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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/RealSphericalHarmonic.hpp" |
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#include "math/SphericalHarmonic.hpp" |
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|
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namespace oopse { |
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|
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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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|
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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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|
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// Set the l for the spherical harmonic, it doesn't change |
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// Q can take values from 0 to 1 |
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|
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sphericalHarmonic.setL(lNumber_); |
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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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|
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delta_Q = 1.0 / nbins; |
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delta_W = 2.0 / 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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|
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Q_histogram_.resize(nbins); |
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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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} |
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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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|
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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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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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int myIndex; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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Molecule::AtomIterator ai; |
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StuntDouble* sd; |
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RealType theta; |
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Vector3d vec; |
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RealType costheta; |
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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, RealType> QBar_lm; |
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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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RealSphericalHarmonic sphericalHarmonic; |
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SphericalHarmonic sphericalHarmonic; |
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int i, j; |
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|
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|
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// Make arrays for Wigner3jm |
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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 m1Pass, m2Min, m2Max; |
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int error, m1, m2, m3; |
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|
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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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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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|
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if (evaluator_.isDynamic()) { |
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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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|
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// For this central atom, zero out nBonds and QBar_lm |
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nBonds = 0; |
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for (atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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if (atom->getGlobalIndex() != myIndex) { |
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Vector3d vec = sd->getPos() - atom->getPos(); |
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currentSnapshot_->wrapVector(vec); |
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|
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// Calculate "bonds" and build Q_lm(r) where |
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// Q_lm = Y_lm(theta(r),phi(r)) |
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// The spherical harmonics are wrt any arbitrary coordinate |
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// system, we choose standard spherical coordinates |
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r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
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// Check to see if neighbor is in bond cutoff |
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|
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if (r < rCut_) { |
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theta = atan2(vec.y(), vec.x()); |
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phi = acos(vec.z()/r); |
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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(theta,phi); |
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} |
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nBonds++; |
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} |
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vec = sd->getPos() - atom->getPos(); |
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currentSnapshot_->wrapVector(vec); |
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|
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// Calculate "bonds" and build Q_lm(r) where |
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// Q_lm = Y_lm(theta(r),phi(r)) |
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// The spherical harmonics are wrt any arbitrary coordinate |
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// system, we choose standard spherical coordinates |
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|
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r = vec.length(); |
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|
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// Check to see if neighbor is in bond cutoff |
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|
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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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|
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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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} |
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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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// Normalize Qbar |
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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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std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n"; |
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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 += pow(QBar_lm[m], 2); |
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QSq_l += norm(QBar_lm[m]); |
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} |
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std::cout << "qsq_l = " << QSq_l << "\n"; |
