, 3> newInd = permuteBackward(perm, newInd_permuted);
250
251 // get actual index
252 unsigned long cellIndex = threeDimensionalMapping::threeToOneD(newInd, this->_dims);
@@ -392,8 +392,8 @@
320inline bool SlicedCellPairTraversal<CellTemplate>::isApplicable(
321 const std::array<unsigned long, 3>& dims) {
322 using std::array;
-
323 const array<unsigned long, 3> start = { 0, 0, 0 };
-
324 array<unsigned long, 3> end;
+
323 const std::array<unsigned long, 3> start = { 0, 0, 0 };
+
324 std::array<unsigned long, 3> end;
325 for (int d = 0; d < 3; ++d) {
326 end[d] = dims[d] - 1;
327 }
@@ -409,9 +409,9 @@
337 using namespace Permute3Elements;
338 using std::array;
339
-
340 array<unsigned long, 3> dims = {end[0] - start[0], end[1] - start[1], end[2] - start[2]};
+
340 std::array<unsigned long, 3> dims = {end[0] - start[0], end[1] - start[1], end[2] - start[2]};
341 Permutation permutation = getPermutationForIncreasingSorting(dims);
-
342 array<unsigned long, 3> dimsPermuted = permuteForward(permutation, dims);
+
342 std::array<unsigned long, 3> dimsPermuted = permuteForward(permutation, dims);
343
344 int num_threads = mardyn_get_max_threads();
345
@@ -450,7 +450,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SolidHarmonicsExpansion_8h_source.html b/SolidHarmonicsExpansion_8h_source.html index e89a3edf60..6bd7a2d2e2 100644 --- a/SolidHarmonicsExpansion_8h_source.html +++ b/SolidHarmonicsExpansion_8h_source.html @@ -302,32 +302,32 @@
551#endif /* SOLIDHARMONICSEXPANSION_H_ */
FFTAccelerableExpansion
Definition: FFTAccelerableExpansion.h:21
bhfmm::SolidHarmonicsExpansion
Definition: SolidHarmonicsExpansion.h:75
-
bhfmm::SolidHarmonicsExpansion::operator*=
SolidHarmonicsExpansion & operator*=(double scalar)
Definition: SolidHarmonicsExpansion.cpp:61
+
bhfmm::SolidHarmonicsExpansion::operator*=
SolidHarmonicsExpansion & operator*=(double scalar)
Definition: SolidHarmonicsExpansion.cpp:59
bhfmm::SolidHarmonicsExpansion::writeValuesToMPIBuffer
void writeValuesToMPIBuffer(double *buf, int &position) const
Definition: SolidHarmonicsExpansion.h:321
bhfmm::SolidHarmonicsExpansion::getS
double & getS(int l, int m)
Definition: SolidHarmonicsExpansion.h:299
-
bhfmm::SolidHarmonicsExpansion::operator+=
SolidHarmonicsExpansion & operator+=(const SolidHarmonicsExpansion &RHS)
Definition: SolidHarmonicsExpansion.cpp:49
-
bhfmm::SolidHarmonicsExpansion::evaluateLOfR
void evaluateLOfR(Vector3< double > r)
Definition: SolidHarmonicsExpansion.cpp:79
+
bhfmm::SolidHarmonicsExpansion::operator+=
SolidHarmonicsExpansion & operator+=(const SolidHarmonicsExpansion &RHS)
Definition: SolidHarmonicsExpansion.cpp:47
+
bhfmm::SolidHarmonicsExpansion::evaluateLOfR
void evaluateLOfR(Vector3< double > r)
Definition: SolidHarmonicsExpansion.cpp:77
bhfmm::SolidHarmonicsExpansion::getOrder
int getOrder() const
Definition: SolidHarmonicsExpansion.h:275
-
bhfmm::SolidHarmonicsExpansion::evaluateMOfR
void evaluateMOfR(Vector3< double > r)
Definition: SolidHarmonicsExpansion.cpp:125
-
bhfmm::SolidHarmonicsExpansion::convoluteLL_Z
void convoluteLL_Z(const SolidHarmonicsExpansion &LE1, const SolidHarmonicsExpansion &LE2)
Definition: SolidHarmonicsExpansion.cpp:213
-
bhfmm::SolidHarmonicsExpansion::setAtMinusR
void setAtMinusR()
Definition: SolidHarmonicsExpansion.cpp:507
-
bhfmm::SolidHarmonicsExpansion::~SolidHarmonicsExpansion
virtual ~SolidHarmonicsExpansion()
Definition: SolidHarmonicsExpansion.cpp:32
-
bhfmm::SolidHarmonicsExpansion::scaleM
void scaleM(double factor)
Definition: SolidHarmonicsExpansion.cpp:390
-
bhfmm::SolidHarmonicsExpansion::convoluteL_ZM
void convoluteL_ZM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:340
-
bhfmm::SolidHarmonicsExpansion::operator=
SolidHarmonicsExpansion & operator=(SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:43
-
bhfmm::SolidHarmonicsExpansion::potentialML
friend double potentialML(const SolidHarmonicsExpansion &ME, const SolidHarmonicsExpansion &LE)
Definition: SolidHarmonicsExpansion.cpp:524
-
bhfmm::SolidHarmonicsExpansion::swap
friend void swap(SolidHarmonicsExpansion &s1, SolidHarmonicsExpansion &s2)
Definition: SolidHarmonicsExpansion.cpp:35
-
bhfmm::SolidHarmonicsExpansion::convoluteLL
void convoluteLL(const SolidHarmonicsExpansion &LE1, const SolidHarmonicsExpansion &LE2)
Definition: SolidHarmonicsExpansion.cpp:169
-
bhfmm::SolidHarmonicsExpansion::print
void print() const
Definition: SolidHarmonicsExpansion.cpp:642
-
bhfmm::SolidHarmonicsExpansion::convoluteLM
void convoluteLM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:253
-
bhfmm::SolidHarmonicsExpansion::clearMonopole
void clearMonopole()
Definition: SolidHarmonicsExpansion.cpp:502
-
bhfmm::SolidHarmonicsExpansion::clear
void clear()
Definition: SolidHarmonicsExpansion.cpp:73
-
bhfmm::SolidHarmonicsExpansion::convoluteLM_Z
void convoluteLM_Z(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:298
+
bhfmm::SolidHarmonicsExpansion::evaluateMOfR
void evaluateMOfR(Vector3< double > r)
Definition: SolidHarmonicsExpansion.cpp:123
+
bhfmm::SolidHarmonicsExpansion::convoluteLL_Z
void convoluteLL_Z(const SolidHarmonicsExpansion &LE1, const SolidHarmonicsExpansion &LE2)
Definition: SolidHarmonicsExpansion.cpp:211
+
bhfmm::SolidHarmonicsExpansion::setAtMinusR
void setAtMinusR()
Definition: SolidHarmonicsExpansion.cpp:505
+
bhfmm::SolidHarmonicsExpansion::~SolidHarmonicsExpansion
virtual ~SolidHarmonicsExpansion()
Definition: SolidHarmonicsExpansion.cpp:30
+
bhfmm::SolidHarmonicsExpansion::scaleM
void scaleM(double factor)
Definition: SolidHarmonicsExpansion.cpp:388
+
bhfmm::SolidHarmonicsExpansion::convoluteL_ZM
void convoluteL_ZM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:338
+
bhfmm::SolidHarmonicsExpansion::operator=
SolidHarmonicsExpansion & operator=(SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:41
+
bhfmm::SolidHarmonicsExpansion::potentialML
friend double potentialML(const SolidHarmonicsExpansion &ME, const SolidHarmonicsExpansion &LE)
Definition: SolidHarmonicsExpansion.cpp:522
+
bhfmm::SolidHarmonicsExpansion::swap
friend void swap(SolidHarmonicsExpansion &s1, SolidHarmonicsExpansion &s2)
Definition: SolidHarmonicsExpansion.cpp:33
+
bhfmm::SolidHarmonicsExpansion::convoluteLL
void convoluteLL(const SolidHarmonicsExpansion &LE1, const SolidHarmonicsExpansion &LE2)
Definition: SolidHarmonicsExpansion.cpp:167
+
bhfmm::SolidHarmonicsExpansion::print
void print() const
Definition: SolidHarmonicsExpansion.cpp:640
+
bhfmm::SolidHarmonicsExpansion::convoluteLM
void convoluteLM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:251
+
bhfmm::SolidHarmonicsExpansion::clearMonopole
void clearMonopole()
Definition: SolidHarmonicsExpansion.cpp:500
+
bhfmm::SolidHarmonicsExpansion::clear
void clear()
Definition: SolidHarmonicsExpansion.cpp:71
+
bhfmm::SolidHarmonicsExpansion::convoluteLM_Z
void convoluteLM_Z(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:296
bhfmm::SolidHarmonicsExpansion::getC
double & getC(int l, int m)
Definition: SolidHarmonicsExpansion.h:285
-
bhfmm::SolidHarmonicsExpansion::SolidHarmonicsExpansion
SolidHarmonicsExpansion(int order, bool initializeToZero=true)
Definition: SolidHarmonicsExpansion.cpp:18
-
bhfmm::SolidHarmonicsExpansion::scaleL
void scaleL(double factor)
Definition: SolidHarmonicsExpansion.cpp:379
-
bhfmm::SolidHarmonicsExpansion::forceLAndGradM
friend Vector3< double > forceLAndGradM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:604
-
bhfmm::SolidHarmonicsExpansion::forceGradLAndM
friend Vector3< double > forceGradLAndM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:547
+
bhfmm::SolidHarmonicsExpansion::SolidHarmonicsExpansion
SolidHarmonicsExpansion(int order, bool initializeToZero=true)
Definition: SolidHarmonicsExpansion.cpp:16
+
bhfmm::SolidHarmonicsExpansion::scaleL
void scaleL(double factor)
Definition: SolidHarmonicsExpansion.cpp:377
+
bhfmm::SolidHarmonicsExpansion::forceLAndGradM
friend Vector3< double > forceLAndGradM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:602
+
bhfmm::SolidHarmonicsExpansion::forceGradLAndM
friend Vector3< double > forceGradLAndM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:545
bhfmm::SolidHarmonicsStorage::index
int index(int l, int m) const
Definition: SolidHarmonicsStorage.h:96
bhfmm::SolidHarmonicsStorage::getTotalNumValues
int getTotalNumValues() const
Definition: SolidHarmonicsStorage.cpp:82
bhfmm::SolidHarmonicsStorage::getValueConst
double getValueConst(int l, int m) const
Definition: SolidHarmonicsStorage.h:129
@@ -337,24 +337,24 @@
bhfmm::Vector3
Definition: Vector3.h:34
bhfmm::WignerMatrix
Definition: WignerMatrix.h:22
bhfmm
Definition: L2PCellProcessor.cpp:15
-
bhfmm::forceLAndGradM
Vector3< double > forceLAndGradM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:604
-
bhfmm::operator*
SolidHarmonicsExpansion operator*(double scalar, SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:67
-
bhfmm::evaluateLOfR
SolidHarmonicsExpansion evaluateLOfR(int order, Vector3< double > r)
Definition: SolidHarmonicsExpansion.cpp:118
-
bhfmm::convoluteLL
SolidHarmonicsExpansion convoluteLL(const SolidHarmonicsExpansion &LE1, const SolidHarmonicsExpansion &LE2)
Definition: SolidHarmonicsExpansion.cpp:205
-
bhfmm::evaluateMOfR
SolidHarmonicsExpansion evaluateMOfR(int order, Vector3< double > r)
Definition: SolidHarmonicsExpansion.cpp:162
-
bhfmm::operator+
SolidHarmonicsExpansion operator+(SolidHarmonicsExpansion LHS, const SolidHarmonicsExpansion &RHS)
Definition: SolidHarmonicsExpansion.cpp:56
-
bhfmm::forceGradLAndM
Vector3< double > forceGradLAndM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:547
-
bhfmm::potentialML
double potentialML(const SolidHarmonicsExpansion &ME, const SolidHarmonicsExpansion &LE)
Definition: SolidHarmonicsExpansion.cpp:524
-
bhfmm::convoluteLM_Z
SolidHarmonicsExpansion convoluteLM_Z(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:332
-
bhfmm::convoluteLM
SolidHarmonicsExpansion convoluteLM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:290
-
bhfmm::rotatePhi
SolidHarmonicsExpansion rotatePhi(const SolidHarmonicsExpansion &E, const double *CosSinPhi, int negate)
Definition: SolidHarmonicsExpansion.cpp:475
-
bhfmm::convoluteL_ZM
SolidHarmonicsExpansion convoluteL_ZM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:371
-
bhfmm::convoluteLL_Z
SolidHarmonicsExpansion convoluteLL_Z(const SolidHarmonicsExpansion &LE1, const SolidHarmonicsExpansion &LE2)
Definition: SolidHarmonicsExpansion.cpp:245
-
bhfmm::swap
void swap(SolidHarmonicsExpansion &s1, SolidHarmonicsExpansion &s2)
Definition: SolidHarmonicsExpansion.cpp:35
+
bhfmm::forceLAndGradM
Vector3< double > forceLAndGradM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:602
+
bhfmm::operator*
SolidHarmonicsExpansion operator*(double scalar, SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:65
+
bhfmm::evaluateLOfR
SolidHarmonicsExpansion evaluateLOfR(int order, Vector3< double > r)
Definition: SolidHarmonicsExpansion.cpp:116
+
bhfmm::convoluteLL
SolidHarmonicsExpansion convoluteLL(const SolidHarmonicsExpansion &LE1, const SolidHarmonicsExpansion &LE2)
Definition: SolidHarmonicsExpansion.cpp:203
+
bhfmm::evaluateMOfR
SolidHarmonicsExpansion evaluateMOfR(int order, Vector3< double > r)
Definition: SolidHarmonicsExpansion.cpp:160
+
bhfmm::operator+
SolidHarmonicsExpansion operator+(SolidHarmonicsExpansion LHS, const SolidHarmonicsExpansion &RHS)
Definition: SolidHarmonicsExpansion.cpp:54
+
bhfmm::forceGradLAndM
Vector3< double > forceGradLAndM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:545
+
bhfmm::potentialML
double potentialML(const SolidHarmonicsExpansion &ME, const SolidHarmonicsExpansion &LE)
Definition: SolidHarmonicsExpansion.cpp:522
+
bhfmm::convoluteLM_Z
SolidHarmonicsExpansion convoluteLM_Z(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:330
+
bhfmm::convoluteLM
SolidHarmonicsExpansion convoluteLM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:288
+
bhfmm::rotatePhi
SolidHarmonicsExpansion rotatePhi(const SolidHarmonicsExpansion &E, const double *CosSinPhi, int negate)
Definition: SolidHarmonicsExpansion.cpp:473
+
bhfmm::convoluteL_ZM
SolidHarmonicsExpansion convoluteL_ZM(const SolidHarmonicsExpansion &LE, const SolidHarmonicsExpansion &ME)
Definition: SolidHarmonicsExpansion.cpp:369
+
bhfmm::convoluteLL_Z
SolidHarmonicsExpansion convoluteLL_Z(const SolidHarmonicsExpansion &LE1, const SolidHarmonicsExpansion &LE2)
Definition: SolidHarmonicsExpansion.cpp:243
+
bhfmm::swap
void swap(SolidHarmonicsExpansion &s1, SolidHarmonicsExpansion &s2)
Definition: SolidHarmonicsExpansion.cpp:33
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SolidHarmonicsStorage_8h_source.html b/SolidHarmonicsStorage_8h_source.html index 1841e5dd96..793c746691 100644 --- a/SolidHarmonicsStorage_8h_source.html +++ b/SolidHarmonicsStorage_8h_source.html @@ -164,13 +164,13 @@
bhfmm::SolidHarmonicsStorage::operator*=
SolidHarmonicsStorage & operator*=(double scalar)
Definition: SolidHarmonicsStorage.cpp:65
bhfmm::SolidHarmonicsStorage::getNumRows
int getNumRows() const
Definition: SolidHarmonicsStorage.cpp:78
bhfmm
Definition: L2PCellProcessor.cpp:15
-
bhfmm::operator*
SolidHarmonicsExpansion operator*(double scalar, SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:67
-
bhfmm::operator+
SolidHarmonicsExpansion operator+(SolidHarmonicsExpansion LHS, const SolidHarmonicsExpansion &RHS)
Definition: SolidHarmonicsExpansion.cpp:56
-
bhfmm::swap
void swap(SolidHarmonicsExpansion &s1, SolidHarmonicsExpansion &s2)
Definition: SolidHarmonicsExpansion.cpp:35
+
bhfmm::operator*
SolidHarmonicsExpansion operator*(double scalar, SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:65
+
bhfmm::operator+
SolidHarmonicsExpansion operator+(SolidHarmonicsExpansion LHS, const SolidHarmonicsExpansion &RHS)
Definition: SolidHarmonicsExpansion.cpp:54
+
bhfmm::swap
void swap(SolidHarmonicsExpansion &s1, SolidHarmonicsExpansion &s2)
Definition: SolidHarmonicsExpansion.cpp:33
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SpatialProfile_8h_source.html b/SpatialProfile_8h_source.html index 17ce8145c5..e2d306e675 100644 --- a/SpatialProfile_8h_source.html +++ b/SpatialProfile_8h_source.html @@ -186,7 +186,7 @@
149#endif //MARDYN_TRUNK_SPATIALPROFILE_H
DOFProfile
Records (NO OUTPUT) the DOF of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DOFProfile.h:15
DensityProfile
Outputs the number density of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DensityProfile.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
KineticProfile
Records (NO OUTPUT) the 2xKinetic Profile of molecules per bin specified by Sampling grid in Kartesia...
Definition: KineticProfile.h:14
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -214,7 +214,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SteereoIntegration_8h_source.html b/SteereoIntegration_8h_source.html index 9fa6d7f1ea..017825896a 100644 --- a/SteereoIntegration_8h_source.html +++ b/SteereoIntegration_8h_source.html @@ -97,11 +97,11 @@
25#endif /* STEEREOINTEGRATION_H_ */
26#endif /* STEEREO */
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
-
Simulation
Controls the simulation process.
Definition: Simulation.h:70
+
Simulation
Controls the simulation process.
Definition: Simulation.h:72
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/String__utils_8h_source.html b/String__utils_8h_source.html index f7c5a5c211..80b10ca08f 100644 --- a/String__utils_8h_source.html +++ b/String__utils_8h_source.html @@ -126,7 +126,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SysMonOutput_8h_source.html b/SysMonOutput_8h_source.html index ebb9ab7621..5bd396375b 100644 --- a/SysMonOutput_8h_source.html +++ b/SysMonOutput_8h_source.html @@ -88,7 +88,7 @@
18
19 void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain,
20 unsigned long simstep);
-
21
+
21
23 void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain);
24
25 std::string getPluginName() {
@@ -102,22 +102,22 @@
34};
35
36#endif /* SYSMONOUTPUT_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
SysMonOutput
Definition: SysMonOutput.h:8
-
SysMonOutput::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: SysMonOutput.cpp:48
+
SysMonOutput::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: SysMonOutput.cpp:46
SysMonOutput::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: SysMonOutput.h:25
-
SysMonOutput::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: SysMonOutput.cpp:60
-
SysMonOutput::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: SysMonOutput.cpp:16
-
SysMonOutput::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: SysMonOutput.cpp:41
+
SysMonOutput::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: SysMonOutput.cpp:58
+
SysMonOutput::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: SysMonOutput.cpp:14
+
SysMonOutput::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Definition: SysMonOutput.cpp:39
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SysMon_8cpp.html b/SysMon_8cpp.html index c9ebd0ca8f..22b59f5087 100644 --- a/SysMon_8cpp.html +++ b/SysMon_8cpp.html @@ -86,7 +86,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SysMon_8h.html b/SysMon_8h.html index ecb7e7903b..950bb70d5f 100644 --- a/SysMon_8h.html +++ b/SysMon_8h.html @@ -108,7 +108,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/SysMon_8h_source.html b/SysMon_8h_source.html index 0f2d7d39ea..92648394ec 100644 --- a/SysMon_8h_source.html +++ b/SysMon_8h_source.html @@ -129,7 +129,7 @@
61 static const MPI_Datatype mpiTvalue;
62 static const int mpiRootRank;
63#endif
-
64
+
64
65private: // Singleton
66 static SysMon* s_sysmoninstance;
67 SysMon(const SysMon&);
@@ -139,7 +139,7 @@
71 SysMon() { _variableset=new Expression::VariableSet(); }
72#endif
73 ~SysMon() { clear(); delete(_variableset); s_sysmoninstance=NULL; }
-
74
+
74
75public:
76 static SysMon* getSysMon()
77 {
@@ -147,7 +147,7 @@
79 s_sysmoninstance = new SysMon();
80 return s_sysmoninstance;
81 }
-
82
+
82
83 void clear();
84 int addExpression(const std::string& exprstr);
85 int addExpression(const std::string& exprstr, const std::string& label)
@@ -179,7 +179,7 @@
111 return oss.str();
112 }
113 operator std::string() const { return InfoString(); }
-
114
+
114
115private:
116 Expression::VariableSet* _variableset;
117 std::list<Expression> _expressions;
@@ -192,7 +192,7 @@
124 std::vector<Tvalue> _valuesMaxMin;
125 MPI_Comm _mpicomm;
126#endif
-
127
+
127
128private:
129 unsigned int updateVariables_sysconf();
130 unsigned int updateVariables_sysinfo();
@@ -222,7 +222,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TaskTimingProfiler_8h_source.html b/TaskTimingProfiler_8h_source.html index 18000d23d5..05cbcad8ba 100644 --- a/TaskTimingProfiler_8h_source.html +++ b/TaskTimingProfiler_8h_source.html @@ -115,7 +115,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TcTS_8h_source.html b/TcTS_8h_source.html index 41987e6a7c..5b5b4f8ba2 100644 --- a/TcTS_8h_source.html +++ b/TcTS_8h_source.html @@ -100,19 +100,19 @@
48};
49
50#endif /* TCTS_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
InputBase
interface for any kind of input class
Definition: InputBase.h:18
MkTcTSGenerator
Generates a scenario of two layers of the same component but with different densities.
Definition: TcTS.h:12
-
MkTcTSGenerator::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MkTcTSGenerator and all its included objects.
Definition: TcTS.cpp:21
-
MkTcTSGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: TcTS.cpp:42
-
MkTcTSGenerator::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *domain, double timestep)
read the phase space components and header information
Definition: TcTS.cpp:38
+
MkTcTSGenerator::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for MkTcTSGenerator and all its included objects.
Definition: TcTS.cpp:19
+
MkTcTSGenerator::readPhaseSpace
unsigned long readPhaseSpace(ParticleContainer *particleContainer, Domain *domain, DomainDecompBase *domainDecomp)
read the actual phase space information
Definition: TcTS.cpp:40
+
MkTcTSGenerator::readPhaseSpaceHeader
void readPhaseSpaceHeader(Domain *domain, double timestep)
read the phase space components and header information
Definition: TcTS.cpp:36
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TemperatureControl_8h_source.html b/TemperatureControl_8h_source.html index 597147ccd5..4fd1c16c46 100644 --- a/TemperatureControl_8h_source.html +++ b/TemperatureControl_8h_source.html @@ -255,10 +255,10 @@
CommVar
Definition: CommVar.h:17
ControlInstance
Definition: Region.h:29
ControlRegionT
Definition: TemperatureControl.h:30
-
ControlRegionT::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for TemperatureControl and all its included objects.
Definition: TemperatureControl.cpp:90
+
ControlRegionT::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for TemperatureControl and all its included objects.
Definition: TemperatureControl.cpp:89
CuboidRegionObs
Definition: Region.h:109
-
DistControl
Definition: DistControl.h:48
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DistControl
Definition: DistControl.h:47
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
FullMolecule::setv
void setv(unsigned short d, double v) override
Definition: FullMolecule.h:57
@@ -268,15 +268,15 @@
Random
Definition: Random.h:12
SubjectBase
Definition: ObserverBase.h:20
TemperatureControl
Definition: TemperatureControl.h:167
-
TemperatureControl::DoLoopsOverMolecules
void DoLoopsOverMolecules(DomainDecompBase *, ParticleContainer *particleContainer, unsigned long simstep)
Decide which ControlMethod to use.
Definition: TemperatureControl.cpp:714
-
TemperatureControl::VelocityScalingPreparation
void VelocityScalingPreparation(DomainDecompBase *, ParticleContainer *, unsigned long simstep)
Prepare for VelocityScaling control method.
Definition: TemperatureControl.cpp:745
+
TemperatureControl::DoLoopsOverMolecules
void DoLoopsOverMolecules(DomainDecompBase *, ParticleContainer *particleContainer, unsigned long simstep)
Decide which ControlMethod to use.
Definition: TemperatureControl.cpp:713
+
TemperatureControl::VelocityScalingPreparation
void VelocityScalingPreparation(DomainDecompBase *, ParticleContainer *, unsigned long simstep)
Prepare for VelocityScaling control method.
Definition: TemperatureControl.cpp:744
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
ControlRegionT::Ramp::Update
Definition: TemperatureControl.h:159
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TemperatureProfile_8h_source.html b/TemperatureProfile_8h_source.html index 50883150b0..246cbc18d7 100644 --- a/TemperatureProfile_8h_source.html +++ b/TemperatureProfile_8h_source.html @@ -98,7 +98,7 @@
29 void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final {
30 _globalProfile[uID] = domainDecomp->collCommGetLongDouble();
31 }
-
32 void output(string prefix, long unsigned accumulatedDatasets) final;
+
32 void output(std::string prefix, long unsigned accumulatedDatasets) final;
33 void reset(unsigned long uID) final {
34 _localProfile[uID] = 0.0;
35 _globalProfile[uID] = 0.0;
@@ -114,13 +114,13 @@
45 // Global 1D Profile
46 std::map<unsigned, long double> _globalProfile;
47
-
48 void writeDataEntry(unsigned long uID, ofstream &outfile) const final;
+
48 void writeDataEntry(unsigned long uID, std::ofstream &outfile) const final;
49};
50
51
52#endif //MARDYN_TEMPERATUREPROFILE_H
DOFProfile
Records (NO OUTPUT) the DOF of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DOFProfile.h:15
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
KineticProfile
Records (NO OUTPUT) the 2xKinetic Profile of molecules per bin specified by Sampling grid in Kartesia...
Definition: KineticProfile.h:14
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
@@ -128,13 +128,14 @@
TemperatureProfile::reset
void reset(unsigned long uID) final
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
Definition: TemperatureProfile.h:33
TemperatureProfile::record
void record(Molecule &mol, unsigned long uID) final
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
Definition: TemperatureProfile.h:23
TemperatureProfile::collectRetrieve
void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
Definition: TemperatureProfile.h:29
-
TemperatureProfile::output
void output(string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: TemperatureProfile.cpp:10
TemperatureProfile::collectAppend
void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID) final
Append all necessary communication per bin to the DomainDecomposition. Append from e....
Definition: TemperatureProfile.h:26
TemperatureProfile::comms
int comms() final
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
Definition: TemperatureProfile.h:37
+
TemperatureProfile::output
void output(std::string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: TemperatureProfile.cpp:10
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TestPlugin_8h_source.html b/TestPlugin_8h_source.html index ca7a832b04..e9c7e649c2 100644 --- a/TestPlugin_8h_source.html +++ b/TestPlugin_8h_source.html @@ -89,51 +89,51 @@
17
23 void init(ParticleContainer* particleContainer,
24 DomainDecompBase* domainDecomp, Domain* domain) {
-
25 global_log->debug() << "[TESTPLUGIN] TESTPLUGIN INIT" << std::endl;
+
25 Log::global_log->debug() << "[TESTPLUGIN] TESTPLUGIN INIT" << std::endl;
26 }
27
28 void readXML(XMLfileUnits& xmlconfig) {
-
29 global_log -> debug() << "[TESTPLUGIN] READING XML" << endl;
+
29 Log::global_log -> debug() << "[TESTPLUGIN] READING XML" << std::endl;
30 }
31
33 void beforeEventNewTimestep(
34 ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
35 unsigned long simstep
36 ) {
-
37 global_log -> debug() << "[TESTPLUGIN] BEFORE EVENT NEW TIMESTEP" << endl;
+
37 Log::global_log -> debug() << "[TESTPLUGIN] BEFORE EVENT NEW TIMESTEP" << std::endl;
38 };
39
45 void beforeForces(
46 ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
47 unsigned long simstep
48 ) {
-
49 global_log -> debug() << "[TESTPLUGIN] BEFORE FORCES" << endl;
+
49 Log::global_log -> debug() << "[TESTPLUGIN] BEFORE FORCES" << std::endl;
50 }
51
56 void afterForces(
57 ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
58 unsigned long simstep
59 ) {
-
60 global_log->debug() << "[TESTPLUGIN] TESTPLUGIN AFTER FORCES" << endl;
+
60 Log::global_log->debug() << "[TESTPLUGIN] TESTPLUGIN AFTER FORCES" << std::endl;
61 }
62
71 void endStep(
72 ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
73 Domain* domain, unsigned long simstep
74 ) {
-
75 global_log->debug() << "[TESTPLUGIN] ENDSTEP" << endl;
+
75 Log::global_log->debug() << "[TESTPLUGIN] ENDSTEP" << std::endl;
76 }
77
86 void finish(ParticleContainer* particleContainer,
87 DomainDecompBase* domainDecomp, Domain* domain) {
-
88 global_log->debug() << "[TESTPLUGIN] FINISHING" << endl;
+
88 Log::global_log->debug() << "[TESTPLUGIN] FINISHING" << std::endl;
89 }
90
92 std::string getPluginName() {
-
93 global_log->debug() << "[TESTPLUGIN] GETTING NAME" << endl;
+
93 Log::global_log->debug() << "[TESTPLUGIN] GETTING NAME" << std::endl;
94 return "TestPlugin";}
95 static PluginBase* createInstance() {
-
96 global_log->debug() << "[TESTPLUGIN] CREATE INSTANCE" << endl;
+
96 Log::global_log->debug() << "[TESTPLUGIN] CREATE INSTANCE" << std::endl;
97 return new TestPlugin(); }
98
99private:
@@ -144,7 +144,7 @@
104};
105
106#endif /* SRC_UTILS_TESTPLUGIN_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -162,7 +162,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TestWithSimulationSetup_8h_source.html b/TestWithSimulationSetup_8h_source.html index 0315342255..b8f4f2d761 100644 --- a/TestWithSimulationSetup_8h_source.html +++ b/TestWithSimulationSetup_8h_source.html @@ -123,7 +123,7 @@
90#endif /* UNIT_TESTS */
91
92#endif /* TESTWITHSIMULATIONSETUP_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
@@ -131,7 +131,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Testing_8h_source.html b/Testing_8h_source.html index 616b2f1ff8..048c6ad49e 100644 --- a/Testing_8h_source.html +++ b/Testing_8h_source.html @@ -196,12 +196,12 @@
199#endif /* UNIT_TESTS */
200
201#endif /* TESTING_H_ */
-
Log::Logger
The Logger class provides a simple interface to handle log messages.
Definition: Logger.h:90
+
Log::Logger
The Logger class provides a simple interface to handle log messages.
Definition: Logger.h:89
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ThermostatVariables_8h_source.html b/ThermostatVariables_8h_source.html index 3d85f7a3a4..ff2180fdd9 100644 --- a/ThermostatVariables_8h_source.html +++ b/ThermostatVariables_8h_source.html @@ -109,7 +109,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ThreeElementPermutations_8h_source.html b/ThreeElementPermutations_8h_source.html index 5ce619fec5..d7b1b8f31d 100644 --- a/ThreeElementPermutations_8h_source.html +++ b/ThreeElementPermutations_8h_source.html @@ -196,7 +196,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TimerProfiler_8h_source.html b/TimerProfiler_8h_source.html index 2bfc783fe5..7be49abc07 100644 --- a/TimerProfiler_8h_source.html +++ b/TimerProfiler_8h_source.html @@ -179,28 +179,28 @@
286
287#endif /* SRC_IO_TIMERPROFILER_H_ */
TimerProfiler
Class for managing timers across the simulation.
Definition: TimerProfiler.h:28
-
TimerProfiler::start
void start(std::string timerName)
Starts the timer "timerName".
Definition: TimerProfiler.cpp:110
-
TimerProfiler::getTimer
Timer * getTimer(std::string timerName)
Gets a pointer to the timer with name "timerName".
Definition: TimerProfiler.cpp:46
-
TimerProfiler::getTime
double getTime(std::string timerName)
Gets the time collected by timer "timerName".
Definition: TimerProfiler.cpp:257
+
TimerProfiler::start
void start(std::string timerName)
Starts the timer "timerName".
Definition: TimerProfiler.cpp:109
+
TimerProfiler::getTimer
Timer * getTimer(std::string timerName)
Gets a pointer to the timer with name "timerName".
Definition: TimerProfiler.cpp:45
+
TimerProfiler::getTime
double getTime(std::string timerName)
Gets the time collected by timer "timerName".
Definition: TimerProfiler.cpp:256
TimerProfiler::getNumElapsedIterations
unsigned long getNumElapsedIterations() const
get the number of iterations since the last resetting of all timers.
Definition: TimerProfiler.h:197
-
TimerProfiler::setSyncTimer
void setSyncTimer(std::string timerName, bool sync)
Sets sync mode of the timer "timerName".
Definition: TimerProfiler.cpp:81
+
TimerProfiler::setSyncTimer
void setSyncTimer(std::string timerName, bool sync)
Sets sync mode of the timer "timerName".
Definition: TimerProfiler.cpp:80
TimerProfiler::incrementTimerTimestepCounter
void incrementTimerTimestepCounter()
Increment the timestep-counter.
Definition: TimerProfiler.h:188
-
TimerProfiler::resetTimers
void resetTimers(std::string timerName=_baseTimerName)
Resets the timer "timerName" and all of its descendants.
Definition: TimerProfiler.cpp:145
-
TimerProfiler::setOutputString
void setOutputString(std::string timerName, std::string outputString)
Sets the output string for the timer output.
Definition: TimerProfiler.cpp:240
-
TimerProfiler::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for TimerProfiler.
Definition: TimerProfiler.cpp:27
-
TimerProfiler::readInitialTimersFromFile
void readInitialTimersFromFile(std::string fileName)
Sets up initial configuration of the timers during the simulation.
Definition: TimerProfiler.cpp:157
-
TimerProfiler::activateTimer
void activateTimer(std::string timerName)
Activates the timer "timerName".
Definition: TimerProfiler.cpp:71
-
TimerProfiler::printTimers
void printTimers(std::string timerName=_baseTimerName, std::string outputPrefix="")
Prints time collected by timer "timerName" and the time from all of its descendants.
Definition: TimerProfiler.cpp:99
-
TimerProfiler::registerTimer
void registerTimer(std::string timerName, std::vector< std::string > parentTimerNames, Timer *timer=nullptr, bool activate=true)
Adds a timer in the container.
Definition: TimerProfiler.cpp:54
-
TimerProfiler::TimerProfiler
TimerProfiler()
Constructor of TimerProfiler.
Definition: TimerProfiler.cpp:22
-
TimerProfiler::deactivateTimer
void deactivateTimer(std::string timerName)
Deactivates the timer "timerName".
Definition: TimerProfiler.cpp:76
+
TimerProfiler::resetTimers
void resetTimers(std::string timerName=_baseTimerName)
Resets the timer "timerName" and all of its descendants.
Definition: TimerProfiler.cpp:144
+
TimerProfiler::setOutputString
void setOutputString(std::string timerName, std::string outputString)
Sets the output string for the timer output.
Definition: TimerProfiler.cpp:239
+
TimerProfiler::readXML
void readXML(XMLfileUnits &xmlconfig)
Read in XML configuration for TimerProfiler.
Definition: TimerProfiler.cpp:26
+
TimerProfiler::readInitialTimersFromFile
void readInitialTimersFromFile(std::string fileName)
Sets up initial configuration of the timers during the simulation.
Definition: TimerProfiler.cpp:156
+
TimerProfiler::activateTimer
void activateTimer(std::string timerName)
Activates the timer "timerName".
Definition: TimerProfiler.cpp:70
+
TimerProfiler::printTimers
void printTimers(std::string timerName=_baseTimerName, std::string outputPrefix="")
Prints time collected by timer "timerName" and the time from all of its descendants.
Definition: TimerProfiler.cpp:98
+
TimerProfiler::registerTimer
void registerTimer(std::string timerName, std::vector< std::string > parentTimerNames, Timer *timer=nullptr, bool activate=true)
Adds a timer in the container.
Definition: TimerProfiler.cpp:53
+
TimerProfiler::TimerProfiler
TimerProfiler()
Constructor of TimerProfiler.
Definition: TimerProfiler.cpp:21
+
TimerProfiler::deactivateTimer
void deactivateTimer(std::string timerName)
Deactivates the timer "timerName".
Definition: TimerProfiler.cpp:75
Timer
This class is used to measure times in sequential and parallel versions.
Definition: Timer.h:59
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TimerWriter_8h_source.html b/TimerWriter_8h_source.html index 72dc2b0c21..5e445aa337 100644 --- a/TimerWriter_8h_source.html +++ b/TimerWriter_8h_source.html @@ -106,7 +106,7 @@
60 std::vector<double> _times{};
61 unsigned long _stepsSinceLastWrite{0ul};
62};
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -121,7 +121,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Timer_8h_source.html b/Timer_8h_source.html index 31e5814716..deecbc478b 100644 --- a/Timer_8h_source.html +++ b/Timer_8h_source.html @@ -85,8 +85,8 @@
13
14/* PAPI hardware performance counter support */
15/*
-
16 * Take care when using multiple timers because calls to the constructor
-
17 * reset the hw counters to zero!
+
16 * Take care when using multiple timers because calls to the constructor
+
17 * reset the hw counters to zero!
18 */
19#ifdef WITH_PAPI
20#include <papi.h>
@@ -147,7 +147,7 @@
77 bool _active; // timer can be active or not; if not active, then all function calls will have no effect on the timer
78
79public:
-
80 Timer() :
+
80 Timer() :
81 _start(0), _stop(0), _etime(0), _state(TIMER_HALTED), _synced(false), _active(true)
82#ifdef WITH_PAPI
83 , _papi_start(0), _papi_stop(0), _papi_counter(0), _papi_num_counters(0), _papi_num_avail_counters(0), _papi_EventSet(0), _collect_papi(false)
@@ -173,7 +173,7 @@
103 void start();
104 void stop();
105 void reset();
-
106
+
106
107 double get_start() {
108 return _start;
109 }
@@ -269,7 +269,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TransferFunctionManagerAPI_8h_source.html b/TransferFunctionManagerAPI_8h_source.html index bb1875aaba..84d439f12c 100644 --- a/TransferFunctionManagerAPI_8h_source.html +++ b/TransferFunctionManagerAPI_8h_source.html @@ -95,7 +95,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TransferFunctionManager_8h_source.html b/TransferFunctionManager_8h_source.html index 46910b91b3..bc2904c17b 100644 --- a/TransferFunctionManager_8h_source.html +++ b/TransferFunctionManager_8h_source.html @@ -117,7 +117,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TransferFunctionManager__UniformGrid_8h_source.html b/TransferFunctionManager__UniformGrid_8h_source.html index 53c882de57..35c090f615 100644 --- a/TransferFunctionManager__UniformGrid_8h_source.html +++ b/TransferFunctionManager__UniformGrid_8h_source.html @@ -121,7 +121,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/TraversalTuner_8h_source.html b/TraversalTuner_8h_source.html index 0969e55e7b..194ca6b7eb 100644 --- a/TraversalTuner_8h_source.html +++ b/TraversalTuner_8h_source.html @@ -89,373 +89,372 @@
17#include "LinkedCellTraversals/NeutralTerritoryTraversal.h"
18#include "LinkedCellTraversals/SlicedCellPairTraversal.h"
19
-
20using Log::global_log;
-
21
-
22template<class CellTemplate>
-
23class TraversalTuner {
-
24 friend class LinkedCellsTest;
-
25
-
26public:
-
27 // Probably remove this once autotuning is implemented
-
28 enum traversalNames {
-
29 ORIGINAL = 0,
-
30 C08 = 1,
-
31 C04 = 2,
-
32 SLICED = 3,
-
33 HS = 4,
-
34 MP = 5,
-
35 C08ES = 6,
-
36 NT = 7,
-
37 // quicksched has to be the last traversal!
-
38 QSCHED = 8,
-
39 };
-
40
-
41 TraversalTuner();
-
42
-
43 ~TraversalTuner();
-
44
-
45 void findOptimalTraversal();
-
46
-
47 void readXML(XMLfileUnits &xmlconfig);
-
48
-
56 void rebuild(std::vector<CellTemplate> &cells,
-
57 const std::array<unsigned long, 3> &dims, double cellLength[3], double cutoff);
-
58
-
59 void traverseCellPairs(CellProcessor &cellProcessor);
-
60
-
61 void traverseCellPairs(traversalNames name, CellProcessor &cellProcessor);
-
62
-
63 void traverseCellPairsOuter(CellProcessor &cellProcessor);
-
64
-
65 void traverseCellPairsInner(CellProcessor &cellProcessor, unsigned stage, unsigned stageCount);
+
20
+
21template<class CellTemplate>
+
22class TraversalTuner {
+
