Change Molecule constructor to require passing all parameters

Remove the default parameters for the Molecule constructor to prevent unintentional incorrect initialization of molecules. Fix all related places in the code with the appropriate initialization values. Signed-off-by: Christoph Niethammer <[email protected]>
ls1mardyn · Apr 16, 2024 · be75df9 · be75df9
1 parent 561259f
commit be75df9
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Showing 12 changed files with 24 additions and 25 deletions.
diff --git a/src/io/ASCIIReader.cpp b/src/io/ASCIIReader.cpp
@@ -410,8 +410,7 @@ ASCIIReader::readPhaseSpace(ParticleContainer* particleContainer, Domain* domain
 		Log::global_log->debug() << "broadcasting(sending/receiving) particles with buffer_position " << particle_buff_pos << std::endl;
 		MPI_Bcast(particle_buff, PARTICLE_BUFFER_SIZE, mpi_Particle, 0, MPI_COMM_WORLD); // TODO: MPI_COMM_WORLD
 		for (int j = 0; j < particle_buff_pos; j++) {
-			Molecule m;
-			ParticleData::ParticleDataToMolecule(particle_buff[j], m);
+			Molecule m = ParticleData::ParticleDataToMolecule(particle_buff[j]);
 			// only add particle if it is inside of the own domain!
 			if(particleContainer->isInBoundingBox(m.r_arr().data())) {
 				particleContainer->addParticle(m, true, false);

diff --git a/src/io/BinaryReader.cpp b/src/io/BinaryReader.cpp
@@ -261,8 +261,7 @@ BinaryReader::readPhaseSpace(ParticleContainer* particleContainer, Domain* domai
 		MPI_Bcast(particle_buff, PARTICLE_BUFFER_SIZE, mpi_Particle, 0,
 				MPI_COMM_WORLD); // TODO: MPI_COMM_WORLD
 		for (int j = 0; j < particle_buff_pos; j++) {
-			Molecule m;
-			ParticleData::ParticleDataToMolecule(particle_buff[j], m);
+			Molecule m = ParticleData::ParticleDataToMolecule(particle_buff[j]);
 			// only add particle if it is inside of the own domain!
 			if(particleContainer->isInBoundingBox(m.r_arr().data())) {
 				particleContainer->addParticle(m, true, false);

diff --git a/src/io/MPI_IOReader.cpp b/src/io/MPI_IOReader.cpp
@@ -504,10 +504,9 @@ MPI_IOReader::readPhaseSpace(ParticleContainer* particleContainer, Domain* domai
 
 		if (globalNumParticlesPerCell[index] > 0) {
 
-			Molecule m;
 			for (int l = 0; l < globalNumParticlesPerCell[index]; l++) {
 
-				ParticleData::ParticleDataToMolecule(data[l], m);
+				Molecule m = ParticleData::ParticleDataToMolecule(data[l]);
 
 				// only add particle if it is inside of the own domain!
 				if(particleContainer->isInBoundingBox(m.r_arr().data())) {

diff --git a/src/io/ObjectGenerator.cpp b/src/io/ObjectGenerator.cpp
@@ -126,7 +126,7 @@ ObjectGenerator::readPhaseSpace(ParticleContainer* particleContainer, Domain* do
 	_filler->setObject(boundedObject);
 	_filler->init();
 
-	Molecule molecule;
+	Molecule molecule(0, nullptr, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0);
 	unsigned long moleculeID = _moleculeIdPool->getNewMoleculeId();
 	while(_filler->getMolecule(&molecule) > 0) {
 		molecule.setid(moleculeID);

diff --git a/src/io/PerCellGenerator.cpp b/src/io/PerCellGenerator.cpp
@@ -120,7 +120,7 @@ void PerCellGenerator::fillContainer(ParticleContainer *particleContainer, Compo
 						std::array pos = {uniform_dists[0](randomEngine), uniform_dists[1](randomEngine),
 										  uniform_dists[2](randomEngine)};
 
-						Molecule m(id, component, pos[0], pos[1], pos[2], 0., 0., 0.);
+						Molecule m(id, component, pos[0], pos[1], pos[2], 0., 0., 0., 1., 0., 0., 0., 0., 0., 0.);
 						if (isHalo) {
 							particleContainer->addHaloParticle(m, true);
 						} else {
@@ -160,7 +160,7 @@ void PerCellGenerator::generateTwoParticles(ParticleContainer *particleContainer
 	for (auto id = 0; id < 2; ++id) {
 		std::array pos = {uniform_dists[0](randomEngine), uniform_dists[1](randomEngine),
 						  uniform_dists[2](randomEngine)};
-		Molecule m(id, component, pos[0], pos[1], pos[2], 0., 0., 0.);
+		Molecule m(id, component, pos[0], pos[1], pos[2], 0., 0., 0., 1., 0., 0., 0., 0., 0., 0.);
 		particleContainer->addParticle(m, true);
 	}
 }
diff --git a/src/molecules/FullMolecule.h b/src/molecules/FullMolecule.h
@@ -22,11 +22,11 @@ class FullMolecule : public MoleculeInterface {
 	// but if it is left away, all pointer data is not initialized (which is not
 	// neccessarily bad), but then assertions fail (e.g. in the destructor) and we can't
 	// use it's instances.
-	FullMolecule(unsigned long id = 0, Component *component = nullptr,
-	         double rx = 0., double ry = 0., double rz = 0.,
-	         double vx = 0., double vy = 0., double vz = 0.,
-	         double qw = 0., double qx = 0., double qy = 0., double qz = 0.,
-	         double Dx = 0., double Dy = 0., double Dz = 0.
+	FullMolecule(unsigned long id, Component *component,
+	         double rx, double ry, double rz,
+	         double vx, double vy, double vz,
+	         double qw, double qx, double qy, double qz,
+	         double Dx, double Dy, double Dz
 	);
 	FullMolecule(const FullMolecule& m);
 

