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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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namespace oopse { |
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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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MaxQ_ = 3.0; |
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deltaQ_ = (MaxQ_ - MinQ_) / nbins; |
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Q_histogram_.resize(nbins); |
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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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// 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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// Set the l for the spherical harmonic, it doesn't change |
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sphericalHarmonic.setL(lNumber_); |
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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 (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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// 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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// 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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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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// 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 = vec.length(); |
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// Check to see if neighbor is in bond cutoff |
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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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} |
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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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// 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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} |
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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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Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); |
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// Find Third Order Invariant W_l |
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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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Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / |
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(2.0*(RealType)lNumber_ + 1.0)); |
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RealType W_l; |
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RealType W_l_hat; |
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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[i] = 0.0; |
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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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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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Wigner3jm(&l_, &l_, &l_, |
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&m1Pass, &m2Min, &m2Max, |
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THRCOF, &mSize_, &error); |
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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[m_index]*QBar_lm[m1+lNumber_]*QBar_lm[m2+lNumber_]*QBar_lm[m3+lNumber_]; |
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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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} |
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W_l_hat = W_l / pow(QSq_l, 1.5); |
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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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// 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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osq << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
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} |
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osq.close(); |
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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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osw << Wval << "\t" << (RealType)W_histogram_[i] / (RealType)Wcount_ << "\n"; |
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} |
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osw.close(); |