23 friend class LinkedCellsTest;
+
24
+
25public:
+
26 // Probably remove this once autotuning is implemented
+
27 enum traversalNames {
+
28 ORIGINAL = 0,
+
29 C08 = 1,
+
30 C04 = 2,
+
31 SLICED = 3,
+
32 HS = 4,
+
33 MP = 5,
+
34 C08ES = 6,
+
35 NT = 7,
+
36 // quicksched has to be the last traversal!
+
37 QSCHED = 8,
+
38 };
+
39
+
40 TraversalTuner();
+
41
+
42 ~TraversalTuner();
+
43
+
44 void findOptimalTraversal();
+
45
+
46 void readXML(XMLfileUnits &xmlconfig);
+
47
+
55 void rebuild(std::vector<CellTemplate> &cells,
+
56 const std::array<unsigned long, 3> &dims, double cellLength[3], double cutoff);
+
57
+
58 void traverseCellPairs(CellProcessor &cellProcessor);
+
59
+
60 void traverseCellPairs(traversalNames name, CellProcessor &cellProcessor);
+
61
+
62 void traverseCellPairsOuter(CellProcessor &cellProcessor);
+
63
+
64 void traverseCellPairsInner(CellProcessor &cellProcessor, unsigned stage, unsigned stageCount);
+
65
66
-
67
-
68 bool isTraversalApplicable(traversalNames name, const std::array<unsigned long, 3> &dims) const; // new
+
67 bool isTraversalApplicable(traversalNames name, const std::array<unsigned long, 3> &dims) const; // new
+
68
69
-
70
-
71 traversalNames getSelectedTraversal() const {
-
72 return selectedTraversal;
-
73 }
-
74
-
75 CellPairTraversals<ParticleCell> *getCurrentOptimalTraversal() { return _optimalTraversal; }
-
76
-
77private:
-
78 std::vector<CellTemplate>* _cells;
-
79 std::array<unsigned long, 3> _dims;
-
80
-
81 traversalNames selectedTraversal;
-
82
-
83 std::vector<std::pair<CellPairTraversals<CellTemplate> *, CellPairTraversalData *> > _traversals;
-
84
-
85 CellPairTraversals<CellTemplate> *_optimalTraversal;
-
86
-
87 unsigned _cellsInCutoff = 1;
-
88};
-
89
-
90template<class CellTemplate>
-
91TraversalTuner<CellTemplate>::TraversalTuner() : _cells(nullptr), _dims(), _optimalTraversal(nullptr) {
-
92 // defaults:
-
93 selectedTraversal = {
-
94 mardyn_get_max_threads() > 1 ? C08 : SLICED
-
95 };
-
96 auto *c08Data = new C08CellPairTraversalData;
-
97 auto *c04Data = new C04CellPairTraversalData;
-
98 auto *origData = new OriginalCellPairTraversalData;
-
99 auto *slicedData = new SlicedCellPairTraversalData;
-
100 auto *hsData = new HalfShellTraversalData;
-
101 auto *mpData = new MidpointTraversalData;
-
102 auto *ntData = new NeutralTerritoryTraversalData;
-
103 auto *c08esData = new C08CellPairTraversalData;
-
104
-
105 _traversals = {
-
106 make_pair(nullptr, origData),
-
107 make_pair(nullptr, c08Data),
-
108 make_pair(nullptr, c04Data),
-
109 make_pair(nullptr, slicedData),
-
110 make_pair(nullptr, hsData),
-
111 make_pair(nullptr, mpData),
-
112 make_pair(nullptr, ntData),
-
113 make_pair(nullptr, c08esData)
-
114 };
-
115#ifdef QUICKSCHED
-
116 struct QuickschedTraversalData *quiData = new QuickschedTraversalData;
-
117 quiData->taskBlockSize = {{2, 2, 2}};
-
118 if (is_base_of<ParticleCellBase, CellTemplate>::value) {
-
119 _traversals.push_back(make_pair(nullptr, quiData));
-
120 }
-
121#endif
-
122}
-
123
-
124template<class CellTemplate>
-
125TraversalTuner<CellTemplate>::~TraversalTuner() {
-
126 for (auto t : _traversals) {
-
127 if (t.first != nullptr)
-
128 delete (t.first);
-
129 if (t.second != nullptr)
-
130 delete (t.second);
-
131 }
-
132}
-
133
-
134template<class CellTemplate>
-
135void TraversalTuner<CellTemplate>::findOptimalTraversal() {
-
136 // TODO implement autotuning here! At the moment the traversal is chosen via readXML!
-
137
-
138 _optimalTraversal = _traversals[selectedTraversal].first;
-
139
-
140 // log traversal
-
141 if (dynamic_cast<HalfShellTraversal<CellTemplate> *>(_optimalTraversal))
-
142 global_log->info() << "Using HalfShellTraversal." << endl;
-
143 else if (dynamic_cast<OriginalCellPairTraversal<CellTemplate> *>(_optimalTraversal))
-
144 global_log->info() << "Using OriginalCellPairTraversal." << endl;
-
145 else if (dynamic_cast<C08CellPairTraversal<CellTemplate> *>(_optimalTraversal))
-
146 global_log->info() << "Using C08CellPairTraversal without eighthShell." << endl;
-
147 else if (dynamic_cast<C08CellPairTraversal<CellTemplate, true> *>(_optimalTraversal))
-
148 global_log->info() << "Using C08CellPairTraversal with eighthShell." << endl;
-
149 else if (dynamic_cast<C04CellPairTraversal<CellTemplate> *>(_optimalTraversal))
-
150 global_log->info() << "Using C04CellPairTraversal." << endl;
-
151 else if (dynamic_cast<MidpointTraversal<CellTemplate> *>(_optimalTraversal))
-
152 global_log->info() << "Using MidpointTraversal." << endl;
-
153 else if (dynamic_cast<NeutralTerritoryTraversal<CellTemplate> *>(_optimalTraversal))
-
154 global_log->info() << "Using NeutralTerritoryTraversal." << endl;
-
155 else if (dynamic_cast<QuickschedTraversal<CellTemplate> *>(_optimalTraversal)) {
-
156 global_log->info() << "Using QuickschedTraversal." << endl;
-
157#ifndef QUICKSCHED
-
158 global_log->error() << "MarDyn was compiled without Quicksched Support. Aborting!" << endl;
-
159 Simulation::exit(1);
-
160#endif
-
161 } else if (dynamic_cast<SlicedCellPairTraversal<CellTemplate> *>(_optimalTraversal))
-
162 global_log->info() << "Using SlicedCellPairTraversal." << endl;
-
163 else
-
164 global_log->warning() << "Using unknown traversal." << endl;
-
165
-
166 if (_cellsInCutoff > _optimalTraversal->maxCellsInCutoff()) {
-
167 global_log->error() << "Traversal supports up to " << _optimalTraversal->maxCellsInCutoff()
-
168 << " cells in cutoff, but value is chosen as " << _cellsInCutoff << std::endl;
-
169 Simulation::exit(45);
-
170 }
-
171}
-
172
-
173template<class CellTemplate>
-
174void TraversalTuner<CellTemplate>::readXML(XMLfileUnits &xmlconfig) {
-
175 string oldPath(xmlconfig.getcurrentnodepath());
-
176 // read traversal type default values
-
177 string traversalType;
-
178
-
179 xmlconfig.getNodeValue("traversalSelector", traversalType);
-
180 transform(traversalType.begin(), traversalType.end(), traversalType.begin(), ::tolower);
-
181
-
182 if (traversalType.find("c08es") != string::npos)
-
183 selectedTraversal = C08ES;
-
184 else if (traversalType.find("c08") != string::npos)
-
185 selectedTraversal = C08;
-
186 else if (traversalType.find("c04") != string::npos)
-
187 selectedTraversal = C04;
-
188 else if (traversalType.find("qui") != string::npos)
-
189 selectedTraversal = QSCHED;
-
190 else if (traversalType.find("slice") != string::npos)
-
191 selectedTraversal = SLICED;
-
192 else if (traversalType.find("ori") != string::npos)
-
193 selectedTraversal = ORIGINAL;
-
194 else if (traversalType.find("hs") != string::npos)
-
195 selectedTraversal = HS;
-
196 else if (traversalType.find("mp") != string::npos)
-
197 selectedTraversal = MP;
-
198 else if (traversalType.find("nt") != string::npos) {
-
199 selectedTraversal = NT;
-
200 } else {
-
201 // selector already set in constructor, just print a warning here
-
202 if (mardyn_get_max_threads() > 1) {
-
203 global_log->warning() << "No traversal type selected. Defaulting to c08 traversal." << endl;
-
204 } else {
-
205 global_log->warning() << "No traversal type selected. Defaulting to sliced traversal." << endl;
-
206 }
-
207 }
-
208
-
209 _cellsInCutoff = xmlconfig.getNodeValue_int("cellsInCutoffRadius", 1); // This is currently only used for an assert
-
210
-
211 // workaround for stupid iterator:
-
212 // since
-
213 // xmlconfig.changecurrentnode(traversalIterator);
-
214 // does not work resolve paths to traversals manually
-
215 // use iterator only to resolve number of traversals (==iterations)
-
216 string basePath(xmlconfig.getcurrentnodepath());
-
217
-
218 int i = 1;
-
219 XMLfile::Query qry = xmlconfig.query("traversalData");
-
220 for (XMLfile::Query::const_iterator traversalIterator = qry.begin(); traversalIterator; ++traversalIterator) {
-
221 string path(basePath + "/traversalData[" + to_string(i) + "]");
-
222 xmlconfig.changecurrentnode(path);
-
223
-
224 traversalType = xmlconfig.getNodeValue_string("@type", "NOTHING FOUND");
-
225 transform(traversalType.begin(), traversalType.end(), traversalType.begin(), ::tolower);
-
226 if (traversalType == "c08") {
-
227 // nothing to do
-
228 } else if (traversalType.find("qui") != string::npos) {
-
229#ifdef QUICKSCHED
-
230 if (not is_base_of<ParticleCellBase, CellTemplate>::value) {
-
231 global_log->warning() << "Attempting to use Quicksched with cell type that does not store task data!"
-
232 << endl;
-
233 }
-
234 for (auto p : _traversals) {
-
235 if (struct QuickschedTraversalData *quiData = dynamic_cast<QuickschedTraversalData *>(p.second)) {
-
236 // read task block size
-
237 string tag = "taskBlockSize/l";
-
238 char dimension = 'x';
-
239
-
240 for (int j = 0; j < 3; ++j) {
-
241 tag += (dimension + j);
-
242 xmlconfig.getNodeValue(tag, quiData->taskBlockSize[j]);
-
243 if (quiData->taskBlockSize[j] < 2) {
-
244 global_log->error() << "Task block size in "
-
245 << (char) (dimension + j)
-
246 << " direction is <2 and thereby invalid! ("
-
247 << quiData->taskBlockSize[j] << ")"
-
248 << endl;
-
249 Simulation::exit(1);
-
250 }
-
251 }
-
252 break;
-
253 }
-
254 }
-
255#else
-
256 global_log->warning() << "Found quicksched traversal data in config "
-
257 << "but mardyn was compiled without quicksched support! "
-
258 << "(make ENABLE_QUICKSCHED=1)" << endl;
-
259#endif
-
260 } else {
-
261 global_log->warning() << "Unknown traversal type: " << traversalType << endl;
-
262 }
-
263 ++i;
-
264 }
-
265 xmlconfig.changecurrentnode(oldPath);
-
266}
-
267
-
268template<class CellTemplate>
-
269void TraversalTuner<CellTemplate>::rebuild(std::vector<CellTemplate> &cells, const std::array<unsigned long, 3> &dims,
-
270 double cellLength[3], double cutoff) {
-
271 _cells = &cells; // new - what for?
-
272 _dims = dims; // new - what for?
-
273
-
274 for (size_t i = 0ul; i < _traversals.size(); ++i) {
-
275 auto& [traversalPointerReference, traversalData] = _traversals[i];
-
276 // decide whether to initialize or rebuild
-
277 if (traversalPointerReference == nullptr) {
-
278 switch (i) {
-
279 case traversalNames ::ORIGINAL:
-
280 traversalPointerReference = new OriginalCellPairTraversal<CellTemplate>(cells, dims);
-
281 break;
-
282 case traversalNames::C08:
-
283 traversalPointerReference = new C08CellPairTraversal<CellTemplate>(cells, dims);
-
284 break;
-
285 case traversalNames::C04:
-
286 traversalPointerReference = new C04CellPairTraversal<CellTemplate>(cells, dims);
-
287 break;
-
288 case traversalNames::SLICED:
-
289 traversalPointerReference = new SlicedCellPairTraversal<CellTemplate>(cells, dims);
-
290 break;
-
291 case traversalNames::HS:
-
292 traversalPointerReference = new HalfShellTraversal<CellTemplate>(cells, dims);
-
293 break;
-
294 case traversalNames::MP:
-
295 traversalPointerReference = new MidpointTraversal<CellTemplate>(cells, dims);
-
296 break;
-
297 case traversalNames::NT:
-
298 traversalPointerReference =
-
299 new NeutralTerritoryTraversal<CellTemplate>(cells, dims, cellLength, cutoff);
-
300 break;
-
301 case traversalNames::C08ES:
-
302 traversalPointerReference = new C08CellPairTraversal<CellTemplate, true>(cells, dims);
-
303 break;
-
304 case traversalNames::QSCHED: {
-
305 mardyn_assert((is_base_of<ParticleCellBase, CellTemplate>::value));
-
306 auto *quiData = dynamic_cast<QuickschedTraversalData *>(traversalData);
-
307 traversalPointerReference = new QuickschedTraversal<CellTemplate>(cells, dims, quiData->taskBlockSize);
-
308 } break;
-
309 default:
-
310 global_log->error() << "Unknown traversal data found in TraversalTuner._traversals!" << endl;
-
311 Simulation::exit(1);
-
312 }
-
313 }
-
314 traversalPointerReference->rebuild(cells, dims, cellLength, cutoff, traversalData);
-
315 }
-
316 _optimalTraversal = nullptr;
-
317}
-
318
-
319template<class CellTemplate>
-
320void TraversalTuner<CellTemplate>::traverseCellPairs(CellProcessor &cellProcessor) {
-
321 if (not _optimalTraversal) {
-
322 findOptimalTraversal();
-
323 }
-
324 _optimalTraversal->traverseCellPairs(cellProcessor);
-
325}
-
326
-
327template<class CellTemplate>
-
328inline void TraversalTuner<CellTemplate>::traverseCellPairs(traversalNames name,
-
329 CellProcessor& cellProcessor) {
-
330 if (name == getSelectedTraversal()) {
-
331 traverseCellPairs(cellProcessor);
-
332 } else {
-
333 SlicedCellPairTraversal<CellTemplate> slicedTraversal(*_cells, _dims);
-
334 switch(name) {
-
335 case SLICED:
-
336 slicedTraversal.traverseCellPairs(cellProcessor);
-
337 break;
-
338 default:
-
339 Log::global_log->error()<< "Calling traverseCellPairs(traversalName, CellProcessor&) for something else than the Sliced Traversal is disabled for now. Aborting." << std::endl;
-
340 mardyn_exit(1);
-
341 break;
-
342 }
-
343 }
-
344}
-
345
-
346template<class CellTemplate>
-
347void TraversalTuner<CellTemplate>::traverseCellPairsOuter(CellProcessor &cellProcessor) {
-
348 if (not _optimalTraversal) {
-
349 findOptimalTraversal();
-
350 }
-
351 _optimalTraversal->traverseCellPairsOuter(cellProcessor);
-
352}
-
353
-
354template<class CellTemplate>
-
355void TraversalTuner<CellTemplate>::traverseCellPairsInner(CellProcessor &cellProcessor, unsigned stage,
-
356 unsigned stageCount) {
-
357 if (not _optimalTraversal) {
-
358 findOptimalTraversal();
-
359 }
-
360 _optimalTraversal->traverseCellPairsInner(cellProcessor, stage, stageCount);
-
361}
-
362
-
363template<class CellTemplate>
-
364inline bool TraversalTuner<CellTemplate>::isTraversalApplicable(
-
365 traversalNames name, const std::array<unsigned long, 3> &dims) const {
-
366 bool ret = true;
-
367 switch(name) {
-
368 case SLICED:
-
369 ret = SlicedCellPairTraversal<CellTemplate>::isApplicable(dims);
-
370 break;
-
371 case QSCHED:
-
372#ifdef QUICKSCHED
-
373 ret = true;
-
374#else
-
375 ret = false;
-
376#endif
-
377 break;
-
378 case C08:
-
379 ret = true;
-
380 break;
-
381 case C04:
-
382 ret = true;
-
383 break;
-
384 case ORIGINAL:
-
385 ret = true;
-
386 break;
-
387 default:
-
388 global_log->warning() << "unknown traversal given in TraversalTuner::isTraversalApplicable, assuming that is applicable" << std::endl;
-
389 }
-
390 return ret;
-
391}
-
392
-
393#endif //TRAVERSALTUNER_H_
+
70 traversalNames getSelectedTraversal() const {
+
71 return selectedTraversal;
+
72 }
+
73
+
74 CellPairTraversals<ParticleCell> *getCurrentOptimalTraversal() { return _optimalTraversal; }
+
75
+
76private:
+
77 std::vector<CellTemplate>* _cells;
+
78 std::array<unsigned long, 3> _dims;
+
79
+
80 traversalNames selectedTraversal;
+
81
+
82 std::vector<std::pair<CellPairTraversals<CellTemplate> *, CellPairTraversalData *> > _traversals;
+
83
+
84 CellPairTraversals<CellTemplate> *_optimalTraversal;
+
85
+
86 unsigned _cellsInCutoff = 1;
+
87};
+
88
+
89template<class CellTemplate>
+
90TraversalTuner<CellTemplate>::TraversalTuner() : _cells(nullptr), _dims(), _optimalTraversal(nullptr) {
+
91 // defaults:
+
92 selectedTraversal = {
+
93 mardyn_get_max_threads() > 1 ? C08 : SLICED
+
94 };
+
95 auto *c08Data = new C08CellPairTraversalData;
+
96 auto *c04Data = new C04CellPairTraversalData;
+
97 auto *origData = new OriginalCellPairTraversalData;
+
98 auto *slicedData = new SlicedCellPairTraversalData;
+
99 auto *hsData = new HalfShellTraversalData;
+
100 auto *mpData = new MidpointTraversalData;
+
101 auto *ntData = new NeutralTerritoryTraversalData;
+
102 auto *c08esData = new C08CellPairTraversalData;
+
103
+
104 _traversals = {
+
105 std::make_pair(nullptr, origData),
+
106 std::make_pair(nullptr, c08Data),
+
107 std::make_pair(nullptr, c04Data),
+
108 std::make_pair(nullptr, slicedData),
+
109 std::make_pair(nullptr, hsData),
+
110 std::make_pair(nullptr, mpData),
+
111 std::make_pair(nullptr, ntData),
+
112 std::make_pair(nullptr, c08esData)
+
113 };
+
114#ifdef QUICKSCHED
+
115 struct QuickschedTraversalData *quiData = new QuickschedTraversalData;
+
116 quiData->taskBlockSize = {{2, 2, 2}};
+
117 if (std::is_base_of<ParticleCellBase, CellTemplate>::value) {
+
118 _traversals.push_back(std::make_pair(nullptr, quiData));
+
119 }
+
120#endif
+
121}
+
122
+
123template<class CellTemplate>
+
124TraversalTuner<CellTemplate>::~TraversalTuner() {
+
125 for (auto t : _traversals) {
+
126 if (t.first != nullptr)
+
127 delete (t.first);
+
128 if (t.second != nullptr)
+
129 delete (t.second);
+
130 }
+
131}
+
132
+
133template<class CellTemplate>
+
134void TraversalTuner<CellTemplate>::findOptimalTraversal() {
+
135 // TODO implement autotuning here! At the moment the traversal is chosen via readXML!
+
136
+
137 _optimalTraversal = _traversals[selectedTraversal].first;
+
138
+
139 // log traversal
+
140 if (dynamic_cast<HalfShellTraversal<CellTemplate> *>(_optimalTraversal))
+
141 Log::global_log->info() << "Using HalfShellTraversal." << std::endl;
+
142 else if (dynamic_cast<OriginalCellPairTraversal<CellTemplate> *>(_optimalTraversal))
+
143 Log::global_log->info() << "Using OriginalCellPairTraversal." << std::endl;
+
144 else if (dynamic_cast<C08CellPairTraversal<CellTemplate> *>(_optimalTraversal))
+
145 Log::global_log->info() << "Using C08CellPairTraversal without eighthShell." << std::endl;
+
146 else if (dynamic_cast<C08CellPairTraversal<CellTemplate, true> *>(_optimalTraversal))
+
147 Log::global_log->info() << "Using C08CellPairTraversal with eighthShell." << std::endl;
+
148 else if (dynamic_cast<C04CellPairTraversal<CellTemplate> *>(_optimalTraversal))
+
149 Log::global_log->info() << "Using C04CellPairTraversal." << std::endl;
+
150 else if (dynamic_cast<MidpointTraversal<CellTemplate> *>(_optimalTraversal))
+
151 Log::global_log->info() << "Using MidpointTraversal." << std::endl;
+
152 else if (dynamic_cast<NeutralTerritoryTraversal<CellTemplate> *>(_optimalTraversal))
+
153 Log::global_log->info() << "Using NeutralTerritoryTraversal." << std::endl;
+
154 else if (dynamic_cast<QuickschedTraversal<CellTemplate> *>(_optimalTraversal)) {
+
155 Log::global_log->info() << "Using QuickschedTraversal." << std::endl;
+
156#ifndef QUICKSCHED
+
157 Log::global_log->error() << "MarDyn was compiled without Quicksched Support. Aborting!" << std::endl;
+
158 Simulation::exit(1);
+
159#endif
+
160 } else if (dynamic_cast<SlicedCellPairTraversal<CellTemplate> *>(_optimalTraversal))
+
161 Log::global_log->info() << "Using SlicedCellPairTraversal." << std::endl;
+
162 else
+
163 Log::global_log->warning() << "Using unknown traversal." << std::endl;
+
164
+
165 if (_cellsInCutoff > _optimalTraversal->maxCellsInCutoff()) {
+
166 Log::global_log->error() << "Traversal supports up to " << _optimalTraversal->maxCellsInCutoff()
+
167 << " cells in cutoff, but value is chosen as " << _cellsInCutoff << std::endl;
+
168 Simulation::exit(45);
+
169 }
+
170}
+
171
+
172template<class CellTemplate>
+
173void TraversalTuner<CellTemplate>::readXML(XMLfileUnits &xmlconfig) {
+
174 std::string oldPath(xmlconfig.getcurrentnodepath());
+
175 // read traversal type default values
+
176 std::string traversalType;
+
177
+
178 xmlconfig.getNodeValue("traversalSelector", traversalType);
+
179 transform(traversalType.begin(), traversalType.end(), traversalType.begin(), ::tolower);
+
180
+
181 if (traversalType.find("c08es") != std::string::npos)
+
182 selectedTraversal = C08ES;
+
183 else if (traversalType.find("c08") != std::string::npos)
+
184 selectedTraversal = C08;
+
185 else if (traversalType.find("c04") != std::string::npos)
+
186 selectedTraversal = C04;
+
187 else if (traversalType.find("qui") != std::string::npos)
+
188 selectedTraversal = QSCHED;
+
189 else if (traversalType.find("slice") != std::string::npos)
+
190 selectedTraversal = SLICED;
+
191 else if (traversalType.find("ori") != std::string::npos)
+
192 selectedTraversal = ORIGINAL;
+
193 else if (traversalType.find("hs") != std::string::npos)
+
194 selectedTraversal = HS;
+
195 else if (traversalType.find("mp") != std::string::npos)
+
196 selectedTraversal = MP;
+
197 else if (traversalType.find("nt") != std::string::npos) {
+
198 selectedTraversal = NT;
+
199 } else {
+
200 // selector already set in constructor, just print a warning here
+
201 if (mardyn_get_max_threads() > 1) {
+
202 Log::global_log->warning() << "No traversal type selected. Defaulting to c08 traversal." << std::endl;
+
203 } else {
+
204 Log::global_log->warning() << "No traversal type selected. Defaulting to sliced traversal." << std::endl;
+
205 }
+
206 }
+
207
+
208 _cellsInCutoff = xmlconfig.getNodeValue_int("cellsInCutoffRadius", 1); // This is currently only used for an assert
+
209
+
210 // workaround for stupid iterator:
+
211 // since
+
212 // xmlconfig.changecurrentnode(traversalIterator);
+
213 // does not work resolve paths to traversals manually
+
214 // use iterator only to resolve number of traversals (==iterations)
+
215 std::string basePath(xmlconfig.getcurrentnodepath());
+
216
+
217 int i = 1;
+
218 XMLfile::Query qry = xmlconfig.query("traversalData");
+
219 for (XMLfile::Query::const_iterator traversalIterator = qry.begin(); traversalIterator; ++traversalIterator) {
+
220 std::string path(basePath + "/traversalData[" + std::to_string(i) + "]");
+
221 xmlconfig.changecurrentnode(path);
+
222
+
223 traversalType = xmlconfig.getNodeValue_string("@type", "NOTHING FOUND");
+
224 transform(traversalType.begin(), traversalType.end(), traversalType.begin(), ::tolower);
+
225 if (traversalType == "c08") {
+
226 // nothing to do
+
227 } else if (traversalType.find("qui") != std::string::npos) {
+
228#ifdef QUICKSCHED
+
229 if (not std::is_base_of<ParticleCellBase, CellTemplate>::value) {
+
230 Log::global_log->warning() << "Attempting to use Quicksched with cell type that does not store task data!"
+
231 << std::endl;
+
232 }
+
233 for (auto p : _traversals) {
+
234 if (struct QuickschedTraversalData *quiData = dynamic_cast<QuickschedTraversalData *>(p.second)) {
+
235 // read task block size
+
236 std::string tag = "taskBlockSize/l";
+
237 char dimension = 'x';
+
238
+
239 for (int j = 0; j < 3; ++j) {
+
240 tag += (dimension + j);
+
241 xmlconfig.getNodeValue(tag, quiData->taskBlockSize[j]);
+
242 if (quiData->taskBlockSize[j] < 2) {
+
243 Log::global_log->error() << "Task block size in "
+
244 << (char) (dimension + j)
+
245 << " direction is <2 and thereby invalid! ("
+
246 << quiData->taskBlockSize[j] << ")"
+
247 << std::endl;
+
248 Simulation::exit(1);
+
249 }
+
250 }
+
251 break;
+
252 }
+
253 }
+
254#else
+
255 Log::global_log->warning() << "Found quicksched traversal data in config "
+
256 << "but mardyn was compiled without quicksched support! "
+
257 << "(make ENABLE_QUICKSCHED=1)" << std::endl;
+
258#endif
+
259 } else {
+
260 Log::global_log->warning() << "Unknown traversal type: " << traversalType << std::endl;
+
261 }
+
262 ++i;
+
263 }
+
264 xmlconfig.changecurrentnode(oldPath);
+
265}
+
266
+
267template<class CellTemplate>
+
268void TraversalTuner<CellTemplate>::rebuild(std::vector<CellTemplate> &cells, const std::array<unsigned long, 3> &dims,
+
269 double cellLength[3], double cutoff) {
+
270 _cells = &cells; // new - what for?
+
271 _dims = dims; // new - what for?
+
272
+
273 for (size_t i = 0ul; i < _traversals.size(); ++i) {
+
274 auto& [traversalPointerReference, traversalData] = _traversals[i];
+
275 // decide whether to initialize or rebuild
+
276 if (traversalPointerReference == nullptr) {
+
277 switch (i) {
+
278 case traversalNames ::ORIGINAL:
+
279 traversalPointerReference = new OriginalCellPairTraversal<CellTemplate>(cells, dims);
+
280 break;
+
281 case traversalNames::C08:
+
282 traversalPointerReference = new C08CellPairTraversal<CellTemplate>(cells, dims);
+
283 break;
+
284 case traversalNames::C04:
+
285 traversalPointerReference = new C04CellPairTraversal<CellTemplate>(cells, dims);
+
286 break;
+
287 case traversalNames::SLICED:
+
288 traversalPointerReference = new SlicedCellPairTraversal<CellTemplate>(cells, dims);
+
289 break;
+
290 case traversalNames::HS:
+
291 traversalPointerReference = new HalfShellTraversal<CellTemplate>(cells, dims);
+
292 break;
+
293 case traversalNames::MP:
+
294 traversalPointerReference = new MidpointTraversal<CellTemplate>(cells, dims);
+
295 break;
+
296 case traversalNames::NT:
+
297 traversalPointerReference =
+
298 new NeutralTerritoryTraversal<CellTemplate>(cells, dims, cellLength, cutoff);
+
299 break;
+
300 case traversalNames::C08ES:
+
301 traversalPointerReference = new C08CellPairTraversal<CellTemplate, true>(cells, dims);
+
302 break;
+
303 case traversalNames::QSCHED: {
+
304 mardyn_assert((std::is_base_of<ParticleCellBase, CellTemplate>::value));
+
305 auto *quiData = dynamic_cast<QuickschedTraversalData *>(traversalData);
+
306 traversalPointerReference = new QuickschedTraversal<CellTemplate>(cells, dims, quiData->taskBlockSize);
+
307 } break;
+
308 default:
+
309 Log::global_log->error() << "Unknown traversal data found in TraversalTuner._traversals!" << std::endl;
+
310 Simulation::exit(1);
+
311 }
+
312 }
+
313 traversalPointerReference->rebuild(cells, dims, cellLength, cutoff, traversalData);
+
314 }
+
315 _optimalTraversal = nullptr;
+
316}
+
317
+
318template<class CellTemplate>
+
319void TraversalTuner<CellTemplate>::traverseCellPairs(CellProcessor &cellProcessor) {
+
320 if (not _optimalTraversal) {
+
321 findOptimalTraversal();
+
322 }
+
323 _optimalTraversal->traverseCellPairs(cellProcessor);
+
324}
+
325
+
326template<class CellTemplate>
+
327inline void TraversalTuner<CellTemplate>::traverseCellPairs(traversalNames name,
+
328 CellProcessor& cellProcessor) {
+
329 if (name == getSelectedTraversal()) {
+
330 traverseCellPairs(cellProcessor);
+
331 } else {
+
332 SlicedCellPairTraversal<CellTemplate> slicedTraversal(*_cells, _dims);
+
333 switch(name) {
+
334 case SLICED:
+
335 slicedTraversal.traverseCellPairs(cellProcessor);
+
336 break;
+
337 default:
+
338 Log::global_log->error()<< "Calling traverseCellPairs(traversalName, CellProcessor&) for something else than the Sliced Traversal is disabled for now. Aborting." << std::endl;
+
339 mardyn_exit(1);
+
340 break;
+
341 }
+
342 }
+
343}
+
344
+
345template<class CellTemplate>
+
346void TraversalTuner<CellTemplate>::traverseCellPairsOuter(CellProcessor &cellProcessor) {
+
347 if (not _optimalTraversal) {
+
348 findOptimalTraversal();
+
349 }
+
350 _optimalTraversal->traverseCellPairsOuter(cellProcessor);
+
351}
+
352
+
353template<class CellTemplate>
+
354void TraversalTuner<CellTemplate>::traverseCellPairsInner(CellProcessor &cellProcessor, unsigned stage,
+
355 unsigned stageCount) {
+
356 if (not _optimalTraversal) {
+
357 findOptimalTraversal();
+
358 }
+
359 _optimalTraversal->traverseCellPairsInner(cellProcessor, stage, stageCount);
+
360}
+
361
+
362template<class CellTemplate>
+
363inline bool TraversalTuner<CellTemplate>::isTraversalApplicable(
+
364 traversalNames name, const std::array<unsigned long, 3> &dims) const {
+
365 bool ret = true;
+
366 switch(name) {
+
367 case SLICED:
+
368 ret = SlicedCellPairTraversal<CellTemplate>::isApplicable(dims);
+
369 break;
+
370 case QSCHED:
+
371#ifdef QUICKSCHED
+
372 ret = true;
+
373#else
+
374 ret = false;
+
375#endif
+
376 break;
+
377 case C08:
+
378 ret = true;
+
379 break;
+
380 case C04:
+
381 ret = true;
+
382 break;
+
383 case ORIGINAL:
+
384 ret = true;
+
385 break;
+
386 default:
+
387 Log::global_log->warning() << "unknown traversal given in TraversalTuner::isTraversalApplicable, assuming that is applicable" << std::endl;
+
388 }
+
389 return ret;
+
390}
+
391
+
392#endif //TRAVERSALTUNER_H_
C04CellPairTraversal
Definition: C04CellPairTraversal.h:20
C08CellPairTraversal
Definition: C08CellPairTraversal.h:20
CellPairTraversals
Definition: CellPairTraversals.h:21
@@ -464,22 +463,23 @@
MidpointTraversal
Definition: MidpointTraversal.h:18
NeutralTerritoryTraversal
Definition: NeutralTerritoryTraversal.h:25
OriginalCellPairTraversal
Definition: OriginalCellPairTraversal.h:21
-
QuickschedTraversal
Definition: QuickschedTraversal.h:27
-
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:162
+
QuickschedTraversal
Definition: QuickschedTraversal.h:26
+
Simulation::exit
static void exit(int exitcode)
Terminate simulation with given exit code.
Definition: Simulation.cpp:159
SlicedCellPairTraversal
Definition: SlicedCellPairTraversal.h:19
-
TraversalTuner
Definition: TraversalTuner.h:23
-
TraversalTuner::rebuild
void rebuild(std::vector< CellTemplate > &cells, const std::array< unsigned long, 3 > &dims, double cellLength[3], double cutoff)
Definition: TraversalTuner.h:269
+
TraversalTuner
Definition: TraversalTuner.h:22
+
TraversalTuner::rebuild
void rebuild(std::vector< CellTemplate > &cells, const std::array< unsigned long, 3 > &dims, double cellLength[3], double cutoff)
Definition: TraversalTuner.h:268
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
XMLfile::Query::const_iterator
Definition: xmlfile.h:240
XMLfile::Query
Definition: xmlfile.h:232
XMLfile::Query::begin
const_iterator begin() const
get starting iterator return an iterator to the first node
Definition: xmlfile.h:344
-
XMLfile::query
Query query(const std::string &querystr) const
perform a query return a query to a given query expression
-
XMLfile::changecurrentnode
long changecurrentnode(const std::string &nodepath=std::string("/"))
set current node set a node, relative queries start with
+
XMLfile::query
Query query(const std::string &querystr) const
perform a query return a query to a given query expression
Definition: xmlfile.cpp:123
+
XMLfile::changecurrentnode
long changecurrentnode(const std::string &nodepath=std::string("/"))
set current node set a node, relative queries start with
Definition: xmlfile.cpp:86
XMLfile::getNodeValue_int
int getNodeValue_int(const std::string &nodepath, int defaultvalue=0) const
get node value as int get the node content and convert it to an integer
Definition: xmlfile.h:514
XMLfile::getNodeValue_string
std::string getNodeValue_string(const std::string &nodepath, const std::string defaultvalue=std::string()) const
get node value as string get the node content
Definition: xmlfile.h:499
XMLfile::getNodeValue
unsigned long getNodeValue(const std::string &nodepath, T &value) const
get node value get the node content and convert it to a given type
Definition: xmlfile.h:484
XMLfile::getcurrentnodepath
std::string getcurrentnodepath() const
get current node path
Definition: xmlfile.h:477
xml_schema::name
::xsd::cxx::tree::name< char, token > name
C++ type corresponding to the Name XML Schema built-in type.
Definition: xml-schema.h:286
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
C04CellPairTraversalData
Definition: C04CellPairTraversal.h:16
C08CellPairTraversalData
Definition: C08CellPairTraversal.h:16
CellPairTraversalData
Definition: CellPairTraversals.h:16
@@ -487,12 +487,12 @@
MidpointTraversalData
Definition: MidpointTraversal.h:14
NeutralTerritoryTraversalData
Definition: NeutralTerritoryTraversal.h:13
OriginalCellPairTraversalData
Definition: OriginalCellPairTraversal.h:17
-
QuickschedTraversalData
Definition: QuickschedTraversal.h:22
+
QuickschedTraversalData
Definition: QuickschedTraversal.h:21
SlicedCellPairTraversalData
Definition: SlicedCellPairTraversal.h:15
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/UniformPseudoParticleContainer_8h_source.html b/UniformPseudoParticleContainer_8h_source.html index cd8b1a1e0a..a43a692366 100644 --- a/UniformPseudoParticleContainer_8h_source.html +++ b/UniformPseudoParticleContainer_8h_source.html @@ -353,7 +353,7 @@
346} /* namespace bhfmm */
347
348#endif /* UNIFORMPSEUDOPARTICLECONTAINER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FFTAccelerationAPI
Definition: FFTAccelerationAPI.h:22
HaloBufferNoOverlap
Definition: HaloBufferNoOverlap.h:11
@@ -373,7 +373,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/UnorderedVector_8h_source.html b/UnorderedVector_8h_source.html index befc7fef84..7906cc9b3e 100644 --- a/UnorderedVector_8h_source.html +++ b/UnorderedVector_8h_source.html @@ -108,7 +108,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VCP1CLJRMM_8h_source.html b/VCP1CLJRMM_8h_source.html index 7eb79b7940..e673738b6f 100644 --- a/VCP1CLJRMM_8h_source.html +++ b/VCP1CLJRMM_8h_source.html @@ -103,9 +103,9 @@
31
35 void initTraversal();
39 void preprocessCell(ParticleCell& /*cell*/) {}
-
40
+
40
41 void processCellPair(ParticleCell& cell1, ParticleCell& cell2, bool sumAll = false /* related to ZonalMethod */);
-
42
+
42
43 double processSingleMolecule(Molecule* /*m1*/, ParticleCell& /*cell2*/) {
44 return 0.0;
45 }
@@ -121,7 +121,7 @@
64 double getDtInvm() const {
65 return _dtInvm;
66 }
-
67
+
67
68private:
72 Domain & _domain;
73
@@ -193,7 +193,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VISWriter_8h_source.html b/VISWriter_8h_source.html index ac571f43db..810c40cc1a 100644 --- a/VISWriter_8h_source.html +++ b/VISWriter_8h_source.html @@ -79,13 +79,13 @@
7#include <list>
8
9class ParticleContainer;
-
10class DomainDecompBase;
+
10class DomainDecompBase;
11class Domain;
12
13class VISWriter : public PluginBase {
14public:
15 VISWriter(){}
-
29 VISWriter(unsigned long writeFrequency, std::string outputPrefix);
+
29 VISWriter(unsigned long writeFrequency, std::string outputPrefix);
30 ~VISWriter();
31
32 void readXML(XMLfileUnits& xmlconfig);
@@ -99,7 +99,7 @@
40 );
41 void finish(ParticleContainer *particleContainer,
42 DomainDecompBase *domainDecomp, Domain *domain);
-
43
+
43
44 std::string getPluginName() {
45 return std::string("VISWriter");
46 }
@@ -112,23 +112,22 @@
53};
54
55#endif /* VISWRITER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
VISWriter
Definition: VISWriter.h:13
-
VISWriter::VISWriter
VISWriter(unsigned long writeFrequency, std::string outputPrefix)
Writes out a file (using *.vis-format) containing coordinates + orientation (using quaternions) of ea...
VISWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: VISWriter.h:44
-
VISWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: VISWriter.cpp:60
-
VISWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: VISWriter.cpp:145
-
VISWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: VISWriter.cpp:53
-
VISWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: VISWriter.cpp:36
+
VISWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Method endStep will be called at the end of each time step.
Definition: VISWriter.cpp:58
+
VISWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method finish will be called at the end of the simulation.
Definition: VISWriter.cpp:143
+
VISWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: VISWriter.cpp:51
+
VISWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: VISWriter.cpp:34
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VTKGridCell_8h_source.html b/VTKGridCell_8h_source.html index 21dcf0be72..98a185ffdd 100644 --- a/VTKGridCell_8h_source.html +++ b/VTKGridCell_8h_source.html @@ -126,7 +126,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VTKGridVertex_8h_source.html b/VTKGridVertex_8h_source.html index 5dc4ddf443..bc28de71be 100644 --- a/VTKGridVertex_8h_source.html +++ b/VTKGridVertex_8h_source.html @@ -107,7 +107,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VTKGridWriterImplementation_8h_source.html b/VTKGridWriterImplementation_8h_source.html index 5730f8a398..865ce9eec9 100644 --- a/VTKGridWriterImplementation_8h_source.html +++ b/VTKGridWriterImplementation_8h_source.html @@ -132,16 +132,16 @@
VTKFile_t
Class corresponding to the VTKFile_t schema type.
Definition: vtk-punstructured.h:548
VTKGridCell
Definition: VTKGridCell.h:16
VTKGridWriterImplementation
Definition: VTKGridWriterImplementation.h:23
-
VTKGridWriterImplementation::initializeVTKFile
void initializeVTKFile()
Definition: VTKGridWriterImplementation.cpp:36
-
VTKGridWriterImplementation::plotCell
void plotCell(VTKGridCell &molecule)
Definition: VTKGridWriterImplementation.cpp:78
-
VTKGridWriterImplementation::VTKGridWriterImplementation
VTKGridWriterImplementation(int rank, const std::vector< double > *processorSpeeds=nullptr)
Definition: VTKGridWriterImplementation.cpp:18
-
VTKGridWriterImplementation::initializeParallelVTKFile
void initializeParallelVTKFile(const std::vector< std::string > &fileNames)
Definition: VTKGridWriterImplementation.cpp:148
-
VTKGridWriterImplementation::writeParallelVTKFile
void writeParallelVTKFile(const std::string &fileName)
Definition: VTKGridWriterImplementation.cpp:190
+
VTKGridWriterImplementation::initializeVTKFile
void initializeVTKFile()
Definition: VTKGridWriterImplementation.cpp:35
+
VTKGridWriterImplementation::plotCell
void plotCell(VTKGridCell &molecule)
Definition: VTKGridWriterImplementation.cpp:77
+
VTKGridWriterImplementation::VTKGridWriterImplementation
VTKGridWriterImplementation(int rank, const std::vector< double > *processorSpeeds=nullptr)
Definition: VTKGridWriterImplementation.cpp:17
+
VTKGridWriterImplementation::initializeParallelVTKFile
void initializeParallelVTKFile(const std::vector< std::string > &fileNames)
Definition: VTKGridWriterImplementation.cpp:147
+
VTKGridWriterImplementation::writeParallelVTKFile
void writeParallelVTKFile(const std::string &fileName)
Definition: VTKGridWriterImplementation.cpp:189
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VTKGridWriter_8h_source.html b/VTKGridWriter_8h_source.html index 12a6903a50..eb5bb0db41 100644 --- a/VTKGridWriter_8h_source.html +++ b/VTKGridWriter_8h_source.html @@ -144,7 +144,7 @@
92};
93
94#endif /* MARDYN_AUTOPAS */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
LinkedCells
Linked Cell Data Structure.
Definition: LinkedCells.h:51
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
@@ -153,12 +153,12 @@
VTKGridVertex
Definition: VTKGridVertex.h:14
VTKGridWriterImplementation
Definition: VTKGridWriterImplementation.h:23
VTKGridWriter
Definition: VTKGridWriter.h:24
-
VTKGridWriter::finish
virtual void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
NOP.
Definition: VTKGridWriter.cpp:188
-
VTKGridWriter::endStep
virtual void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: VTKGridWriter.cpp:43
-
VTKGridWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: VTKGridWriter.cpp:31
-
VTKGridWriter::VTKGridWriter
VTKGridWriter()
Definition: VTKGridWriter.cpp:21
+
VTKGridWriter::finish
virtual void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
NOP.
Definition: VTKGridWriter.cpp:187
+
VTKGridWriter::endStep
virtual void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: VTKGridWriter.cpp:42
+
VTKGridWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: VTKGridWriter.cpp:30
+
VTKGridWriter::VTKGridWriter
VTKGridWriter()
Definition: VTKGridWriter.cpp:20
VTKGridWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: VTKGridWriter.h:74
-
VTKGridWriter::init
virtual void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: VTKGridWriter.cpp:113
+
VTKGridWriter::init
virtual void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
Method init will be called at the begin of the simulation.
Definition: VTKGridWriter.cpp:112
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::name
::xsd::cxx::tree::name< char, token > name
C++ type corresponding to the Name XML Schema built-in type.
Definition: xml-schema.h:286
xml_schema::container
typedef::xsd::cxx::tree::type container
Alias for the anyType type.
Definition: xml-schema.h:128
@@ -166,7 +166,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VTKMoleculeWriterImplementation_8h_source.html b/VTKMoleculeWriterImplementation_8h_source.html index 734b6d5445..f3ae517b76 100644 --- a/VTKMoleculeWriterImplementation_8h_source.html +++ b/VTKMoleculeWriterImplementation_8h_source.html @@ -134,16 +134,16 @@
Quadrupole
Quadrupole center.
Definition: Site.h:343
VTKFile_t
Class corresponding to the VTKFile_t schema type.
Definition: vtk-punstructured.h:548
VTKMoleculeWriterImplementation
Definition: VTKMoleculeWriterImplementation.h:26
-
VTKMoleculeWriterImplementation::initializeParallelVTKFile
void initializeParallelVTKFile(const std::vector< std::string > &fileNames)
Definition: VTKMoleculeWriterImplementation.cpp:176
-
VTKMoleculeWriterImplementation::plotMolecule
void plotMolecule(Molecule &molecule)
Definition: VTKMoleculeWriterImplementation.cpp:74
-
VTKMoleculeWriterImplementation::initializeVTKFile
void initializeVTKFile()
Definition: VTKMoleculeWriterImplementation.cpp:33
-
VTKMoleculeWriterImplementation::writeParallelVTKFile
void writeParallelVTKFile(const std::string &fileName)
Definition: VTKMoleculeWriterImplementation.cpp:218
-
VTKMoleculeWriterImplementation::VTKMoleculeWriterImplementation
VTKMoleculeWriterImplementation(int rank, bool plotCenters=false)
Definition: VTKMoleculeWriterImplementation.cpp:17
+
VTKMoleculeWriterImplementation::initializeParallelVTKFile
void initializeParallelVTKFile(const std::vector< std::string > &fileNames)
Definition: VTKMoleculeWriterImplementation.cpp:175
+
VTKMoleculeWriterImplementation::plotMolecule
void plotMolecule(Molecule &molecule)
Definition: VTKMoleculeWriterImplementation.cpp:73
+
VTKMoleculeWriterImplementation::initializeVTKFile
void initializeVTKFile()
Definition: VTKMoleculeWriterImplementation.cpp:32
+
VTKMoleculeWriterImplementation::writeParallelVTKFile
void writeParallelVTKFile(const std::string &fileName)
Definition: VTKMoleculeWriterImplementation.cpp:217
+
VTKMoleculeWriterImplementation::VTKMoleculeWriterImplementation
VTKMoleculeWriterImplementation(int rank, bool plotCenters=false)
Definition: VTKMoleculeWriterImplementation.cpp:16
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VTKMoleculeWriter_8h_source.html b/VTKMoleculeWriter_8h_source.html index d71f0267c7..f9a9bd9811 100644 --- a/VTKMoleculeWriter_8h_source.html +++ b/VTKMoleculeWriter_8h_source.html @@ -128,24 +128,24 @@
78};
79
80#endif /* VTKWRITER_H_ */
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
VTKMoleculeWriterImplementation
Definition: VTKMoleculeWriterImplementation.h:26
VTKMoleculeWriter
Definition: VTKMoleculeWriter.h:22
VTKMoleculeWriter::getPluginName
std::string getPluginName()
return the name of the plugin
Definition: VTKMoleculeWriter.h:67
-
VTKMoleculeWriter::endStep
virtual void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: VTKMoleculeWriter.cpp:46
-
VTKMoleculeWriter::init
virtual void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
NOP.
Definition: VTKMoleculeWriter.cpp:108
-
VTKMoleculeWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: VTKMoleculeWriter.cpp:27
-
VTKMoleculeWriter::finish
virtual void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
NOP.
Definition: VTKMoleculeWriter.cpp:112
+
VTKMoleculeWriter::endStep
virtual void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep)
Definition: VTKMoleculeWriter.cpp:44
+
VTKMoleculeWriter::init
virtual void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
NOP.
Definition: VTKMoleculeWriter.cpp:106
+
VTKMoleculeWriter::readXML
void readXML(XMLfileUnits &xmlconfig)
Method readXML will be called once for each plugin section in the input file.
Definition: VTKMoleculeWriter.cpp:25
+
VTKMoleculeWriter::finish
virtual void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain)
NOP.
Definition: VTKMoleculeWriter.cpp:110
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
xml_schema::name
::xsd::cxx::tree::name< char, token > name
C++ type corresponding to the Name XML Schema built-in type.
Definition: xml-schema.h:286
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VTKWriter.html b/VTKWriter.html index 08e0e21a3b..5fdbf23003 100644 --- a/VTKWriter.html +++ b/VTKWriter.html @@ -88,7 +88,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Vector3_8h_source.html b/Vector3_8h_source.html index c529098fb6..ac99911143 100644 --- a/Vector3_8h_source.html +++ b/Vector3_8h_source.html @@ -245,12 +245,12 @@
bhfmm::Vector3
Definition: Vector3.h:34
type
Enumeration class corresponding to the type schema type.
Definition: vtk-unstructured.h:1198
bhfmm
Definition: L2PCellProcessor.cpp:15
-
bhfmm::operator*
SolidHarmonicsExpansion operator*(double scalar, SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:67
+
bhfmm::operator*
SolidHarmonicsExpansion operator*(double scalar, SolidHarmonicsExpansion RHS)
Definition: SolidHarmonicsExpansion.cpp:65
bhfmm::operator<<
std::ostream & operator<<(std::ostream &stream, const Vector3< type > &v)
Definition: Vector3.h:22
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizationTuner_8h_source.html b/VectorizationTuner_8h_source.html index 1cae362c8a..5d40e09627 100644 --- a/VectorizationTuner_8h_source.html +++ b/VectorizationTuner_8h_source.html @@ -223,7 +223,7 @@
270 double gflopsOwnZero, double gflopsPairZero) override;
271 void close() override;
272 private:
-
273 ofstream _myfile;
+
273 std::ofstream _myfile;
274 };
275
276 class VTWriterStatistics: public VTWriterI {
@@ -246,7 +246,7 @@
FlopCounter.h
A CellProcessor that produces Flop information.
CellProcessor
Definition: CellProcessor.h:29
Component
Class implementing molecules as rigid rotators consisting out of different interaction sites (LJcente...
Definition: Component.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
FlopCounter
Definition: FlopCounter.h:60
FullParticleCell
FullParticleCell data structure. Renamed from ParticleCell.
Definition: FullParticleCell.h:49
@@ -269,7 +269,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedCellProcessor_8cpp.html b/VectorizedCellProcessor_8cpp.html index fd8fdc54d6..3299e92cd1 100644 --- a/VectorizedCellProcessor_8cpp.html +++ b/VectorizedCellProcessor_8cpp.html @@ -131,7 +131,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedCellProcessor_8h.html b/VectorizedCellProcessor_8h.html index a28fd65dc8..15ea53118c 100644 --- a/VectorizedCellProcessor_8h.html +++ b/VectorizedCellProcessor_8h.html @@ -99,7 +99,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedCellProcessor_8h_source.html b/VectorizedCellProcessor_8h_source.html index 86e26791e8..50da4b3b48 100644 --- a/VectorizedCellProcessor_8h_source.html +++ b/VectorizedCellProcessor_8h_source.html @@ -108,9 +108,9 @@
55 }
56
60 void processCell(ParticleCell& cell);
-
61
+
61
62 void processCellPair(ParticleCell& cell1, ParticleCell& cell2, bool sumAll = false);
-
63
+
63
67 void postprocessCell(ParticleCell& /*cell*/) {}
71 void endTraversal();
72
@@ -296,17 +296,17 @@
VectorizedCellProcessor
Vectorized calculation of the force.
Definition: VectorizedCellProcessor.h:29
VectorizedCellProcessor::preprocessCell
void preprocessCell(ParticleCell &)
Load the CellDataSoA for cell.
Definition: VectorizedCellProcessor.h:51
VectorizedCellProcessor::postprocessCell
void postprocessCell(ParticleCell &)
Free the LennardJonesSoA for cell.
Definition: VectorizedCellProcessor.h:67
-
VectorizedCellProcessor::processCellPair
void processCellPair(ParticleCell &cell1, ParticleCell &cell2, bool sumAll=false)
Definition: VectorizedCellProcessor.cpp:2746
-
VectorizedCellProcessor::endTraversal
void endTraversal()
Store macroscopic values in the Domain.
Definition: VectorizedCellProcessor.cpp:124
-
VectorizedCellProcessor::processCell
void processCell(ParticleCell &cell)
Calculate forces between pairs of Molecules in cell.
Definition: VectorizedCellProcessor.cpp:2734
-
VectorizedCellProcessor::initTraversal
void initTraversal()
Reset macroscopic values to 0.0.
Definition: VectorizedCellProcessor.cpp:111
-
VectorizedCellProcessor::VectorizedCellProcessor
VectorizedCellProcessor(Domain &domain, double cutoffRadius, double LJcutoffRadius)
Construct and set up the internal parameter table.
Definition: VectorizedCellProcessor.cpp:21
+
VectorizedCellProcessor::processCellPair
void processCellPair(ParticleCell &cell1, ParticleCell &cell2, bool sumAll=false)
Definition: VectorizedCellProcessor.cpp:2744
+
VectorizedCellProcessor::endTraversal
void endTraversal()
Store macroscopic values in the Domain.
Definition: VectorizedCellProcessor.cpp:122
+
VectorizedCellProcessor::processCell
void processCell(ParticleCell &cell)
Calculate forces between pairs of Molecules in cell.
Definition: VectorizedCellProcessor.cpp:2732
+
VectorizedCellProcessor::initTraversal
void initTraversal()
Reset macroscopic values to 0.0.
Definition: VectorizedCellProcessor.cpp:109
+
VectorizedCellProcessor::VectorizedCellProcessor
VectorizedCellProcessor(Domain &domain, double cutoffRadius, double LJcutoffRadius)
Construct and set up the internal parameter table.
Definition: VectorizedCellProcessor.cpp:19
vcp::MaskVec
Definition: MaskVec.h:16
vcp::RealVec
Definition: RealVec.h:22
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedChargeP2PCellProcessor_8cpp.html b/VectorizedChargeP2PCellProcessor_8cpp.html index 7c8bd53390..cfd5c4edd6 100644 --- a/VectorizedChargeP2PCellProcessor_8cpp.html +++ b/VectorizedChargeP2PCellProcessor_8cpp.html @@ -135,7 +135,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedChargeP2PCellProcessor_8h.html b/VectorizedChargeP2PCellProcessor_8h.html index d4bdf05042..30c0118a23 100644 --- a/VectorizedChargeP2PCellProcessor_8h.html +++ b/VectorizedChargeP2PCellProcessor_8h.html @@ -107,7 +107,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedChargeP2PCellProcessor_8h_source.html b/VectorizedChargeP2PCellProcessor_8h_source.html index 2ceb66bbbd..f536439a6d 100644 --- a/VectorizedChargeP2PCellProcessor_8h_source.html +++ b/VectorizedChargeP2PCellProcessor_8h_source.html @@ -173,20 +173,20 @@
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
bhfmm::ParticleCellPointers
Definition: ParticleCellPointers.h:44
bhfmm::VectorizedChargeP2PCellProcessor
Vectorized calculation of the force.
Definition: VectorizedChargeP2PCellProcessor.h:32
-
bhfmm::VectorizedChargeP2PCellProcessor::processCellPair
void processCellPair(ParticleCellPointers &cell1, ParticleCellPointers &cell2)
Calculate forces between pairs of Molecules in cell1 and cell2.
Definition: VectorizedChargeP2PCellProcessor.cpp:541
-
bhfmm::VectorizedChargeP2PCellProcessor::processCell
void processCell(ParticleCellPointers &cell)
Calculate forces between pairs of Molecules in cell.
Definition: VectorizedChargeP2PCellProcessor.cpp:531
-
bhfmm::VectorizedChargeP2PCellProcessor::preprocessCell
void preprocessCell(ParticleCellPointers &cell)
Load the CellDataSoA for cell.
Definition: VectorizedChargeP2PCellProcessor.cpp:117
-
bhfmm::VectorizedChargeP2PCellProcessor::initTraversal
void initTraversal()
Reset macroscopic values to 0.0.
Definition: VectorizedChargeP2PCellProcessor.cpp:74
-
bhfmm::VectorizedChargeP2PCellProcessor::endTraversal
void endTraversal()
Store macroscopic values in the Domain.
Definition: VectorizedChargeP2PCellProcessor.cpp:87
-
bhfmm::VectorizedChargeP2PCellProcessor::VectorizedChargeP2PCellProcessor
VectorizedChargeP2PCellProcessor(Domain &domain, double cutoffRadius=0, double LJcutoffRadius=0)
Construct and set up the internal parameter table.
Definition: VectorizedChargeP2PCellProcessor.cpp:20
-
bhfmm::VectorizedChargeP2PCellProcessor::postprocessCell
void postprocessCell(ParticleCellPointers &cell)
Free the LennardJonesSoA for cell.
Definition: VectorizedChargeP2PCellProcessor.cpp:194
+
bhfmm::VectorizedChargeP2PCellProcessor::processCellPair
void processCellPair(ParticleCellPointers &cell1, ParticleCellPointers &cell2)
Calculate forces between pairs of Molecules in cell1 and cell2.
Definition: VectorizedChargeP2PCellProcessor.cpp:539
+
bhfmm::VectorizedChargeP2PCellProcessor::processCell
void processCell(ParticleCellPointers &cell)
Calculate forces between pairs of Molecules in cell.
Definition: VectorizedChargeP2PCellProcessor.cpp:529
+
bhfmm::VectorizedChargeP2PCellProcessor::preprocessCell
void preprocessCell(ParticleCellPointers &cell)
Load the CellDataSoA for cell.
Definition: VectorizedChargeP2PCellProcessor.cpp:115
+
bhfmm::VectorizedChargeP2PCellProcessor::initTraversal
void initTraversal()
Reset macroscopic values to 0.0.
Definition: VectorizedChargeP2PCellProcessor.cpp:72
+
bhfmm::VectorizedChargeP2PCellProcessor::endTraversal
void endTraversal()
Store macroscopic values in the Domain.
Definition: VectorizedChargeP2PCellProcessor.cpp:85
+
bhfmm::VectorizedChargeP2PCellProcessor::VectorizedChargeP2PCellProcessor
VectorizedChargeP2PCellProcessor(Domain &domain, double cutoffRadius=0, double LJcutoffRadius=0)
Construct and set up the internal parameter table.
Definition: VectorizedChargeP2PCellProcessor.cpp:18
+
bhfmm::VectorizedChargeP2PCellProcessor::postprocessCell
void postprocessCell(ParticleCellPointers &cell)
Free the LennardJonesSoA for cell.
Definition: VectorizedChargeP2PCellProcessor.cpp:192
vcp::MaskVec
Definition: MaskVec.h:16
vcp::RealVec
Definition: RealVec.h:22
bhfmm
Definition: L2PCellProcessor.cpp:15
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedLJP2PCellProcessor_8cpp.html b/VectorizedLJP2PCellProcessor_8cpp.html index f2bd0e448f..686c525db1 100644 --- a/VectorizedLJP2PCellProcessor_8cpp.html +++ b/VectorizedLJP2PCellProcessor_8cpp.html @@ -96,7 +96,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedLJP2PCellProcessor_8h.html b/VectorizedLJP2PCellProcessor_8h.html index 11ec6330f3..d2b168d0f8 100644 --- a/VectorizedLJP2PCellProcessor_8h.html +++ b/VectorizedLJP2PCellProcessor_8h.html @@ -106,7 +106,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VectorizedLJP2PCellProcessor_8h_source.html b/VectorizedLJP2PCellProcessor_8h_source.html index 7b6e2e7a97..c6bc264f3f 100644 --- a/VectorizedLJP2PCellProcessor_8h_source.html +++ b/VectorizedLJP2PCellProcessor_8h_source.html @@ -107,7 +107,7 @@
54 }
55
59 void processCell(ParticleCell& cell);
-
60
+
60
61 void processCellPair(ParticleCell& c1, ParticleCell& c2, bool sumAll = false);
65 void postprocessCell(ParticleCell& /*cell*/) {}
69 void endTraversal();
@@ -189,11 +189,11 @@
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
FullParticleCell
FullParticleCell data structure. Renamed from ParticleCell.
Definition: FullParticleCell.h:49
bhfmm::VectorizedLJP2PCellProcessor
Vectorized calculation of the force.
Definition: VectorizedLJP2PCellProcessor.h:31
-
bhfmm::VectorizedLJP2PCellProcessor::processCell
void processCell(ParticleCell &cell)
Calculate forces between pairs of Molecules in cell.
Definition: VectorizedLJP2PCellProcessor.cpp:469
-
bhfmm::VectorizedLJP2PCellProcessor::processCellPair
void processCellPair(ParticleCell &c1, ParticleCell &c2, bool sumAll=false)
Definition: VectorizedLJP2PCellProcessor.cpp:480
-
bhfmm::VectorizedLJP2PCellProcessor::VectorizedLJP2PCellProcessor
VectorizedLJP2PCellProcessor(Domain &domain, double cutoffRadius, double LJcutoffRadius)
Construct and set up the internal parameter table.
Definition: VectorizedLJP2PCellProcessor.cpp:21
-
bhfmm::VectorizedLJP2PCellProcessor::initTraversal
void initTraversal()
Reset macroscopic values to 0.0.
Definition: VectorizedLJP2PCellProcessor.cpp:120
-
bhfmm::VectorizedLJP2PCellProcessor::endTraversal
void endTraversal()
Store macroscopic values in the Domain.
Definition: VectorizedLJP2PCellProcessor.cpp:134
+
bhfmm::VectorizedLJP2PCellProcessor::processCell
void processCell(ParticleCell &cell)
Calculate forces between pairs of Molecules in cell.
Definition: VectorizedLJP2PCellProcessor.cpp:467
+
bhfmm::VectorizedLJP2PCellProcessor::processCellPair
void processCellPair(ParticleCell &c1, ParticleCell &c2, bool sumAll=false)
Definition: VectorizedLJP2PCellProcessor.cpp:478
+
bhfmm::VectorizedLJP2PCellProcessor::VectorizedLJP2PCellProcessor
VectorizedLJP2PCellProcessor(Domain &domain, double cutoffRadius, double LJcutoffRadius)
Construct and set up the internal parameter table.
Definition: VectorizedLJP2PCellProcessor.cpp:19
+
bhfmm::VectorizedLJP2PCellProcessor::initTraversal
void initTraversal()
Reset macroscopic values to 0.0.
Definition: VectorizedLJP2PCellProcessor.cpp:118
+
bhfmm::VectorizedLJP2PCellProcessor::endTraversal
void endTraversal()
Store macroscopic values in the Domain.
Definition: VectorizedLJP2PCellProcessor.cpp:132
bhfmm::VectorizedLJP2PCellProcessor::preprocessCell
void preprocessCell(ParticleCell &)
Load the CellDataSoA for cell.
Definition: VectorizedLJP2PCellProcessor.h:50
bhfmm::VectorizedLJP2PCellProcessor::postprocessCell
void postprocessCell(ParticleCell &)
Free the LennardJonesSoA for cell.
Definition: VectorizedLJP2PCellProcessor.h:65
vcp::MaskVec
Definition: MaskVec.h:16
@@ -202,7 +202,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Velocity3dProfile_8h_source.html b/Velocity3dProfile_8h_source.html index 8c5fbf40c5..73d6496371 100644 --- a/Velocity3dProfile_8h_source.html +++ b/Velocity3dProfile_8h_source.html @@ -105,7 +105,7 @@
36 _global3dProfile[uID][d] = domainDecomp->collCommGetDouble();
37 }
38 }
-
39 void output(string prefix, long unsigned accumulatedDatasets) final;
+
39 void output(std::string prefix, long unsigned accumulatedDatasets) final;
40 void reset(unsigned long uID) final {
41 for(unsigned d = 0; d < 3; d++){
42 _local3dProfile[uID][d] = 0.0;
@@ -123,26 +123,27 @@
54 // Global 3D Profile
55 std::map<unsigned, std::array<double,3>> _global3dProfile;
56
-
57 void writeDataEntry(unsigned long uID, ofstream &outfile) const final;
+
57 void writeDataEntry(unsigned long uID, std::ofstream &outfile) const final;
58};
59
60
61#endif //MARDYN_TRUNK_VELOCITYPROFILE_H
DensityProfile
Outputs the number density of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DensityProfile.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
Velocity3dProfile
Outputs the XYZ velocity components per bin specified by Sampling grid in KartesianProfile.
Definition: Velocity3dProfile.h:18
Velocity3dProfile::comms
int comms() final
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
Definition: Velocity3dProfile.h:47
-
Velocity3dProfile::output
void output(string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: Velocity3dProfile.cpp:9
+
Velocity3dProfile::output
void output(std::string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: Velocity3dProfile.cpp:9
Velocity3dProfile::collectRetrieve
void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
Definition: Velocity3dProfile.h:34
Velocity3dProfile::reset
void reset(unsigned long uID) final
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
Definition: Velocity3dProfile.h:40
Velocity3dProfile::collectAppend
void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID) final
Append all necessary communication per bin to the DomainDecomposition. Append from e....
Definition: Velocity3dProfile.h:29
Velocity3dProfile::record
void record(Molecule &mol, unsigned long uID) final
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
Definition: Velocity3dProfile.h:24
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VelocityAbsProfile_8h_source.html b/VelocityAbsProfile_8h_source.html index a3103b2d46..1ca634ed14 100644 --- a/VelocityAbsProfile_8h_source.html +++ b/VelocityAbsProfile_8h_source.html @@ -104,7 +104,7 @@
35 void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final {
36 _globalProfile[uID] = domainDecomp->collCommGetDouble();
37 }
-
38 void output(string prefix, long unsigned accumulatedDatasets) final;
+
38 void output(std::string prefix, long unsigned accumulatedDatasets) final;
39 void reset(unsigned long uID) final {
40 _localProfile[uID] = 0.0;
41 _globalProfile[uID] = 0.0;
@@ -120,25 +120,26 @@
51 // Global 1D Profile
52 std::map<unsigned, double> _globalProfile;
53
-
54 void writeDataEntry(unsigned long uID, ofstream &outfile) const final;
+
54 void writeDataEntry(unsigned long uID, std::ofstream &outfile) const final;
55};
56
57#endif //MARDYN_TRUNK_VELOCITYABSPROFILE_H
DensityProfile
Outputs the number density of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DensityProfile.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
VelocityAbsProfile
Outputs the magnitude of the velocity per bin specified by Sampling grid in KartesianProfile.
Definition: VelocityAbsProfile.h:16
VelocityAbsProfile::record
void record(Molecule &mol, unsigned long uID) final
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
Definition: VelocityAbsProfile.h:22
VelocityAbsProfile::collectAppend
void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID) final
Append all necessary communication per bin to the DomainDecomposition. Append from e....
Definition: VelocityAbsProfile.h:32
VelocityAbsProfile::collectRetrieve
void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
Definition: VelocityAbsProfile.h:35
+
VelocityAbsProfile::output
void output(std::string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: VelocityAbsProfile.cpp:8
VelocityAbsProfile::comms
int comms() final
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
Definition: VelocityAbsProfile.h:44
-
VelocityAbsProfile::output
void output(string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: VelocityAbsProfile.cpp:8
VelocityAbsProfile::reset
void reset(unsigned long uID) final
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
Definition: VelocityAbsProfile.h:39
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VelocityAssignerBase_8h_source.html b/VelocityAssignerBase_8h_source.html index c74333f5cc..038cdc5a60 100644 --- a/VelocityAssignerBase_8h_source.html +++ b/VelocityAssignerBase_8h_source.html @@ -92,7 +92,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VelocityCellProcessorRMM_8h_source.html b/VelocityCellProcessorRMM_8h_source.html index 8592de8aa7..80e14ecafd 100644 --- a/VelocityCellProcessorRMM_8h_source.html +++ b/VelocityCellProcessorRMM_8h_source.html @@ -130,7 +130,7 @@
58 _summv2 = 0.0;
59 } // end pragma omp master
60
-
61 global_log->debug() << "VelocityCellProcessorRMM::initTraversal()." << std::endl;
+
61 Log::global_log->debug() << "VelocityCellProcessorRMM::initTraversal()." << std::endl;
62 }
63
64 void endTraversal() {
@@ -247,7 +247,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VelocityExchange_8h_source.html b/VelocityExchange_8h_source.html index d1f43f0930..bd08980b68 100644 --- a/VelocityExchange_8h_source.html +++ b/VelocityExchange_8h_source.html @@ -151,7 +151,7 @@
111 static PluginBase* createInstance() { return new VelocityExchange(); }
112};
CommVar
Definition: CommVar.h:17
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
@@ -168,7 +168,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VelocityScalingThermostat_8h_source.html b/VelocityScalingThermostat_8h_source.html index 48a8a653ae..b32103db99 100644 --- a/VelocityScalingThermostat_8h_source.html +++ b/VelocityScalingThermostat_8h_source.html @@ -117,7 +117,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/Virial2DProfile_8h_source.html b/Virial2DProfile_8h_source.html index eaf521a8a3..9914f2369f 100644 --- a/Virial2DProfile_8h_source.html +++ b/Virial2DProfile_8h_source.html @@ -93,8 +93,8 @@
21 }
22
23 ~Virial2DProfile() final = default;
-
24
-
25
+
24
+
25
26 void record(Molecule& mol, unsigned long uID) final {
27 for (unsigned short d = 0; d < 3; d++) {
28 _local3dProfile[uID][d] += mol.Vi(d);
@@ -114,7 +114,7 @@
42 }
43
44
-
45 void output(string prefix, long unsigned accumulatedDatasets) final;
+
45 void output(std::string prefix, long unsigned accumulatedDatasets) final;
46
47 void reset(unsigned long uID) final {
48 for (unsigned d = 0; d < 3; d++) {
@@ -136,7 +136,7 @@
64 std::map<unsigned, std::array<double, 3>> _global3dProfile;
65
66 // Only needed because its abstract, all output handled by output()
-
67 void writeDataEntry(unsigned long uID, ofstream& outfile) const final;
+
67 void writeDataEntry(unsigned long uID, std::ofstream& outfile) const final;
68
69};
70
@@ -144,7 +144,7 @@
72#endif //MARDYN_VIRIAL_H
DOFProfile
Records (NO OUTPUT) the DOF of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DOFProfile.h:15
DensityProfile
Outputs the number density of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DensityProfile.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
KineticProfile
Records (NO OUTPUT) the 2xKinetic Profile of molecules per bin specified by Sampling grid in Kartesia...
Definition: KineticProfile.h:14
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
@@ -152,13 +152,14 @@
Virial2DProfile::record
void record(Molecule &mol, unsigned long uID) final
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
Definition: Virial2DProfile.h:26
Virial2DProfile::collectRetrieve
void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
Definition: Virial2DProfile.h:38
Virial2DProfile::comms
int comms() final
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
Definition: Virial2DProfile.h:54
-
Virial2DProfile::output
void output(string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: Virial2DProfile.cpp:11
Virial2DProfile::reset
void reset(unsigned long uID) final
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
Definition: Virial2DProfile.h:47
+
Virial2DProfile::output
void output(std::string prefix, long unsigned accumulatedDatasets) final
Whatever is necessary to output for this profile.
Definition: Virial2DProfile.cpp:11
Virial2DProfile::collectAppend
void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID) final
Append all necessary communication per bin to the DomainDecomposition. Append from e....
Definition: Virial2DProfile.h:32
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/VirialProfile_8h_source.html b/VirialProfile_8h_source.html index 1e3a649cd7..a514aea3b5 100644 --- a/VirialProfile_8h_source.html +++ b/VirialProfile_8h_source.html @@ -114,7 +114,7 @@
42 }
43 }
44
-
50 void output(string prefix, long unsigned accumulatedDatasets) final;
+
50 void output(std::string prefix, long unsigned accumulatedDatasets) final;
51
52 void reset(unsigned long uID) final {
53 for (unsigned d = 0; d < 3; d++) {
@@ -134,27 +134,28 @@
67 std::map<unsigned, std::array<double, 3>> _global3dProfile;
68
69 // Only needed because its abstract, all output handled by output()
-
70 void writeDataEntry(unsigned long uID, ofstream& outfile) const final {};
+
70 void writeDataEntry(unsigned long uID, std::ofstream& outfile) const final {};
71
72};
73
74
75#endif //MARDYN_VIRIAL_H
DensityProfile
Outputs the number density of molecules per bin specified by Sampling grid in KartesianProfile.
Definition: DensityProfile.h:14
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
FullMolecule
FullMolecule modeled as LJ sphere with point polarities.
Definition: FullMolecule.h:18
ProfileBase
Base class for all Profile outputs used by KartesianProfile.
Definition: ProfileBase.h:34
VirialProfile
Definition: VirialProfile.h:20
+
VirialProfile::output
void output(std::string prefix, long unsigned accumulatedDatasets) final
Definition: VirialProfile.cpp:8
VirialProfile::collectAppend
void collectAppend(DomainDecompBase *domainDecomp, unsigned long uID) final
Append all necessary communication per bin to the DomainDecomposition. Append from e....
Definition: VirialProfile.h:33
VirialProfile::collectRetrieve
void collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) final
Get global values after AllReduceSum per bin. Write to e.g. _globalProfile.
Definition: VirialProfile.h:39
-
VirialProfile::output
void output(string prefix, long unsigned accumulatedDatasets) final
Definition: VirialProfile.cpp:8
VirialProfile::reset
void reset(unsigned long uID) final
Used to reset all array contents for a specific uID in order to start the next recording timeframe.
Definition: VirialProfile.h:52
VirialProfile::comms
int comms() final
1D profiles like a number density profile should return 1 here. 3D profiles that have 3 entries per b...
Definition: VirialProfile.h:59
VirialProfile::record
void record(Molecule &mol, unsigned long uID) final
The recording step defines what kind of data needs to be recorded for a single molecule with a corres...
Definition: VirialProfile.h:27
+
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/WallPotential_8h_source.html b/WallPotential_8h_source.html index 8a3046f879..0d58ff777d 100644 --- a/WallPotential_8h_source.html +++ b/WallPotential_8h_source.html @@ -138,7 +138,7 @@
94 };
95
96 void init(ParticleContainer* particleContainer, DomainDecompBase* domainDecomp, Domain* domain) override {
-
97 global_log -> debug() << "[WallPotential] Wall enabled" << std::endl;
+
97 Log::global_log -> debug() << "[WallPotential] Wall enabled" << std::endl;
98 _domain = domain;
99 }
100
@@ -155,11 +155,11 @@
111
112 static PluginBase* createInstance(){return new WallPotential();}
113
-
114 void initializeLJ93(const vector<Component> *components, double in_rhoWall, double in_sigWall, double in_epsWall,
-
115 vector<double> in_xi, vector<double> in_eta, double in_yOffWall, double in_yWallCut);
+
114 void initializeLJ93(const std::vector<Component> *components, double in_rhoWall, double in_sigWall, double in_epsWall,
+
115 std::vector<double> in_xi, std::vector<double> in_eta, double in_yOffWall, double in_yWallCut);
116
-
117 void initializeLJ1043(const vector<Component> *components, double in_rhoWall, double in_sigWall, double in_epsWall,
-
118 vector<double> in_xi, vector<double> in_eta, double in_yOffWall, double in_yWallCut);
+
117 void initializeLJ1043(const std::vector<Component> *components, double in_rhoWall, double in_sigWall, double in_epsWall,
+
118 std::vector<double> in_xi, std::vector<double> in_eta, double in_yOffWall, double in_yWallCut);
119
120 void calcTSLJ_9_3(ParticleContainer *partContainer);
121
@@ -171,17 +171,17 @@
127
128
129#endif //MARDYN_TRUNK_WALLPOTENTIAL_H
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
WallPotential
WallPotential exerts the force of a Lennard-Jones potential on the Lennard-Jones centers of particles...
Definition: WallPotential.h:42
-
WallPotential::initializeLJ93
void initializeLJ93(const vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, vector< double > in_xi, vector< double > in_eta, double in_yOffWall, double in_yWallCut)
initialize the LJ93 potential and calculate potential energy at cutoff
Definition: WallPotential.cpp:105
WallPotential::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: WallPotential.h:110
WallPotential::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: WallPotential.h:107
+
WallPotential::initializeLJ93
void initializeLJ93(const std::vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, std::vector< double > in_xi, std::vector< double > in_eta, double in_yOffWall, double in_yWallCut)
initialize the LJ93 potential and calculate potential energy at cutoff
Definition: WallPotential.cpp:105
WallPotential::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: WallPotential.h:103
-
WallPotential::initializeLJ1043
void initializeLJ1043(const vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, vector< double > in_xi, vector< double > in_eta, double in_yOffWall, double in_yWallCut)
initialize the LJ1043 potential and calculate potential energy at cutoff
Definition: WallPotential.cpp:147
WallPotential::siteWiseForces
void siteWiseForces(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, unsigned long simstep) override
gets called during the force update step. calls the appropriate calculation function.
Definition: WallPotential.cpp:351
+
WallPotential::initializeLJ1043
void initializeLJ1043(const std::vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, std::vector< double > in_xi, std::vector< double > in_eta, double in_yOffWall, double in_yWallCut)
initialize the LJ1043 potential and calculate potential energy at cutoff
Definition: WallPotential.cpp:147
WallPotential::calcTSLJ_10_4
void calcTSLJ_10_4(ParticleContainer *partContainer)
Calculate and add forces to lennard-jones-sites. Also calculate new potential energy addition.
Definition: WallPotential.cpp:264
WallPotential::readXML
void readXML(XMLfileUnits &xmlconfig) override
reads in configuration from config.xml. see class doc for example .xml
Definition: WallPotential.cpp:13
WallPotential::calcTSLJ_9_3
void calcTSLJ_9_3(ParticleContainer *partContainer)
Calculate and add forces to lennard-jones-sites. Also calculate new potential energy addition.
Definition: WallPotential.cpp:193
@@ -191,7 +191,7 @@
-Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
diff --git a/WignerMatrix_8h_source.html b/WignerMatrix_8h_source.html index b4f6a90529..dc0185746a 100644 --- a/WignerMatrix_8h_source.html +++ b/WignerMatrix_8h_source.html @@ -186,7 +186,7 @@
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/WrapOpenMP_8h_source.html b/WrapOpenMP_8h_source.html index 74fb03153c..6ea57c7fb6 100644 --- a/WrapOpenMP_8h_source.html +++ b/WrapOpenMP_8h_source.html @@ -119,7 +119,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/XyzWriter_8h_source.html b/XyzWriter_8h_source.html index a76032fc3a..a2cbae7841 100644 --- a/XyzWriter_8h_source.html +++ b/XyzWriter_8h_source.html @@ -99,7 +99,7 @@
45 std::string getPluginName() override {
46 return std::string("XyzWriter");
47 }
-
48
+
48
49 static PluginBase* createInstance() { return new XyzWriter(); }
50private:
51 std::string _outputPrefix;
@@ -109,22 +109,22 @@
55};
56
57#endif // SRC_IO_XYZWRITER_H_
-
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:51
+
DomainDecompBase
handle boundary region and multiple processes
Definition: DomainDecompBase.h:53
Domain
This class is used to read in the phasespace and to handle macroscopic values.
Definition: Domain.h:47
ParticleContainer
This Interface is used to get access to particles and pairs of particles.
Definition: ParticleContainer.h:69
PluginBase
The PluginBase class provides the interface for any kind of output/plugin classes - called "(output) ...
Definition: PluginBase.h:47
XMLfileUnits
XML file with unit attributes abstraction.
Definition: xmlfileUnits.h:25
XyzWriter
Writes out an ASCII file in the *.xyz-format containing coordinates of each molecule.
Definition: XyzWriter.h:14
XyzWriter::getPluginName
std::string getPluginName() override
return the name of the plugin
Definition: XyzWriter.h:45
-
XyzWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: XyzWriter.cpp:37
-
XyzWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: XyzWriter.cpp:34
-
XyzWriter::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DecompWriter.
Definition: XyzWriter.cpp:18
-
XyzWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: XyzWriter.cpp:110
+
XyzWriter::endStep
void endStep(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain, unsigned long simstep) override
Method endStep will be called at the end of each time step.
Definition: XyzWriter.cpp:34
+
XyzWriter::init
void init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method init will be called at the begin of the simulation.
Definition: XyzWriter.cpp:31
+
XyzWriter::readXML
void readXML(XMLfileUnits &xmlconfig) override
Read in XML configuration for DecompWriter.
Definition: XyzWriter.cpp:15
+
XyzWriter::finish
void finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) override
Method finish will be called at the end of the simulation.
Definition: XyzWriter.cpp:107
xml_schema::string
::xsd::cxx::tree::string< char, simple_type > string
C++ type corresponding to the string XML Schema built-in type.
Definition: xml-schema.h:268
-Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
diff --git a/ZonalMethod_8h_source.html b/ZonalMethod_8h_source.html index 5436b2fda8..c99ca10e75 100644 --- a/ZonalMethod_8h_source.html +++ b/ZonalMethod_8h_source.html @@ -130,7 +130,7 @@
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diff --git a/citelist.html b/citelist.html index 7be782d7c5..39fc3680e3 100644 --- a/citelist.html +++ b/citelist.html @@ -70,7 +70,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classALLLoadBalancer-members.html b/classALLLoadBalancer-members.html index e9ad473204..e3b127facf 100644 --- a/classALLLoadBalancer-members.html +++ b/classALLLoadBalancer-members.html @@ -78,7 +78,7 @@