diff --git a/src/molecules/MoleculeRMM.h b/src/molecules/MoleculeRMM.h
@@ -18,11 +18,11 @@ class MoleculeRMM : public MoleculeInterface {
 	};
 
 public:
-	MoleculeRMM(unsigned long id = 0, Component *component = nullptr,
-        double rx = 0., double ry = 0., double rz = 0.,
-        double vx = 0., double vy = 0., double vz = 0.,
-        double qw = 0., double qx = 0., double qy = 0., double qz = 0.,
-        double Dx = 0., double Dy = 0., double Dz = 0.
+	MoleculeRMM(unsigned long id, Component *component,
+        double rx, double ry, double rz,
+        double vx, double vy, double vz,
+        double qw, double qx, double qy, double qz,
+        double Dx, double Dy, double Dz
 	) {
 		_state = STORAGE_AOS;
 		_r[0] = rx;

diff --git a/src/parallel/ParticleDataFull.cpp b/src/parallel/ParticleDataFull.cpp
@@ -60,9 +60,9 @@ void ParticleDataFull::MoleculeToParticleData(ParticleDataFull &particleStruct,
 	particleStruct.D[2] = molecule.D(2);
 }
 
-void ParticleDataFull::ParticleDataToMolecule(const ParticleDataFull &particleStruct, Molecule &molecule) {
+Molecule ParticleDataFull::ParticleDataToMolecule(const ParticleDataFull &particleStruct) {
 	Component* component = _simulation.getEnsemble()->getComponent(particleStruct.cid);
-	molecule = Molecule(particleStruct.id, component,
+	return Molecule(particleStruct.id, component,
 						particleStruct.r[0], particleStruct.r[1], particleStruct.r[2],
 						particleStruct.v[0], particleStruct.v[1], particleStruct.v[2],
 						particleStruct.q[0], particleStruct.q[1], particleStruct.q[2], particleStruct.q[3],

diff --git a/src/parallel/ParticleDataFull.h b/src/parallel/ParticleDataFull.h
@@ -25,7 +25,7 @@ class ParticleDataFull {
 	static void MoleculeToParticleData(ParticleDataFull &particleStruct, Molecule &molecule);
 
 	//! @brief copy data from object of class ParticleDataFull to object of class Molecule
-	static void ParticleDataToMolecule(const ParticleDataFull &particleStruct, Molecule &molecule);
+	static Molecule ParticleDataToMolecule(const ParticleDataFull &particleStruct);
 
 	double r[3];  //! position
 	double v[3];  //! velocity

diff --git a/src/parallel/ParticleDataRMM.cpp b/src/parallel/ParticleDataRMM.cpp
@@ -66,7 +66,7 @@ void ParticleDataRMM::MoleculeToParticleData(ParticleDataRMM &particleStruct, Mo
 	particleStruct.v[2] = molecule.v(2);
 }
 
-void ParticleDataRMM::ParticleDataToMolecule(const ParticleDataRMM &particleStruct, Molecule &molecule) {
+Molecule ParticleDataRMM::ParticleDataToMolecule(const ParticleDataRMM &particleStruct) {
 	Component* component = _simulation.getEnsemble()->getComponent(0);
 	molecule = Molecule(particleStruct.id, component,
 						particleStruct.r[0], particleStruct.r[1], particleStruct.r[2],

diff --git a/src/parallel/ParticleDataRMM.h b/src/parallel/ParticleDataRMM.h
@@ -26,7 +26,7 @@ class ParticleDataRMM {
 	static void MoleculeToParticleData(ParticleDataRMM &particleStruct, Molecule &molecule);
 
 	//! @brief copy data from object of class class ParticleDataRMM to object of class Molecule
-	static void ParticleDataToMolecule(const ParticleDataRMM &particleStruct, Molecule &molecule);
+	static Molecule ParticleDataToMolecule(const ParticleDataRMM &particleStruct);
 
 	unsigned long id;
 	vcp_real_calc r[3];

diff --git a/src/particleContainer/adapter/CellDataSoARMM.h b/src/particleContainer/adapter/CellDataSoARMM.h
@@ -72,7 +72,9 @@ class CellDataSoARMM : public CellDataSoABase {
 		return Molecule (
 			getMolUid(index), nullptr,
 			getMolR(0,index), getMolR(1,index), getMolR(2,index),
-			getMolV(0,index), getMolV(1,index), getMolV(2,index));
+			getMolV(0,index), getMolV(1,index), getMolV(2,index),
+			1.0, 0.0, 0.0, 0.0,
+			0.0, 0.0, 0.0);
 	}
 
 	void readImmutableMolecule(size_t index, MoleculeInterface& m) const {