void P2OrderParameter::process() {
Molecule* mol;
RigidBody* rb;
SimInfo::MoleculeIterator mi;
Molecule::RigidBodyIterator rbIter;
StuntDouble* sd1;
StuntDouble* sd2;
int ii;
int jj;
int vecCount;
bool usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
DumpReader reader(info_, dumpFilename_);
int nFrames = reader.getNFrames();
for (int i = 0; i < nFrames; i += step_) {
reader.readFrame(i);
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
//change the positions of atoms which belong to the rigidbodies
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
rb->updateAtoms();
}
}
Mat3x3d orderTensor(0.0);
vecCount = 0;
seleMan1_.setSelectionSet(evaluator1_.evaluate());
if (doVect_) {
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
sd1 = seleMan1_.nextSelected(ii)) {
if (sd1->isDirectional()) {
Vector3d vec = sd1->getA().transpose()*V3Z;
vec.normalize();
orderTensor += outProduct(vec, vec);
vecCount++;
}
}
orderTensor /= vecCount;
} else {
if (doOffset_) {
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
sd1 = seleMan1_.nextSelected(ii)) {
// This will require careful rewriting if StaticProps is
// ever parallelized. For an example, see
// Thermo::getTaggedAtomPairDistance
int sd2Index = sd1->getGlobalIndex() + seleOffset_;
sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
Vector3d vec = sd1->getPos() - sd2->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(vec);
vec.normalize();
orderTensor +=outProduct(vec, vec);
vecCount++;
}
orderTensor /= vecCount;
} else {
seleMan2_.setSelectionSet(evaluator2_.evaluate());
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
sprintf( painCave.errMsg,
"In frame %d, the number of selected StuntDoubles are\n"
"\tnot the same in --sele1 and sele2\n", i);
painCave.severity = OPENMD_INFO;
painCave.isFatal = 0;
simError();
}
for (sd1 = seleMan1_.beginSelected(ii),
sd2 = seleMan2_.beginSelected(jj);
sd1 != NULL && sd2 != NULL;
sd1 = seleMan1_.nextSelected(ii),
sd2 = seleMan2_.nextSelected(jj)) {
Vector3d vec = sd1->getPos() - sd2->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(vec);
vec.normalize();
orderTensor +=outProduct(vec, vec);
vecCount++;
}
orderTensor /= vecCount;
}
}
if (vecCount == 0) {
sprintf( painCave.errMsg,
"In frame %d, the number of selected vectors was zero.\n"
"\tThis will not give a meaningful order parameter.", i);
painCave.severity = OPENMD_ERROR;
painCave.isFatal = 1;
simError();
}
orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
Vector3d eigenvalues;
Mat3x3d eigenvectors;
Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
int which(-1);
RealType maxEval = 0.0;
for(int k = 0; k< 3; k++) {
if(fabs(eigenvalues[k]) > maxEval) {
which = k;
maxEval = fabs(eigenvalues[k]);
}
}
RealType p2 = 1.5 * maxEval;
//the eigen vector is already normalized in SquareMatrix3::diagonalize
Vector3d director = eigenvectors.getColumn(which);
if (director[0] < 0) {
director.negate();
}
RealType angle = 0.0;
vecCount = 0;
if (doVect_) {
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
sd1 = seleMan1_.nextSelected(ii)) {
if (sd1->isDirectional()) {
Vector3d vec = sd1->getA().transpose()*V3Z;
vec.normalize();
angle += acos(dot(vec, director));
vecCount++;
}
}
angle = angle/(vecCount*NumericConstant::PI)*180.0;
} else {
if (doOffset_) {
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
sd1 = seleMan1_.nextSelected(ii)) {
// This will require careful rewriting if StaticProps is
// ever parallelized. For an example, see
// Thermo::getTaggedAtomPairDistance
int sd2Index = sd1->getGlobalIndex() + seleOffset_;
sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
Vector3d vec = sd1->getPos() - sd2->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(vec);
vec.normalize();
angle += acos(dot(vec, director)) ;
vecCount++;
}
angle = angle / (vecCount * NumericConstant::PI) * 180.0;
} else {
for (sd1 = seleMan1_.beginSelected(ii),
sd2 = seleMan2_.beginSelected(jj);
sd1 != NULL && sd2 != NULL;
sd1 = seleMan1_.nextSelected(ii),
sd2 = seleMan2_.nextSelected(jj)) {
Vector3d vec = sd1->getPos() - sd2->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(vec);
vec.normalize();
angle += acos(dot(vec, director)) ;
vecCount++;
}
angle = angle / (vecCount * NumericConstant::PI) * 180.0;
}
}
OrderParam param;
param.p2 = p2;
param.director = director;
param.angle = angle;
orderParams_.push_back(param);
}
writeP2();
}
void MomentumCorrFunc::correlateFrames(int frame1, int frame2) {
SimInfo::MoleculeIterator mi1;
SimInfo::MoleculeIterator mi2;
Molecule* mol1;
Molecule* mol2;
Molecule::AtomIterator ai1;
Molecule::AtomIterator ai2;
Atom* atom1;
Atom* atom2;
std::vector<Vector3d> atomPositions1;
std::vector<Vector3d> atomPositions2;
std::vector<Vector3d> atomVelocity1;
std::vector<Vector3d> atomVelocity2;
int thisAtom1, thisAtom2;
Snapshot* snapshot1 = bsMan_->getSnapshot(frame1);
Snapshot* snapshot2 = bsMan_->getSnapshot(frame2);
assert(snapshot1 && snapshot2);
RealType time1 = snapshot1->getTime();
RealType time2 = snapshot2->getTime();
int timeBin = int ((time2 - time1) /deltaTime_ + 0.5);
updateFrame(frame1);
atomPositions1.clear();
for (mol1 = info_->beginMolecule(mi1); mol1 != NULL;
mol1 = info_->nextMolecule(mi1)) {
for(atom1 = mol1->beginAtom(ai1); atom1 != NULL;
atom1 = mol1->nextAtom(ai1)) {
atomPositions1.push_back(atom1->getPos(frame1));
atomVelocity1.push_back(atom1->getVel(frame1));
}
}
updateFrame(frame2);
atomPositions2.clear();
for (mol2 = info_->beginMolecule(mi2); mol2 != NULL;
mol2 = info_->nextMolecule(mi2)) {
for(atom2 = mol2->beginAtom(ai2); atom2 != NULL;
atom2 = mol2->nextAtom(ai2)) {
atomPositions2.push_back(atom2->getPos(frame2));
atomVelocity2.push_back(atom2->getVel(frame2));
}
}
thisAtom1 = 0;
for (mol1 = info_->beginMolecule(mi1); mol1 != NULL;
mol1 = info_->nextMolecule(mi1)) {
for(atom1 = mol1->beginAtom(ai1); atom1 != NULL;
atom1 = mol1->nextAtom(ai1)) {
Vector3d r1 = atomPositions1[thisAtom1];
Vector3d p1 = atom1->getMass() * atomVelocity1[thisAtom1];
thisAtom2 = 0;
for (mol2 = info_->beginMolecule(mi2); mol2 != NULL;
mol2 = info_->nextMolecule(mi2)) {
for(atom2 = mol2->beginAtom(ai2); atom2 != NULL;
atom2 = mol2->nextAtom(ai2)) {
Vector3d r2 = atomPositions2[thisAtom2];
Vector3d p2 = atom2->getMass() * atomVelocity1[thisAtom1];
Vector3d deltaPos = (r2-r1);
Vector3d dp2( deltaPos.x() * deltaPos.x(),
deltaPos.y() * deltaPos.y(),
deltaPos.z() * deltaPos.z());
Vector3d pprod( p1.x() * p2.x(),
p1.y() * p2.y(),
p1.z() * p2.z());
histogram_[timeBin] += outProduct(dp2, pprod);
thisAtom2++;
}
}
thisAtom1++;
}
}
count_[timeBin]++;
}
