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Fix quaternion default initialisation #300

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Fix quaternion default initialisation #300

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879cbf3
Change default initialization for Quaternions to 0 + 0i + 0j + 0k
cniethammer Mar 20, 2024
32d6e83
Align names of parameters in Molecule constructors with Quaternion pa…
cniethammer Mar 20, 2024
4fe755b
Fix initialization of molecule orientation in internal generator code
cniethammer Mar 20, 2024
561259f
Add cubic_gird_generator example to test configuration list
cniethammer Mar 20, 2024
be75df9
Change Molecule constructor to require passing all parameters
cniethammer Apr 16, 2024
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3 changes: 1 addition & 2 deletions src/io/ASCIIReader.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -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);
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3 changes: 1 addition & 2 deletions src/io/BinaryReader.cpp
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Expand Up @@ -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);
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3 changes: 1 addition & 2 deletions src/io/MPI_IOReader.cpp
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Expand Up @@ -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())) {
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2 changes: 1 addition & 1 deletion src/io/ObjectGenerator.cpp
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Expand Up @@ -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);
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4 changes: 2 additions & 2 deletions src/io/PerCellGenerator.cpp
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Expand Up @@ -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 {
Expand Down Expand Up @@ -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);
}
}
10 changes: 5 additions & 5 deletions src/molecules/FullMolecule.h
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Expand Up @@ -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);

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10 changes: 5 additions & 5 deletions src/molecules/MoleculeRMM.h
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Expand Up @@ -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;
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4 changes: 2 additions & 2 deletions src/parallel/ParticleDataFull.cpp
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Expand Up @@ -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) {
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Out of interest: Is the whole object returned or just a pointer?
If former, isn't this quite bad since a Molecule object is rather big?

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],
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2 changes: 1 addition & 1 deletion src/parallel/ParticleDataFull.h
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion src/parallel/ParticleDataRMM.cpp
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Expand Up @@ -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],
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2 changes: 1 addition & 1 deletion src/parallel/ParticleDataRMM.h
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Expand Up @@ -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];
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4 changes: 3 additions & 1 deletion src/particleContainer/adapter/CellDataSoARMM.h
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Expand Up @@ -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 {
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