Functions

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diff --git a/classCavityEnsemble-members.html b/classCavityEnsemble-members.html index 1d6968d060..d606d178c2 100644 --- a/classCavityEnsemble-members.html +++ b/classCavityEnsemble-members.html @@ -92,7 +92,7 @@
-Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classCavityEnsemble.html b/classCavityEnsemble.html index 88a1ba4ff0..e071fa811f 100644 --- a/classCavityEnsemble.html +++ b/classCavityEnsemble.html @@ -114,12 +114,12 @@ unsigned long numCavities ()   - -map< unsigned long, Molecule * > * particleContainer () -  - -map< unsigned long, Molecule * > activeParticleContainer () -  + +std::map< unsigned long, Molecule * > * particleContainer () +  + +std::map< unsigned long, Molecule * > activeParticleContainer () +  void determineBoundary ()   @@ -137,7 +137,7 @@
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classDOFProfile-members.html b/classDOFProfile-members.html index 26fa05387c..214a0a6e89 100644 --- a/classDOFProfile-members.html +++ b/classDOFProfile-members.html @@ -77,19 +77,19 @@ comms() finalDOFProfileinlinevirtual getGlobalDOF(unsigned long uid) const (defined in DOFProfile)DOFProfileinline init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets) finalDOFProfilevirtual + output(std::string prefix, long unsigned accumulatedDatasets) finalDOFProfilevirtual record(Molecule &mol, unsigned long uID) finalDOFProfileinlinevirtual reset(unsigned long uID) finalDOFProfileinlinevirtual - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~DOFProfile() final=default (defined in DOFProfile)DOFProfile ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual
-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classDOFProfile.html b/classDOFProfile.html index 2b145bcc83..46ca291470 100644 --- a/classDOFProfile.html +++ b/classDOFProfile.html @@ -95,9 +95,9 @@ void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID) final  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -void output (string prefix, long unsigned accumulatedDatasets) final - Whatever is necessary to output for this profile. More...
-  +void output (std::string prefix, long unsigned accumulatedDatasets) final + Whatever is necessary to output for this profile. More...
+  void reset (unsigned long uID) final  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -115,22 +115,22 @@

Additional Inherited Members

- Protected Member Functions inherited from ProfileBase -void writeMatrix (ofstream &outfile) - Matrix writing routine to avoid code duplication. More...
-  - -void writeKartMatrix (ofstream &outfile) -  -void writeSimpleMatrix (ofstream &outfile) - STUB for simple Matrix output without headers. More...
-  -void writeCylMatrix (ofstream &outfile) - cylinder Matrix output More...
-  +void writeMatrix (std::ofstream &outfile) + Matrix writing routine to avoid code duplication. More...
+  + +void writeKartMatrix (std::ofstream &outfile) +  +void writeSimpleMatrix (std::ofstream &outfile) + STUB for simple Matrix output without headers. More...
+  +void writeCylMatrix (std::ofstream &outfile) + cylinder Matrix output More...
+  - Protected Attributes inherited from ProfileBase - -string _profilePrefix -  + +std::string _profilePrefix +  SamplingInformation _samplInfo   @@ -265,8 +265,8 @@

-

◆ output()

+ +

◆ output()

@@ -277,7 +277,7 @@

void DOFProfile::output ( - string  + std::string  prefix, @@ -307,7 +307,7 @@

ProfileBase.

+

Implements ProfileBase.

@@ -401,7 +401,7 @@

-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classDensityControl-members.html b/classDensityControl-members.html index 5ffcd490e6..17e0ab2e07 100644 --- a/classDensityControl-members.html +++ b/classDensityControl-members.html @@ -88,7 +88,7 @@
-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classDensityControl.html b/classDensityControl.html index 9edf5094fc..e4ed155aab 100644 --- a/classDensityControl.html +++ b/classDensityControl.html @@ -426,7 +426,7 @@

-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classDensityProfile-members.html b/classDensityProfile-members.html index 131350fb65..c13e077642 100644 --- a/classDensityProfile-members.html +++ b/classDensityProfile-members.html @@ -77,19 +77,19 @@ comms() finalDensityProfileinlinevirtual getGlobalNumber(unsigned long uid) const (defined in DensityProfile)DensityProfileinline init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets) finalDensityProfilevirtual + output(std::string prefix, long unsigned accumulatedDatasets) finalDensityProfilevirtual record(Molecule &mol, unsigned long uID) finalDensityProfileinlinevirtual reset(unsigned long uID) finalDensityProfileinlinevirtual - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~DensityProfile() final=default (defined in DensityProfile)DensityProfile ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual
-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classDensityProfile.html b/classDensityProfile.html index a3e06d276a..6617612c59 100644 --- a/classDensityProfile.html +++ b/classDensityProfile.html @@ -95,9 +95,9 @@ void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID) final  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -void output (string prefix, long unsigned accumulatedDatasets) final - Whatever is necessary to output for this profile. More...
-  +void output (std::string prefix, long unsigned accumulatedDatasets) final + Whatever is necessary to output for this profile. More...
+  void reset (unsigned long uID) final  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -115,22 +115,22 @@

Additional Inherited Members

- Protected Member Functions inherited from ProfileBase -void writeMatrix (ofstream &outfile) - Matrix writing routine to avoid code duplication. More...
-  - -void writeKartMatrix (ofstream &outfile) -  -void writeSimpleMatrix (ofstream &outfile) - STUB for simple Matrix output without headers. More...
-  -void writeCylMatrix (ofstream &outfile) - cylinder Matrix output More...
-  +void writeMatrix (std::ofstream &outfile) + Matrix writing routine to avoid code duplication. More...
+  + +void writeKartMatrix (std::ofstream &outfile) +  +void writeSimpleMatrix (std::ofstream &outfile) + STUB for simple Matrix output without headers. More...
+  +void writeCylMatrix (std::ofstream &outfile) + cylinder Matrix output More...
+  - Protected Attributes inherited from ProfileBase - -string _profilePrefix -  + +std::string _profilePrefix +  SamplingInformation _samplInfo   @@ -265,8 +265,8 @@

-

◆ output()

+ +

◆ output()

@@ -277,7 +277,7 @@

void DensityProfile::output ( - string  + std::string  prefix, @@ -307,7 +307,7 @@

ProfileBase.

+

Implements ProfileBase.

@@ -401,7 +401,7 @@

-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classDomain-members.html b/classDomain-members.html index 686e486508..8562097554 100644 --- a/classDomain-members.html +++ b/classDomain-members.html @@ -101,7 +101,7 @@ getLocalUpotCompSpecific()Domain getLocalVirial() constDomain getMaxMoleculeID() constDomain - getmixcoeff()Domain + getmixcoeff()Domain getNumberOfComponents() (defined in Domain)Domain getNumFluidComponents()Domain getNumFluidMolecules()Domain @@ -152,7 +152,7 @@
-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classDomain.html b/classDomain.html index 0c9072c07f..27a8562148 100644 --- a/classDomain.html +++ b/classDomain.html @@ -164,10 +164,10 @@ void setTargetTemperature (int thermostatID, double T)   - + std::vector< double > & getmixcoeff () - get the mixcoeff
-  + get the mixcoeff
+  double getepsilonRF () const  get the epsilonRF
@@ -355,8 +355,7 @@

This class is responsible for all macroscopic values. It is important to differentiate between local and global version of those values Macroscopic values are values that aggregate some property of a set of molecules. As this program is designed to run on a parallel computer, there are typically several processes. Each process has an instance of this class, but with a different subset of molecules. Therefore, also the macroscopic values are only representative for the "local" domain of that process.

member variables that represent "local" macroscopic values begin with _local

properties of the global system begin with _global if only the rank 0 process obtains the correct value (e.g., as a sum over corresponding local properties) and with _universal if the global value must be communicated to all processes.

-

At some points of the simulation, macroscopic values for the whole set of molecules have to be calculated. Those values are stored in member variables beginning with _global.
-

+

At some points of the simulation, macroscopic values for the whole set of molecules have to be calculated. Those values are stored in member variables beginning with _global.

Member Function Documentation

◆ calculateGlobalValues()

@@ -615,8 +614,7 @@

-

by Stefan Becker: determine and return the totel number of fluid molecules this method assumes all molecules with a component-ID less than _numFluidComponent to be fluid molecules
-

+

by Stefan Becker: determine and return the totel number of fluid molecules this method assumes all molecules with a component-ID less than _numFluidComponent to be fluid molecules

@@ -1020,7 +1018,7 @@

-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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get value type

-

parameter Evaltype
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+

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@@ -470,7 +469,7 @@

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diff --git a/classKineticProfile-members.html b/classKineticProfile-members.html index d2ca345b63..99576c418c 100644 --- a/classKineticProfile-members.html +++ b/classKineticProfile-members.html @@ -77,19 +77,19 @@ comms() finalKineticProfileinlinevirtual getGlobalKineticEnergy(unsigned long uid) const (defined in KineticProfile)KineticProfileinline init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets) finalKineticProfilevirtual + output(std::string prefix, long unsigned accumulatedDatasets) finalKineticProfilevirtual record(Molecule &mol, unsigned long uID) finalKineticProfileinlinevirtual reset(unsigned long uID) finalKineticProfileinlinevirtual - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~KineticProfile() final=default (defined in KineticProfile)KineticProfile ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual
-Generated on Wed Sep 27 2023 09:33:54 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:40 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classKineticProfile.html b/classKineticProfile.html index d59e161ee8..b446d1867b 100644 --- a/classKineticProfile.html +++ b/classKineticProfile.html @@ -95,9 +95,9 @@ void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID) final  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -void output (string prefix, long unsigned accumulatedDatasets) final - Whatever is necessary to output for this profile. More...
-  +void output (std::string prefix, long unsigned accumulatedDatasets) final + Whatever is necessary to output for this profile. More...
+  void reset (unsigned long uID) final  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -115,22 +115,22 @@

Additional Inherited Members

- Protected Member Functions inherited from ProfileBase -void writeMatrix (ofstream &outfile) - Matrix writing routine to avoid code duplication. More...
-  - -void writeKartMatrix (ofstream &outfile) -  -void writeSimpleMatrix (ofstream &outfile) - STUB for simple Matrix output without headers. More...
-  -void writeCylMatrix (ofstream &outfile) - cylinder Matrix output More...
-  +void writeMatrix (std::ofstream &outfile) + Matrix writing routine to avoid code duplication. More...
+  + +void writeKartMatrix (std::ofstream &outfile) +  +void writeSimpleMatrix (std::ofstream &outfile) + STUB for simple Matrix output without headers. More...
+  +void writeCylMatrix (std::ofstream &outfile) + cylinder Matrix output More...
+  - Protected Attributes inherited from ProfileBase - -string _profilePrefix -  + +std::string _profilePrefix +  SamplingInformation _samplInfo   @@ -265,8 +265,8 @@

-

◆ output()

+ +

◆ output()

@@ -277,7 +277,7 @@

void KineticProfile::output ( - string  + std::string  prefix, @@ -307,7 +307,7 @@

ProfileBase.

+

Implements ProfileBase.

@@ -401,7 +401,7 @@

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diff --git a/classLinkedCells.html b/classLinkedCells.html index 0abc04b697..9b1e63658e 100644 --- a/classLinkedCells.html +++ b/classLinkedCells.html @@ -196,8 +196,8 @@   std::vector< unsigned long > getParticleCellStatistics () override   -std::string getConfigurationAsString () override -  +std::string getConfigurationAsString () override +  - Public Member Functions inherited from ParticleContainer  ParticleContainer (double bBoxMin[3], double bBoxMax[3])  The constructor. More...
@@ -640,8 +640,8 @@

-

◆ getConfigurationAsString()

+ +

◆ getConfigurationAsString()

@@ -650,7 +650,7 @@

- + @@ -1474,7 +1474,7 @@

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string LinkedCells::getConfigurationAsString std::string LinkedCells::getConfigurationAsString ( )

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diff --git a/classLog_1_1Logger-members.html b/classLog_1_1Logger-members.html index 3b986138b2..3285b170ff 100644 --- a/classLog_1_1Logger-members.html +++ b/classLog_1_1Logger-members.html @@ -99,7 +99,7 @@
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Detailed Description

The Logger class provides a simple interface to handle log messages.

Provides easy interface to handle log messages. Initialize either with output level and stream or output level and filename or use default constructor values (Error, &(std::cout)). With a given file basename and MPI Support each rank will create and write to his own file. For writing log messages use fatal(), error(), warning(), info() or debug() as with normal streams, e.g.

-

log.error() << "Wrong parameter." << endl;

+

log.error() << "Wrong parameter." << std::endl;

For easy handling of output within MPI applications there are the following methods: set_mpi_output_root(int root) set_mpi_output_rall() set_mpi_output_ranks(int num_ranks, int * ranks) Please include std::endl statements at the end of output as they will flush the stream buffers. If ENABLE_MPI is enabled logger initialization has to take place after the MPI_Init call.

Constructor & Destructor Documentation

@@ -207,7 +207,7 @@

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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classODF.html b/classODF.html index a83b9bf127..06fec8d81c 100644 --- a/classODF.html +++ b/classODF.html @@ -102,9 +102,9 @@ void collect (DomainDecompBase *domainDecomp)   - -void calculateOrientation (const array< double, 3 > &simBoxSize, const Molecule &mol1, const Molecule &mol2, const array< double, 3 > &orientationVector1) -  + +void calculateOrientation (const std::array< double, 3 > &simBoxSize, const Molecule &mol1, const Molecule &mol2, const std::array< double, 3 > &orientationVector1) +  void output (Domain *domain, long unsigned timestep)   @@ -436,7 +436,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classODFCellProcessor-members.html b/classODFCellProcessor-members.html index 141b2f3387..ca0437e21a 100644 --- a/classODFCellProcessor-members.html +++ b/classODFCellProcessor-members.html @@ -92,7 +92,7 @@
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classODFCellProcessor.html b/classODFCellProcessor.html index 375c0d8be1..b1be96b56a 100644 --- a/classODFCellProcessor.html +++ b/classODFCellProcessor.html @@ -385,7 +385,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classObject-members.html b/classObject-members.html index 9e0b24edfd..75190c05ac 100644 --- a/classObject-members.html +++ b/classObject-members.html @@ -81,7 +81,7 @@
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classPPointData.html b/classPPointData.html index 0811256d06..aae6bb042f 100644 --- a/classPPointData.html +++ b/classPPointData.html @@ -377,7 +377,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticleCellBase-members.html b/classParticleCellBase-members.html index fd9e759423..6c29260f4f 100644 --- a/classParticleCellBase-members.html +++ b/classParticleCellBase-members.html @@ -120,7 +120,7 @@
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticleContainer-members.html b/classParticleContainer-members.html index fefb47c728..a7fe39c52f 100644 --- a/classParticleContainer-members.html +++ b/classParticleContainer-members.html @@ -118,7 +118,7 @@
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticleContainer.html b/classParticleContainer.html index df5449afc5..c963036d3f 100644 --- a/classParticleContainer.html +++ b/classParticleContainer.html @@ -642,7 +642,7 @@

Returns
-

Implemented in AutoPasContainer, LinkedCells, and ParticleContainerToBasisWrapper.

+

Implemented in AutoPasContainer, LinkedCells, and ParticleContainerToBasisWrapper.

@@ -1154,7 +1154,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticleContainerToBasisWrapper-members.html b/classParticleContainerToBasisWrapper-members.html index 521e2f1379..907caef9aa 100644 --- a/classParticleContainerToBasisWrapper-members.html +++ b/classParticleContainerToBasisWrapper-members.html @@ -83,7 +83,7 @@ getBoundingBoxMax(int dimension) const overrideParticleContainerToBasisWrapperinlinevirtual getBoundingBoxMin(int dimension) const overrideParticleContainerToBasisWrapperinlinevirtual getCellLength() override (defined in ParticleContainerToBasisWrapper)ParticleContainerToBasisWrapperinlinevirtual - getConfigurationAsString() overrideParticleContainerToBasisWrapperinlinevirtual + getConfigurationAsString() overrideParticleContainerToBasisWrapperinlinevirtual getCutoff() const override (defined in ParticleContainerToBasisWrapper)ParticleContainerToBasisWrapperinlinevirtual getEnergy(ParticlePairsHandler *particlePairsHandler, Molecule *m1, CellProcessor &cellProcessor) override (defined in ParticleContainerToBasisWrapper)ParticleContainerToBasisWrapperinlinevirtual getHaloSize()ParticleContainerinlinevirtual @@ -122,7 +122,7 @@
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticleContainerToBasisWrapper.html b/classParticleContainerToBasisWrapper.html index 75d562f7bb..88301d99a8 100644 --- a/classParticleContainerToBasisWrapper.html +++ b/classParticleContainerToBasisWrapper.html @@ -160,8 +160,8 @@   double * getCellLength () override   -string getConfigurationAsString () override -  +std::string getConfigurationAsString () override +  - Public Member Functions inherited from ParticleContainer  ParticleContainer (double bBoxMin[3], double bBoxMax[3])  The constructor. More...
@@ -555,8 +555,8 @@

-

◆ getConfigurationAsString()

+ +

◆ getConfigurationAsString()

@@ -565,7 +565,7 @@

- + @@ -1238,7 +1238,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticleDataFull-members.html b/classParticleDataFull-members.html index 13640949d0..cc378b5830 100644 --- a/classParticleDataFull-members.html +++ b/classParticleDataFull-members.html @@ -81,7 +81,7 @@

string ParticleContainerToBasisWrapper::getConfigurationAsString std::string ParticleContainerToBasisWrapper::getConfigurationAsString ( )

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticleIterator.html b/classParticleIterator.html index e031891340..6ff98b5203 100644 --- a/classParticleIterator.html +++ b/classParticleIterator.html @@ -164,7 +164,7 @@
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticlePairs2LoadCalcAdapter-members.html b/classParticlePairs2LoadCalcAdapter-members.html index a8eb33966c..8d84505f3f 100644 --- a/classParticlePairs2LoadCalcAdapter-members.html +++ b/classParticlePairs2LoadCalcAdapter-members.html @@ -83,7 +83,7 @@
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classParticlePairsHandler.html b/classParticlePairsHandler.html index bcc011b3a7..ed15b99c2f 100644 --- a/classParticlePairsHandler.html +++ b/classParticlePairsHandler.html @@ -253,7 +253,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classPermittivity.html b/classPermittivity.html index 46df5dd129..73b0c934af 100644 --- a/classPermittivity.html +++ b/classPermittivity.html @@ -386,7 +386,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:41 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classPressureGradient.html b/classPressureGradient.html index 6495e9a7e3..0323720118 100644 --- a/classPressureGradient.html +++ b/classPressureGradient.html @@ -270,7 +270,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classProfileBase-members.html b/classProfileBase-members.html index 8eaf4d0452..b1987ae571 100644 --- a/classProfileBase-members.html +++ b/classProfileBase-members.html @@ -76,19 +76,19 @@ collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID)=0ProfileBasepure virtual comms()=0ProfileBasepure virtual init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets)=0ProfileBasepure virtual + output(std::string prefix, long unsigned accumulatedDatasets)=0ProfileBasepure virtual record(Molecule &mol, unsigned long uID)=0ProfileBasepure virtual reset(unsigned long uID)=0ProfileBasepure virtual - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeDataEntry(unsigned long uID, ofstream &outfile) const =0ProfileBaseprotectedpure virtual - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeDataEntry(unsigned long uID, std::ofstream &outfile) const =0ProfileBaseprotectedpure virtual + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classProfileBase.html b/classProfileBase.html index e90363b563..ff873cf665 100644 --- a/classProfileBase.html +++ b/classProfileBase.html @@ -107,9 +107,9 @@ virtual void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID)=0  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -virtual void output (string prefix, long unsigned accumulatedDatasets)=0 - Whatever is necessary to output for this profile. More...
-  +virtual void output (std::string prefix, long unsigned accumulatedDatasets)=0 + Whatever is necessary to output for this profile. More...
+  virtual void reset (unsigned long uID)=0  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -119,27 +119,27 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + +

Protected Member Functions

virtual void writeDataEntry (unsigned long uID, ofstream &outfile) const =0
 Write Single Data Entry for Matrix with given uID to outfile. More...
 
void writeMatrix (ofstream &outfile)
 Matrix writing routine to avoid code duplication. More...
 
-void writeKartMatrix (ofstream &outfile)
 
void writeSimpleMatrix (ofstream &outfile)
 STUB for simple Matrix output without headers. More...
 
void writeCylMatrix (ofstream &outfile)
 cylinder Matrix output More...
 
virtual void writeDataEntry (unsigned long uID, std::ofstream &outfile) const =0
 Write Single Data Entry for Matrix with given uID to outfile. More...
 
void writeMatrix (std::ofstream &outfile)
 Matrix writing routine to avoid code duplication. More...
 
+void writeKartMatrix (std::ofstream &outfile)
 
void writeSimpleMatrix (std::ofstream &outfile)
 STUB for simple Matrix output without headers. More...
 
void writeCylMatrix (std::ofstream &outfile)
 cylinder Matrix output More...
 
- - + + @@ -310,8 +310,8 @@

-

◆ output()

+ +

◆ output()

@@ -322,7 +322,7 @@

virtual void ProfileBase::output

- + @@ -352,7 +352,7 @@

DensityProfile, DOFProfile, KineticProfile, TemperatureProfile, Velocity3dProfile, VelocityAbsProfile, Virial2DProfile, and VirialProfile.

+

Implemented in DensityProfile, DOFProfile, KineticProfile, TemperatureProfile, Velocity3dProfile, VelocityAbsProfile, Virial2DProfile, and VirialProfile.

@@ -439,8 +439,8 @@

-

◆ writeCylMatrix()

+ +

◆ writeCylMatrix()

@@ -451,7 +451,7 @@

void ProfileBase::writeCylMatrix

- + @@ -473,8 +473,8 @@

-

◆ writeDataEntry()

+ +

◆ writeDataEntry()

@@ -491,7 +491,7 @@

- + @@ -518,8 +518,8 @@

-

◆ writeMatrix()

+ +

◆ writeMatrix()

@@ -530,7 +530,7 @@

void ProfileBase::writeMatrix

- + @@ -552,8 +552,8 @@

-

◆ writeSimpleMatrix()

+ +

◆ writeSimpleMatrix()

@@ -564,7 +564,7 @@

void ProfileBase::writeSimpleMatrix

- + @@ -593,7 +593,7 @@

-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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Protected Attributes

-string _profilePrefix
 
+std::string _profilePrefix
 
SamplingInformation _samplInfo
 
(string std::string  prefix,
(ofstream & std::ofstream &  outfile)
ofstream & std::ofstream &  outfile 
(ofstream & std::ofstream &  outfile)
(ofstream & std::ofstream &  outfile)
-Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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diff --git a/classSubjectBase.html b/classSubjectBase.html index 033914e44b..ef02851014 100644 --- a/classSubjectBase.html +++ b/classSubjectBase.html @@ -97,7 +97,7 @@
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diff --git a/classSysMon-members.html b/classSysMon-members.html index 6b6cf6567d..d2a325a0c2 100644 --- a/classSysMon-members.html +++ b/classSysMon-members.html @@ -88,7 +88,7 @@
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diff --git a/classSysMon.html b/classSysMon.html index 2df6ab4aac..cd759516b4 100644 --- a/classSysMon.html +++ b/classSysMon.html @@ -105,9 +105,9 @@ std::pair< Tvalue, Tvalue > getExpressionMinMaxPeakValues (unsigned int index) const   - + std::pair< Tvalue, Tvalue > getExpressionMinMaxValues (unsigned int index) const -  +  void writeExpressionValues (std::ostream &ostrm=std::cout, std::string header=std::string(), std::string lineprefix=std::string(), std::string sep=std::string("\t"), std::string eol=std::string("\n")) const   @@ -140,7 +140,7 @@
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-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classTemperatureControl-members.html b/classTemperatureControl-members.html index d1f1b52138..ee285c211b 100644 --- a/classTemperatureControl-members.html +++ b/classTemperatureControl-members.html @@ -94,7 +94,7 @@
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classTemperatureControl.html b/classTemperatureControl.html index fe19a4b8c4..5eafc0b7de 100644 --- a/classTemperatureControl.html +++ b/classTemperatureControl.html @@ -258,7 +258,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classTemperatureProfile-members.html b/classTemperatureProfile-members.html index 521d88a95f..4cea7ccb0e 100644 --- a/classTemperatureProfile-members.html +++ b/classTemperatureProfile-members.html @@ -76,20 +76,20 @@ collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) finalTemperatureProfileinlinevirtual comms() finalTemperatureProfileinlinevirtual init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets) finalTemperatureProfilevirtual + output(std::string prefix, long unsigned accumulatedDatasets) finalTemperatureProfilevirtual record(Molecule &mol, unsigned long uID) finalTemperatureProfileinlinevirtual reset(unsigned long uID) finalTemperatureProfileinlinevirtual TemperatureProfile(DOFProfile *dofProf, KineticProfile *kinProf) (defined in TemperatureProfile)TemperatureProfileinline - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual ~TemperatureProfile() final=default (defined in TemperatureProfile)TemperatureProfile
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classTemperatureProfile.html b/classTemperatureProfile.html index 28e2166a5d..d6b6879e13 100644 --- a/classTemperatureProfile.html +++ b/classTemperatureProfile.html @@ -98,9 +98,9 @@ void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID) final  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -void output (string prefix, long unsigned accumulatedDatasets) final - Whatever is necessary to output for this profile. More...
-  +void output (std::string prefix, long unsigned accumulatedDatasets) final + Whatever is necessary to output for this profile. More...
+  void reset (unsigned long uID) final  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -115,22 +115,22 @@

Additional Inherited Members

- Protected Member Functions inherited from ProfileBase -void writeMatrix (ofstream &outfile) - Matrix writing routine to avoid code duplication. More...
-  - -void writeKartMatrix (ofstream &outfile) -  -void writeSimpleMatrix (ofstream &outfile) - STUB for simple Matrix output without headers. More...
-  -void writeCylMatrix (ofstream &outfile) - cylinder Matrix output More...
-  +void writeMatrix (std::ofstream &outfile) + Matrix writing routine to avoid code duplication. More...
+  + +void writeKartMatrix (std::ofstream &outfile) +  +void writeSimpleMatrix (std::ofstream &outfile) + STUB for simple Matrix output without headers. More...
+  +void writeCylMatrix (std::ofstream &outfile) + cylinder Matrix output More...
+  - Protected Attributes inherited from ProfileBase - -string _profilePrefix -  + +std::string _profilePrefix +  SamplingInformation _samplInfo   @@ -265,8 +265,8 @@

-

◆ output()

+ +

◆ output()

@@ -277,7 +277,7 @@

void TemperatureProfile::output ( - string  + std::string  prefix, @@ -307,7 +307,7 @@

ProfileBase.

+

Implements ProfileBase.

@@ -401,7 +401,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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diff --git a/classTimerProfiler-members.html b/classTimerProfiler-members.html index 806cb86f94..4f2ed8a869 100644 --- a/classTimerProfiler-members.html +++ b/classTimerProfiler-members.html @@ -94,7 +94,7 @@
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diff --git a/classTimerProfiler.html b/classTimerProfiler.html index c01c7aee1e..609674dce1 100644 --- a/classTimerProfiler.html +++ b/classTimerProfiler.html @@ -139,9 +139,9 @@ void setOutputString (std::string timerName, std::string outputString)  Sets the output string for the timer output. More...
  - + std::string getOutputString (std::string timerName) -  +  double getTime (std::string timerName)  Gets the time collected by timer "timerName". More...
  @@ -592,7 +592,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classVelocity3dProfile-members.html b/classVelocity3dProfile-members.html index 7c9e23a0dc..903c29bf7b 100644 --- a/classVelocity3dProfile-members.html +++ b/classVelocity3dProfile-members.html @@ -76,20 +76,20 @@ collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) finalVelocity3dProfileinlinevirtual comms() finalVelocity3dProfileinlinevirtual init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets) finalVelocity3dProfilevirtual + output(std::string prefix, long unsigned accumulatedDatasets) finalVelocity3dProfilevirtual record(Molecule &mol, unsigned long uID) finalVelocity3dProfileinlinevirtual reset(unsigned long uID) finalVelocity3dProfileinlinevirtual Velocity3dProfile(DensityProfile *densProf) (defined in Velocity3dProfile)Velocity3dProfileinline - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual ~Velocity3dProfile() final=default (defined in Velocity3dProfile)Velocity3dProfile
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classVelocity3dProfile.html b/classVelocity3dProfile.html index 45d498bb1f..f1aff46e97 100644 --- a/classVelocity3dProfile.html +++ b/classVelocity3dProfile.html @@ -98,9 +98,9 @@ void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID) final  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -void output (string prefix, long unsigned accumulatedDatasets) final - Whatever is necessary to output for this profile. More...
-  +void output (std::string prefix, long unsigned accumulatedDatasets) final + Whatever is necessary to output for this profile. More...
+  void reset (unsigned long uID) final  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -115,22 +115,22 @@

Additional Inherited Members

- Protected Member Functions inherited from ProfileBase -void writeMatrix (ofstream &outfile) - Matrix writing routine to avoid code duplication. More...
-  - -void writeKartMatrix (ofstream &outfile) -  -void writeSimpleMatrix (ofstream &outfile) - STUB for simple Matrix output without headers. More...
-  -void writeCylMatrix (ofstream &outfile) - cylinder Matrix output More...
-  +void writeMatrix (std::ofstream &outfile) + Matrix writing routine to avoid code duplication. More...
+  + +void writeKartMatrix (std::ofstream &outfile) +  +void writeSimpleMatrix (std::ofstream &outfile) + STUB for simple Matrix output without headers. More...
+  +void writeCylMatrix (std::ofstream &outfile) + cylinder Matrix output More...
+  - Protected Attributes inherited from ProfileBase - -string _profilePrefix -  + +std::string _profilePrefix +  SamplingInformation _samplInfo   @@ -265,8 +265,8 @@

-

◆ output()

+ +

◆ output()

@@ -277,7 +277,7 @@

void Velocity3dProfile::output ( - string  + std::string  prefix, @@ -307,7 +307,7 @@

ProfileBase.

+

Implements ProfileBase.

@@ -401,7 +401,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classVelocityAbsProfile-members.html b/classVelocityAbsProfile-members.html index fdf7b0f3d7..0a68dd0988 100644 --- a/classVelocityAbsProfile-members.html +++ b/classVelocityAbsProfile-members.html @@ -76,20 +76,20 @@ collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) finalVelocityAbsProfileinlinevirtual comms() finalVelocityAbsProfileinlinevirtual init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets) finalVelocityAbsProfilevirtual + output(std::string prefix, long unsigned accumulatedDatasets) finalVelocityAbsProfilevirtual record(Molecule &mol, unsigned long uID) finalVelocityAbsProfileinlinevirtual reset(unsigned long uID) finalVelocityAbsProfileinlinevirtual VelocityAbsProfile(DensityProfile *dens) (defined in VelocityAbsProfile)VelocityAbsProfileinline - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual ~VelocityAbsProfile() final=default (defined in VelocityAbsProfile)VelocityAbsProfile
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classVelocityAbsProfile.html b/classVelocityAbsProfile.html index cbaae182c0..f266df545d 100644 --- a/classVelocityAbsProfile.html +++ b/classVelocityAbsProfile.html @@ -98,9 +98,9 @@ void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID) final  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -void output (string prefix, long unsigned accumulatedDatasets) final - Whatever is necessary to output for this profile. More...
-  +void output (std::string prefix, long unsigned accumulatedDatasets) final + Whatever is necessary to output for this profile. More...
+  void reset (unsigned long uID) final  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -115,22 +115,22 @@

Additional Inherited Members

- Protected Member Functions inherited from ProfileBase -void writeMatrix (ofstream &outfile) - Matrix writing routine to avoid code duplication. More...
-  - -void writeKartMatrix (ofstream &outfile) -  -void writeSimpleMatrix (ofstream &outfile) - STUB for simple Matrix output without headers. More...
-  -void writeCylMatrix (ofstream &outfile) - cylinder Matrix output More...
-  +void writeMatrix (std::ofstream &outfile) + Matrix writing routine to avoid code duplication. More...
+  + +void writeKartMatrix (std::ofstream &outfile) +  +void writeSimpleMatrix (std::ofstream &outfile) + STUB for simple Matrix output without headers. More...
+  +void writeCylMatrix (std::ofstream &outfile) + cylinder Matrix output More...
+  - Protected Attributes inherited from ProfileBase - -string _profilePrefix -  + +std::string _profilePrefix +  SamplingInformation _samplInfo   @@ -265,8 +265,8 @@

-

◆ output()

+ +

◆ output()

@@ -277,7 +277,7 @@

void VelocityAbsProfile::output ( - string  + std::string  prefix, @@ -307,7 +307,7 @@

ProfileBase.

+

Implements ProfileBase.

@@ -401,7 +401,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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diff --git a/classVelocityScalingThermostat.html b/classVelocityScalingThermostat.html index 88ba0df569..c6545377a1 100644 --- a/classVelocityScalingThermostat.html +++ b/classVelocityScalingThermostat.html @@ -119,7 +119,7 @@
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classVirial2DProfile-members.html b/classVirial2DProfile-members.html index ea28dbb402..acce321078 100644 --- a/classVirial2DProfile-members.html +++ b/classVirial2DProfile-members.html @@ -76,20 +76,20 @@ collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) finalVirial2DProfileinlinevirtual comms() finalVirial2DProfileinlinevirtual init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets) finalVirial2DProfilevirtual + output(std::string prefix, long unsigned accumulatedDatasets) finalVirial2DProfilevirtual record(Molecule &mol, unsigned long uID) finalVirial2DProfileinlinevirtual reset(unsigned long uID) finalVirial2DProfileinlinevirtual Virial2DProfile(DensityProfile *densProf, DOFProfile *dofProf, KineticProfile *kinProf) (defined in Virial2DProfile)Virial2DProfileinline - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual ~Virial2DProfile() final=default (defined in Virial2DProfile)Virial2DProfile
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classVirial2DProfile.html b/classVirial2DProfile.html index 940c333dc2..7f355b434b 100644 --- a/classVirial2DProfile.html +++ b/classVirial2DProfile.html @@ -93,9 +93,9 @@ void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID) final  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -void output (string prefix, long unsigned accumulatedDatasets) final - Whatever is necessary to output for this profile. More...
-  +void output (std::string prefix, long unsigned accumulatedDatasets) final + Whatever is necessary to output for this profile. More...
+  void reset (unsigned long uID) final  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -110,22 +110,22 @@

Additional Inherited Members

- Protected Member Functions inherited from ProfileBase -void writeMatrix (ofstream &outfile) - Matrix writing routine to avoid code duplication. More...
-  - -void writeKartMatrix (ofstream &outfile) -  -void writeSimpleMatrix (ofstream &outfile) - STUB for simple Matrix output without headers. More...
-  -void writeCylMatrix (ofstream &outfile) - cylinder Matrix output More...
-  +void writeMatrix (std::ofstream &outfile) + Matrix writing routine to avoid code duplication. More...
+  + +void writeKartMatrix (std::ofstream &outfile) +  +void writeSimpleMatrix (std::ofstream &outfile) + STUB for simple Matrix output without headers. More...
+  +void writeCylMatrix (std::ofstream &outfile) + cylinder Matrix output More...
+  - Protected Attributes inherited from ProfileBase - -string _profilePrefix -  + +std::string _profilePrefix +  SamplingInformation _samplInfo   @@ -258,8 +258,8 @@

-

◆ output()

+ +

◆ output()

@@ -270,7 +270,7 @@

void Virial2DProfile::output ( - string  + std::string  prefix, @@ -300,7 +300,7 @@

ProfileBase.

+

Implements ProfileBase.

@@ -394,7 +394,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classVirialProfile-members.html b/classVirialProfile-members.html index d54e6f5ab9..2ca41da801 100644 --- a/classVirialProfile-members.html +++ b/classVirialProfile-members.html @@ -76,20 +76,20 @@ collectRetrieve(DomainDecompBase *domainDecomp, unsigned long uID) finalVirialProfileinlinevirtual comms() finalVirialProfileinlinevirtual init(SamplingInformation &samplingInformation)ProfileBaseinlinevirtual - output(string prefix, long unsigned accumulatedDatasets) finalVirialProfilevirtual + output(std::string prefix, long unsigned accumulatedDatasets) finalVirialProfilevirtual record(Molecule &mol, unsigned long uID) finalVirialProfileinlinevirtual reset(unsigned long uID) finalVirialProfileinlinevirtual VirialProfile(DensityProfile *densProf) (defined in VirialProfile)VirialProfileinline - writeCylMatrix(ofstream &outfile)ProfileBaseprotected - writeKartMatrix(ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected - writeMatrix(ofstream &outfile)ProfileBaseprotected - writeSimpleMatrix(ofstream &outfile)ProfileBaseprotected + writeCylMatrix(std::ofstream &outfile)ProfileBaseprotected + writeKartMatrix(std::ofstream &outfile) (defined in ProfileBase)ProfileBaseprotected + writeMatrix(std::ofstream &outfile)ProfileBaseprotected + writeSimpleMatrix(std::ofstream &outfile)ProfileBaseprotected ~ProfileBase() (defined in ProfileBase)ProfileBaseinlinevirtual ~VirialProfile()=default (defined in VirialProfile)VirialProfile
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classVirialProfile.html b/classVirialProfile.html index dba29345ad..e2b14760fa 100644 --- a/classVirialProfile.html +++ b/classVirialProfile.html @@ -93,8 +93,8 @@ void collectRetrieve (DomainDecompBase *domainDecomp, unsigned long uID) final  Get global values after AllReduceSum per bin. Write to e.g. _globalProfile. More...
  -void output (string prefix, long unsigned accumulatedDatasets) final -  +void output (std::string prefix, long unsigned accumulatedDatasets) final +  void reset (unsigned long uID) final  Used to reset all array contents for a specific uID in order to start the next recording timeframe. More...
  @@ -109,22 +109,22 @@

Additional Inherited Members

- Protected Member Functions inherited from ProfileBase -void writeMatrix (ofstream &outfile) - Matrix writing routine to avoid code duplication. More...
-  - -void writeKartMatrix (ofstream &outfile) -  -void writeSimpleMatrix (ofstream &outfile) - STUB for simple Matrix output without headers. More...
-  -void writeCylMatrix (ofstream &outfile) - cylinder Matrix output More...
-  +void writeMatrix (std::ofstream &outfile) + Matrix writing routine to avoid code duplication. More...
+  + +void writeKartMatrix (std::ofstream &outfile) +  +void writeSimpleMatrix (std::ofstream &outfile) + STUB for simple Matrix output without headers. More...
+  +void writeCylMatrix (std::ofstream &outfile) + cylinder Matrix output More...
+  - Protected Attributes inherited from ProfileBase - -string _profilePrefix -  + +std::string _profilePrefix +  SamplingInformation _samplInfo   @@ -257,8 +257,8 @@

-

◆ output()

+ +

◆ output()

@@ -269,7 +269,7 @@

void VirialProfile::output ( - string  + std::string  prefix, @@ -299,7 +299,7 @@

ProfileBase.

+

Implements ProfileBase.

