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Cleanup of readers #332

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Cleanup of readers #332

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c7f4729
Deprecate readPhaseSpaceHeader of ASCII reader
HomesGH Jul 26, 2024
b47d637
Add meaning full error message when using ASCII readPhaseSpaceHeader
HomesGH Jul 26, 2024
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205 changes: 3 additions & 202 deletions src/io/ASCIIReader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -46,208 +46,9 @@ void ASCIIReader::readXML(XMLfileUnits& xmlconfig) {
}

void ASCIIReader::readPhaseSpaceHeader(Domain* domain, double timestep) {
std::string token;

Log::global_log->info() << "Opening phase space header file " << _phaseSpaceHeaderFile << std::endl;
_phaseSpaceHeaderFileStream.open(_phaseSpaceHeaderFile.c_str());
_phaseSpaceHeaderFileStream >> token;
if(token != "mardyn") {
Log::global_log->error() << _phaseSpaceHeaderFile << " not a valid mardyn input file." << std::endl;
Simulation::exit(1);
}

std::string inputversion;
_phaseSpaceHeaderFileStream >> token >> inputversion;
// FIXME: remove tag trunk from file specification?
if(token != "trunk") {
Log::global_log->error() << "Wrong input file specifier (\'" << token << "\' instead of \'trunk\')." << std::endl;
Simulation::exit(1);
}

if(std::stoi(inputversion) < 20080701) {
Log::global_log->error() << "Input version too old (" << inputversion << ")" << std::endl;
Simulation::exit(1);
}

Log::global_log->info() << "Reading phase space header from file " << _phaseSpaceHeaderFile << std::endl;

std::vector<Component>& dcomponents = *(_simulation.getEnsemble()->getComponents());
bool header = true; // When the last header element is reached, "header" is set to false

while(header) {
char c;
_phaseSpaceHeaderFileStream >> c;
if(c == '#') {
// comment line
_phaseSpaceHeaderFileStream.ignore(INT_MAX, '\n');
continue;
}
_phaseSpaceHeaderFileStream.putback(c);

token.clear();
_phaseSpaceHeaderFileStream >> token;
Log::global_log->info() << "{{" << token << "}}" << std::endl;

if((token == "currentTime") || (token == "t")) {
// set current simulation time
_phaseSpaceHeaderFileStream >> token;
_simulation.setSimulationTime(strtod(token.c_str(), NULL));
} else if((token == "Temperature") || (token == "T")) {
// set global thermostat temperature
domain->disableComponentwiseThermostat(); //disable component wise thermostats
double targetT;
_phaseSpaceHeaderFileStream >> targetT;
domain->setGlobalTemperature(targetT);
} else if((token == "ThermostatTemperature") || (token == "ThT") || (token == "h")) {
// set up a new thermostat
int thermostat_id;
double targetT;
_phaseSpaceHeaderFileStream >> thermostat_id;
_phaseSpaceHeaderFileStream >> targetT;
Log::global_log->info() << "Thermostat number " << thermostat_id << " has T = " << targetT << ".\n";
domain->setTargetTemperature(thermostat_id, targetT);
} else if((token == "ComponentThermostat") || (token == "CT") || (token == "o")) {
// specify a thermostat for a component
if(!domain->severalThermostats())
domain->enableComponentwiseThermostat();
int component_id;
int thermostat_id;
_phaseSpaceHeaderFileStream >> component_id >> thermostat_id;
Log::global_log->info() << "Component " << component_id << " (internally: " << component_id - 1
<< ") is regulated by thermostat number " << thermostat_id << ".\n";
component_id--; // FIXME thermostat IDs start with 0 in the program but not in the config file?!
if(thermostat_id < 0) // thermostat IDs start with 0
continue;
domain->setComponentThermostat(component_id, thermostat_id);
} else if((token == "Undirected") || (token == "U")) {
// set undirected thermostat
int thermostat_id;
_phaseSpaceHeaderFileStream >> thermostat_id;
domain->enableUndirectedThermostat(thermostat_id);
} else if((token == "Length") || (token == "L")) {
// simulation box dimensions
double globalLength[3];
_phaseSpaceHeaderFileStream >> globalLength[0] >> globalLength[1] >> globalLength[2];
delete _simulation.getEnsemble()->domain();
_simulation.getEnsemble()->domain() = new BoxDomain();
for(int d = 0; d < 3; d++) {
static_cast<BoxDomain*>(_simulation.getEnsemble()->domain())->setLength(d, globalLength[d]);
domain->setGlobalLength(d, _simulation.getEnsemble()->domain()->length(d));
}
} else if((token == "HeatCapacity") || (token == "cv") || (token == "I")) {
unsigned N;
double U, UU;
_phaseSpaceFileStream >> N >> U >> UU;
domain->init_cv(N, U, UU);
} else if((token == "NumberOfComponents") || (token == "C")) {
// read in component definitions and
// read in mixing coefficients

