void RCorrFuncZ::computeFrame(int istep) {
hmat_ = currentSnapshot_->getHmat();
halfBoxZ_ = hmat_(2,2) / 2.0;
StuntDouble* sd;
int isd1, isd2;
unsigned int index;
if (evaluator1_.isDynamic()) {
seleMan1_.setSelectionSet(evaluator1_.evaluate());
}
if (uniqueSelections_ && evaluator2_.isDynamic()) {
seleMan2_.setSelectionSet(evaluator2_.evaluate());
}
for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
sd = seleMan1_.nextSelected(isd1)) {
index = computeProperty1(istep, sd);
if (index == sele1ToIndex_[istep].size()) {
sele1ToIndex_[istep].push_back(sd->getGlobalIndex());
} else {
sele1ToIndex_[istep].resize(index+1);
sele1ToIndex_[istep][index] = sd->getGlobalIndex();
}
}
if (uniqueSelections_) {
for (sd = seleMan2_.beginSelected(isd2); sd != NULL;
sd = seleMan2_.nextSelected(isd2)) {
index = computeProperty1(istep, sd);
if (index == sele2ToIndex_[istep].size()) {
sele2ToIndex_[istep].push_back(sd->getGlobalIndex());
} else {
sele2ToIndex_[istep].resize(index+1);
sele2ToIndex_[istep][index] = sd->getGlobalIndex();
}
}
}
}
void BondAngleDistribution::process() {
Molecule* mol;
Atom* atom;
RigidBody* rb;
int myIndex;
SimInfo::MoleculeIterator mi;
Molecule::RigidBodyIterator rbIter;
Molecule::AtomIterator ai;
StuntDouble* sd;
Vector3d vec;
std::vector<Vector3d> bondvec;
RealType r;
int nBonds;
int i;
bool usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
DumpReader reader(info_, dumpFilename_);
int nFrames = reader.getNFrames();
frameCounter_ = 0;
nTotBonds_ = 0;
for (int istep = 0; istep < nFrames; istep += step_) {
reader.readFrame(istep);
frameCounter_++;
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
if (evaluator_.isDynamic()) {
seleMan_.setSelectionSet(evaluator_.evaluate());
}
// update the positions of atoms which belong to the rigidbodies
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
rb->updateAtoms();
}
}
// outer loop is over the selected StuntDoubles:
for (sd = seleMan_.beginSelected(i); sd != NULL;
sd = seleMan_.nextSelected(i)) {
myIndex = sd->getGlobalIndex();
nBonds = 0;
bondvec.clear();
// inner loop is over all other atoms in the system:
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
for (atom = mol->beginAtom(ai); atom != NULL;
atom = mol->nextAtom(ai)) {
if (atom->getGlobalIndex() != myIndex) {
vec = sd->getPos() - atom->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(vec);
// Calculate "bonds" and make a pair list
r = vec.length();
// Check to see if neighbor is in bond cutoff
if (r < rCut_) {
// Add neighbor to bond list's
bondvec.push_back(vec);
nBonds++;
nTotBonds_++;
}
}
}
for (int i = 0; i < nBonds-1; i++ ){
Vector3d vec1 = bondvec[i];
vec1.normalize();
for(int j = i+1; j < nBonds; j++){
Vector3d vec2 = bondvec[j];
vec2.normalize();
RealType theta = acos(dot(vec1,vec2))*180.0/NumericConstant::PI;
if (theta > 180.0){
theta = 360.0 - theta;
}
int whichBin = int(theta/deltaTheta_);
histogram_[whichBin] += 2;
}
}
}
}
}
writeBondAngleDistribution();
}
void TetrahedralityParam::process() {
Molecule* mol;
StuntDouble* sd;
StuntDouble* sd2;
StuntDouble* sdi;
StuntDouble* sdj;
RigidBody* rb;
int myIndex;
SimInfo::MoleculeIterator mi;
Molecule::RigidBodyIterator rbIter;
Molecule::IntegrableObjectIterator ioi;
Vector3d vec;
Vector3d ri, rj, rk, rik, rkj, dposition, tposition;
RealType r;
RealType cospsi;
RealType Qk;
std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
int isd;
