--- trunk/src/applications/staticProps/BondOrderParameter.cpp 2006/09/19 21:14:11 1039 +++ trunk/src/applications/staticProps/BondOrderParameter.cpp 2006/09/21 18:04:52 1044 @@ -51,18 +51,16 @@ #include "io/DumpReader.hpp" #include "primitives/Molecule.hpp" #include "utils/NumericConstant.hpp" -#include "math/RealSphericalHarmonic.hpp" +#include "math/SphericalHarmonic.hpp" + namespace oopse { - BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele, - double rCut, int lNumber, int nbins) - : StaticAnalyser(info, filename), selectionScript_(sele), - evaluator_(info), seleMan_(info){ + double rCut, int lNumber, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ - setOutputName(getPrefix(filename) + ".obo"); + setOutputName(getPrefix(filename) + ".bo"); evaluator_.loadScriptString(sele); if (!evaluator_.isDynamic()) { @@ -75,18 +73,28 @@ namespace oopse { rCut_ = rCut; mSize_ = 2*lNumber_+1; - // Set the l for the spherical harmonic, it doesn't change + // Q can take values from 0 to 1 - sphericalHarmonic.setL(lNumber_); + MinQ_ = 0.0; + MaxQ_ = 1.0; + deltaQ_ = (MaxQ_ - MinQ_) / nbins; + Q_histogram_.resize(nbins); - delta_Q = 1.0 / nbins; - delta_W = 2.0 / nbins; + // W_6 for icosahedral clusters is 11 / sqrt(4199) = 0.169754, so we'll + // use values for MinW_ and MaxW_ that are slightly larger than this: - Q_histogram_.resize(nbins); + MinW_ = -0.18; + MaxW_ = 0.18; + deltaW_ = (MaxW_ - MinW_) / nbins; W_histogram_.resize(nbins); } + BondOrderParameter::~BondOrderParameter() { + Q_histogram_.clear(); + W_histogram_.clear(); + } + void BondOrderParameter::initalizeHistogram() { std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); std::fill(W_histogram_.begin(), W_histogram_.end(), 0); @@ -96,28 +104,41 @@ namespace oopse { Molecule* mol; Atom* atom; RigidBody* rb; + int myIndex; SimInfo::MoleculeIterator mi; Molecule::RigidBodyIterator rbIter; Molecule::AtomIterator ai; StuntDouble* sd; - RealType theta; + Vector3d vec; + RealType costheta; RealType phi; RealType r; RealType dist; - std::map QBar_lm; + std::map QBar_lm; RealType QSq_l; RealType Q_l; + ComplexType W_l; + ComplexType W_l_hat; int nBonds; - RealSphericalHarmonic sphericalHarmonic; + SphericalHarmonic sphericalHarmonic; int i, j; - - + // Make arrays for Wigner3jm + double* THRCOF = new double[mSize_]; + // Variables for Wigner routine + double l_ = (double)lNumber_; + double m1Pass, m2Min, m2Max; + int error, m1, m2, m3; + + // Set the l for the spherical harmonic, it doesn't change + sphericalHarmonic.setL(lNumber_); + DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); + frameCounter_ = 0; - for (int istep = 0; istep < nFrames; istep += step_) { reader.readFrame(istep); + frameCounter_++; currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); if (evaluator_.isDynamic()) { @@ -139,6 +160,8 @@ namespace oopse { for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { + myIndex = sd->getGlobalIndex(); + // For this central atom, zero out nBonds and QBar_lm nBonds = 0; @@ -154,139 +177,166 @@ namespace oopse { for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + if (atom->getGlobalIndex() != myIndex) { - Vector3d vec = sd->getPos() - atom->getPos(); - currentSnapshot_->wrapVector(vec); - - // Calculate "bonds" and build Q_lm(r) where - // Q_lm = Y_lm(theta(r),phi(r)) - // The spherical harmonics are wrt any arbitrary coordinate - // system, we choose standard spherical coordinates - - r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); - - // Check to see if neighbor is in bond cutoff - - if (r < rCut_) { - theta = atan2(vec.y(), vec.x()); - phi = acos(vec.z()/r); - for(int m = -lNumber_; m <= lNumber_; m++){ - sphericalHarmonic.setM(m); - QBar_lm[m] += sphericalHarmonic.getValueAt(theta,phi); - } - nBonds++; - } + vec = sd->getPos() - atom->getPos(); + currentSnapshot_->wrapVector(vec); + + // Calculate "bonds" and build Q_lm(r) where + // Q_lm = Y_lm(theta(r),phi(r)) + // The spherical harmonics are wrt any arbitrary coordinate + // system, we choose standard spherical coordinates + + r = vec.length(); + + // Check to see if neighbor is in bond cutoff + + if (r < rCut_) { + costheta = vec.z() / r; + phi = atan2(vec.y(), vec.x()); + + for(int m = -lNumber_; m <= lNumber_; m++){ + sphericalHarmonic.setM(m); + QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); + } + nBonds++; + } + } } } - // Normalize Qbar + // Normalize Qbar2 for (int m = -lNumber_;m <= lNumber_; m++){ QBar_lm[m] /= nBonds; + std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n"; } // Find second order invariant Q_l QSq_l = 0.0; for (int m = -lNumber_; m <= lNumber_; m++){ - QSq_l += pow(QBar_lm[m], 2); + QSq_l += norm(QBar_lm[m]); } - Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); - - // Find Third Order Invariant W_l + std::cout << "qsq_l = " << QSq_l << "\n"; + Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / + (2.0*(RealType)lNumber_ + 1.0)); - // Make arrays for Wigner3jm - double* THRCOF = new double[mSize_]; - // Variables for Wigner routine - double l_ = (double)lNumber_; - double m2Min, m2Max; - int error, m1, m2, m3; + // Find Third Order Invariant W_l - W_l_ = 0.0; + W_l = 0.0; for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { // Zero work array - for (int ii = 0; ii < mSize_; ii+){ + for (int ii = 0; ii < mSize_; ii++){ THRCOF[i] = 0.0; } // Get Wigner coefficients - Wigner3jm(&l_, &l_, &l_, &(double)m1, &m2Min, &m2Max, THRCOF, &mSize_, &error); - for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { + m1Pass = (double)m1; + Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error); + for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) { m2 = floor(m2Min) + m_index - 1; m3 = -m1-m2; - W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; + W_l += THRCOF[m_index]*QBar_lm[m1]*QBar_lm[m2]*QBar_lm[m3]; } } - - W_l_hat = W_l_ / pow(QSq_l, 1.5); - + + W_l_hat = W_l / pow(QSq_l, 1.5); + // accumulate histogram data for Q_l and W_l_hat: - collectHistogram(Q_l, W_l_hat); + std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n"; + collectHistogram(Q_l, real(W_l_hat)); } } - // Normalize by number of frames - for (int m = -lNumber_; m <= lNumber_; m++){ - QBar_lm[m] /= nFrames; - } - - - - - writeOrderParameter(); } - - void BondOrderParameter::processHistogram() { - - int nPairs = getNPairs(); - RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); - RealType pairDensity = nPairs /volume * 2.0; - RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; - for(int i = 0 ; i < histogram_.size(); ++i){ + void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { - RealType rLower = i * deltaR_; - RealType rUpper = rLower + deltaR_; - RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); - RealType nIdeal = volSlice * pairConstant; - - avgGofr_[i] += histogram_[i] / nIdeal; + if (Q_l >= MinQ_ && Q_l < MaxQ_) { + int qbin = (Q_l - MinQ_) / deltaQ_; + Q_histogram_[qbin] += 1; + Qcount_++; + sumQ_ += Q_l; + sumQ2_ += Q_l * Q_l; + } else { + sprintf( painCave.errMsg, + "Q_l value outside reasonable range\n"); + painCave.severity = OOPSE_ERROR; + painCave.isFatal = 1; + simError(); } - } - - void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { - - if (Q_l < Max_Q) { - int whichBin = Q_l / deltaQ_; - Q_histogram_[whichBin] += 1; + if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { + int wbin = (W_l_hat - MinW_) / deltaW_; + W_histogram_[wbin] += 1; + Wcount_++; + sumW_ += W_l_hat; + sumW2_ += W_l_hat*W_l_hat; + } else { + sprintf( painCave.errMsg, + "W_l_hat value outside reasonable range\n"); + painCave.severity = OOPSE_ERROR; + painCave.isFatal = 1; + simError(); } - if (W_l_hat < Max_W) { - int whichBin = W_l_hat / deltaW_; - W_histogram_[whichBin] += 1; - } - } - + } void BondOrderParameter::writeOrderParameter() { - std::ofstream os(getOutputFileName().c_str()); - os << "#Bond Order Parameter\n"; - os << "#selection: (" << selectionScript_ << ")\n"; + std::ofstream osq((getOutputFileName() + "q").c_str()); - for (std::size_t i = 0; i < orderParams_.size(); ++i) { - os << orderParams_[i].p2 << "\t" - << orderParams_[i].director[0] << "\t" - << orderParams_[i].director[1] << "\t" - << orderParams_[i].director[2] << "\t" - << orderParams_[i].angle << "\n"; + if (osq.is_open()) { + RealType qAvg = sumQ_ / (RealType) Qcount_; + RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; + + osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; + osq << "# selection: (" << selectionScript_ << ")\n"; + osq << "# : " << qAvg << "\n"; + osq << "# std. dev.: " << qStdDev << "\n"; + + // Normalize by number of frames and write it out: + for (int i = 0; i < Q_histogram_.size(); ++i) { + RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; + osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; + } + + osq.close(); + } else { + sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", + (getOutputFileName() + "q").c_str()); + painCave.isFatal = 1; + simError(); } - } + std::ofstream osw((getOutputFileName() + "w").c_str()); + if (osw.is_open()) { + RealType wAvg = sumW_ / (RealType) Wcount_; + RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; + + osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; + osw << "# selection: (" << selectionScript_ << ")\n"; + osw << "# : " << wAvg << "\n"; + osw << "# std. dev.: " << wStdDev << "\n"; + + // Normalize by number of frames and write it out: + for (int i = 0; i < W_histogram_.size(); ++i) { + RealType Wval = MinW_ + (i + 0.5) * deltaW_; + osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; + } + + osw.close(); + } else { + sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", + (getOutputFileName() + "w").c_str()); + painCave.isFatal = 1; + simError(); + } + } }