@@ -393,7 +393,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classWallPotential-members.html b/classWallPotential-members.html index 45c8f0b3dd..188245be7f 100644 --- a/classWallPotential-members.html +++ b/classWallPotential-members.html @@ -80,8 +80,8 @@ finish(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) overrideWallPotentialinlinevirtual getPluginName() overrideWallPotentialinlinevirtual init(ParticleContainer *particleContainer, DomainDecompBase *domainDecomp, Domain *domain) overrideWallPotentialinlinevirtual - initializeLJ1043(const vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, vector< double > in_xi, vector< double > in_eta, double in_yOffWall, double in_yWallCut)WallPotential - initializeLJ93(const vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, vector< double > in_xi, vector< double > in_eta, double in_yOffWall, double in_yWallCut)WallPotential + initializeLJ1043(const std::vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, std::vector< double > in_xi, std::vector< double > in_eta, double in_yOffWall, double in_yWallCut)WallPotential + initializeLJ93(const std::vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, std::vector< double > in_xi, std::vector< double > in_eta, double in_yOffWall, double in_yWallCut)WallPotential PluginBase()PluginBaseinline readXML(XMLfileUnits &xmlconfig) overrideWallPotentialvirtual registerCallbacks(std::map< std::string, FunctionWrapper > &callbackMap)PluginBaseinlinevirtual @@ -92,7 +92,7 @@
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classWallPotential.html b/classWallPotential.html index 560a4be9f5..52c34b4e30 100644 --- a/classWallPotential.html +++ b/classWallPotential.html @@ -102,12 +102,12 @@ std::string getPluginName () override  return the name of the plugin More...
  -void initializeLJ93 (const vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, vector< double > in_xi, vector< double > in_eta, double in_yOffWall, double in_yWallCut) - initialize the LJ93 potential and calculate potential energy at cutoff More...
-  -void initializeLJ1043 (const vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, vector< double > in_xi, vector< double > in_eta, double in_yOffWall, double in_yWallCut) - initialize the LJ1043 potential and calculate potential energy at cutoff More...
-  +void initializeLJ93 (const std::vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, std::vector< double > in_xi, std::vector< double > in_eta, double in_yOffWall, double in_yWallCut) + initialize the LJ93 potential and calculate potential energy at cutoff More...
+  +void initializeLJ1043 (const std::vector< Component > *components, double in_rhoWall, double in_sigWall, double in_epsWall, std::vector< double > in_xi, std::vector< double > in_eta, double in_yOffWall, double in_yWallCut) + initialize the LJ1043 potential and calculate potential energy at cutoff More...
+  void calcTSLJ_9_3 (ParticleContainer *partContainer)  Calculate and add forces to lennard-jones-sites. Also calculate new potential energy addition. More...
  @@ -418,8 +418,8 @@

-

◆ initializeLJ1043()

+ +

◆ initializeLJ1043()

@@ -427,7 +427,7 @@

void WallPotential::initializeLJ1043 ( - const vector< Component > *  + const std::vector< Component > *  components, @@ -497,8 +497,8 @@

-

◆ initializeLJ93()

+ +

◆ initializeLJ93()

@@ -506,7 +506,7 @@

void WallPotential::initializeLJ93 ( - const vector< Component > *  + const std::vector< Component > *  components, @@ -673,7 +673,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfile-members.html b/classXMLfile-members.html index fe7c51deae..0f57f95d8d 100644 --- a/classXMLfile-members.html +++ b/classXMLfile-members.html @@ -95,7 +95,7 @@ operator std::string() constXMLfile print(std::ostream &ostrm=std::cout) constXMLfile printXML(std::ostream &ostrm=std::cout) constXMLfile - query(const std::string &querystr) constXMLfile + query(const std::string &querystr) constXMLfile Query::xmlfile_register (defined in XMLfile)XMLfilefriend Query::xmlfile_unregister (defined in XMLfile)XMLfilefriend queryattrtag (defined in XMLfile)XMLfilestatic @@ -107,7 +107,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfile.html b/classXMLfile.html index 8ef8407481..a07be18109 100644 --- a/classXMLfile.html +++ b/classXMLfile.html @@ -181,9 +181,9 @@ void save (std::string filepath=std::string())  save save node content as XML-file More...
  -Query query (const std::string &querystr) const - perform a query return a query to a given query expression More...
-  +Query query (const std::string &querystr) const + perform a query return a query to a given query expression More...
+   operator std::string () const  std::string cast operator XMLfile will cast to a string with XML content
@@ -1162,14 +1162,14 @@

-

◆ query()

+ +

◆ query()

- + @@ -1222,7 +1222,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfileUnits-members.html b/classXMLfileUnits-members.html index da993dca6d..30afd5c451 100644 --- a/classXMLfileUnits-members.html +++ b/classXMLfileUnits-members.html @@ -108,7 +108,7 @@

- + @@ -130,7 +130,7 @@
Query XMLfile::query XMLfile::Query XMLfile::query ( const std::string &  querystr)
prefixsymbols (defined in XMLfileUnits)XMLfileUnitsstatic
print(std::ostream &ostrm=std::cout) constXMLfile
printXML(std::ostream &ostrm=std::cout) constXMLfile
query(const std::string &querystr) constXMLfile
query(const std::string &querystr) constXMLfile
queryattrtag (defined in XMLfile)XMLfilestatic
refunitstag (defined in XMLfileUnits)XMLfileUnitsstatic
roottag (defined in XMLfileUnits)XMLfileUnitsstatic
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfileUnits.html b/classXMLfileUnits.html index cb78a36024..9607b48beb 100644 --- a/classXMLfileUnits.html +++ b/classXMLfileUnits.html @@ -214,9 +214,9 @@ void save (std::string filepath=std::string())  save save node content as XML-file More...
  -Query query (const std::string &querystr) const - perform a query return a query to a given query expression More...
-  +Query query (const std::string &querystr) const + perform a query return a query to a given query expression More...
+   operator std::string () const  std::string cast operator XMLfile will cast to a string with XML content
@@ -452,7 +452,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfileUnits_1_1ValueUnit-members.html b/classXMLfileUnits_1_1ValueUnit-members.html index 72ea9f05ea..89d21d0a55 100644 --- a/classXMLfileUnits_1_1ValueUnit-members.html +++ b/classXMLfileUnits_1_1ValueUnit-members.html @@ -90,7 +90,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfileUnits_1_1ValueUnit.html b/classXMLfileUnits_1_1ValueUnit.html index 45a040a488..f86a2f51ed 100644 --- a/classXMLfileUnits_1_1ValueUnit.html +++ b/classXMLfileUnits_1_1ValueUnit.html @@ -101,9 +101,9 @@ UnitType unittype () const   - + std::string unittypesymbol () const -  +  bool iscompatible (const ValueUnit &vu) const   @@ -151,8 +151,7 @@

XMLfileUnits::ValueUnit constructor.

Parameters
- +
doublevalue
-
doublevalue
@@ -196,10 +195,8 @@

XMLfileUnits::ValueUnit constructor.

Parameters
- - + +
doublevalue
-
conststd::string& symbol
-
doublevalue
conststd::string& symbol
@@ -375,7 +372,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfile_1_1Node-members.html b/classXMLfile_1_1Node-members.html index 89edf4fe7a..5ab2eb1c8d 100644 --- a/classXMLfile_1_1Node-members.html +++ b/classXMLfile_1_1Node-members.html @@ -83,44 +83,43 @@ ENTITY_Node enum value (defined in XMLfile::Node)XMLfile::Node ENTITY_REFERENCE_Node enum value (defined in XMLfile::Node)XMLfile::Node getValue(T &value) constXMLfile::Node - getValue(string &value) const (defined in XMLfile::Node)XMLfile::Node - getValue(int &value) const (defined in XMLfile::Node)XMLfile::Node - getValue(long &value) const (defined in XMLfile::Node)XMLfile::Node - getValue(float &value) const (defined in XMLfile::Node)XMLfile::Node - getValue(double &value) const (defined in XMLfile::Node)XMLfile::Node - getValue(bool &value) const (defined in XMLfile::Node)XMLfile::Node - Invalid_Node enum value (defined in XMLfile::Node)XMLfile::Node - invalidate()XMLfile::Nodeinline - isLeafNode() constXMLfile::Node - isRootNode() constXMLfile::Nodeinline - name() constXMLfile::Nodeinline - Node()XMLfile::Nodeinline - Node(const Node &n)XMLfile::Nodeinline - nodepath() constXMLfile::Nodeinline - NodeType enum nameXMLfile::Node - NOTATION_Node enum value (defined in XMLfile::Node)XMLfile::Node - operator bool() constXMLfile::Nodeinline - operator T() constXMLfile::Nodeinline - operator=(const Node &n)XMLfile::Nodeinline - operator=(Node &node) (defined in XMLfile::Node)XMLfile::Nodeinline - print(std::ostream &ostrm=std::cout) constXMLfile::Node - printXML(std::ostream &ostrm=std::cout) constXMLfile::Node - PROCESSING_INSTRUCTION_Node enum value (defined in XMLfile::Node)XMLfile::Node - Query (defined in XMLfile::Node)XMLfile::Nodefriend - TEXT_Node enum value (defined in XMLfile::Node)XMLfile::Node - type() constXMLfile::Nodeinline - Unknown_Node enum value (defined in XMLfile::Node)XMLfile::Node - value_bool(bool defaultvalue=false) constXMLfile::Node - value_double(double defaultvalue=0.) constXMLfile::Node - value_float(float defaultvalue=0.) constXMLfile::Node - value_int(int defaultvalue=0) constXMLfile::Node - value_long(long defaultvalue=0) constXMLfile::Node - value_string(std::string defaultvalue=std::string()) constXMLfile::Node - XMLfile (defined in XMLfile::Node)XMLfile::Nodefriend + getValue(int &value) const (defined in XMLfile::Node)XMLfile::Node + getValue(long &value) const (defined in XMLfile::Node)XMLfile::Node + getValue(float &value) const (defined in XMLfile::Node)XMLfile::Node + getValue(double &value) const (defined in XMLfile::Node)XMLfile::Node + getValue(bool &value) const (defined in XMLfile::Node)XMLfile::Node + Invalid_Node enum value (defined in XMLfile::Node)XMLfile::Node + invalidate()XMLfile::Nodeinline + isLeafNode() constXMLfile::Node + isRootNode() constXMLfile::Nodeinline + name() constXMLfile::Nodeinline + Node()XMLfile::Nodeinline + Node(const Node &n)XMLfile::Nodeinline + nodepath() constXMLfile::Nodeinline + NodeType enum nameXMLfile::Node + NOTATION_Node enum value (defined in XMLfile::Node)XMLfile::Node + operator bool() constXMLfile::Nodeinline + operator T() constXMLfile::Nodeinline + operator=(const Node &n)XMLfile::Nodeinline + operator=(Node &node) (defined in XMLfile::Node)XMLfile::Nodeinline + print(std::ostream &ostrm=std::cout) constXMLfile::Node + printXML(std::ostream &ostrm=std::cout) constXMLfile::Node + PROCESSING_INSTRUCTION_Node enum value (defined in XMLfile::Node)XMLfile::Node + Query (defined in XMLfile::Node)XMLfile::Nodefriend + TEXT_Node enum value (defined in XMLfile::Node)XMLfile::Node + type() constXMLfile::Nodeinline + Unknown_Node enum value (defined in XMLfile::Node)XMLfile::Node + value_bool(bool defaultvalue=false) constXMLfile::Node + value_double(double defaultvalue=0.) constXMLfile::Node + value_float(float defaultvalue=0.) constXMLfile::Node + value_int(int defaultvalue=0) constXMLfile::Node + value_long(long defaultvalue=0) constXMLfile::Node + value_string(std::string defaultvalue=std::string()) constXMLfile::Node + XMLfile (defined in XMLfile::Node)XMLfile::Nodefriend

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfile_1_1Node.html b/classXMLfile_1_1Node.html index 6cb3bdc1ae..11ef9aa595 100644 --- a/classXMLfile_1_1Node.html +++ b/classXMLfile_1_1Node.html @@ -134,9 +134,9 @@ bool getValue (T &value) const  get the node value returns the node value converted to a given type More...
  -std::string value_string (std::string defaultvalue=std::string()) const - get the node string value returns the node value as string value or default value, if node is invalid More...
-  +std::string value_string (std::string defaultvalue=std::string()) const + get the node string value returns the node value as string value or default value, if node is invalid More...
+  int value_int (int defaultvalue=0) const  get the node int value returns the node value as int value or default value, if node is invalid More...
  @@ -173,10 +173,6 @@ Node & operator= (Node &node)   - -template<> -bool getValue (string &value) const -  template<> bool getValue (int &value) const @@ -616,14 +612,14 @@

-

◆ value_string()

+ +

◆ value_string()

- + @@ -650,7 +646,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfile_1_1Query-members.html b/classXMLfile_1_1Query-members.html index 181ba16aea..f7bbe8d28e 100644 --- a/classXMLfile_1_1Query-members.html +++ b/classXMLfile_1_1Query-members.html @@ -100,7 +100,7 @@

string XMLfile::Node::value_string std::string XMLfile::Node::value_string ( std::string  defaultvalue = std::string())
-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfile_1_1Query.html b/classXMLfile_1_1Query.html index 713aed9b0c..8a3c15dd18 100644 --- a/classXMLfile_1_1Query.html +++ b/classXMLfile_1_1Query.html @@ -729,7 +729,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfile_1_1Query_1_1const__iterator-members.html b/classXMLfile_1_1Query_1_1const__iterator-members.html index 58e37c6f0d..e2baf5d459 100644 --- a/classXMLfile_1_1Query_1_1const__iterator-members.html +++ b/classXMLfile_1_1Query_1_1const__iterator-members.html @@ -85,7 +85,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXMLfile_1_1Query_1_1const__iterator.html b/classXMLfile_1_1Query_1_1const__iterator.html index 09640d0d27..55e073195f 100644 --- a/classXMLfile_1_1Query_1_1const__iterator.html +++ b/classXMLfile_1_1Query_1_1const__iterator.html @@ -259,7 +259,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXyzWriter-members.html b/classXyzWriter-members.html index 5b5950b489..e5d9e53eb8 100644 --- a/classXyzWriter-members.html +++ b/classXyzWriter-members.html @@ -88,7 +88,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classXyzWriter.html b/classXyzWriter.html index f78223846e..d2d2d62499 100644 --- a/classXyzWriter.html +++ b/classXyzWriter.html @@ -374,7 +374,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classZonalMethod-members.html b/classZonalMethod-members.html index e2dbff214b..2f9784b4ab 100644 --- a/classZonalMethod-members.html +++ b/classZonalMethod-members.html @@ -82,7 +82,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
diff --git a/classZonalMethod.html b/classZonalMethod.html index c0a57a335a..68b2584a47 100644 --- a/classZonalMethod.html +++ b/classZonalMethod.html @@ -403,7 +403,7 @@

-Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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diff --git a/classoptparse_1_1Option.html b/classoptparse_1_1Option.html index 11dfe7a622..51b580350d 100644 --- a/classoptparse_1_1Option.html +++ b/classoptparse_1_1Option.html @@ -156,7 +156,7 @@
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diff --git a/compile__info_8h_source.html b/compile__info_8h_source.html index 9baf02b84a..4ef1c1542f 100644 --- a/compile__info_8h_source.html +++ b/compile__info_8h_source.html @@ -130,7 +130,7 @@
58# else
59 sprintf(info_str, "GNU %d.%d", __GNUC__, __GNUC_MINOR__);
60# endif
-
61
+
61
62 /* unknown */
63#else
64 sprintf(info_str, "unknown");
@@ -248,7 +248,7 @@
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- _ -

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      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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        -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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        - c -

          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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              -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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              - f -

                -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                  -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                    -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                    - b -

                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                      - c -

                        -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                        - d -

                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                          - e -

                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                            diff --git a/functions_func_f.html b/functions_func_f.html index 9c67e81145..c9e55d1be4 100644 --- a/functions_func_f.html +++ b/functions_func_f.html @@ -101,7 +101,7 @@

                            - f -

                              -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                              diff --git a/functions_func_g.html b/functions_func_g.html index 7885d34fbb..90bbf6352a 100644 --- a/functions_func_g.html +++ b/functions_func_g.html @@ -102,7 +102,7 @@

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                                  • -
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                                  • @@ -235,7 +235,7 @@

                                  - g -

                                    -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                    - h -

                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                        • -
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                                        • @@ -110,7 +110,7 @@

                                        - i -

                                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                          - k -

                                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                              -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                              - m -

                                                -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                - n -

                                                  -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                  - o -

                                                  -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                    -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                    -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                        -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                              • -
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                                                              • @@ -95,7 +95,7 @@

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                                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                      - ~ -

                                                                        -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                        diff --git a/functions_g.html b/functions_g.html index b96e51ca8e..31aaa21772 100644 --- a/functions_g.html +++ b/functions_g.html @@ -102,7 +102,7 @@

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                                                                          • @@ -152,7 +152,7 @@

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                                                                                -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                  • @@ -111,7 +111,7 @@

                                                                                  - i -

                                                                                    -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                              -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                - s -

                                                                                                  -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                  - t -

                                                                                                    -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                    diff --git a/functions_type.html b/functions_type.html index 3a03073099..6c20c18ff2 100644 --- a/functions_type.html +++ b/functions_type.html @@ -157,7 +157,7 @@

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                                                                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                      diff --git a/functions_u.html b/functions_u.html index 085f127ce1..51662f4ce4 100644 --- a/functions_u.html +++ b/functions_u.html @@ -92,7 +92,7 @@

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                                                                                                        -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                        - v -

                                                                                                        • value_float() : XMLfile::Node
                                                                                                        • value_int() : XMLfile::Node
                                                                                                        • value_long() : XMLfile::Node
                                                                                                          • -
                                                                                                        • value_string() : XMLfile::Node
                                                                                                          • +
                                                                                                        • value_string() : XMLfile::Node
                                                                                                        • ValueUnit() : XMLfileUnits::ValueUnit
                                                                                                        • VectorizationTuner() : VectorizationTuner
                                                                                                        • VectorizedCellProcessor() : VectorizedCellProcessor
                                                                                                          • @@ -99,7 +99,7 @@

                                                                                                          - v -

                                                                                                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                            diff --git a/functions_vars.html b/functions_vars.html index 79e8f1b38d..22e598153e 100644 --- a/functions_vars.html +++ b/functions_vars.html @@ -214,7 +214,7 @@

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                                                                                                              -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                              diff --git a/functions_w.html b/functions_w.html index cb3277e225..0b8ee6446c 100644 --- a/functions_w.html +++ b/functions_w.html @@ -70,19 +70,19 @@

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                                                                                                              -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                              - x -

                                                                                                                -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                diff --git a/functions_y.html b/functions_y.html index 20fe1984f8..bb5a4f4d6c 100644 --- a/functions_y.html +++ b/functions_y.html @@ -71,7 +71,7 @@

                                                                                                                - y -

                                                                                                                  -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                  diff --git a/functions_z.html b/functions_z.html index df6a1474db..6ac8dfb6a9 100644 --- a/functions_z.html +++ b/functions_z.html @@ -71,7 +71,7 @@

                                                                                                                  - z -

                                                                                                                    -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                    diff --git a/functions_~.html b/functions_~.html index 5b9bb16709..0a71dcac88 100644 --- a/functions_~.html +++ b/functions_~.html @@ -125,7 +125,7 @@

                                                                                                                    - ~ -

                                                                                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/globals_func.html b/globals_func.html index cf2148af13..9f1177dce5 100644 --- a/globals_func.html +++ b/globals_func.html @@ -72,7 +72,7 @@
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/hierarchy.html b/hierarchy.html index 157d8e26e5..d2b3e476ff 100644 --- a/hierarchy.html +++ b/hierarchy.html @@ -516,7 +516,7 @@
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/index.html b/index.html index 698fc24ac0..9ed91b091e 100644 --- a/index.html +++ b/index.html @@ -103,7 +103,7 @@

                                                                                                                      Publications

                                                                                                                      -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/iteratePairwiseLJFunctorNoShiftMix_8cpp.html b/iteratePairwiseLJFunctorNoShiftMix_8cpp.html index c01a8c0174..f6025f6f39 100644 --- a/iteratePairwiseLJFunctorNoShiftMix_8cpp.html +++ b/iteratePairwiseLJFunctorNoShiftMix_8cpp.html @@ -79,7 +79,7 @@
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/iteratePairwiseLJFunctorNoShiftNoMix_8cpp.html b/iteratePairwiseLJFunctorNoShiftNoMix_8cpp.html index 0dd41cbecd..a509b966dc 100644 --- a/iteratePairwiseLJFunctorNoShiftNoMix_8cpp.html +++ b/iteratePairwiseLJFunctorNoShiftNoMix_8cpp.html @@ -79,7 +79,7 @@
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/iteratePairwiseLJFunctorShiftMix_8cpp.html b/iteratePairwiseLJFunctorShiftMix_8cpp.html index f5c34813b8..5a6c414246 100644 --- a/iteratePairwiseLJFunctorShiftMix_8cpp.html +++ b/iteratePairwiseLJFunctorShiftMix_8cpp.html @@ -79,7 +79,7 @@
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/iteratePairwiseLJFunctorShiftNoMix_8cpp.html b/iteratePairwiseLJFunctorShiftNoMix_8cpp.html index b9c7afabdf..9c54b6a874 100644 --- a/iteratePairwiseLJFunctorShiftNoMix_8cpp.html +++ b/iteratePairwiseLJFunctorShiftNoMix_8cpp.html @@ -79,7 +79,7 @@
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/ls1GeneralPlugins.html b/ls1GeneralPlugins.html index a110245d77..18bf460b80 100644 --- a/ls1GeneralPlugins.html +++ b/ls1GeneralPlugins.html @@ -106,7 +106,7 @@

                                                                                                                      Background

                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/ls1MarDynInputFiles.html b/ls1MarDynInputFiles.html index 0538dacce7..10b972a4fe 100644 --- a/ls1MarDynInputFiles.html +++ b/ls1MarDynInputFiles.html @@ -132,7 +132,7 @@

                                                                                                                      Old Config file format (used up to ls1-MarDyn 1.1)

                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/ls1Todos.html b/ls1Todos.html index 7d310b39dd..e9ff8ea1a3 100644 --- a/ls1Todos.html +++ b/ls1Todos.html @@ -77,7 +77,7 @@
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/mardyn__assert_8h_source.html b/mardyn__assert_8h_source.html index ea3ccb6f20..3935c79224 100644 --- a/mardyn__assert_8h_source.html +++ b/mardyn__assert_8h_source.html @@ -108,7 +108,7 @@
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/md_examples_Mamico_couette_readme.html b/md_examples_Mamico_couette_readme.html index 6eb6c4e2d4..13f2b411af 100644 --- a/md_examples_Mamico_couette_readme.html +++ b/md_examples_Mamico_couette_readme.html @@ -81,7 +81,7 @@

                                                                                                                      Parallelization

                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/megaMolSnapshotCommand_8h_source.html b/megaMolSnapshotCommand_8h_source.html index 7bb757ca23..722cc0ee63 100644 --- a/megaMolSnapshotCommand_8h_source.html +++ b/megaMolSnapshotCommand_8h_source.html @@ -109,11 +109,11 @@
                                                                                                                      37
                                                                                                                      38#endif /* MEGAMOLSNAPSHOTCOMMAND_H_ */
                                                                                                                      39#endif /* STEEREO */
                                                                                                                      -
                                                                                                                      Simulation
                                                                                                                      Controls the simulation process.
                                                                                                                      Definition: Simulation.h:70
                                                                                                                      +
                                                                                                                      Simulation
                                                                                                                      Controls the simulation process.
                                                                                                                      Definition: Simulation.h:72
                                                                                                                      -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                      diff --git a/namespaceConcSites.html b/namespaceConcSites.html index f062b83116..5efd9f20ec 100644 --- a/namespaceConcSites.html +++ b/namespaceConcSites.html @@ -90,7 +90,7 @@
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                                                                                                                      - u -

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                                                                                                                        -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                        - u -

                                                                                                                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                          diff --git a/namespacemembers_vars.html b/namespacemembers_vars.html index bcdfa04590..89b6bba758 100644 --- a/namespacemembers_vars.html +++ b/namespacemembers_vars.html @@ -76,7 +76,7 @@
                                                                                                                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                          diff --git a/namespaceoptparse.html b/namespaceoptparse.html index 8fe48c8544..bc2ac43472 100644 --- a/namespaceoptparse.html +++ b/namespaceoptparse.html @@ -146,12 +146,12 @@

                                                                                                                          using optparse::OptionParser;

                                                                                                                          OptionParser parser = OptionParser() .description("just an example");

                                                                                                                          parser.add_option("-f", "--file") .dest("filename") .help("write report to FILE") .metavar("FILE"); parser.add_option("-q", "--quiet") .action("store_false") .dest("verbose") .set_default("1") .help("don't print status messages to stdout");

                                                                                                                          -

                                                                                                                          optparse::Values options = parser.parse_args(argc, argv); vector<string> args = parser.args();

                                                                                                                          -

                                                                                                                          if (options.get("verbose")) cout << options["filename"] << endl;

                                                                                                                          +

                                                                                                                          optparse::Values options = parser.parse_args(argc, argv); std::vector<std::string> args = parser.args();

                                                                                                                          +

                                                                                                                          if (options.get("verbose")) cout << options["filename"] << std::endl;

                                                                                                                          -Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          diff --git a/namespacexml__schema.html b/namespacexml__schema.html index f084c2f5fc..6774976296 100644 --- a/namespacexml__schema.html +++ b/namespacexml__schema.html @@ -379,7 +379,7 @@
                                                                                                                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          diff --git a/nnls_8h_source.html b/nnls_8h_source.html index 67a8617fa6..150510df50 100644 --- a/nnls_8h_source.html +++ b/nnls_8h_source.html @@ -76,7 +76,7 @@
                                                                                                                          -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                          diff --git a/optFFT__API_8h_source.html b/optFFT__API_8h_source.html index 245acf5d66..aaa7cd453a 100644 --- a/optFFT__API_8h_source.html +++ b/optFFT__API_8h_source.html @@ -105,7 +105,7 @@
                                                                                                                          -Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                          diff --git a/optFFT__API__Factory_8h_source.html b/optFFT__API__Factory_8h_source.html index 663cb6557d..8793dbf803 100644 --- a/optFFT__API__Factory_8h_source.html +++ b/optFFT__API__Factory_8h_source.html @@ -100,14 +100,14 @@
                                                                                                                          40};
                                                                                                                          41
                                                                                                                          42#endif
                                                                                                                          -
                                                                                                                          FakedOptFFT
                                                                                                                          Definition: FakedOptFFT.h:39
                                                                                                                          +
                                                                                                                          FakedOptFFT
                                                                                                                          Definition: FakedOptFFT.h:37
                                                                                                                          optFFT_API_Factory
                                                                                                                          Definition: optFFT_API_Factory.h:14
                                                                                                                          optFFT_API_Factory::getOptFFT_API
                                                                                                                          static optFFT_API * getOptFFT_API(const int order, const bool square_matrix)
                                                                                                                          Definition: optFFT_API_Factory.h:29
                                                                                                                          optFFT_API
                                                                                                                          Definition: optFFT_API.h:18
                                                                                                                          -Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                          diff --git a/pages.html b/pages.html index bbccf922e8..630b6311bd 100644 --- a/pages.html +++ b/pages.html @@ -87,7 +87,7 @@
                                                                                                                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                          diff --git a/potforce_8h_source.html b/potforce_8h_source.html index ed0b63ecfe..0ee4bb1fe1 100644 --- a/potforce_8h_source.html +++ b/potforce_8h_source.html @@ -524,7 +524,7 @@
                                                                                                                          497
                                                                                                                          498 mi.Viadd(Virial);
                                                                                                                          499 mj.Viadd(Virial);
                                                                                                                          -
                                                                                                                          500
                                                                                                                          +
                                                                                                                          500
                                                                                                                          501 // check whether all parameters were used
                                                                                                                          502 mardyn_assert(params.eos());
                                                                                                                          503}
                                                                                                                          @@ -684,7 +684,7 @@
                                                                                                                          -Generated on Wed Sep 27 2023 09:33:51 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:38 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                          diff --git a/snapshotCommand_8h_source.html b/snapshotCommand_8h_source.html index ae7921605b..642b21aa86 100644 --- a/snapshotCommand_8h_source.html +++ b/snapshotCommand_8h_source.html @@ -78,7 +78,7 @@
                                                                                                                          6#include <steereo/steereoCommand.h>
                                                                                                                          7
                                                                                                                          8
                                                                                                                          -
                                                                                                                          9class SnapshotCommand : public SteereoCommand
                                                                                                                          +
                                                                                                                          9class SnapshotCommand : public SteereoCommand
                                                                                                                          10{
                                                                                                                          11 public:
                                                                                                                          12 SnapshotCommand ();
                                                                                                                          @@ -87,17 +87,17 @@
                                                                                                                          15 void setParameters (std::list<std::string> params);
                                                                                                                          16 static void setSimData (Simulation* simu) {sim = simu;};
                                                                                                                          17 static SteereoCommand* generateNewInstance ();
                                                                                                                          -
                                                                                                                          18
                                                                                                                          +
                                                                                                                          18
                                                                                                                          19 bool condition ();
                                                                                                                          20 void setStepInterval (int interval) {stepInterval = interval;};
                                                                                                                          -
                                                                                                                          21
                                                                                                                          -
                                                                                                                          22
                                                                                                                          +
                                                                                                                          21
                                                                                                                          +
                                                                                                                          22
                                                                                                                          23 private:
                                                                                                                          24 // parameters needed for execution
                                                                                                                          25 int sockfd;
                                                                                                                          26 static Simulation* sim;
                                                                                                                          27 static int startStep;
                                                                                                                          -
                                                                                                                          28 int stepInterval;
                                                                                                                          +
                                                                                                                          28 int stepInterval;
                                                                                                                          29 bool sendVelocity;
                                                                                                                          30 bool sendForces;
                                                                                                                          31 bool sendV2;
                                                                                                                          @@ -108,11 +108,11 @@
                                                                                                                          36#endif
                                                                                                                          37
                                                                                                                          38#endif
                                                                                                                          -
                                                                                                                          Simulation
                                                                                                                          Controls the simulation process.
                                                                                                                          Definition: Simulation.h:70
                                                                                                                          +
                                                                                                                          Simulation
                                                                                                                          Controls the simulation process.
                                                                                                                          Definition: Simulation.h:72
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                                                                                                                          -Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          -Generated on Wed Sep 27 2023 09:33:55 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          -Generated on Wed Sep 27 2023 09:33:56 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:42 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          -Generated on Wed Sep 27 2023 09:33:54 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:40 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                          diff --git a/structoptparse_1_1str__wrap-members.html b/structoptparse_1_1str__wrap-members.html index 1ef2c92c03..a34173401f 100644 --- a/structoptparse_1_1str__wrap-members.html +++ b/structoptparse_1_1str__wrap-members.html @@ -74,14 +74,14 @@

                                                                                                                          This is the complete list of members for optparse::str_wrap, including all inherited members.

                                                                                                                          - + - - + +
                                                                                                                          lwrap (defined in optparse::str_wrap)optparse::str_wrap
                                                                                                                          operator()(const string &s) (defined in optparse::str_wrap)optparse::str_wrapinline
                                                                                                                          operator()(const std::string &s) (defined in optparse::str_wrap)optparse::str_wrapinline
                                                                                                                          rwrap (defined in optparse::str_wrap)optparse::str_wrap
                                                                                                                          str_wrap(const string &l, const string &r) (defined in optparse::str_wrap)optparse::str_wrapinline
                                                                                                                          str_wrap(const string &w) (defined in optparse::str_wrap)optparse::str_wrapinline
                                                                                                                          str_wrap(const std::string &l, const std::string &r) (defined in optparse::str_wrap)optparse::str_wrapinline
                                                                                                                          str_wrap(const std::string &w) (defined in optparse::str_wrap)optparse::str_wrapinline
                                                                                                                          -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                          Public Member Functions

                                                                                                                          - str_wrap (const string &l, const string &r)
                                                                                                                           
                                                                                                                          - str_wrap (const string &w)
                                                                                                                           
                                                                                                                          -string operator() (const string &s)
                                                                                                                           
                                                                                                                          + str_wrap (const std::string &l, const std::string &r)
                                                                                                                           
                                                                                                                          + str_wrap (const std::string &w)
                                                                                                                           
                                                                                                                          +std::string operator() (const std::string &s)
                                                                                                                           
                                                                                                                          - - - - + + + +

                                                                                                                          Public Attributes

                                                                                                                          -const string lwrap
                                                                                                                           
                                                                                                                          -const string rwrap
                                                                                                                           
                                                                                                                          +const std::string lwrap
                                                                                                                           
                                                                                                                          +const std::string rwrap
                                                                                                                           
                                                                                                                          The documentation for this struct was generated from the following file:
                                                                                                                          • src/utils/OptionParser.cpp
                                                                                                                            • @@ -102,7 +102,7 @@
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                                                                                                                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/structxsd_1_1cxx_1_1tree_1_1traits_3_01long_01double_00_01char_00_01schema__type_1_1decimal_01_4-members.html b/structxsd_1_1cxx_1_1tree_1_1traits_3_01long_01double_00_01char_00_01schema__type_1_1decimal_01_4-members.html index 1f520fc564..ba39a97ad9 100644 --- a/structxsd_1_1cxx_1_1tree_1_1traits_3_01long_01double_00_01char_00_01schema__type_1_1decimal_01_4-members.html +++ b/structxsd_1_1cxx_1_1tree_1_1traits_3_01long_01double_00_01char_00_01schema__type_1_1decimal_01_4-members.html @@ -80,7 +80,7 @@
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/structxsd_1_1cxx_1_1tree_1_1traits_3_01long_01double_00_01char_00_01schema__type_1_1decimal_01_4.html b/structxsd_1_1cxx_1_1tree_1_1traits_3_01long_01double_00_01char_00_01schema__type_1_1decimal_01_4.html index fb886f3f1b..53835fa0ce 100644 --- a/structxsd_1_1cxx_1_1tree_1_1traits_3_01long_01double_00_01char_00_01schema__type_1_1decimal_01_4.html +++ b/structxsd_1_1cxx_1_1tree_1_1traits_3_01long_01double_00_01char_00_01schema__type_1_1decimal_01_4.html @@ -263,7 +263,7 @@

                                                                                                                            -Generated on Wed Sep 27 2023 09:33:57 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:43 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/threeDimensionalMapping_8h_source.html b/threeDimensionalMapping_8h_source.html index 03a48370f0..ebe61b610c 100644 --- a/threeDimensionalMapping_8h_source.html +++ b/threeDimensionalMapping_8h_source.html @@ -107,11 +107,11 @@
                                                                                                                            35
                                                                                                                            36
                                                                                                                            37#endif /* SRC_UTILS_THREEDIMENSIONALMAPPING_H_ */
                                                                                                                            -
                                                                                                                            pos
                                                                                                                            Definition: FakedOptFFT.h:23
                                                                                                                            +
                                                                                                                            pos
                                                                                                                            Definition: FakedOptFFT.h:21
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                                                                                                                            -Generated on Wed Sep 27 2023 09:33:53 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:40 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                            Writing the test header

                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
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                                                                                                                            40 {
                                                                                                                            41 namespace tree
                                                                                                                            42 {
                                                                                                                            -
                                                                                                                            43
                                                                                                                            +
                                                                                                                            43
                                                                                                                            44 template <>
                                                                                                                            45 struct traits<long double, char, schema_type::decimal>
                                                                                                                            46 {
                                                                                                                            -
                                                                                                                            47
                                                                                                                            +
                                                                                                                            47
                                                                                                                            48 typedef long double type;
                                                                                                                            49
                                                                                                                            58 static type
                                                                                                                            @@ -118,7 +118,7 @@
                                                                                                                            74 {
                                                                                                                            75 return create (xml::transcode<char> (a.getValue ()), 0, f, c);
                                                                                                                            76 }
                                                                                                                            -
                                                                                                                            77
                                                                                                                            +
                                                                                                                            77
                                                                                                                            84 static type
                                                                                                                            85 create (const std::string& s,
                                                                                                                            86 const xercesc::DOMElement*,
                                                                                                                            @@ -167,7 +167,7 @@
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                                                                                                                            511 operator= (const PUnstructuredGrid_t& x);
                                                                                                                            512
                                                                                                                            514
                                                                                                                            -
                                                                                                                            518 virtual
                                                                                                                            +
                                                                                                                            518 virtual
                                                                                                                            519 ~PUnstructuredGrid_t ();
                                                                                                                            520
                                                                                                                            521 // Implementation.
                                                                                                                            @@ -428,7 +428,7 @@
                                                                                                                            894 operator= (const VTKFile_t& x);
                                                                                                                            895
                                                                                                                            897
                                                                                                                            -
                                                                                                                            901 virtual
                                                                                                                            +
                                                                                                                            901 virtual
                                                                                                                            902 ~VTKFile_t ();
                                                                                                                            903
                                                                                                                            904 // Implementation.
                                                                                                                            @@ -496,7 +496,7 @@
                                                                                                                            1058 operator= (const PPointData& x);
                                                                                                                            1059
                                                                                                                            1061
                                                                                                                            -
                                                                                                                            1065 virtual
                                                                                                                            +
                                                                                                                            1065 virtual
                                                                                                                            1066 ~PPointData ();
                                                                                                                            1067
                                                                                                                            1068 // Implementation.
                                                                                                                            @@ -558,7 +558,7 @@
                                                                                                                            1216 operator= (const PCellData& x);
                                                                                                                            1217
                                                                                                                            1219
                                                                                                                            -
                                                                                                                            1223 virtual
                                                                                                                            +
                                                                                                                            1223 virtual
                                                                                                                            1224 ~PCellData ();
                                                                                                                            1225
                                                                                                                            1226 // Implementation.
                                                                                                                            @@ -620,7 +620,7 @@
                                                                                                                            1374 operator= (const PPoints& x);
                                                                                                                            1375
                                                                                                                            1377
                                                                                                                            -
                                                                                                                            1381 virtual
                                                                                                                            +
                                                                                                                            1381 virtual
                                                                                                                            1382 ~PPoints ();
                                                                                                                            1383
                                                                                                                            1384 // Implementation.
                                                                                                                            @@ -682,7 +682,7 @@
                                                                                                                            1532 operator= (const PCells& x);
                                                                                                                            1533
                                                                                                                            1535
                                                                                                                            -
                                                                                                                            1539 virtual
                                                                                                                            +
                                                                                                                            1539 virtual
                                                                                                                            1540 ~PCells ();
                                                                                                                            1541
                                                                                                                            1542 // Implementation.
                                                                                                                            @@ -741,7 +741,7 @@
                                                                                                                            1684 operator= (const Piece& x);
                                                                                                                            1685
                                                                                                                            1687
                                                                                                                            -
                                                                                                                            1691 virtual
                                                                                                                            +
                                                                                                                            1691 virtual
                                                                                                                            1692 ~Piece ();
                                                                                                                            1693
                                                                                                                            1694 // Implementation.
                                                                                                                            @@ -866,14 +866,14 @@
                                                                                                                            1993
                                                                                                                            2005void
                                                                                                                            2006VTKFile (::std::ostream& os,
                                                                                                                            -
                                                                                                                            2007 const ::VTKFile_t& x,
                                                                                                                            +
                                                                                                                            2007 const ::VTKFile_t& x,
                                                                                                                            2008 const ::xml_schema::namespace_infomap& m = ::xml_schema::namespace_infomap (),
                                                                                                                            2009 const ::std::string& e = "UTF-8",
                                                                                                                            2010 ::xml_schema::flags f = 0);
                                                                                                                            2011
                                                                                                                            2025void
                                                                                                                            2026VTKFile (::std::ostream& os,
                                                                                                                            -
                                                                                                                            2027 const ::VTKFile_t& x,
                                                                                                                            +
                                                                                                                            2027 const ::VTKFile_t& x,
                                                                                                                            2028 ::xml_schema::error_handler& eh,
                                                                                                                            2029 const ::xml_schema::namespace_infomap& m = ::xml_schema::namespace_infomap (),
                                                                                                                            2030 const ::std::string& e = "UTF-8",
                                                                                                                            @@ -881,7 +881,7 @@
                                                                                                                            2032
                                                                                                                            2047void
                                                                                                                            2048VTKFile (::std::ostream& os,
                                                                                                                            -
                                                                                                                            2049 const ::VTKFile_t& x,
                                                                                                                            +
                                                                                                                            2049 const ::VTKFile_t& x,
                                                                                                                            2050 ::xercesc::DOMErrorHandler& eh,
                                                                                                                            2051 const ::xml_schema::namespace_infomap& m = ::xml_schema::namespace_infomap (),
                                                                                                                            2052 const ::std::string& e = "UTF-8",
                                                                                                                            @@ -889,14 +889,14 @@
                                                                                                                            2054
                                                                                                                            2066void
                                                                                                                            2067VTKFile (::xercesc::XMLFormatTarget& ft,
                                                                                                                            -
                                                                                                                            2068 const ::VTKFile_t& x,
                                                                                                                            +
                                                                                                                            2068 const ::VTKFile_t& x,
                                                                                                                            2069 const ::xml_schema::namespace_infomap& m = ::xml_schema::namespace_infomap (),
                                                                                                                            2070 const ::std::string& e = "UTF-8",
                                                                                                                            2071 ::xml_schema::flags f = 0);
                                                                                                                            2072
                                                                                                                            2087void
                                                                                                                            2088VTKFile (::xercesc::XMLFormatTarget& ft,
                                                                                                                            -
                                                                                                                            2089 const ::VTKFile_t& x,
                                                                                                                            +
                                                                                                                            2089 const ::VTKFile_t& x,
                                                                                                                            2090 ::xml_schema::error_handler& eh,
                                                                                                                            2091 const ::xml_schema::namespace_infomap& m = ::xml_schema::namespace_infomap (),
                                                                                                                            2092 const ::std::string& e = "UTF-8",
                                                                                                                            @@ -904,7 +904,7 @@
                                                                                                                            2094
                                                                                                                            2109void
                                                                                                                            2110VTKFile (::xercesc::XMLFormatTarget& ft,
                                                                                                                            -
                                                                                                                            2111 const ::VTKFile_t& x,
                                                                                                                            +
                                                                                                                            2111 const ::VTKFile_t& x,
                                                                                                                            2112 ::xercesc::DOMErrorHandler& eh,
                                                                                                                            2113 const ::xml_schema::namespace_infomap& m = ::xml_schema::namespace_infomap (),
                                                                                                                            2114 const ::std::string& e = "UTF-8",
                                                                                                                            @@ -916,7 +916,7 @@
                                                                                                                            2131 ::xml_schema::flags f = 0);
                                                                                                                            2132
                                                                                                                            2141::xml_schema::dom::unique_ptr< ::xercesc::DOMDocument >
                                                                                                                            -
                                                                                                                            2142VTKFile (const ::VTKFile_t& x,
                                                                                                                            +
                                                                                                                            2142VTKFile (const ::VTKFile_t& x,
                                                                                                                            2143 const ::xml_schema::namespace_infomap& m = ::xml_schema::namespace_infomap (),
                                                                                                                            2144 ::xml_schema::flags f = 0);
                                                                                                                            2145
                                                                                                                            @@ -1064,7 +1064,7 @@
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/vtk-unstructured_8h.html b/vtk-unstructured_8h.html index 7ad4903f65..beddb0138a 100644 --- a/vtk-unstructured_8h.html +++ b/vtk-unstructured_8h.html @@ -177,7 +177,7 @@
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/vtk-unstructured_8h_source.html b/vtk-unstructured_8h_source.html index 10b49b4552..6a65e7bdff 100644 --- a/vtk-unstructured_8h_source.html +++ b/vtk-unstructured_8h_source.html @@ -194,7 +194,7 @@
                                                                                                                            201 _clone (::xml_schema::flags f = 0,
                                                                                                                            202 ::xml_schema::container* c = 0) const;
                                                                                                                            203
                                                                                                                            -
                                                                                                                            207 virtual
                                                                                                                            +
                                                                                                                            207 virtual
                                                                                                                            208 ~DataArrayList_t ();
                                                                                                                            209};
                                                                                                                            210
                                                                                                                            @@ -310,7 +310,7 @@
                                                                                                                            555 operator= (const DataArray_t& x);
                                                                                                                            556
                                                                                                                            558
                                                                                                                            -
                                                                                                                            562 virtual
                                                                                                                            +
                                                                                                                            562 virtual
                                                                                                                            563 ~DataArray_t ();
                                                                                                                            564
                                                                                                                            565 // Implementation.
                                                                                                                            @@ -470,7 +470,7 @@
                                                                                                                            1000 operator= (const PieceUnstructuredGrid_t& x);
                                                                                                                            1001
                                                                                                                            1003
                                                                                                                            -
                                                                                                                            1007 virtual
                                                                                                                            +
                                                                                                                            1007 virtual
                                                                                                                            1008 ~PieceUnstructuredGrid_t ();
                                                                                                                            1009
                                                                                                                            1010 // Implementation.
                                                                                                                            @@ -536,7 +536,7 @@
                                                                                                                            1167 operator= (const UnstructuredGrid_t& x);
                                                                                                                            1168
                                                                                                                            1170
                                                                                                                            -
                                                                                                                            1174 virtual
                                                                                                                            +
                                                                                                                            1174 virtual
                                                                                                                            1175 ~UnstructuredGrid_t ();
                                                                                                                            1176
                                                                                                                            1177 // Implementation.
                                                                                                                            @@ -667,7 +667,7 @@
                                                                                                                            1478 operator= (const PointData& x);
                                                                                                                            1479
                                                                                                                            1481
                                                                                                                            -
                                                                                                                            1485 virtual
                                                                                                                            +
                                                                                                                            1485 virtual
                                                                                                                            1486 ~PointData ();
                                                                                                                            1487
                                                                                                                            1488 // Implementation.
                                                                                                                            @@ -729,7 +729,7 @@
                                                                                                                            1636 operator= (const CellData& x);
                                                                                                                            1637
                                                                                                                            1639
                                                                                                                            -
                                                                                                                            1643 virtual
                                                                                                                            +
                                                                                                                            1643 virtual
                                                                                                                            1644 ~CellData ();
                                                                                                                            1645
                                                                                                                            1646 // Implementation.
                                                                                                                            @@ -791,7 +791,7 @@
                                                                                                                            1794 operator= (const Points& x);
                                                                                                                            1795
                                                                                                                            1797
                                                                                                                            -
                                                                                                                            1801 virtual
                                                                                                                            +
                                                                                                                            1801 virtual
                                                                                                                            1802 ~Points ();
                                                                                                                            1803
                                                                                                                            1804 // Implementation.
                                                                                                                            @@ -853,7 +853,7 @@
                                                                                                                            1952 operator= (const Cells& x);
                                                                                                                            1953
                                                                                                                            1955
                                                                                                                            -
                                                                                                                            1959 virtual
                                                                                                                            +
                                                                                                                            1959 virtual
                                                                                                                            1960 ~Cells ();
                                                                                                                            1961
                                                                                                                            1962 // Implementation.
                                                                                                                            @@ -1056,7 +1056,7 @@
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/xml-schema_8h.html b/xml-schema_8h.html index 75eaa6d4ca..a0ac17d4dc 100644 --- a/xml-schema_8h.html +++ b/xml-schema_8h.html @@ -428,7 +428,7 @@
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/xml-schema_8h_source.html b/xml-schema_8h_source.html index 96941df88d..b33937e816 100644 --- a/xml-schema_8h_source.html +++ b/xml-schema_8h_source.html @@ -481,7 +481,7 @@
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:50 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:37 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/xmlfileUnits_8cpp.html b/xmlfileUnits_8cpp.html index f408e06264..89cac538bd 100644 --- a/xmlfileUnits_8cpp.html +++ b/xmlfileUnits_8cpp.html @@ -84,7 +84,7 @@
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/xmlfileUnits_8h.html b/xmlfileUnits_8h.html index ca9ce54c72..06b05a330f 100644 --- a/xmlfileUnits_8h.html +++ b/xmlfileUnits_8h.html @@ -151,7 +151,7 @@

                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/xmlfileUnits_8h_source.html b/xmlfileUnits_8h_source.html index 1b7c40baff..3bfe7f3a07 100644 --- a/xmlfileUnits_8h_source.html +++ b/xmlfileUnits_8h_source.html @@ -87,7 +87,7 @@
                                                                                                                            27 static const char *const roottag;
                                                                                                                            28 static const char *const refunitstag;
                                                                                                                            29 static const char *const unitattributetag;
                                                                                                                            -
                                                                                                                            30
                                                                                                                            +
                                                                                                                            30
                                                                                                                            31 enum UnitType { Unknown_Unit=-1, No_Unit=0,
                                                                                                                            32 Length_Unit=1,
                                                                                                                            33 Mass_Unit=2,
                                                                                                                            @@ -102,55 +102,55 @@
                                                                                                                            42 static const short int unittypequantifiers[numUnitTypes][8]; // Q
                                                                                                                            43 static const char *const unittypesymbols[numUnitTypes]; // corresponding symbols
                                                                                                                            44 static const char *const unittypequalifiers[numUnitTypes]; // XML qualifiers
                                                                                                                            -
                                                                                                                            45
                                                                                                                            +
                                                                                                                            45
                                                                                                                            46 static const int numPrefixes=21;
                                                                                                                            47 static const char *const prefixsymbols[numPrefixes]; // corresponding symbols
                                                                                                                            48 static const short int prefixquantifiers[numPrefixes]; // corresponds to Q[0]
                                                                                                                            -
                                                                                                                            49
                                                                                                                            +
                                                                                                                            49
                                                                                                                            50//+XMLfileUnits::ValueUnit======================================================
                                                                                                                            51 class ValueUnit
                                                                                                                            52 {
                                                                                                                            53 public:
                                                                                                                            54 static std::size_t string_endswith(std::string str, const char* suffix); // util/helper function
                                                                                                                            -
                                                                                                                            55
                                                                                                                            +
                                                                                                                            55
                                                                                                                            58 ValueUnit(double value=0.)
                                                                                                                            59 { initialize(value); }
                                                                                                                            63 ValueUnit(double value, const std::string& symbol)
                                                                                                                            64 { initialize(value,symbol); }
                                                                                                                            -
                                                                                                                            65
                                                                                                                            +
                                                                                                                            65
                                                                                                                            69 ValueUnit(const ValueUnit& vu)
                                                                                                                            70 : m_value(vu.m_value)
                                                                                                                            71 { for(int i=0;i<numUnitTypes;++i) m_Q[i]=vu.m_Q[i];}
                                                                                                                            72
                                                                                                                            77 ValueUnit& operator =(const ValueUnit& vu)
                                                                                                                            78 { m_value=vu.m_value; for(int i=0;i<numUnitTypes;++i) m_Q[i]=vu.m_Q[i]; return *this; }
                                                                                                                            -
                                                                                                                            79
                                                                                                                            +
                                                                                                                            79
                                                                                                                            84 ValueUnit& operator =(const double d)
                                                                                                                            85 { m_value=d; for(int i=0;i<numUnitTypes;++i) m_Q[i]=0; return *this; }
                                                                                                                            -
                                                                                                                            86
                                                                                                                            +
                                                                                                                            86
                                                                                                                            90 ValueUnit operator /(const ValueUnit& vu) const;
                                                                                                                            -
                                                                                                                            91
                                                                                                                            +
                                                                                                                            91
                                                                                                                            92 double value() const
                                                                                                                            93 { return m_value; }
                                                                                                                            -
                                                                                                                            94
                                                                                                                            +
                                                                                                                            94
                                                                                                                            95 UnitType unittype() const;
                                                                                                                            96 std::string unittypesymbol() const;
                                                                                                                            -
                                                                                                                            97
                                                                                                                            +
                                                                                                                            97
                                                                                                                            98 bool iscompatible(const ValueUnit& vu) const
                                                                                                                            99 { return m_Q[1]==vu.m_Q[1]&&m_Q[2]==vu.m_Q[2]&&m_Q[3]==vu.m_Q[3]&&m_Q[4]==vu.m_Q[4]
                                                                                                                            100 &&m_Q[5]==vu.m_Q[5]&&m_Q[6]==vu.m_Q[6]&&m_Q[7]==vu.m_Q[7]; }
                                                                                                                            101 bool iscompatible(UnitType ut) const
                                                                                                                            102 { return ut==unittype(); }
                                                                                                                            -
                                                                                                                            103
                                                                                                                            +
                                                                                                                            103
                                                                                                                            104 ValueUnit normalized() const;
                                                                                                                            -
                                                                                                                            105
                                                                                                                            +
                                                                                                                            105
                                                                                                                            109 void print(std::ostream& ostrm=std::cout, bool simplify=true) const;
                                                                                                                            110
                                                                                                                            111 private:
                                                                                                                            -
                                                                                                                            112
                                                                                                                            +
                                                                                                                            112
                                                                                                                            113 void initialize(double value=0.);
                                                                                                                            114 void initialize(double value,const std::string& symbol);
                                                                                                                            -
                                                                                                                            115
                                                                                                                            +
                                                                                                                            115
                                                                                                                            116 double m_value; // value
                                                                                                                            117 short int m_Q[numUnitTypes]; // quantity exponents: 10^Q[0]*m^Q[1]*g^Q[2]*s^Q[3]*A^Q[4]*K^Q[5]*mol^Q[6]*cd^Q[7]
                                                                                                                            118 /* In contrast to the SI base units, gram ("g") instead of kilogram ("kg")
                                                                                                                            @@ -158,16 +158,16 @@
                                                                                                                            120 This seems to be more consistent related to the handling of prefixes */
                                                                                                                            121 };
                                                                                                                            122//-XMLfileUnits::ValueUnit======================================================
                                                                                                                            -
                                                                                                                            123
                                                                                                                            +
                                                                                                                            123
                                                                                                                            124 XMLfileUnits(const std::string& filepath);
                                                                                                                            -
                                                                                                                            125
                                                                                                                            +
                                                                                                                            125
                                                                                                                            126 unsigned long getNodeValueUnit(const char* nodepath, ValueUnit& value) const;
                                                                                                                            127 unsigned long getNodeValueUnit(const std::string& nodepath, ValueUnit& value) const
                                                                                                                            128 { return getNodeValueUnit(nodepath.c_str(),value); }
                                                                                                                            129 unsigned long getNodeValueReduced(const char* nodepath, double& value, UnitType ut=Unknown_Unit) const;
                                                                                                                            130 unsigned long getNodeValueReduced(const std::string& nodepath, double& value, UnitType ut=Unknown_Unit) const
                                                                                                                            131 { return getNodeValueReduced(nodepath.c_str(),value,ut); }
                                                                                                                            -
                                                                                                                            132
                                                                                                                            +
                                                                                                                            132
                                                                                                                            133private:
                                                                                                                            134 ValueUnit m_refunits[numUnitTypes];
                                                                                                                            135};
                                                                                                                            @@ -182,8 +182,8 @@
                                                                                                                            149#endif
                                                                                                                            XMLfileUnits::ValueUnit
                                                                                                                            Definition: xmlfileUnits.h:52
                                                                                                                            XMLfileUnits::ValueUnit::ValueUnit
                                                                                                                            ValueUnit(const ValueUnit &vu)
                                                                                                                            XMLfileUnits::ValueUnit copy constructor duplicate a ValueNode.
                                                                                                                            Definition: xmlfileUnits.h:69
                                                                                                                            -
                                                                                                                            XMLfileUnits::ValueUnit::operator/
                                                                                                                            ValueUnit operator/(const ValueUnit &vu) const
                                                                                                                            divide operator divide other ValueUnit
                                                                                                                            Definition: xmlfileUnits.cpp:106
                                                                                                                            -
                                                                                                                            XMLfileUnits::ValueUnit::print
                                                                                                                            void print(std::ostream &ostrm=std::cout, bool simplify=true) const
                                                                                                                            print data to stream print the node data
                                                                                                                            Definition: xmlfileUnits.cpp:164
                                                                                                                            +
                                                                                                                            XMLfileUnits::ValueUnit::operator/
                                                                                                                            ValueUnit operator/(const ValueUnit &vu) const
                                                                                                                            divide operator divide other ValueUnit
                                                                                                                            Definition: xmlfileUnits.cpp:105
                                                                                                                            +
                                                                                                                            XMLfileUnits::ValueUnit::print
                                                                                                                            void print(std::ostream &ostrm=std::cout, bool simplify=true) const
                                                                                                                            print data to stream print the node data
                                                                                                                            Definition: xmlfileUnits.cpp:163
                                                                                                                            XMLfileUnits::ValueUnit::ValueUnit
                                                                                                                            ValueUnit(double value=0.)
                                                                                                                            XMLfileUnits::ValueUnit constructor.
                                                                                                                            Definition: xmlfileUnits.h:58
                                                                                                                            XMLfileUnits::ValueUnit::ValueUnit
                                                                                                                            ValueUnit(double value, const std::string &symbol)
                                                                                                                            XMLfileUnits::ValueUnit constructor.
                                                                                                                            Definition: xmlfileUnits.h:63
                                                                                                                            XMLfileUnits::ValueUnit::operator=
                                                                                                                            ValueUnit & operator=(const ValueUnit &vu)
                                                                                                                            assignment operator copy/duplicate other ValueUnit content to ValueUnit
                                                                                                                            Definition: xmlfileUnits.h:77
                                                                                                                            @@ -195,7 +195,7 @@
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/xmlfile_8cpp.html b/xmlfile_8cpp.html index 3c267d5820..57d10710cf 100644 --- a/xmlfile_8cpp.html +++ b/xmlfile_8cpp.html @@ -67,6 +67,8 @@
                                                                                                                            +
                                                                                                                            +Functions
                                                                                                                            xmlfile.cpp File Reference
                                                                                                                            @@ -84,13 +86,21 @@ #include "rapidxml/rapidxml_print.hpp"
                                                                                                                            #include "String_utils.h"
                                                                                                                            #include "Simulation.h"
                                                                                                                            -

                                                                                                                            Detailed Description

                                                                                                                            + + + + + +

                                                                                                                            +Functions

                                                                                                                            +template<>
                                                                                                                            bool XMLfile::Node::getValue< std::string > (std::string &value) const
                                                                                                                             
                                                                                                                            +

                                                                                                                            Detailed Description

                                                                                                                            XML file.

                                                                                                                            Author
                                                                                                                            Martin Bernreuther bernr.nosp@m.euth.nosp@m.er@hl.nosp@m.rs.d.nosp@m.e
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/xmlfile_8h.html b/xmlfile_8h.html index 83a07f809e..28fbc6a09b 100644 --- a/xmlfile_8h.html +++ b/xmlfile_8h.html @@ -258,7 +258,7 @@