bool usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
DumpReader reader(info_, dumpFilename_);
int nFrames = reader.getNFrames();
frameCounter_ = 0;
Distorted_.clear();
Tetrahedral_.clear();
for (int istep = 0; istep < nFrames; istep += step_) {
reader.readFrame(istep);
frameCounter_++;
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
if (evaluator_.isDynamic()) {
seleMan_.setSelectionSet(evaluator_.evaluate());
}
// update the positions of atoms which belong to the rigidbodies
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
rb->updateAtoms();
}
}
// outer loop is over the selected StuntDoubles:
for (sd = seleMan_.beginSelected(isd); sd != NULL;
sd = seleMan_.nextSelected(isd)) {
myIndex = sd->getGlobalIndex();
Qk = 1.0;
myNeighbors.clear();
// inner loop is over all StuntDoubles in the system:
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
for (sd2 = mol->beginIntegrableObject(ioi); sd2 != NULL;
sd2 = mol->nextIntegrableObject(ioi)) {
if (sd2->getGlobalIndex() != myIndex) {
vec = sd->getPos() - sd2->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(vec);
r = vec.length();
// Check to see if neighbor is in bond cutoff
if (r < rCut_) {
myNeighbors.push_back(std::make_pair(r,sd2));
}
}
}
}
// Sort the vector using predicate and std::sort
std::sort(myNeighbors.begin(), myNeighbors.end());
//std::cerr << myNeighbors.size() << " neighbors within "
// << rCut_ << " A" << " \n";
// Use only the 4 closest neighbors to do the rest of the work:
int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size();
int nang = int (0.5 * (nbors * (nbors - 1)));
rk = sd->getPos();
//std::cerr<<nbors<<endl;
for (int i = 0; i < nbors-1; i++) {
sdi = myNeighbors[i].second;
ri = sdi->getPos();
rik = rk - ri;
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(rik);
rik.normalize();
for (int j = i+1; j < nbors; j++) {
sdj = myNeighbors[j].second;
rj = sdj->getPos();
rkj = rk - rj;
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(rkj);
rkj.normalize();
cospsi = dot(rik,rkj);
//std::cerr << "cos(psi) = " << cospsi << " \n";
// Calculates scaled Qk for each molecule using calculated
// angles from 4 or fewer nearest neighbors.
Qk = Qk - (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
//std::cerr<<Qk<<"\t"<<nang<<endl;
}
}
//std::cerr<<nang<<endl;
if (nang > 0) {
collectHistogram(Qk);
// Saves positions of StuntDoubles & neighbors with distorted
// coordination (low Qk value)
if ((Qk < 0.55) && (Qk > 0.45)) {
//std::cerr<<Distorted_.size()<<endl;
Distorted_.push_back(sd);
//std::cerr<<Distorted_.size()<<endl;
dposition = sd->getPos();
//std::cerr << "distorted position \t" << dposition << "\n";
}
// Saves positions of StuntDoubles & neighbors with
// tetrahedral coordination (high Qk value)
if (Qk > 0.05) {
Tetrahedral_.push_back(sd);
tposition = sd->getPos();
//std::cerr << "tetrahedral position \t" << tposition << "\n";
}
//std::cerr<<Tetrahedral_.size()<<endl;
}
}
}
writeOrderParameter();
std::cerr << "number of distorted StuntDoubles = "
<< Distorted_.size() << "\n";
std::cerr << "number of tetrahedral StuntDoubles = "
<< Tetrahedral_.size() << "\n";
}
void TetrahedralityParamXYZ::process() {
Molecule* mol;
StuntDouble* sd;
StuntDouble* sd2;
StuntDouble* sdi;
StuntDouble* sdj;
RigidBody* rb;
int myIndex;
SimInfo::MoleculeIterator mi;
Molecule::RigidBodyIterator rbIter;
Vector3d vec;
Vector3d ri, rj, rk, rik, rkj;
