Fixes to mamico plugin after mamico refactor

src/plugins/MamicoCoupling.cpp

@@ -1,64 +1,49 @@
+#ifdef MAMICO_COUPLING
+
 #include "MamicoCoupling.h"
 #include "Domain.h"
 
-void MamicoCoupling::readXML(XMLfileUnits& xmlconfig)
-{
-	return;
-}
-
-void MamicoCoupling::init(ParticleContainer* particleContainer,
-		DomainDecompBase* domainDecomp, Domain* domain)
-{
-#ifdef MAMICO_COUPLING
-	//code to print to log that plugin is initialised
-	Log::global_log->info() << "MaMiCo coupling plugin initialized" << std::endl;
-#endif
-}
-
-void MamicoCoupling::beforeEventNewTimestep(ParticleContainer* particleContainer,
-		DomainDecompBase* domainDecomp, unsigned long simstep)
-{
+void MamicoCoupling::readXML(XMLfileUnits &xmlconfig) {}
 
+void MamicoCoupling::init(ParticleContainer *particleContainer,
+                          DomainDecompBase *domainDecomp, Domain *domain) {
+  Log::global_log->info() << "MaMiCo coupling plugin initialized" << std::endl;
 }
 
-void MamicoCoupling::beforeForces(ParticleContainer* particleContainer,
-		DomainDecompBase* domainDecomp, unsigned long simstep)
-{
-#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
-		_macroscopicCellService->processInnerMacroscopicCellAfterMDTimestep();
-		_macroscopicCellService->distributeMass(simstep);
-		_macroscopicCellService->applyTemperatureToMolecules(simstep);
+void MamicoCoupling::beforeEventNewTimestep(
+    ParticleContainer *particleContainer, DomainDecompBase *domainDecomp,
+    unsigned long simstep) {}
+
+void MamicoCoupling::beforeForces(ParticleContainer *particleContainer,
+                                  DomainDecompBase *domainDecomp,
+                                  unsigned long simstep) {
+  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
+    _couplingCellService->processInnerCouplingCellAfterMDTimestep();
+    _couplingCellService->distributeMass(simstep);
+    _couplingCellService->applyTemperatureToMolecules(simstep);
 #ifndef MARDYN_AUTOPAS
-		particleContainer->deleteOuterParticles();
-#endif
-	}
+    particleContainer->deleteOuterParticles();
 #endif
+  }
 }
 
-void MamicoCoupling::afterForces(ParticleContainer* particleContainer,
-		DomainDecompBase* domainDecomp, unsigned long simstep)
-{
-#ifdef MAMICO_COUPLING
-	if(_couplingEnabled)
-	{
-		_macroscopicCellService->distributeMomentum(simstep);
-		_macroscopicCellService->applyBoundaryForce(simstep);
-	}
-#endif
+void MamicoCoupling::afterForces(ParticleContainer *particleContainer,
+                                 DomainDecompBase *domainDecomp,
+                                 unsigned long simstep) {
+  if (_couplingEnabled) {
+    _couplingCellService->distributeMomentum(simstep);
+    _couplingCellService->applyBoundaryForce(simstep);
+  }
 }
 
-void MamicoCoupling::endStep(ParticleContainer* particleContainer,
-		DomainDecompBase* domainDecomp, Domain* domain, unsigned long simstep)
-{
+void MamicoCoupling::endStep(ParticleContainer *particleContainer,
+                             DomainDecompBase *domainDecomp, Domain *domain,
+                             unsigned long simstep) {}
 
-}
-
-void MamicoCoupling::finish(ParticleContainer* particleContainer,
-		DomainDecompBase* domainDecomp, Domain* domain)
-{
+void MamicoCoupling::finish(ParticleContainer *particleContainer,
+                            DomainDecompBase *domainDecomp, Domain *domain) {}
 
