docs and indent cleanup

src/Simulation.cpp

@@ -326,8 +326,9 @@ void Simulation::readXML(XMLfileUnits& xmlconfig) {
 			else if(parallelisationtype == "DomainDecomposition") {
 				delete _domainDecomposition;
 				_domainDecomposition = new DomainDecomposition(
-#ifdef MAMICO_COUPLING	coupling::interface::LS1StaticCommData::getInstance().getLocalCommunicator(),
-															coupling::interface::LS1StaticCommData::getInstance().getDomainGridDecomp()
+#ifdef MAMICO_COUPLING	
+				coupling::interface::LS1StaticCommData::getInstance().getLocalCommunicator(),
+				coupling::interface::LS1StaticCommData::getInstance().getDomainGridDecomp()
 #endif
 				);
 			}

src/plugins/MamicoCoupling.cpp

@@ -2,22 +2,17 @@
 #include "Domain.h"
 
 void MamicoCoupling::readXML(XMLfileUnits& xmlconfig)
-{	
+{
 	return;
 }
 
-/** @brief Ensures _macroscopicCellService is initialized, and switches the ls1 thermostat off.
- * 
- * MaMiCo uses its own thermostat, which will conflict with the ls1 thermostat. */
 void MamicoCoupling::init(ParticleContainer* particleContainer,
 		DomainDecompBase* domainDecomp, Domain* domain)
 {
-	#ifdef MAMICO_COUPLING
-	//since using mamico thermostat, switch off ls1 thermostat 
-	domain->thermostatOff();
+#ifdef MAMICO_COUPLING
 	//code to print to log that plugin is initialised
 	global_log->info() << "MaMiCo coupling plugin initialized" << std::endl;
-	#endif
+#endif
 }
 
 void MamicoCoupling::beforeEventNewTimestep(ParticleContainer* particleContainer,
@@ -26,21 +21,11 @@ void MamicoCoupling::beforeEventNewTimestep(ParticleContainer* particleContainer
 
 }
 
-/** @brief Takes coupling steps such as particle insertion, to make sure they are accounted for before forces are calculated.
- * 
- * Following steps are taken, if coupling is switched on:
- * - Iterate over cells to average values like momentum and mass, to pass to macroscopic solvers
- * - Distribute incoming mass from macroscopic solver by inserting perticles (if enabled)
- * - Run the MaMiCo thermostat cell by cell
- * 
- * The distributeMass method calls the updateParticleContainerAndDecomposition() function at the end, so we end up with a container with halo particles present.
- * Hence a manual halo clearance is done to restore the state of the container.
- * */
 void MamicoCoupling::beforeForces(ParticleContainer* particleContainer,
 		DomainDecompBase* domainDecomp, unsigned long simstep)        
 {
-	#ifdef MAMICO_COUPLING
-	if(_couplingEnabled) //only perform coupling steps if coupling is enabled
+#ifdef MAMICO_COUPLING
+	if(_couplingEnabled)
 	{
 		// This object should be set by MaMiCo after the plugins are created in the simulation readxml file
 		// Even though this method is called before the object is set, at this point the coupling switch is always off
@@ -50,26 +35,20 @@ void MamicoCoupling::beforeForces(ParticleContainer* particleContainer,
 #ifndef MARDYN_AUTOPAS
 		particleContainer->deleteOuterParticles();
 #endif
-    }
-	#endif
+	}
+#endif
 }
 
-/** @brief Performs adjustments after force calculation 
- * 
- * Following steps are taken, if coupling is switched on:
- * - Distribute incoming momentum among affected cells
- * - Apply boundary force to molecules near microscopic domain boundary
- * */
 void MamicoCoupling::afterForces(ParticleContainer* particleContainer,
 		DomainDecompBase* domainDecomp, unsigned long simstep)
 {
-	#ifdef MAMICO_COUPLING
+#ifdef MAMICO_COUPLING
 	if(_couplingEnabled)
 	{
 		_macroscopicCellService->distributeMomentum(simstep);
 		_macroscopicCellService->applyBoundaryForce(simstep);
 	}
-	#endif
+#endif
 }
 
 void MamicoCoupling::endStep(ParticleContainer* particleContainer,

src/plugins/MamicoCoupling.h

@@ -23,21 +23,41 @@ class MamicoCoupling: public PluginBase {
 	MamicoCoupling() {}
 	virtual ~MamicoCoupling() {}
 
