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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "math/RealSphericalHarmonic.hpp" |
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namespace oopse { |
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BondOrderParameter::BondOrderParameter(SimInfo* info, |
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const std::string& filename, |
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const std::string& sele, |
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double rCut, int lNumber, int nbins) |
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: StaticAnalyser(info, filename), selectionScript_(sele), |
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evaluator_(info), seleMan_(info){ |
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double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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setOutputName(getPrefix(filename) + ".obo"); |
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setOutputName(getPrefix(filename) + ".bo"); |
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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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rCut_ = rCut; |
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mSize_ = 2*lNumber_+1; |
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deltaQ_ = 1.0 / nbins; |
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deltaW_ = 2.0 / nbins; |
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// Q can take values from 0 to 1 |
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MinQ_ = 0.0; |
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MaxQ_ = 1.0; |
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deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
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Q_histogram_.resize(nbins); |
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// W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll |
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// use values for MinW_ and MaxW_ that are slightly larger than this: |
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MinW_ = -0.18; |
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MaxW_ = 0.18; |
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deltaW_ = (MaxW_ - MinW_) / nbins; |
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W_histogram_.resize(nbins); |
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} |
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BondOrderParameter::~BondOrderParameter() { |
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Q_histogram_.clear(); |
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W_histogram_.clear(); |
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} |
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void BondOrderParameter::initalizeHistogram() { |
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std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); |
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std::fill(W_histogram_.begin(), W_histogram_.end(), 0); |
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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frameCounter_ = 0; |
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for (int istep = 0; istep < nFrames; istep += step_) { |
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reader.readFrame(istep); |
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frameCounter_++; |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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if (evaluator_.isDynamic()) { |
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double* THRCOF = new double[mSize_]; |
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// Variables for Wigner routine |
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double l_ = (double)lNumber_; |
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double m2Min, m2Max; |
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double m1Pass, m2Min, m2Max; |
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int error, m1, m2, m3; |
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RealType W_l; |
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THRCOF[i] = 0.0; |
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} |
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// Get Wigner coefficients |
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Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
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m1Pass = (double)m1; |
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Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error); |
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for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
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m2 = floor(m2Min) + m_index - 1; |
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m3 = -m1-m2; |
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} |
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} |
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// Normalize by number of frames |
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for (int m = -lNumber_; m <= lNumber_; m++){ |
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QBar_lm[m] /= nFrames; |
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} |
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writeOrderParameter(); |
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} |
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void BondOrderParameter::processHistogram() { |
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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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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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} |
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} |
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void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
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if (Q_l < MaxQ_) { |
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int whichBin = Q_l / deltaQ_; |
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Q_histogram_[whichBin] += 1; |
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if (Q_l >= MinQ_ && Q_l < MaxQ_) { |
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int qbin = (Q_l - MinQ_) / deltaQ_; |
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Q_histogram_[qbin] += 1; |
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Qcount_++; |
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sumQ_ += Q_l; |
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sumQ2_ += Q_l * Q_l; |
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} else { |
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sprintf( painCave.errMsg, |
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"Q_l value outside reasonable range\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (W_l_hat < MaxW_) { |
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int whichBin = W_l_hat / deltaW_; |
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W_histogram_[whichBin] += 1; |
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if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
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int wbin = (W_l_hat - MinW_) / deltaW_; |
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W_histogram_[wbin] += 1; |
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Wcount_++; |
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sumW_ += W_l_hat; |
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sumW2_ += W_l_hat*W_l_hat; |
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} else { |
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sprintf( painCave.errMsg, |
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"W_l_hat value outside reasonable range\n"); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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void BondOrderParameter::writeOrderParameter() { |
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std::ofstream os(getOutputFileName().c_str()); |
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os << "#Bond Order Parameter\n"; |
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os << "#selection: (" << selectionScript_ << ")\n"; |
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std::ofstream osq((getOutputFileName() + "q").c_str()); |
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for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
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os << orderParams_[i].p2 << "\t" |
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<< orderParams_[i].director[0] << "\t" |
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<< orderParams_[i].director[1] << "\t" |
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<< orderParams_[i].director[2] << "\t" |
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<< orderParams_[i].angle << "\n"; |
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if (osq.is_open()) { |
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RealType qAvg = sumQ_ / (RealType) Qcount_; |
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RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
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osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
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osq << "# selection: (" << selectionScript_ << ")\n"; |
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osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
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osq << "# std. dev.: " << qStdDev << "\n"; |
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|
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// Normalize by number of frames and write it out: |
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for (int i = 0; i < Q_histogram_.size(); ++i) { |
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RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
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osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; |
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} |
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osq.close(); |
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} else { |
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sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
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(getOutputFileName() + "q").c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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std::ofstream osw((getOutputFileName() + "w").c_str()); |
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if (osw.is_open()) { |
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RealType wAvg = sumW_ / (RealType) Wcount_; |
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RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
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osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
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osw << "# selection: (" << selectionScript_ << ")\n"; |
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osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
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osw << "# std. dev.: " << wStdDev << "\n"; |
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|
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// Normalize by number of frames and write it out: |
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for (int i = 0; i < W_histogram_.size(); ++i) { |
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RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
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osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; |
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} |
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osw.close(); |
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} else { |
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sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
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(getOutputFileName() + "w").c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |