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namespace OpenMD { |
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TetrahedralityParamZ::TetrahedralityParamZ(SimInfo* info, |
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const std::string& filename, |
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< |
const std::string& sele, |
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> |
const std::string& sele1, |
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> |
const std::string& sele2, |
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double rCut, int nzbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), |
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seleMan_(info), nZBins_(nzbins) { |
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> |
: StaticAnalyser(info, filename), selectionScript1_(sele1), |
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evaluator1_(info), seleMan1_(info), selectionScript2_(sele2), |
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> |
evaluator2_(info), seleMan2_(info), nZBins_(nzbins) { |
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|
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< |
evaluator_.loadScriptString(sele); |
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< |
if (!evaluator_.isDynamic()) { |
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< |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
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> |
evaluator1_.loadScriptString(sele1); |
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> |
if (!evaluator1_.isDynamic()) { |
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> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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+ |
evaluator2_.loadScriptString(sele2); |
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+ |
if (!evaluator2_.isDynamic()) { |
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+ |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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} |
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|
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// Set up cutoff radius: |
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rCut_ = rCut; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Molecule::IntegrableObjectIterator ioi; |
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Molecule::RigidBodyIterator rbIter; |
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Vector3d vec; |
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Vector3d ri, rj, rk, rik, rkj; |
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RealType cospsi; |
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RealType Qk; |
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std::vector<std::pair<RealType,StuntDouble*> > myNeighbors; |
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int isd; |
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> |
int isd1; |
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> |
int isd2; |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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|
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RealType halfBoxZ_ = hmat(2,2) / 2.0; |
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|
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< |
if (evaluator_.isDynamic()) { |
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< |
seleMan_.setSelectionSet(evaluator_.evaluate()); |
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> |
if (evaluator1_.isDynamic()) { |
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> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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|
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+ |
if (evaluator2_.isDynamic()) { |
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+ |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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+ |
} |
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+ |
|
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// update the positions of atoms which belong to the rigidbodies |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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mol = info_->nextMolecule(mi)) { |
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} |
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|
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// outer loop is over the selected StuntDoubles: |
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for (sd = seleMan_.beginSelected(isd); sd != NULL; |
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< |
sd = seleMan_.nextSelected(isd)) { |
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> |
for (sd = seleMan1_.beginSelected(isd1); sd != NULL; |
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> |
sd = seleMan1_.nextSelected(isd1)) { |
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|
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myIndex = sd->getGlobalIndex(); |
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|
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Qk = 1.0; |
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myNeighbors.clear(); |
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|
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< |
// inner loop is over all StuntDoubles in the system: |
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< |
|
| 140 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; |
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< |
mol = info_->nextMolecule(mi)) { |
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> |
Qk = 1.0; |
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> |
myNeighbors.clear(); |
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|
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< |
for (sd2 = mol->beginIntegrableObject(ioi); sd2 != NULL; |
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< |
sd2 = mol->nextIntegrableObject(ioi)) { |
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> |
for (sd2 = seleMan2_.beginSelected(isd2); sd2 != NULL; |
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> |
sd2 = seleMan2_.nextSelected(isd2)) { |
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> |
|
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> |
if (sd2->getGlobalIndex() != myIndex) { |
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|
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< |
if (sd2->getGlobalIndex() != myIndex) { |
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< |
|
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< |
vec = sd->getPos() - sd2->getPos(); |
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< |
|
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< |
if (usePeriodicBoundaryConditions_) |
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< |
currentSnapshot_->wrapVector(vec); |
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< |
|
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< |
r = vec.length(); |
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< |
|
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< |
// Check to see if neighbor is in bond cutoff |
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< |
|
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< |
if (r < rCut_) { |
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< |
myNeighbors.push_back(std::make_pair(r,sd2)); |
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< |
} |
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> |
vec = sd->getPos() - sd2->getPos(); |
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> |
|
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> |
if (usePeriodicBoundaryConditions_) |
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> |
currentSnapshot_->wrapVector(vec); |
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> |
|
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> |
r = vec.length(); |
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> |
|
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> |
// Check to see if neighbor is in bond cutoff |
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> |
|
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> |
if (r < rCut_) { |
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> |
myNeighbors.push_back(std::make_pair(r,sd2)); |
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} |
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} |
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} |
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int nang = int (0.5 * (nbors * (nbors - 1))); |
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|
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rk = sd->getPos(); |
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< |
|
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> |
|
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for (int i = 0; i < nbors-1; i++) { |
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< |
|
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> |
|
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sdi = myNeighbors[i].second; |
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ri = sdi->getPos(); |
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rik = rk - ri; |
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currentSnapshot_->wrapVector(rik); |
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|
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rik.normalize(); |
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< |
|
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> |
|
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for (int j = i+1; j < nbors; j++) { |
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< |
|
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> |
|
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sdj = myNeighbors[j].second; |
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rj = sdj->getPos(); |
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rkj = rk - rj; |
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rkj.normalize(); |
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|
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cospsi = dot(rik,rkj); |
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< |
|
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> |
|
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// Calculates scaled Qk for each molecule using calculated |
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// angles from 4 or fewer nearest neighbors. |
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Qk -= (pow(cospsi + 1.0 / 3.0, 2) * 2.25 / nang); |
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} |
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} |
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< |
|
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> |
|
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if (nang > 0) { |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(rk); |
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if (qZstream.is_open()) { |
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qZstream << "#Tetrahedrality Parameters (z)\n"; |
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qZstream << "#nFrames:\t" << zBox_.size() << "\n"; |
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< |
qZstream << "#selection: (" << selectionScript_ << ")\n"; |
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> |
qZstream << "#selection 1: (" << selectionScript1_ << ")\n"; |
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> |
qZstream << "#selection 2: (" << selectionScript2_ << ")\n"; |
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qZstream << "#z\tQk\n"; |
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for (unsigned int i = 0; i < sliceQ_.size(); ++i) { |
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RealType z = zAve * (i+0.5) / sliceQ_.size(); |
