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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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#include "math/SphericalHarmonic.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) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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double rCut, int lMax, int nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ |
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setOutputName(getPrefix(filename) + ".bo"); |
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// Set up cutoff radius and order of the Legendre Polynomial: |
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lNumber_ = lNumber; |
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lMax_ = lMax; |
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rCut_ = rCut; |
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mSize_ = 2*lNumber_+1; |
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nBins_ = nbins; |
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Qcount_.resize(lMax_+1); |
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Wcount_.resize(lMax_+1); |
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|
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// Q can take values from 0 to 1 |
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MinQ_ = 0.0; |
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MaxQ_ = 1.1; |
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deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
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|
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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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} |
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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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for (int bin = 0; bin < nBins_; bin++) { |
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for (int l = 0; l <= lMax_; l++) { |
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Q_histogram_[std::make_pair(bin,l)] = 0; |
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W_histogram_[std::make_pair(bin,l)] = 0; |
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} |
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} |
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} |
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void BondOrderParameter::process() { |
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Molecule* mol; |
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Atom* atom; |
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RealType phi; |
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RealType r; |
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RealType dist; |
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std::map<int,ComplexType> QBar_lm; |
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RealType QSq_l; |
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RealType Q_l; |
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ComplexType W_l; |
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ComplexType W_l_hat; |
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int nBonds; |
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std::map<std::pair<int,int>,ComplexType> q; |
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std::vector<RealType> q_l; |
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std::map<std::pair<int,int>,ComplexType> QBar; |
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std::vector<RealType> Q2; |
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std::vector<RealType> Q; |
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std::vector<ComplexType> W; |
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std::vector<ComplexType> W_hat; |
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int nBonds, Nbonds; |
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SphericalHarmonic sphericalHarmonic; |
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int i, j; |
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// Make arrays for Wigner3jm |
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double* THRCOF = new double[mSize_]; |
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double* THRCOF = new double[2*lMax_+1]; |
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// Variables for Wigner routine |
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double l_ = (double)lNumber_; |
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double m1Pass, m2Min, m2Max; |
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int error, m1, m2, m3; |
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double lPass, m1Pass, m2Min, m2Max; |
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int error, m1, m2, m3, mSize; |
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mSize = 2*lMax_+1; |
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// Set the l for the spherical harmonic, it doesn't change |
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sphericalHarmonic.setL(lNumber_); |
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|
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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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q_l.resize(lMax_+1); |
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Q2.resize(lMax_+1); |
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Q.resize(lMax_+1); |
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W.resize(lMax_+1); |
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W_hat.resize(lMax_+1); |
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|
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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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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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nBonds = 0; |
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for (int m = -lNumber_; m <= lNumber_; m++) { |
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QBar_lm[m] = 0.0; |
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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(i); sd != NULL; |
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sd = seleMan_.nextSelected(i)) { |
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myIndex = sd->getGlobalIndex(); |
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nBonds = 0; |
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++) { |
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q[std::make_pair(l,m)] = 0.0; |
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} |
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} |
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// inner loop is over all other atoms in the system: |
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for (mol = info_->beginMolecule(mi); mol != NULL; |
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if (r < rCut_) { |
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costheta = vec.z() / r; |
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phi = atan2(vec.y(), vec.x()); |
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for(int m = -lNumber_; m <= lNumber_; m++){ |
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sphericalHarmonic.setM(m); |
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QBar_lm[m] += sphericalHarmonic.getValueAt(costheta, phi); |
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for (int l = 0; l <= lMax_; l++) { |
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sphericalHarmonic.setL(l); |
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for(int m = -l; m <= l; m++){ |
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sphericalHarmonic.setM(m); |
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q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); |
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} |
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} |
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nBonds++; |
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} |
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} |
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} |
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} |
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} |
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} |
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for (int l = 0; l <= lMax_; l++) { |
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q_l[l] = 0.0; |
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for(int m = -l; m <= l; m++) { |
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q_l[l] += norm(q[std::make_pair(l,m)]); |
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} |
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q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); |
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q_l[l] = sqrt(q_l[l])/(RealType)nBonds; |
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} |