// components:
unsigned int numcomponents = 0;
_phaseSpaceHeaderFileStream >> numcomponents;
Log::global_log->info() << "Reading " << numcomponents << " components" << std::endl;
dcomponents.resize(numcomponents);
for(unsigned int i = 0; i < numcomponents; i++) {
Log::global_log->info() << "comp. i = " << i << ": " << std::endl;
dcomponents[i].setID(i);
unsigned int numljcenters = 0;
unsigned int numcharges = 0;
unsigned int numdipoles = 0;
unsigned int numquadrupoles = 0;
unsigned int numtersoff = 0; //previously tersoff
_phaseSpaceHeaderFileStream >> numljcenters >> numcharges >> numdipoles
>> numquadrupoles >> numtersoff;
if(numtersoff != 0) {
Log::global_log->error() << "tersoff no longer supported."
<< std::endl;
Simulation::exit(-1);
}
double x, y, z, m;
for(unsigned int j = 0; j < numljcenters; j++) {
double eps, sigma, tcutoff, do_shift;
_phaseSpaceHeaderFileStream >> x >> y >> z >> m >> eps >> sigma >> tcutoff >> do_shift;
dcomponents[i].addLJcenter(x, y, z, m, eps, sigma, tcutoff, (do_shift != 0));
Log::global_log->info() << "LJ at [" << x << " " << y << " " << z << "], mass: " << m << ", epsilon: "
<< eps << ", sigma: " << sigma << std::endl;
}
for(unsigned int j = 0; j < numcharges; j++) {
double q;
_phaseSpaceHeaderFileStream >> x >> y >> z >> m >> q;
dcomponents[i].addCharge(x, y, z, m, q);
Log::global_log->info() << "charge at [" << x << " " << y << " " << z << "], mass: " << m << ", q: " << q
<< std::endl;
}
for(unsigned int j = 0; j < numdipoles; j++) {
double eMyx, eMyy, eMyz, absMy;
_phaseSpaceHeaderFileStream >> x >> y >> z >> eMyx >> eMyy >> eMyz >> absMy;
dcomponents[i].addDipole(x, y, z, eMyx, eMyy, eMyz, absMy);
Log::global_log->info() << "dipole at [" << x << " " << y << " " << z << "] " << std::endl;
}
for(unsigned int j = 0; j < numquadrupoles; j++) {
double eQx, eQy, eQz, absQ;
_phaseSpaceHeaderFileStream >> x >> y >> z >> eQx >> eQy >> eQz >> absQ;
dcomponents[i].addQuadrupole(x, y, z, eQx, eQy, eQz, absQ);
Log::global_log->info() << "quad at [" << x << " " << y << " " << z << "] " << std::endl;
}
double IDummy1, IDummy2, IDummy3;
// FIXME! Was soll das hier? Was ist mit der Initialisierung im Fall I <= 0.
_phaseSpaceHeaderFileStream >> IDummy1 >> IDummy2 >> IDummy3;
if(IDummy1 > 0.) dcomponents[i].setI11(IDummy1);
if(IDummy2 > 0.) dcomponents[i].setI22(IDummy2);
if(IDummy3 > 0.) dcomponents[i].setI33(IDummy3);
domain->setProfiledComponentMass(dcomponents[i].m());
Log::global_log->info() << std::endl;
}

#ifndef NDEBUG
for(unsigned int i = 0; i < numcomponents; i++) {
Log::global_log->debug() << "Component " << (i + 1) << " of " << numcomponents << std::endl;
Log::global_log->debug() << dcomponents[i] << std::endl;
}
#endif

// Mixing coefficients
std::vector<double>& dmixcoeff = domain->getmixcoeff();
dmixcoeff.clear();
for(unsigned int i = 1; i < numcomponents; i++) {
for(unsigned int j = i + 1; j <= numcomponents; j++) {
double xi, eta;
_phaseSpaceHeaderFileStream >> xi >> eta;
dmixcoeff.push_back(xi);
dmixcoeff.push_back(eta);
}
}
// read in global factor \epsilon_{RF}
// FIXME: Maybe this should go better to a seperate token?!
_phaseSpaceHeaderFileStream >> token;
domain->setepsilonRF(strtod(token.c_str(), NULL));
long int fpos;
if(_phaseSpaceFile == _phaseSpaceHeaderFile) {
// in the case of a single phase space header + phase space file
// find out the actual position, because the phase space definition will follow
// FIXME: is there a more elegant way?
fpos = _phaseSpaceHeaderFileStream.tellg();
_phaseSpaceFileStream.seekg(fpos, std::ios::beg);
}
// FIXME: Is there a better solution than skipping the rest of the file?
header = false;
} else if((token == "NumberOfMolecules") || (token == "N")) {
// set number of Molecules
// FIXME: Is this part called in any case as the token is handled in the readPhaseSpace method?
_phaseSpaceHeaderFileStream >> token;
domain->setglobalNumMolecules( strtoul(token.c_str(),NULL,0) );
}
// LOCATION OF OLD PRESSURE GRADIENT TOKENS
else {
Log::global_log->error() << "Invalid token \'" << token << "\' found. Skipping rest of the header." << std::endl;
header = false;
}
}

_simulation.getEnsemble()->setComponentLookUpIDs();

_phaseSpaceHeaderFileStream.close();
Log::global_log->error() << "[ASCII Reader] Using the header of the ASCII checkpoints is deprecated" << std::endl;
Log::global_log->error() << "[ASCII Reader] Use the config xml file instead to set according values" << std::endl;
Simulation::exit(1);
}

unsigned long
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2 changes: 2 additions & 0 deletions src/io/ASCIIReader.h
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@ class ASCIIReader : public InputBase {
//! @brief For this class, header and data are in the same file, so there is no separate header file
void setPhaseSpaceHeaderFile(std::string filename);

//! DEPRECATED!
//! The information stored in the header must be provided via the xml config file
//! @brief reads in header of the input file (including component description)
//!
//! The Header in the input file consists of several elements. An element starts
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