                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2
                                                                                                                            diff --git a/xmlfile_8h_source.html b/xmlfile_8h_source.html index 4d4cf0681f..50278f6f3a 100644 --- a/xmlfile_8h_source.html +++ b/xmlfile_8h_source.html @@ -96,15 +96,15 @@
                                                                                                                            50 typedef rapidxml::xml_node<> t_XMLelement;
                                                                                                                            51 typedef rapidxml::xml_attribute<> t_XMLattribute;
                                                                                                                            52 typedef rapidxml::xml_document<> t_XMLdocument;
                                                                                                                            -
                                                                                                                            53
                                                                                                                            +
                                                                                                                            53
                                                                                                                            54public:
                                                                                                                            55 static const char *const includeattrtag;
                                                                                                                            56 static const char *const queryattrtag;
                                                                                                                            57
                                                                                                                            58 class Query;
                                                                                                                            59 //class Query::const_iterator; forward declaration not possible...
                                                                                                                            -
                                                                                                                            60
                                                                                                                            -
                                                                                                                            61
                                                                                                                            +
                                                                                                                            60
                                                                                                                            +
                                                                                                                            61
                                                                                                                            62//+XMLfile::Node----------------------------------------------------------------
                                                                                                                            63 class Node
                                                                                                                            64 {
                                                                                                                            @@ -119,7 +119,7 @@
                                                                                                                            73 //friend unsigned long query(std::list<Node>& nodeselection, const char* querystr, Node startnode) const;
                                                                                                                            74 //friend bool initfile_local(const std::string& filepath);
                                                                                                                            75 //friend void initstring_local(const char* xmlstring);
                                                                                                                            -
                                                                                                                            76
                                                                                                                            +
                                                                                                                            76
                                                                                                                            77 public:
                                                                                                                            82 enum NodeType { Unknown_Node=-1,
                                                                                                                            83 Invalid_Node=0,
                                                                                                                            @@ -135,50 +135,50 @@
                                                                                                                            93 DOCUMENT_TYPE_Node=10,
                                                                                                                            94 DOCUMENT_FRAGMENT_Node=11,
                                                                                                                            95 NOTATION_Node=12 };
                                                                                                                            -
                                                                                                                            96
                                                                                                                            +
                                                                                                                            96
                                                                                                                            99 Node()
                                                                                                                            100 : m_xmlnode(NULL), m_nodepath(std::string()), m_type(Unknown_Node)
                                                                                                                            101 {}
                                                                                                                            -
                                                                                                                            102
                                                                                                                            +
                                                                                                                            102
                                                                                                                            106 Node(const Node& n)
                                                                                                                            107 : m_xmlnode(n.m_xmlnode), m_nodepath(n.m_nodepath), m_type(n.m_type)
                                                                                                                            108 {}
                                                                                                                            -
                                                                                                                            109
                                                                                                                            +
                                                                                                                            109
                                                                                                                            113 const std::string& nodepath() const
                                                                                                                            114 { return m_nodepath; }
                                                                                                                            -
                                                                                                                            115
                                                                                                                            +
                                                                                                                            115
                                                                                                                            118 std::string name() const
                                                                                                                            119 { return (m_xmlnode) ? std::string(m_xmlnode->name()) : std::string(); }
                                                                                                                            -
                                                                                                                            120
                                                                                                                            +
                                                                                                                            120
                                                                                                                            123 void invalidate()
                                                                                                                            124 { m_xmlnode=NULL; m_nodepath=std::string(); }
                                                                                                                            -
                                                                                                                            125
                                                                                                                            +
                                                                                                                            125
                                                                                                                            129 NodeType type() const
                                                                                                                            130 { return m_type; }
                                                                                                                            -
                                                                                                                            131
                                                                                                                            +
                                                                                                                            131
                                                                                                                            135 bool isRootNode() const
                                                                                                                            136 { if(m_xmlnode && ! m_xmlnode->parent()) return true; else return false; }
                                                                                                                            140 bool isLeafNode() const;
                                                                                                                            -
                                                                                                                            141
                                                                                                                            +
                                                                                                                            141
                                                                                                                            146 template<typename T> bool getValue(T& value) const;
                                                                                                                            -
                                                                                                                            147
                                                                                                                            -
                                                                                                                            152 std::string value_string(std::string defaultvalue=std::string()) const;
                                                                                                                            +
                                                                                                                            147
                                                                                                                            +
                                                                                                                            152 std::string value_string(std::string defaultvalue=std::string()) const;
                                                                                                                            157 int value_int(int defaultvalue=0) const;
                                                                                                                            162 long value_long(long defaultvalue=0) const;
                                                                                                                            167 float value_float(float defaultvalue=0.) const;
                                                                                                                            172 double value_double(double defaultvalue=0.) const;
                                                                                                                            177 bool value_bool(bool defaultvalue=false) const;
                                                                                                                            -
                                                                                                                            178
                                                                                                                            +
                                                                                                                            178
                                                                                                                            183 Node& operator =(const Node& n)
                                                                                                                            184 { m_xmlnode=n.m_xmlnode; m_nodepath=n.m_nodepath; return *this; }
                                                                                                                            187 template<typename T> operator T() const
                                                                                                                            188 { T value; getValue(value); return value; }
                                                                                                                            191 operator bool() const
                                                                                                                            192 { return m_xmlnode!=NULL && m_type!=Invalid_Node; }
                                                                                                                            -
                                                                                                                            193
                                                                                                                            +
                                                                                                                            193
                                                                                                                            197 void printXML(std::ostream& ostrm=std::cout) const;
                                                                                                                            201 void print(std::ostream& ostrm=std::cout) const;
                                                                                                                            -
                                                                                                                            202
                                                                                                                            +
                                                                                                                            202
                                                                                                                            203 Node& operator=(Node& node){
                                                                                                                            204 m_xmlnode = node.m_xmlnode;
                                                                                                                            205 m_nodepath = node.m_nodepath;
                                                                                                                            @@ -198,27 +198,27 @@
                                                                                                                            219 : m_xmlnode(xmldocument), m_nodepath(nodepath), m_type(DOCUMENT_Node)
                                                                                                                            220 { if(!xmldocument) m_type=Invalid_Node; }
                                                                                                                            221 */
                                                                                                                            -
                                                                                                                            222
                                                                                                                            +
                                                                                                                            222
                                                                                                                            223 const t_XMLnode* m_xmlnode;
                                                                                                                            224 std::string m_nodepath;
                                                                                                                            225 NodeType m_type;
                                                                                                                            226 };
                                                                                                                            227//-XMLfile::Node----------------------------------------------------------------
                                                                                                                            -
                                                                                                                            228
                                                                                                                            -
                                                                                                                            229
                                                                                                                            +
                                                                                                                            228
                                                                                                                            +
                                                                                                                            229
                                                                                                                            230//+XMLfile::Query---------------------------------------------------------------
                                                                                                                            231 class Query
                                                                                                                            232 {
                                                                                                                            233 friend class XMLfile;
                                                                                                                            234 //friend Query XMLfile::query(const char* querystr) const;
                                                                                                                            -
                                                                                                                            235
                                                                                                                            +
                                                                                                                            235
                                                                                                                            236 public:
                                                                                                                            -
                                                                                                                            237
                                                                                                                            +
                                                                                                                            237
                                                                                                                            238//+XMLfile::Query::const_iterator...............................................
                                                                                                                            239 class const_iterator
                                                                                                                            240 {
                                                                                                                            241 friend class Query;
                                                                                                                            -
                                                                                                                            242
                                                                                                                            +
                                                                                                                            242
                                                                                                                            243 public:
                                                                                                                            246 const_iterator()
                                                                                                                            247 : m_query(NULL), m_nodesidx(0) {}
                                                                                                                            @@ -235,23 +235,23 @@
                                                                                                                            272 { if(m_nodesidx>=0) m_nodesidx--; return *this; }
                                                                                                                            276 Node operator *() const
                                                                                                                            277 { if(*this) return (*m_query)[m_nodesidx]; else return Node(); }
                                                                                                                            -
                                                                                                                            278
                                                                                                                            +
                                                                                                                            278
                                                                                                                            279 private:
                                                                                                                            280 const Query* m_query;
                                                                                                                            281 long m_nodesidx;
                                                                                                                            -
                                                                                                                            282
                                                                                                                            -
                                                                                                                            283 const_iterator(const Query* query, long idx)
                                                                                                                            -
                                                                                                                            284 : m_query(query), m_nodesidx(idx) {}
                                                                                                                            +
                                                                                                                            282
                                                                                                                            +
                                                                                                                            283 const_iterator(const Query* query, long idx)
                                                                                                                            +
                                                                                                                            284 : m_query(query), m_nodesidx(idx) {}
                                                                                                                            285 };
                                                                                                                            286//-XMLfile::Query::const_iterator...............................................
                                                                                                                            -
                                                                                                                            287
                                                                                                                            +
                                                                                                                            287
                                                                                                                            290 Query() : m_xmlfile(NULL), m_nodes()
                                                                                                                            291 {}
                                                                                                                            295 Query(const Query& q) : m_xmlfile(q.m_xmlfile), m_nodes(q.m_nodes)
                                                                                                                            296 { xmlfile_register(); }
                                                                                                                            299 ~Query()
                                                                                                                            300 { xmlfile_unregister(); }
                                                                                                                            -
                                                                                                                            301
                                                                                                                            +
                                                                                                                            301
                                                                                                                            305 unsigned long card() const { return m_nodes.size(); }
                                                                                                                            309 bool empty() const
                                                                                                                            310 { return card()==0; }
                                                                                                                            @@ -259,7 +259,7 @@
                                                                                                                            314 { xmlfile_unregister(); m_xmlfile=NULL; m_nodes.clear(); }
                                                                                                                            318 Node front() const
                                                                                                                            319 { return (*this)[0]; }
                                                                                                                            -
                                                                                                                            320
                                                                                                                            +
                                                                                                                            320
                                                                                                                            325 Query& operator =(const Query& q);
                                                                                                                            328 operator unsigned long() const
                                                                                                                            329 { return card(); }
                                                                                                                            @@ -267,7 +267,7 @@
                                                                                                                            333 { return m_xmlfile!=NULL; }
                                                                                                                            338 Node operator [](unsigned long idx) const
                                                                                                                            339 { if(idx<m_nodes.size()) return Node(m_nodes[idx]); else return Node(); }
                                                                                                                            -
                                                                                                                            340
                                                                                                                            +
                                                                                                                            340
                                                                                                                            344 const_iterator begin() const
                                                                                                                            345 { return const_iterator(this,0); }
                                                                                                                            349 const_iterator rbegin() const
                                                                                                                            @@ -278,7 +278,7 @@
                                                                                                                            362 bool rend() const
                                                                                                                            363 { return false; }
                                                                                                                            364 */
                                                                                                                            -
                                                                                                                            365
                                                                                                                            +
                                                                                                                            365
                                                                                                                            370 template<typename T> unsigned long getNodeValue(T& value) const;
                                                                                                                            375 std::string getNodeValue_string(const std::string defaultvalue=std::string()) const
                                                                                                                            376 { std::string value(defaultvalue); getNodeValue(value); return value; }
                                                                                                                            @@ -292,88 +292,88 @@
                                                                                                                            400 { double value=defaultvalue; getNodeValue(value); return value; }
                                                                                                                            405 bool getNodeValue_bool(bool defaultvalue=false) const
                                                                                                                            406 { bool value=defaultvalue; getNodeValue(value); return value; }
                                                                                                                            -
                                                                                                                            407
                                                                                                                            +
                                                                                                                            407
                                                                                                                            411 void printXML(std::ostream& ostrm=std::cout) const;
                                                                                                                            415 void print(std::ostream& ostrm=std::cout) const;
                                                                                                                            -
                                                                                                                            416
                                                                                                                            +
                                                                                                                            416
                                                                                                                            417 private:
                                                                                                                            418 const XMLfile* m_xmlfile;
                                                                                                                            419 std::vector<Node> m_nodes; // nodes within the actual query set
                                                                                                                            -
                                                                                                                            420
                                                                                                                            +
                                                                                                                            420
                                                                                                                            421 Query(const XMLfile* xmlfile)
                                                                                                                            422 : m_xmlfile(xmlfile)
                                                                                                                            423 { m_nodes.clear(); }
                                                                                                                            -
                                                                                                                            424
                                                                                                                            +
                                                                                                                            424
                                                                                                                            425 void xmlfile_register()
                                                                                                                            426 { if(m_xmlfile) m_xmlfile->registerQuery(this); }
                                                                                                                            427 void xmlfile_unregister()
                                                                                                                            428 { if(m_xmlfile) m_xmlfile->unregisterQuery(this); }
                                                                                                                            429 };
                                                                                                                            430//-XMLfile::Query---------------------------------------------------------------
                                                                                                                            -
                                                                                                                            431
                                                                                                                            +
                                                                                                                            431
                                                                                                                            432 friend void Query::xmlfile_register();
                                                                                                                            433 friend void Query::xmlfile_unregister();
                                                                                                                            -
                                                                                                                            434
                                                                                                                            +
                                                                                                                            434
                                                                                                                            436 XMLfile();
                                                                                                                            438 virtual ~XMLfile() { clear(); }
                                                                                                                            -
                                                                                                                            439
                                                                                                                            -
                                                                                                                            443 XMLfile(const std::string& filepath);
                                                                                                                            -
                                                                                                                            444
                                                                                                                            +
                                                                                                                            439
                                                                                                                            +
                                                                                                                            443 XMLfile(const std::string& filepath);
                                                                                                                            +
                                                                                                                            444
                                                                                                                            448 bool initfile(const std::string& filepath);
                                                                                                                            -
                                                                                                                            449
                                                                                                                            +
                                                                                                                            449
                                                                                                                            453 void initstring(const char* xmlstring);
                                                                                                                            -
                                                                                                                            454
                                                                                                                            +
                                                                                                                            454
                                                                                                                            458 const std::string getDir() const { return m_filedir; }
                                                                                                                            462 const std::string getFilename() const { return m_filename; }
                                                                                                                            -
                                                                                                                            463
                                                                                                                            -
                                                                                                                            468 long changecurrentnode(const std::string& nodepath=std::string("/"));
                                                                                                                            -
                                                                                                                            473 bool changecurrentnode(const Query::const_iterator& pos);
                                                                                                                            +
                                                                                                                            463
                                                                                                                            +
                                                                                                                            468 long changecurrentnode(const std::string& nodepath=std::string("/"));
                                                                                                                            +
                                                                                                                            473 bool changecurrentnode(const Query::const_iterator& pos);
                                                                                                                            477 std::string getcurrentnodepath() const { return m_currentnode.nodepath(); }
                                                                                                                            -
                                                                                                                            478
                                                                                                                            +
                                                                                                                            478
                                                                                                                            484 template<typename T> unsigned long getNodeValue(const std::string& nodepath, T& value) const
                                                                                                                            485 //{ Query q=query(nodepath.c_str()); if(!q.empty()) q.front().getValue(value); return q.card(); }
                                                                                                                            -
                                                                                                                            486 { return query(nodepath).getNodeValue(value); }
                                                                                                                            +
                                                                                                                            486 { return query(nodepath).getNodeValue(value); }
                                                                                                                            492 template<typename T> unsigned long getNodeValue(const char* nodepath, T& value) const
                                                                                                                            493 { return getNodeValue(std::string(nodepath),value); }
                                                                                                                            499 std::string getNodeValue_string(const std::string& nodepath, const std::string defaultvalue=std::string()) const
                                                                                                                            500 //{ std::string value(defaultvalue); getNodeValue(nodepath,value); return value; }
                                                                                                                            -
                                                                                                                            501 { return query(nodepath).getNodeValue_string(defaultvalue); }
                                                                                                                            +
                                                                                                                            501 { return query(nodepath).getNodeValue_string(defaultvalue); }
                                                                                                                            507 std::string getNodeValue_string(const char* nodepath, std::string defaultvalue=std::string()) const
                                                                                                                            508 { return getNodeValue_string(std::string(nodepath),defaultvalue); }
                                                                                                                            514 int getNodeValue_int(const std::string& nodepath, int defaultvalue=0) const
                                                                                                                            515 //{ int value=defaultvalue; getNodeValue(nodepath,value); return value; }
                                                                                                                            -
                                                                                                                            516 { return query(nodepath).getNodeValue_int(defaultvalue); }
                                                                                                                            +
                                                                                                                            516 { return query(nodepath).getNodeValue_int(defaultvalue); }
                                                                                                                            522 int getNodeValue_int(const char* nodepath, int defaultvalue=0) const
                                                                                                                            523 { return getNodeValue_int(std::string(nodepath),defaultvalue); }
                                                                                                                            529 long getNodeValue_long(const std::string& nodepath, long defaultvalue=0) const
                                                                                                                            530 //{ long value=defaultvalue; getNodeValue(nodepath,value); return value; }
                                                                                                                            -
                                                                                                                            531 { return query(nodepath.c_str()).getNodeValue_long(defaultvalue); }
                                                                                                                            +
                                                                                                                            531 { return query(nodepath.c_str()).getNodeValue_long(defaultvalue); }
                                                                                                                            537 long getNodeValue_long(const char* nodepath, long defaultvalue=0) const
                                                                                                                            538 { return getNodeValue_long(std::string(nodepath),defaultvalue); }
                                                                                                                            544 float getNodeValue_float(const std::string& nodepath, float defaultvalue=0.) const
                                                                                                                            545 //{ float value=defaultvalue; getNodeValue(nodepath,value); return value; }
                                                                                                                            -
                                                                                                                            546 { return query(nodepath).getNodeValue_float(defaultvalue); }
                                                                                                                            +
                                                                                                                            546 { return query(nodepath).getNodeValue_float(defaultvalue); }
                                                                                                                            552 float getNodeValue_float(const char* nodepath, float defaultvalue=0.) const
                                                                                                                            553 { return getNodeValue_float(std::string(nodepath),defaultvalue); }
                                                                                                                            559 double getNodeValue_double(const std::string& nodepath, double defaultvalue=0.) const
                                                                                                                            560 //{ double value=defaultvalue; getNodeValue(nodepath,value); return value; }
                                                                                                                            -
                                                                                                                            561 { return query(nodepath).getNodeValue_double(defaultvalue); }
                                                                                                                            +
                                                                                                                            561 { return query(nodepath).getNodeValue_double(defaultvalue); }
                                                                                                                            567 double getNodeValue_double(const char* nodepath, double defaultvalue=0.) const
                                                                                                                            568 { return getNodeValue_double(std::string(nodepath),defaultvalue); }
                                                                                                                            575 bool getNodeValue_bool(const std::string& nodepath, bool defaultvalue=false) const
                                                                                                                            576 //{ bool value=defaultvalue; getNodeValue(nodepath,value); return value; }
                                                                                                                            -
                                                                                                                            577 { return query(nodepath).getNodeValue_bool(defaultvalue); }
                                                                                                                            +
                                                                                                                            577 { return query(nodepath).getNodeValue_bool(defaultvalue); }
                                                                                                                            583 bool getNodeValue_bool(const char* nodepath, bool defaultvalue=false) const
                                                                                                                            584 { return getNodeValue_bool(std::string(nodepath),defaultvalue); }
                                                                                                                            -
                                                                                                                            585
                                                                                                                            +
                                                                                                                            585
                                                                                                                            589 void printXML(std::ostream& ostrm=std::cout) const;
                                                                                                                            593 void print(std::ostream& ostrm=std::cout) const;
                                                                                                                            597 void save(std::string filepath=std::string());
                                                                                                                            -
                                                                                                                            598
                                                                                                                            -
                                                                                                                            603 Query query(const std::string& querystr) const;
                                                                                                                            -
                                                                                                                            604
                                                                                                                            -
                                                                                                                            607 operator std::string() const;
                                                                                                                            -
                                                                                                                            608
                                                                                                                            +
                                                                                                                            598
                                                                                                                            +
                                                                                                                            603 Query query(const std::string& querystr) const;
                                                                                                                            +
                                                                                                                            604
                                                                                                                            +
                                                                                                                            607 operator std::string() const;
                                                                                                                            +
                                                                                                                            608
                                                                                                                            612 size_t numqueries() const
                                                                                                                            613 { return m_queries.size(); }
                                                                                                                            614
                                                                                                                            @@ -389,14 +389,14 @@
                                                                                                                            624 Node m_currentnode;
                                                                                                                            625 mutable std::set<Query*> m_queries;
                                                                                                                            626 //std::stack<Node> m_lastnodes;
                                                                                                                            -
                                                                                                                            627
                                                                                                                            +
                                                                                                                            627
                                                                                                                            628 void clear();
                                                                                                                            629 bool initfile_local(const std::string& filepath);
                                                                                                                            630 void initstring_local(const char* xmlstring);
                                                                                                                            631 void expandincludes();
                                                                                                                            -
                                                                                                                            632 unsigned long query(std::list<Node>& nodeselection, const std::string& querystring, Node startnode=Node()) const;
                                                                                                                            +
                                                                                                                            632 unsigned long query(std::list<Node>& nodeselection, const std::string& querystring, Node startnode=Node()) const;
                                                                                                                            633 void insertcloneelement(const t_XMLelement* src, t_XMLelement* dest_after);
                                                                                                                            -
                                                                                                                            634
                                                                                                                            +
                                                                                                                            634
                                                                                                                            635 void registerQuery(Query* q) const
                                                                                                                            636 { if(q) m_queries.insert(q); }
                                                                                                                            637 void unregisterQuery(Query* q) const
                                                                                                                            @@ -446,25 +446,25 @@
                                                                                                                            696
                                                                                                                            697#endif
                                                                                                                            XMLfile::Node
                                                                                                                            Definition: xmlfile.h:64
                                                                                                                            -
                                                                                                                            XMLfile::Node::print
                                                                                                                            void print(std::ostream &ostrm=std::cout) const
                                                                                                                            print data to stream print the node data
                                                                                                                            Definition: xmlfile.cpp:689
                                                                                                                            +
                                                                                                                            XMLfile::Node::print
                                                                                                                            void print(std::ostream &ostrm=std::cout) const
                                                                                                                            print data to stream print the node data
                                                                                                                            Definition: xmlfile.cpp:688
                                                                                                                            XMLfile::Node::invalidate
                                                                                                                            void invalidate()
                                                                                                                            invalidate the node set the internal state to invalid
                                                                                                                            Definition: xmlfile.h:123
                                                                                                                            XMLfile::Node::nodepath
                                                                                                                            const std::string & nodepath() const
                                                                                                                            get nodepath returns the full path of the node
                                                                                                                            Definition: xmlfile.h:113
                                                                                                                            XMLfile::Node::isRootNode
                                                                                                                            bool isRootNode() const
                                                                                                                            check, if node is root node return true, if node is a valid root node - false otherwise
                                                                                                                            Definition: xmlfile.h:135
                                                                                                                            +
                                                                                                                            XMLfile::Node::value_string
                                                                                                                            std::string value_string(std::string defaultvalue=std::string()) const
                                                                                                                            get the node string value returns the node value as string value or default value,...
                                                                                                                            Definition: xmlfile.cpp:613
                                                                                                                            XMLfile::Node::type
                                                                                                                            NodeType type() const
                                                                                                                            get node type determine the node type (enumeration)
                                                                                                                            Definition: xmlfile.h:129
                                                                                                                            -
                                                                                                                            XMLfile::Node::value_float
                                                                                                                            float value_float(float defaultvalue=0.) const
                                                                                                                            get the node float value returns the node value as float value or default value, if node is invalid
                                                                                                                            Definition: xmlfile.cpp:644
                                                                                                                            -
                                                                                                                            XMLfile::Node::printXML
                                                                                                                            void printXML(std::ostream &ostrm=std::cout) const
                                                                                                                            print XML data to stream print the node content using XML syntax
                                                                                                                            Definition: xmlfile.cpp:674
                                                                                                                            -
                                                                                                                            XMLfile::Node::value_int
                                                                                                                            int value_int(int defaultvalue=0) const
                                                                                                                            get the node int value returns the node value as int value or default value, if node is invalid
                                                                                                                            Definition: xmlfile.cpp:624
                                                                                                                            +
                                                                                                                            XMLfile::Node::value_float
                                                                                                                            float value_float(float defaultvalue=0.) const
                                                                                                                            get the node float value returns the node value as float value or default value, if node is invalid
                                                                                                                            Definition: xmlfile.cpp:643
                                                                                                                            +
                                                                                                                            XMLfile::Node::printXML
                                                                                                                            void printXML(std::ostream &ostrm=std::cout) const
                                                                                                                            print XML data to stream print the node content using XML syntax
                                                                                                                            Definition: xmlfile.cpp:673
                                                                                                                            +
                                                                                                                            XMLfile::Node::value_int
                                                                                                                            int value_int(int defaultvalue=0) const
                                                                                                                            get the node int value returns the node value as int value or default value, if node is invalid
                                                                                                                            Definition: xmlfile.cpp:623
                                                                                                                            XMLfile::Node::operator=
                                                                                                                            Node & operator=(const Node &n)
                                                                                                                            assignment operator copy/duplicate other node content to node
                                                                                                                            Definition: xmlfile.h:183
                                                                                                                            -
                                                                                                                            XMLfile::Node::value_string
                                                                                                                            std::string value_string(std::string defaultvalue=std::string()) const
                                                                                                                            get the node string value returns the node value as string value or default value,...
                                                                                                                            Definition: xmlfile.cpp:614
                                                                                                                            XMLfile::Node::Node
                                                                                                                            Node()
                                                                                                                            XMLfile::Node constructor sets up an invalid node.
                                                                                                                            Definition: xmlfile.h:99
                                                                                                                            XMLfile::Node::Node
                                                                                                                            Node(const Node &n)
                                                                                                                            XMLfile::Node copy constructor duplicate a node.
                                                                                                                            Definition: xmlfile.h:106
                                                                                                                            -
                                                                                                                            XMLfile::Node::isLeafNode
                                                                                                                            bool isLeafNode() const
                                                                                                                            check, if node is leaf node return true, if node is a valid leaf node - false otherwise
                                                                                                                            Definition: xmlfile.cpp:524
                                                                                                                            +
                                                                                                                            XMLfile::Node::isLeafNode
                                                                                                                            bool isLeafNode() const
                                                                                                                            check, if node is leaf node return true, if node is a valid leaf node - false otherwise
                                                                                                                            Definition: xmlfile.cpp:523
                                                                                                                            XMLfile::Node::NodeType
                                                                                                                            NodeType
                                                                                                                            Node types enumeration associates a number to each XML node type.
                                                                                                                            Definition: xmlfile.h:82
                                                                                                                            -
                                                                                                                            XMLfile::Node::value_double
                                                                                                                            double value_double(double defaultvalue=0.) const
                                                                                                                            get the node double value returns the node value as double value or default value,...
                                                                                                                            Definition: xmlfile.cpp:654
                                                                                                                            +
                                                                                                                            XMLfile::Node::value_double
                                                                                                                            double value_double(double defaultvalue=0.) const
                                                                                                                            get the node double value returns the node value as double value or default value,...
                                                                                                                            Definition: xmlfile.cpp:653
                                                                                                                            XMLfile::Node::name
                                                                                                                            std::string name() const
                                                                                                                            get node name returns the name of the node, if node is valid - otherwise an empty string
                                                                                                                            Definition: xmlfile.h:118
                                                                                                                            -
                                                                                                                            XMLfile::Node::value_long
                                                                                                                            long value_long(long defaultvalue=0) const
                                                                                                                            get the node long value returns the node value as long value or default value, if node is invalid
                                                                                                                            Definition: xmlfile.cpp:634
                                                                                                                            -
                                                                                                                            XMLfile::Node::value_bool
                                                                                                                            bool value_bool(bool defaultvalue=false) const
                                                                                                                            get the node bool value returns the node value as bool value or default value, if node is invalid
                                                                                                                            Definition: xmlfile.cpp:664
                                                                                                                            -
                                                                                                                            XMLfile::Node::getValue
                                                                                                                            bool getValue(T &value) const
                                                                                                                            get the node value returns the node value converted to a given type
                                                                                                                            Definition: xmlfile.cpp:532
                                                                                                                            +
                                                                                                                            XMLfile::Node::value_long
                                                                                                                            long value_long(long defaultvalue=0) const
                                                                                                                            get the node long value returns the node value as long value or default value, if node is invalid
                                                                                                                            Definition: xmlfile.cpp:633
                                                                                                                            +
                                                                                                                            XMLfile::Node::value_bool
                                                                                                                            bool value_bool(bool defaultvalue=false) const
                                                                                                                            get the node bool value returns the node value as bool value or default value, if node is invalid
                                                                                                                            Definition: xmlfile.cpp:663
                                                                                                                            +
                                                                                                                            XMLfile::Node::getValue
                                                                                                                            bool getValue(T &value) const
                                                                                                                            get the node value returns the node value converted to a given type
                                                                                                                            Definition: xmlfile.cpp:531
                                                                                                                            XMLfile::Query::const_iterator
                                                                                                                            Definition: xmlfile.h:240
                                                                                                                            XMLfile::Query::const_iterator::operator++
                                                                                                                            const_iterator & operator++()
                                                                                                                            prefix increment operator put the index to the next position
                                                                                                                            Definition: xmlfile.h:256
                                                                                                                            XMLfile::Query::const_iterator::operator*
                                                                                                                            Node operator*() const
                                                                                                                            access operator return the node, the iterator (index) actually points to or an invalid Node,...
                                                                                                                            Definition: xmlfile.h:276
                                                                                                                            @@ -478,9 +478,9 @@
                                                                                                                            XMLfile::Query::Query
                                                                                                                            Query()
                                                                                                                            XMLfile::Query constructor sets up an invalid query.
                                                                                                                            Definition: xmlfile.h:290
                                                                                                                            XMLfile::Query::getNodeValue_long
                                                                                                                            long getNodeValue_long(long defaultvalue=0) const
                                                                                                                            get node value as long get the node content and convert it to a long
                                                                                                                            Definition: xmlfile.h:387
                                                                                                                            XMLfile::Query::begin
                                                                                                                            const_iterator begin() const
                                                                                                                            get starting iterator return an iterator to the first node
                                                                                                                            Definition: xmlfile.h:344
                                                                                                                            -
                                                                                                                            XMLfile::Query::printXML
                                                                                                                            void printXML(std::ostream &ostrm=std::cout) const
                                                                                                                            print XML data to stream print the query content using XML syntax
                                                                                                                            Definition: xmlfile.cpp:762
                                                                                                                            +
                                                                                                                            XMLfile::Query::printXML
                                                                                                                            void printXML(std::ostream &ostrm=std::cout) const
                                                                                                                            print XML data to stream print the query content using XML syntax
                                                                                                                            Definition: xmlfile.cpp:761
                                                                                                                            XMLfile::Query::getNodeValue_int
                                                                                                                            int getNodeValue_int(int defaultvalue=0) const
                                                                                                                            get node value as int get the node content and convert it to an int
                                                                                                                            Definition: xmlfile.h:381
                                                                                                                            -
                                                                                                                            XMLfile::Query::print
                                                                                                                            void print(std::ostream &ostrm=std::cout) const
                                                                                                                            print data to stream print the query content
                                                                                                                            Definition: xmlfile.cpp:768
                                                                                                                            +
                                                                                                                            XMLfile::Query::print
                                                                                                                            void print(std::ostream &ostrm=std::cout) const
                                                                                                                            print data to stream print the query content
                                                                                                                            Definition: xmlfile.cpp:767
                                                                                                                            XMLfile::Query::end
                                                                                                                            bool end() const
                                                                                                                            get (dummy) iteration end for comparison return false (as dummy) to enable e.g. for(it=query....
                                                                                                                            Definition: xmlfile.h:355
                                                                                                                            XMLfile::Query::rbegin
                                                                                                                            const_iterator rbegin() const
                                                                                                                            get reverse starting iterator return an iterator to the last node
                                                                                                                            Definition: xmlfile.h:349
                                                                                                                            XMLfile::Query::card
                                                                                                                            unsigned long card() const
                                                                                                                            get cardinality of query set return the size of the query set
                                                                                                                            Definition: xmlfile.h:305
                                                                                                                            @@ -490,16 +490,16 @@
                                                                                                                            XMLfile::Query::getNodeValue_string
                                                                                                                            std::string getNodeValue_string(const std::string defaultvalue=std::string()) const
                                                                                                                            get node value as string get the node content
                                                                                                                            Definition: xmlfile.h:375
                                                                                                                            XMLfile::Query::Query
                                                                                                                            Query(const Query &q)
                                                                                                                            copy constructor duplicate a given query and register the new created one at the XMLfile
                                                                                                                            Definition: xmlfile.h:295
                                                                                                                            XMLfile::Query::~Query
                                                                                                                            ~Query()
                                                                                                                            XMLfile::Query destructor unregister the query.
                                                                                                                            Definition: xmlfile.h:299
                                                                                                                            -
                                                                                                                            XMLfile::Query::operator=
                                                                                                                            Query & operator=(const Query &q)
                                                                                                                            assignment operator copy/duplicate other query content to query
                                                                                                                            Definition: xmlfile.cpp:738
                                                                                                                            -
                                                                                                                            XMLfile::Query::getNodeValue
                                                                                                                            unsigned long getNodeValue(T &value) const
                                                                                                                            get node value get the node content and convert it to a given type
                                                                                                                            Definition: xmlfile.cpp:747
                                                                                                                            +
                                                                                                                            XMLfile::Query::operator=
                                                                                                                            Query & operator=(const Query &q)
                                                                                                                            assignment operator copy/duplicate other query content to query
                                                                                                                            Definition: xmlfile.cpp:737
                                                                                                                            +
                                                                                                                            XMLfile::Query::getNodeValue
                                                                                                                            unsigned long getNodeValue(T &value) const
                                                                                                                            get node value get the node content and convert it to a given type
                                                                                                                            Definition: xmlfile.cpp:746
                                                                                                                            XMLfile
                                                                                                                            XML file abstraction.
                                                                                                                            Definition: xmlfile.h:47
                                                                                                                            -
                                                                                                                            XMLfile::query
                                                                                                                            Query query(const std::string &querystr) const
                                                                                                                            perform a query return a query to a given query expression
                                                                                                                            -
                                                                                                                            XMLfile::printXML
                                                                                                                            void printXML(std::ostream &ostrm=std::cout) const
                                                                                                                            print node content as XML print node content to stream using XML
                                                                                                                            Definition: xmlfile.cpp:159
                                                                                                                            +
                                                                                                                            XMLfile::query
                                                                                                                            Query query(const std::string &querystr) const
                                                                                                                            perform a query return a query to a given query expression
                                                                                                                            Definition: xmlfile.cpp:123
                                                                                                                            +
                                                                                                                            XMLfile::printXML
                                                                                                                            void printXML(std::ostream &ostrm=std::cout) const
                                                                                                                            print node content as XML print node content to stream using XML
                                                                                                                            Definition: xmlfile.cpp:158
                                                                                                                            XMLfile::getNodeValue_bool
                                                                                                                            bool getNodeValue_bool(const std::string &nodepath, bool defaultvalue=false) const
                                                                                                                            get node value as bool get the node content and convert it to a bool (an alternative of using <tag>tr...
                                                                                                                            Definition: xmlfile.h:575
                                                                                                                            XMLfile::getNodeValue
                                                                                                                            unsigned long getNodeValue(const char *nodepath, T &value) const
                                                                                                                            get node value get the node content and convert it to a given type
                                                                                                                            Definition: xmlfile.h:492
                                                                                                                            -
                                                                                                                            XMLfile::print
                                                                                                                            void print(std::ostream &ostrm=std::cout) const
                                                                                                                            print node content print node content and debug information to stream
                                                                                                                            Definition: xmlfile.cpp:164
                                                                                                                            -
                                                                                                                            XMLfile::changecurrentnode
                                                                                                                            long changecurrentnode(const std::string &nodepath=std::string("/"))
                                                                                                                            set current node set a node, relative queries start with
                                                                                                                            -
                                                                                                                            XMLfile::save
                                                                                                                            void save(std::string filepath=std::string())
                                                                                                                            save save node content as XML-file
                                                                                                                            Definition: xmlfile.cpp:113
                                                                                                                            +
                                                                                                                            XMLfile::print
                                                                                                                            void print(std::ostream &ostrm=std::cout) const
                                                                                                                            print node content print node content and debug information to stream
                                                                                                                            Definition: xmlfile.cpp:163
                                                                                                                            +
                                                                                                                            XMLfile::changecurrentnode
                                                                                                                            long changecurrentnode(const std::string &nodepath=std::string("/"))
                                                                                                                            set current node set a node, relative queries start with
                                                                                                                            Definition: xmlfile.cpp:86
                                                                                                                            +
                                                                                                                            XMLfile::save
                                                                                                                            void save(std::string filepath=std::string())
                                                                                                                            save save node content as XML-file
                                                                                                                            Definition: xmlfile.cpp:112
                                                                                                                            XMLfile::getNodeValue_long
                                                                                                                            long getNodeValue_long(const char *nodepath, long defaultvalue=0) const
                                                                                                                            get node value as long get the node content and convert it to a long
                                                                                                                            Definition: xmlfile.h:537
                                                                                                                            XMLfile::getNodeValue_int
                                                                                                                            int getNodeValue_int(const std::string &nodepath, int defaultvalue=0) const
                                                                                                                            get node value as int get the node content and convert it to an integer
                                                                                                                            Definition: xmlfile.h:514
                                                                                                                            XMLfile::getNodeValue_bool
                                                                                                                            bool getNodeValue_bool(const char *nodepath, bool defaultvalue=false) const
                                                                                                                            get node value as bool get the node content and convert it to a bool
                                                                                                                            Definition: xmlfile.h:583
                                                                                                                            @@ -508,26 +508,25 @@
                                                                                                                            XMLfile::getFilename
                                                                                                                            const std::string getFilename() const
                                                                                                                            get XML filename if instantiated with a XML-file, return the filename (without directory part of path...
                                                                                                                            Definition: xmlfile.h:462
                                                                                                                            XMLfile::getNodeValue_float
                                                                                                                            float getNodeValue_float(const char *nodepath, float defaultvalue=0.) const
                                                                                                                            get node value as float get the node content and convert it to a float
                                                                                                                            Definition: xmlfile.h:552
                                                                                                                            XMLfile::~XMLfile
                                                                                                                            virtual ~XMLfile()
                                                                                                                            XMLfile default destructor.
                                                                                                                            Definition: xmlfile.h:438
                                                                                                                            -
                                                                                                                            XMLfile::initfile
                                                                                                                            bool initfile(const std::string &filepath)
                                                                                                                            initialize with XML-file instantiating with XML file
                                                                                                                            Definition: xmlfile.cpp:54
                                                                                                                            +
                                                                                                                            XMLfile::initfile
                                                                                                                            bool initfile(const std::string &filepath)
                                                                                                                            initialize with XML-file instantiating with XML file
                                                                                                                            Definition: xmlfile.cpp:53
                                                                                                                            XMLfile::getNodeValue_double
                                                                                                                            double getNodeValue_double(const char *nodepath, double defaultvalue=0.) const
                                                                                                                            get node value as double get the node content and convert it to a double
                                                                                                                            Definition: xmlfile.h:567
                                                                                                                            XMLfile::getNodeValue
                                                                                                                            unsigned long getNodeValue(const std::string &nodepath, T &value) const
                                                                                                                            get node value get the node content and convert it to a given type
                                                                                                                            Definition: xmlfile.h:484
                                                                                                                            XMLfile::getNodeValue_float
                                                                                                                            float getNodeValue_float(const std::string &nodepath, float defaultvalue=0.) const
                                                                                                                            get node value as float get the node content and convert it to a float
                                                                                                                            Definition: xmlfile.h:544
                                                                                                                            XMLfile::getNodeValue_int
                                                                                                                            int getNodeValue_int(const char *nodepath, int defaultvalue=0) const
                                                                                                                            get node value as int get the node content and convert it to an integer
                                                                                                                            Definition: xmlfile.h:522
                                                                                                                            -
                                                                                                                            XMLfile::XMLfile
                                                                                                                            XMLfile(const std::string &filepath)
                                                                                                                            constructor for XML-file constructor calls initfile
                                                                                                                            -
                                                                                                                            XMLfile::XMLfile
                                                                                                                            XMLfile()
                                                                                                                            XMLfile default constructor.
                                                                                                                            Definition: xmlfile.cpp:37
                                                                                                                            +
                                                                                                                            XMLfile::XMLfile
                                                                                                                            XMLfile()
                                                                                                                            XMLfile default constructor.
                                                                                                                            Definition: xmlfile.cpp:36
                                                                                                                            XMLfile::getNodeValue_double
                                                                                                                            double getNodeValue_double(const std::string &nodepath, double defaultvalue=0.) const
                                                                                                                            get node value as double get the node content and convert it to a double
                                                                                                                            Definition: xmlfile.h:559
                                                                                                                            XMLfile::getDir
                                                                                                                            const std::string getDir() const
                                                                                                                            get XML file directory if instantiated with a XML-file, return the directory
                                                                                                                            Definition: xmlfile.h:458
                                                                                                                            XMLfile::getNodeValue_string
                                                                                                                            std::string getNodeValue_string(const char *nodepath, std::string defaultvalue=std::string()) const
                                                                                                                            get node value as string get the node content
                                                                                                                            Definition: xmlfile.h:507
                                                                                                                            XMLfile::numqueries
                                                                                                                            size_t numqueries() const
                                                                                                                            number of registered queries return the number of active queries
                                                                                                                            Definition: xmlfile.h:612
                                                                                                                            -
                                                                                                                            XMLfile::initstring
                                                                                                                            void initstring(const char *xmlstring)
                                                                                                                            initialize with XML-string instantiating with XML-string
                                                                                                                            Definition: xmlfile.cpp:72
                                                                                                                            +
                                                                                                                            XMLfile::initstring
                                                                                                                            void initstring(const char *xmlstring)
                                                                                                                            initialize with XML-string instantiating with XML-string
                                                                                                                            Definition: xmlfile.cpp:71
                                                                                                                            XMLfile::getcurrentnodepath
                                                                                                                            std::string getcurrentnodepath() const
                                                                                                                            get current node path
                                                                                                                            Definition: xmlfile.h:477
                                                                                                                            xml_schema::string
                                                                                                                            ::xsd::cxx::tree::string< char, simple_type > string
                                                                                                                            C++ type corresponding to the string XML Schema built-in type.
                                                                                                                            Definition: xml-schema.h:268
                                                                                                                            -
                                                                                                                            pos
                                                                                                                            Definition: FakedOptFFT.h:23
                                                                                                                            +
                                                                                                                            pos
                                                                                                                            Definition: FakedOptFFT.h:21
                                                                                                                            operator<<
                                                                                                                            std::ostream & operator<<(std::ostream &ostrm, const XMLfile::Node &xmlnode)
                                                                                                                            write a node to a stream write XML node data to an output stream
                                                                                                                            Definition: xmlfile.h:659
                                                                                                                            -Generated on Wed Sep 27 2023 09:33:52 for ls1-MarDyn by doxygen 1.9.2 +Generated on Mon Oct 16 2023 14:20:39 for ls1-MarDyn by doxygen 1.9.2