RealType r;
RealType cospsi;
RealType Qk;
std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
//std::vector<std::pair<Vector3d, RealType> > qvals;
//std::vector<std::pair<Vector3d, RealType> >::iterator qiter;
int isd1;
int isd2;
int kMax = int(5.0 * gaussWidth_ / voxelSize_);
int kSqLim = kMax*kMax;
cerr << "gw = " << gaussWidth_ << " vS = " << voxelSize_ << " kMax = "
<< kMax << " kSqLim = " << kSqLim << "\n";
DumpReader reader(info_, dumpFilename_);
int nFrames = reader.getNFrames();
for (int istep = 0; istep < nFrames; istep += step_) {
reader.readFrame(istep);
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
Mat3x3d hmat = currentSnapshot_->getHmat();
Vector3d halfBox = Vector3d(hmat(0,0), hmat(1,1), hmat(2,2)) / 2.0;
if (evaluator1_.isDynamic()) {
seleMan1_.setSelectionSet(evaluator1_.evaluate());
}
if (evaluator2_.isDynamic()) {
seleMan2_.setSelectionSet(evaluator2_.evaluate());
}
// update the positions of atoms which belong to the rigidbodies
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
rb->updateAtoms();
}
}
//qvals.clear();
// outer loop is over the selected StuntDoubles:
for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
sd = seleMan1_.nextSelected(isd1)) {
myIndex = sd->getGlobalIndex();
Qk = 1.0;
myNeighbors.clear();
for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
sd2 = seleMan2_.nextSelected(isd2)) {
if (sd2->getGlobalIndex() != myIndex) {
vec = sd->getPos() - sd2->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(vec);
r = vec.length();
// Check to see if neighbor is in bond cutoff
if (r < rCut_) {
myNeighbors.push_back(std::make_pair(r,sd2));
}
}
}
// Sort the vector using predicate and std::sort
std::sort(myNeighbors.begin(), myNeighbors.end());
// Use only the 4 closest neighbors to do the rest of the work:
int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size();
int nang = int (0.5 * (nbors * (nbors - 1)));
rk = sd->getPos();
for (int i = 0; i < nbors-1; i++) {
sdi = myNeighbors[i].second;
ri = sdi->getPos();
rik = rk - ri;
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(rik);
rik.normalize();
for (int j = i+1; j < nbors; j++) {
sdj = myNeighbors[j].second;
rj = sdj->getPos();
rkj = rk - rj;
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(rkj);
rkj.normalize();
cospsi = dot(rik,rkj);
// Calculates scaled Qk for each molecule using calculated
// angles from 4 or fewer nearest neighbors.
Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
}
}
if (nang > 0) {
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(rk);
//qvals.push_back(std::make_pair(rk, Qk));
Vector3d pos = rk + halfBox;
Vector3i whichVoxel(int(pos[0] / voxelSize_),
int(pos[1] / voxelSize_),
int(pos[2] / voxelSize_));
for (int l = -kMax; l <= kMax; l++) {
for (int m = -kMax; m <= kMax; m++) {
for (int n = -kMax; n <= kMax; n++) {
int kk = l*l + m*m + n*n;
if(kk <= kSqLim) {
int ll = (whichVoxel[0] + l) % nBins_(0);
ll = ll < 0 ? nBins_(0) + ll : ll;
int mm = (whichVoxel[1] + m) % nBins_(1);
mm = mm < 0 ? nBins_(1) + mm : mm;
int nn = (whichVoxel[2] + n) % nBins_(2);
nn = nn < 0 ? nBins_(2) + nn : nn;
Vector3d bPos = Vector3d(ll,mm,nn) * voxelSize_ - halfBox;
Vector3d d = bPos - rk;
currentSnapshot_->wrapVector(d);
RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3);
RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
RealType weight = exp(exponent) / denom;
count_[ll][mm][nn] += weight;