+	/** @brief Prints to log that mamico coupling is inited
+	 * 
+	 * */
 	void init(ParticleContainer* particleContainer,
 			DomainDecompBase* domainDecomp, Domain* domain) override;
 
+
 	void readXML(XMLfileUnits& xmlconfig) override;
 
 	void beforeEventNewTimestep(
 			ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
 			unsigned long simstep
 	) override;
 
+	/** @brief Takes coupling steps such as particle insertion, to make sure they are accounted for before forces are calculated.
+	 * 
+	 * Following steps are taken, if coupling is switched on:
+	 * - Iterate over cells to average values like momentum and mass, to pass to macroscopic solvers
+	 * - Distribute incoming mass from macroscopic solver by inserting perticles (if enabled)
+	 * - Run the MaMiCo thermostat cell by cell
+	 * 
+	 * The distributeMass method calls the updateParticleContainerAndDecomposition() function at the end, so we end up with a container with halo particles present.
+	 * Hence a manual halo clearance is done to restore the state of the container.
+	 * */
 	void beforeForces(
 			ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
 			unsigned long simstep
 	) override;
 
+	/** @brief Performs adjustments after force calculation 
+	 * 
+	 * Following steps are taken, if coupling is switched on:
+	 * - Distribute incoming momentum among affected cells
+	 * - Apply boundary force to molecules near microscopic domain boundary
+	 * */	
 	void afterForces(
 			ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
 			unsigned long simstep
@@ -57,7 +77,7 @@ class MamicoCoupling: public PluginBase {
 	static PluginBase* createInstance() { return new MamicoCoupling(); }
 
 #ifdef MAMICO_COUPLING
-/** @brief sets the macroscopicCellService object that controls the inner coupling logic.
+/** @brief Sets the macroscopicCellService object that controls the inner coupling logic.
  * 
  * MaMiCo extracts the MamicoCoupling plugin object from the simulation object after initialization and uses this function to set the macroscopicCellCervice.
  * The code for this object can be found in https://github.com/HSU-HPC/MaMiCo/blob/master/coupling/services/MacroscopicCellService.cpph
@@ -66,15 +86,30 @@ class MamicoCoupling: public PluginBase {
 		_macroscopicCellService = static_cast<coupling::services::MacroscopicCellServiceImpl<ls1::LS1RegionWrapper,3>*>
 			(macroscopicCellService);
 	}
+#endif
 
+/** @brief Enables coupling logic, allowing coupling steps to run while simulation is running.
+ * 
+ * Set from within MaMiCo, check https://github.com/HSU-HPC/MaMiCo/blob/master/coupling/interface/MDSimulationFactory.h, class LS1MDSimulation
+ * */
 	void switchOnCoupling(){ _couplingEnabled = true; }
+
+/** @brief Disables coupling logic, not allowing coupling steps to run. Typically done when equilibrating the simulation initially.
+ * 
+ * Set from within MaMiCo, check https://github.com/HSU-HPC/MaMiCo/blob/master/coupling/interface/MDSimulationFactory.h, class LS1MDSimulation
+ * */
 	void switchOffCoupling(){ _couplingEnabled = false; }
+
+/** @brief Getter method for the coupling state.
+ * 
+ * Not used currently, but may be used in future
+ * */
 	bool getCouplingState() { return _couplingEnabled;}
-#endif
+
 
 private:
 #ifdef MAMICO_COUPLING
 	coupling::services::MacroscopicCellServiceImpl<ls1::LS1RegionWrapper,3>* _macroscopicCellService;
-	bool _couplingEnabled = false;
 #endif
+	bool _couplingEnabled = false;
 };