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Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
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|
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// Find Third Order Invariant W_l |
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|
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// Make arrays for Wigner3jm |
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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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int error, m1, m2, m3; |
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// Find Third Order Invariant W_l |
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|
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W_l_ = 0.0; |
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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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for (int ii = 0; ii < mSize_; ii++){ |
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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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for (int m_index = 1; i < (int)(m2Max - m2Min-1.0); m_index++) { |
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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; m_index < (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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W_l_ += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
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W_l += THRCOF[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
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} |
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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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|
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W_l_hat = W_l / pow(QSq_l, 1.5); |
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|
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// accumulate histogram data for Q_l and W_l_hat: |
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collectHistogram(Q_l, W_l_hat); |
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std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n"; |
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collectHistogram(Q_l, real(W_l_hat)); |
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|
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} |
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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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|
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|
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|
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|
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|
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writeOrderParameter(); |
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|
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} |
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|
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|
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void BondOrderParameter::processHistogram() { |
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|
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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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|
256 |
< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
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> |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
257 |
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|
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< |
RealType rLower = i * deltaR_; |
259 |
< |
RealType rUpper = rLower + deltaR_; |
260 |
< |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
261 |
< |
RealType nIdeal = volSlice * pairConstant; |
262 |
< |
|
263 |
< |
avgGofr_[i] += histogram_[i] / nIdeal; |
258 |
> |
if (Q_l >= MinQ_ && Q_l < MaxQ_) { |
259 |
> |
int qbin = (Q_l - MinQ_) / deltaQ_; |
260 |
> |
Q_histogram_[qbin] += 1; |
261 |
> |
Qcount_++; |
262 |
> |
sumQ_ += Q_l; |
263 |
> |
sumQ2_ += Q_l * Q_l; |
264 |
> |
} else { |
265 |
> |
sprintf( painCave.errMsg, |
266 |
> |
"Q_l value outside reasonable range\n"); |
267 |
> |
painCave.severity = OOPSE_ERROR; |
268 |
> |
painCave.isFatal = 1; |
269 |
> |
simError(); |
270 |
|
} |
271 |
|
|
272 |
< |
} |
273 |
< |
|
274 |
< |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
275 |
< |
|
276 |
< |
if (Q_l < Max_Q) { |
277 |
< |
int whichBin = Q_l / deltaQ_; |
278 |
< |
Q_histogram_[whichBin] += 1; |
272 |
> |
if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { |
273 |
> |
int wbin = (W_l_hat - MinW_) / deltaW_; |
274 |
> |
W_histogram_[wbin] += 1; |
275 |
> |
Wcount_++; |
276 |
> |
sumW_ += W_l_hat; |
277 |
> |
sumW2_ += W_l_hat*W_l_hat; |
278 |
> |
} else { |
279 |
> |
sprintf( painCave.errMsg, |
280 |
> |
"W_l_hat value outside reasonable range\n"); |
281 |
> |
painCave.severity = OOPSE_ERROR; |
282 |
> |
painCave.isFatal = 1; |
283 |
> |
simError(); |
284 |
|
} |
285 |
< |
if (W_l_hat < Max_W) { |
268 |
< |
int whichBin = W_l_hat / deltaW_; |
269 |
< |
W_histogram_[whichBin] += 1; |
270 |
< |
} |
271 |
< |
} |
272 |
< |
|
285 |
> |
} |
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|
287 |
|
void BondOrderParameter::writeOrderParameter() { |
288 |
|
|
289 |
< |
std::ofstream os(getOutputFileName().c_str()); |
277 |
< |
os << "#Bond Order Parameter\n"; |
278 |
< |
os << "#selection: (" << selectionScript_ << ")\n"; |
289 |
> |
std::ofstream osq((getOutputFileName() + "q").c_str()); |
290 |
|
|
291 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
281 |
< |
os << orderParams_[i].p2 << "\t" |
282 |
< |
<< orderParams_[i].director[0] << "\t" |
283 |
< |
<< orderParams_[i].director[1] << "\t" |
284 |
< |
<< orderParams_[i].director[2] << "\t" |
285 |
< |
<< orderParams_[i].angle << "\n"; |
291 |
> |
if (osq.is_open()) { |
292 |
|
|
293 |
+ |
RealType qAvg = sumQ_ / (RealType) Qcount_; |
294 |
+ |
RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; |
295 |
+ |
|
296 |
+ |
osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; |
297 |
+ |
osq << "# selection: (" << selectionScript_ << ")\n"; |
298 |
+ |
osq << "# <Q_" << lNumber_ << ">: " << qAvg << "\n"; |
299 |
+ |
osq << "# std. dev.: " << qStdDev << "\n"; |
300 |
+ |
|
301 |
+ |
// Normalize by number of frames and write it out: |
302 |
+ |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
303 |
+ |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
304 |
+ |
osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; |
305 |
+ |
} |
306 |
+ |
|
307 |
+ |
osq.close(); |
308 |
+ |
} else { |
309 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
310 |
+ |
(getOutputFileName() + "q").c_str()); |
311 |
+ |
painCave.isFatal = 1; |
312 |
+ |
simError(); |
313 |
|
} |
288 |
– |
} |
314 |
|
|
315 |
+ |
std::ofstream osw((getOutputFileName() + "w").c_str()); |
316 |
|
|
317 |
+ |
if (osw.is_open()) { |
318 |
|
|
319 |
+ |
RealType wAvg = sumW_ / (RealType) Wcount_; |
320 |
+ |
RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; |
321 |
+ |
|
322 |
+ |
osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; |
323 |
+ |
osw << "# selection: (" << selectionScript_ << ")\n"; |
324 |
+ |
osw << "# <W_" << lNumber_ << ">: " << wAvg << "\n"; |
325 |
+ |
osw << "# std. dev.: " << wStdDev << "\n"; |
326 |
+ |
|
327 |
+ |
// Normalize by number of frames and write it out: |
328 |
+ |
for (int i = 0; i < W_histogram_.size(); ++i) { |
329 |
+ |
RealType Wval = MinW_ + (i + 0.5) * deltaW_; |
330 |
+ |
osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; |
331 |
+ |
} |
332 |
+ |
|
333 |
+ |
osw.close(); |
334 |
+ |
} else { |
335 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
336 |
+ |
(getOutputFileName() + "w").c_str()); |
337 |
+ |
painCave.isFatal = 1; |
338 |
+ |
simError(); |
339 |
+ |
} |
340 |
+ |
} |
341 |
|
} |