-}
+#endif

src/plugins/MamicoCoupling.h

@@ -1,115 +1,134 @@
+#ifdef MAMICO_COUPLING
+
 #pragma once
 
 #include "PluginBase.h"
-#ifdef MAMICO_COUPLING
-#include <coupling/services/MacroscopicCellService.h>
 #include <coupling/interface/impl/ls1/LS1RegionWrapper.h>
-#endif
-
-/** @brief Allows execution of MaMiCo code to enable coupling with MaMiCo.
- * 
- * When MaMiCo is coupled with any simulation software, it needs to control the simulation from both the outside and inside.
- * From the outside, MaMiCo needs to be able to start and stop the simulation, and keep unique simulations distinct.
- * From the inside, MaMiCo code needs to be executed at specific points within the same simulation step. This plugin enables the "inside" behaviour.
- * 
- * MaMiCo coupling requires the MAMICO_COUPLING flag to be set, and the MAMICO_SRD_DIR flag to point to MaMiCo source files. With these enabled, ls1 compiles as a library.
- * To make sure the program compiles and works with tests, the relevant MaMiCo portions for the code are put in #ifdef regions.
- * 
- * */
-
-class MamicoCoupling: public PluginBase {
+#include <coupling/services/CouplingCellService.h>
+
+/**
+ * Allows execution of MaMiCo code to enable coupling with MaMiCo.
+ *
+ * When MaMiCo is coupled with any simulation software, it needs to control the
+ * simulation from both the outside and inside. From the outside, MaMiCo needs
+ * to be able to start and stop the simulation, and keep unique simulations
+ * distinct. From the inside, MaMiCo code needs to be executed at specific
+ * points within the same simulation step. This plugin enables the "inside"
+ * behaviour.
+ *
+ * MaMiCo coupling requires the MAMICO_COUPLING flag to be set, and the
+ * MAMICO_SRD_DIR flag to point to MaMiCo source files. With these enabled, ls1
+ * compiles as a library. To make sure the program compiles and works with
+ * tests, the relevant MaMiCo portions for the code are put in #ifdef regions.
+ */
+class MamicoCoupling : public PluginBase {
 
 public:
-	MamicoCoupling() {}
-	virtual ~MamicoCoupling() {}
-
-	/** @brief Prints to log that mamico coupling is initialized
-	 * 
-	 * */
-	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
-	) override;
-
-	void endStep(
-			ParticleContainer* particleContainer, DomainDecompBase* domainDecomp,
-			Domain* domain, unsigned long simstep) override;
-
-	void finish(ParticleContainer* particleContainer,
-			DomainDecompBase* domainDecomp, Domain* domain) override;
-
-	std::string getPluginName() override {
-		return std::string("MamicoCoupling");
-	}
-
-	static PluginBase* createInstance() { return new MamicoCoupling(); }
-
-#ifdef MAMICO_COUPLING
-/** @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
- * */
-	void setMamicoMacroscopicCellService(coupling::services::MacroscopicCellService<3>* macroscopicCellService){
-		_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; }
+  MamicoCoupling() = default;
+  ~MamicoCoupling() override = default;
+
+  void init(ParticleContainer *particleContainer,
+            DomainDecompBase *domainDecomp, Domain *domain) override;
+
+  /*
+   * No XML tags defined for this plugin, so does nothing
+   */
+  void readXML(XMLfileUnits &xmlconfig) override;
+
+  void beforeEventNewTimestep(ParticleContainer *particleContainer,
+                              DomainDecompBase *domainDecomp,
+                              unsigned long simstep) override;
+
+  /**
+   * 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;
+
+  /**
+   * 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) override;
+
+  void endStep(ParticleContainer *particleContainer,
+               DomainDecompBase *domainDecomp, Domain *domain,
+               unsigned long simstep) override;
+
+  void finish(ParticleContainer *particleContainer,
+              DomainDecompBase *domainDecomp, Domain *domain) override;
+
+  std::string getPluginName() override { return "MamicoCoupling"; }
+
+  static PluginBase *createInstance() { return new MamicoCoupling(); }
+
+  /**
+   * 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/CouplingCellService.cpph
+   */
+  void setMamicoCouplingCellService(
+      coupling::services::CouplingCellService<3> *couplingCellService) {
+    _couplingCellService =
+        static_cast<coupling::services::CouplingCellServiceImpl<
+            ls1::LS1RegionWrapper, 3> *>(couplingCellService);
+  }
+
+  /**
+   * 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; }
+
+  /**
+   * 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; }
+
+  /**
+   * Getter method for the coupling state.
+   *
+   * Not used currently, but may be used in future
+   */
+  bool getCouplingState() const { return _couplingEnabled; }
 
-/** @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;}
+private:
+  coupling::services::CouplingCellServiceImpl<ls1::LS1RegionWrapper, 3>
+      *_couplingCellService = nullptr;
 
+  bool _couplingEnabled = false;
+};
 
-private:
-#ifdef MAMICO_COUPLING
-	coupling::services::MacroscopicCellServiceImpl<ls1::LS1RegionWrapper,3>* _macroscopicCellService;
 #endif
-	bool _couplingEnabled = false;
-};