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namespace oopse { |
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< |
GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: RadialDistrFunc(info, filename, sele1, sele2){ |
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GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, RealType len, int nrbins, int nangleBins) |
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: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){ |
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} |
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deltaR_ = len_ /(double) nRBins_; |
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deltaCosAngle_ = 2.0 / (double)nAngleBins_; |
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histogram_.resize(nRBins_); |
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avgGofr_.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++i) { |
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histogram_[i].resize(nAngleBins_); |
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avgGofr_[i].resize(nAngleBins_); |
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} |
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} |
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void GofRAngle::preProcess() { |
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void GofRAngle::preProcess() { |
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for (int i = 0; i < avgGofr_.size(); ++i) { |
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std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
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std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
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} |
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} |
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} |
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void GofRAngle::initalizeHistogram() { |
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void GofRAngle::initalizeHistogram() { |
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npairs_ = 0; |
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for (int i = 0; i < histogram_.size(); ++i) |
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std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
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} |
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for (int i = 0; i < histogram_.size(); ++i){ |
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std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
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} |
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} |
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void GofRAngle::processHistogram() { |
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void GofRAngle::processHistogram() { |
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int nPairs = getNPairs(); |
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double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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double pairDensity = nPairs /volume; |
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double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
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> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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RealType pairDensity = nPairs /volume; |
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RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
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for(int i = 0 ; i < histogram_.size(); ++i){ |
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double rLower = i * deltaR_; |
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double rUpper = rLower + deltaR_; |
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double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
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double nIdeal = volSlice * pairConstant; |
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RealType rLower = i * deltaR_; |
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RealType rUpper = rLower + deltaR_; |
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RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
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RealType nIdeal = volSlice * pairConstant; |
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for (int j = 0; j < histogram_[i].size(); ++j){ |
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avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
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} |
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for (int j = 0; j < histogram_[i].size(); ++j){ |
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avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
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} |
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} |
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} |
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} |
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void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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if (sd1 == sd2) { |
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return; |
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return; |
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} |
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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos1 - pos2; |
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currentSnapshot_->wrapVector(r12); |
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Vector3d r12 = pos2 - pos1; |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(r12); |
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double distance = r12.length(); |
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RealType distance = r12.length(); |
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int whichRBin = distance / deltaR_; |
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if (distance <= len_) { |
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double cosAngle = evaluateAngle(sd1, sd2); |
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double halfBin = (nAngleBins_ - 1) * 0.5; |
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int whichThetaBin = halfBin * (cosAngle + 1.0); |
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++histogram_[whichRBin][whichThetaBin]; |
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RealType cosAngle = evaluateAngle(sd1, sd2); |
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RealType halfBin = (nAngleBins_ - 1) * 0.5; |
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int whichThetaBin = halfBin * (cosAngle + 1.0); |
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++histogram_[whichRBin][whichThetaBin]; |
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++npairs_; |
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++npairs_; |
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} |
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} |
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} |
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void GofRAngle::writeRdf() { |
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> |
void GofRAngle::writeRdf() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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if (rdfStream.is_open()) { |
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rdfStream << "#radial distribution function\n"; |
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rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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rdfStream << "#r\tcorrValue\n"; |
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for (int i = 0; i < avgGofr_.size(); ++i) { |
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double r = deltaR_ * (i + 0.5); |
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> |
rdfStream << "#radial distribution function\n"; |
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> |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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> |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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> |
rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
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rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; |
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> |
for (int i = 0; i < avgGofr_.size(); ++i) { |
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RealType r = deltaR_ * (i + 0.5); |
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for(int j = 0; j < avgGofr_[i].size(); ++j) { |
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< |
double cosAngle = -1.0 + (i + 0.5)*deltaCosAngle_; |
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< |
rdfStream << r << "\t" << cosAngle << "\t" << avgGofr_[i][j]/nProcessed_ << "\n"; |
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} |
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} |
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for(int j = 0; j < avgGofr_[i].size(); ++j) { |
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> |
RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; |
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> |
rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; |
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} |
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> |
|
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rdfStream << "\n"; |
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} |
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} else { |
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sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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rdfStream.close(); |
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} |
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} |
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< |
double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
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> |
RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos1 - pos2; |
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currentSnapshot_->wrapVector(r12); |
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> |
Vector3d r12 = pos2 - pos1; |
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> |
|
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> |
if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(r12); |
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|
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r12.normalize(); |
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Vector3d dipole = sd1->getElectroFrame().getColumn(2); |
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dipole.normalize(); |
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return dot(r12, dipole); |
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} |
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} |
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< |
double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
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> |
RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
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Vector3d v1 = sd1->getElectroFrame().getColumn(2); |
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Vector3d v2 = sd1->getElectroFrame().getColumn(2); |
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> |
Vector3d v2 = sd2->getElectroFrame().getColumn(2); |
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v1.normalize(); |
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v2.normalize(); |
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return dot(v1, v2); |
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< |
} |
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> |
} |
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} |
