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namespace oopse { |
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< |
GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len) |
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< |
: RadialDistrFunc(info, filename, sele1, sele2){ |
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> |
GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins) |
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> |
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){ |
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< |
deltaR_ = len_ /nRBins_; |
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> |
deltaR_ = len_ /nRBins_; |
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< |
histogram_.resize(nRBins_); |
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< |
avgGofr_.resize(nRBins_); |
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} |
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> |
histogram_.resize(nRBins_); |
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> |
avgGofr_.resize(nRBins_); |
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+ |
setOutputName(getPrefix(filename) + ".gofr"); |
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} |
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< |
void GofR::preProcess() { |
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> |
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> |
void GofR::preProcess() { |
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std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0); |
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< |
} |
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> |
} |
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< |
void GofR::initalizeHistogram() { |
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< |
npairs_ = 0; |
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> |
void GofR::initalizeHistogram() { |
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std::fill(histogram_.begin(), histogram_.end(), 0); |
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< |
} |
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} |
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< |
void GofR::processHistogram() { |
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> |
void GofR::processHistogram() { |
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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 * PI * pairDensity ) / 3.0; |
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> |
int nPairs = getNPairs(); |
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> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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> |
RealType pairDensity = nPairs /volume * 2.0; |
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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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< |
avgGofr_[i] += histogram_[i] / nIdeal; |
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> |
avgGofr_[i] += histogram_[i] / nIdeal; |
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} |
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< |
} |
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> |
} |
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< |
void GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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> |
void GofR::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 whichBin = distance / deltaR_; |
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< |
++histogram_[whichBin]; |
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++npairs_; |
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} |
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> |
if (distance < len_) { |
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> |
int whichBin = distance / deltaR_; |
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> |
histogram_[whichBin] += 2; |
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> |
} |
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> |
} |
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< |
void GofR::writeRdf() { |
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> |
void GofR::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 << r << "\t" << avgGofr_[i]/nProcessed_ << "\n"; |
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< |
} |
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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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> |
RealType r = deltaR_ * (i + 0.5); |
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> |
rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n"; |
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> |
} |
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} else { |
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< |
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> |
sprintf(painCave.errMsg, "GofR: 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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} |
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