hist_[ll][mm][nn] += weight * Qk;
}
}
}
}
}
}
// for (int i = 0; i < nBins_(0); ++i) {
// for(int j = 0; j < nBins_(1); ++j) {
// for(int k = 0; k < nBins_(2); ++k) {
// Vector3d pos = Vector3d(i, j, k) * voxelSize_ - halfBox;
// for(qiter = qvals.begin(); qiter != qvals.end(); ++qiter) {
// Vector3d d = pos - (*qiter).first;
// currentSnapshot_->wrapVector(d);
// RealType denom = pow(2.0 * sqrt(M_PI) * gaussWidth_, 3);
// RealType exponent = -dot(d,d) / pow(2.0*gaussWidth_, 2);
// RealType weight = exp(exponent) / denom;
// count_[i][j][k] += weight;
// hist_[i][j][k] += weight * (*qiter).second;
// }
// }
// }
// }
}
writeQxyz();
}
void TetrahedralityParamZ::process() {
Molecule* mol;
StuntDouble* sd;
StuntDouble* sd2;
StuntDouble* sdi;
StuntDouble* sdj;
RigidBody* rb;
int myIndex;
SimInfo::MoleculeIterator mi;
Molecule::RigidBodyIterator rbIter;
Vector3d vec;
Vector3d ri, rj, rk, rik, rkj;
RealType r;
RealType cospsi;
RealType Qk;
std::vector<std::pair<RealType,StuntDouble*> > myNeighbors;
int isd1;
int isd2;
DumpReader reader(info_, dumpFilename_);
int nFrames = reader.getNFrames();
for (int istep = 0; istep < nFrames; istep += step_) {
reader.readFrame(istep);
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
Mat3x3d hmat = currentSnapshot_->getHmat();
zBox_.push_back(hmat(2,2));
RealType halfBoxZ_ = hmat(2,2) / 2.0;
if (evaluator1_.isDynamic()) {
seleMan1_.setSelectionSet(evaluator1_.evaluate());
}
if (evaluator2_.isDynamic()) {
seleMan2_.setSelectionSet(evaluator2_.evaluate());
}
// update the positions of atoms which belong to the rigidbodies
for (mol = info_->beginMolecule(mi); mol != NULL;
mol = info_->nextMolecule(mi)) {
for (rb = mol->beginRigidBody(rbIter); rb != NULL;
rb = mol->nextRigidBody(rbIter)) {
rb->updateAtoms();
}
}
// outer loop is over the selected StuntDoubles:
for (sd = seleMan1_.beginSelected(isd1); sd != NULL;
sd = seleMan1_.nextSelected(isd1)) {
myIndex = sd->getGlobalIndex();
Qk = 1.0;
myNeighbors.clear();
for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL;
sd2 = seleMan2_.nextSelected(isd2)) {
if (sd2->getGlobalIndex() != myIndex) {
vec = sd->getPos() - sd2->getPos();
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(vec);
r = vec.length();
// Check to see if neighbor is in bond cutoff
if (r < rCut_) {
myNeighbors.push_back(std::make_pair(r,sd2));
}
}
}
// Sort the vector using predicate and std::sort
std::sort(myNeighbors.begin(), myNeighbors.end());
// Use only the 4 closest neighbors to do the rest of the work:
int nbors = myNeighbors.size()> 4 ? 4 : myNeighbors.size();
int nang = int (0.5 * (nbors * (nbors - 1)));
rk = sd->getPos();
for (int i = 0; i < nbors-1; i++) {
sdi = myNeighbors[i].second;
ri = sdi->getPos();
rik = rk - ri;
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(rik);
rik.normalize();
for (int j = i+1; j < nbors; j++) {
sdj = myNeighbors[j].second;
rj = sdj->getPos();
rkj = rk - rj;
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(rkj);
rkj.normalize();
cospsi = dot(rik,rkj);
// Calculates scaled Qk for each molecule using calculated
// angles from 4 or fewer nearest neighbors.
Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang);
}
}
if (nang > 0) {
if (usePeriodicBoundaryConditions_)
currentSnapshot_->wrapVector(rk);
int binNo = int(nZBins_ * (halfBoxZ_ + rk.z()) / hmat(2,2));
sliceQ_[binNo] += Qk;
sliceCount_[binNo] += 1;
}
}
}
writeQz();
}