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collectHistogram(q_l); |
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Nbonds += nBonds; |
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++) { |
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QBar[std::make_pair(l,m)] += q[std::make_pair(l,m)]; |
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} |
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} |
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} |
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} |
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// Normalize Qbar2 |
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for (int m = -lNumber_;m <= lNumber_; m++){ |
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QBar_lm[m] /= nBonds; |
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for (int l = 0; l <= lMax_; l++) { |
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for (int m = -l; m <= l; m++){ |
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QBar[std::make_pair(l,m)] /= Nbonds; |
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} |
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} |
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// Find second order invariant Q_l |
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QSq_l = 0.0; |
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for (int m = -lNumber_; m <= lNumber_; m++){ |
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QSq_l += norm(QBar_lm[m]); |
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for (int l = 0; l <= lMax_; l++) { |
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Q2[l] = 0.0; |
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for (int m = -l; m <= l; m++){ |
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Q2[l] += norm(QBar[std::make_pair(l,m)]); |
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} |
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Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); |
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} |
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std::cout << "qsl = " << QSq_l << "\n"; |
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Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / (RealType)(2*lNumber_ + 1)); |
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// Find Third Order Invariant W_l |
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W_l = 0.0; |
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for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
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// Zero work array |
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for (int ii = 0; ii < mSize_; ii++){ |
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THRCOF[ii] = 0.0; |
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for (int l = 0; l <= lMax_; l++) { |
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W[l] = 0.0; |
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lPass = (double)l; |
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for (int m1 = -l; m1 <= l; m1++) { |
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// Zero work array |
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for (int ii = 0; ii < 2*l + 1; ii++){ |
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THRCOF[ii] = 0.0; |
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} |
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// Get Wigner coefficients |
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m1Pass = (double)m1; |
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|
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Wigner3jm(&lPass, &lPass, &lPass, |
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&m1Pass, &m2Min, &m2Max, |
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THRCOF, &mSize, &error); |
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|
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for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
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m2 = (int)floor(m2Min) + mmm; |
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m3 = -m1-m2; |
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W[l] += THRCOF[mmm] * |
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QBar[std::make_pair(l,m1)] * |
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QBar[std::make_pair(l,m2)] * |
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QBar[std::make_pair(l,m3)]; |
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} |
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} |
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// Get Wigner coefficients |
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m1Pass = (double)m1; |
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|
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< |
Wigner3jm(&l_, &l_, &l_, |
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< |
&m1Pass, &m2Min, &m2Max, |
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< |
THRCOF, &mSize_, &error); |
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< |
|
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< |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
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< |
m2 = (int)floor(m2Min) + mmm; |
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< |
m3 = -m1-m2; |
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< |
W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3]; |
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< |
} |
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> |
W_hat[l] = W[l] / pow(Q2[l], 1.5); |
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} |
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|
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< |
W_l_hat = W_l / pow(QSq_l, 1.5); |
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< |
|
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< |
writeOrderParameter(Q_l, real(W_l_hat)); |
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> |
writeOrderParameter(Q, W_hat); |
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} |
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void BondOrderParameter::collectHistogram(std::vector<RealType> q) { |
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|
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< |
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
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> |
for (int l = 0; l <= lMax_; l++) { |
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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_[std::make_pair(qbin,l)] += 1; |
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Qcount_[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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} |
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std::ofstream os(getOutputFileName().c_str()); |
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> |
} |
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|
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void BondOrderParameter::writeOrderParameter(std::vector<RealType> Q, std::vector<ComplexType> What) { |
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|
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std::ofstream os(getOutputFileName().c_str()); |
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|
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if (os.is_open()) { |
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os << "# Bond Order Parameters\n"; |
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os << "# selection: (" << selectionScript_ << ")\n"; |
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< |
os << "# \n"; |
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< |
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
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< |
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
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> |
for (int l = 0; l <= lMax_; l++) { |
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> |
os << "# \n"; |
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> |
os << "# <Q_" << l << ">: " << Q[l] << "\n"; |
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> |
os << "# <W_" << l << ">: " << real(What[l]) << "\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 < nBins_; ++i) { |
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> |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
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> |
os << Qval; |
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> |
for (int l = 0; l <= lMax_; l++) { |
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> |
os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; |
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} |
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> |
os << "\n"; |
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> |
} |
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> |
|
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os.close(); |
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} else { |
