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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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evaluator_.loadScriptString(sele); |
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if (!evaluator_.isDynamic()) { |
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lNumber_ = lNumber; |
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rCut_ = rCut; |
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mSize_ = 2*lNumber_+1; |
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mSize_ = 2*lNumber_+1; |
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|
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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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|
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MinQ_ = 0.0; |
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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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|
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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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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> q_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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int nBonds; |
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RealSphericalHarmonic sphericalHarmonic; |
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ComplexType W_l; |
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ComplexType W_l_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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|
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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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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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rb = mol->nextRigidBody(rbIter)) { |
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rb->updateAtoms(); |
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} |
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} |
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|
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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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// For this central atom, zero out nBonds and QBar_lm |
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myIndex = sd->getGlobalIndex(); |
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nBonds = 0; |
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|
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for (int m = -lNumber_; m <= lNumber_; m++) { |
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QBar_lm[m] = 0.0; |
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q_lm[m] = 0.0; |
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} |
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// inner loop is over all other atoms in the system: |
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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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|
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r = sqrt(pow(vec.x(),2)+pow(vec.y(),2)+pow(vec.z(),2)); |
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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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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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q_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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for (int m = -lNumber_;m <= lNumber_; m++){ |
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QBar_lm[m] /= nBonds; |
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} |
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RealType ql = 0.0; |
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for(int m=-lNumber_; m<=lNumber_; m++) { |
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ql += norm(QBar_lm[m]); |
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} |
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ql *= 4.0*NumericConstant::PI/(RealType)(2*lNumber_+1); |
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collectHistogram(sqrt(ql)/(RealType)nBonds); |
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|
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// Find second order invariant Q_l |
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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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} |
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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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|
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RealType W_l; |
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RealType W_l_hat; |
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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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} |
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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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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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} |
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Nbonds += nBonds; |
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for (int m=-lNumber_; m<=lNumber_; m++) { |
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QBar_lm[m] += q_lm[m]; |
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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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|
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collectHistogram(Q_l, W_l_hat); |
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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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} |
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|
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< |
// Normalize by number of frames |
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> |
// Find second order invariant Q_l |
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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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QBar_lm[m] /= nFrames; |
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> |
QSq_l += norm(QBar_lm[m]); |
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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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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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|
233 |
< |
} |
241 |
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|
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|
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< |
void BondOrderParameter::processHistogram() { |
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> |
// Find Third Order Invariant W_l |
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|
|
235 |
< |
int nPairs = getNPairs(); |
236 |
< |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
237 |
< |
RealType pairDensity = nPairs /volume * 2.0; |
238 |
< |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
239 |
< |
|
240 |
< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
241 |
< |
|
242 |
< |
RealType rLower = i * deltaR_; |
243 |
< |
RealType rUpper = rLower + deltaR_; |
244 |
< |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
245 |
< |
RealType nIdeal = volSlice * pairConstant; |
246 |
< |
|
247 |
< |
avgGofr_[i] += histogram_[i] / nIdeal; |
235 |
> |
W_l = 0.0; |
236 |
> |
for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { |
237 |
> |
// Zero work array |
238 |
> |
for (int ii = 0; ii < mSize_; ii++){ |
239 |
> |
THRCOF[ii] = 0.0; |
240 |
> |
} |
241 |
> |
// Get Wigner coefficients |
242 |
> |
m1Pass = (double)m1; |
243 |
> |
|
244 |
> |
Wigner3jm(&l_, &l_, &l_, |
245 |
> |
&m1Pass, &m2Min, &m2Max, |
246 |
> |
THRCOF, &mSize_, &error); |
247 |
> |
|
248 |
> |
for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { |
249 |
> |
m2 = (int)floor(m2Min) + mmm; |
250 |
> |
m3 = -m1-m2; |
251 |
> |
W_l += THRCOF[mmm] * QBar_lm[m1] * QBar_lm[m2] * QBar_lm[m3]; |
252 |
> |
} |
253 |
|
} |
254 |
< |
|
254 |
> |
|
255 |
> |
W_l_hat = W_l / pow(QSq_l, 1.5); |
256 |
> |
|
257 |
> |
writeOrderParameter(Q_l, real(W_l_hat)); |
258 |
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} |
259 |
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|
260 |
< |
void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { |
260 |
> |
void BondOrderParameter::collectHistogram(RealType q_l) { |
261 |
|
|
262 |
< |
if (Q_l < MaxQ_) { |
263 |
< |
int whichBin = Q_l / deltaQ_; |
264 |
< |
Q_histogram_[whichBin] += 1; |
262 |
> |
if (q_l >= MinQ_ && q_l < MaxQ_) { |
263 |
> |
int qbin = (q_l - MinQ_) / deltaQ_; |
264 |
> |
Q_histogram_[qbin] += 1; |
265 |
> |
Qcount_++; |
266 |
> |
sumQ_ += q_l; |
267 |
> |
sumQ2_ += q_l * q_l; |
268 |
> |
} else { |
269 |
> |
sprintf( painCave.errMsg, |
270 |
> |
"q_l value outside reasonable range\n"); |
271 |
> |
painCave.severity = OOPSE_ERROR; |
272 |
> |
painCave.isFatal = 1; |
273 |
> |
simError(); |
274 |
|
} |
268 |
– |
if (W_l_hat < MaxW_) { |
269 |
– |
int whichBin = W_l_hat / deltaW_; |
270 |
– |
W_histogram_[whichBin] += 1; |
271 |
– |
} |
272 |
– |
} |
273 |
– |
|
275 |
|
|
276 |
< |
void BondOrderParameter::writeOrderParameter() { |
276 |
> |
} |
277 |
|
|
277 |
– |
std::ofstream os(getOutputFileName().c_str()); |
278 |
– |
os << "#Bond Order Parameter\n"; |
279 |
– |
os << "#selection: (" << selectionScript_ << ")\n"; |
278 |
|
|
279 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
282 |
< |
os << orderParams_[i].p2 << "\t" |
283 |
< |
<< orderParams_[i].director[0] << "\t" |
284 |
< |
<< orderParams_[i].director[1] << "\t" |
285 |
< |
<< orderParams_[i].director[2] << "\t" |
286 |
< |
<< orderParams_[i].angle << "\n"; |
279 |
> |
void BondOrderParameter::writeOrderParameter(RealType ql, RealType Wlhat) { |
280 |
|
|
281 |
< |
} |
289 |
< |
} |
281 |
> |
std::ofstream os(getOutputFileName().c_str()); |
282 |
|
|
283 |
+ |
if (os.is_open()) { |
284 |
+ |
|
285 |
+ |
os << "# Bond Order Parameters\n"; |
286 |
+ |
os << "# selection: (" << selectionScript_ << ")\n"; |
287 |
+ |
os << "# \n"; |
288 |
+ |
os << "# <Q_" << lNumber_ << ">: " << ql << "\n"; |
289 |
+ |
os << "# <W_" << lNumber_ << ">: " << Wlhat << "\n"; |
290 |
+ |
// Normalize by number of frames and write it out: |
291 |
+ |
for (int i = 0; i < Q_histogram_.size(); ++i) { |
292 |
+ |
RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; |
293 |
+ |
os << Qval << "\t" << (RealType)Q_histogram_[i] / (RealType)Qcount_ << "\n"; |
294 |
+ |
} |
295 |
|
|
296 |
+ |
os.close(); |
297 |
|
|
298 |
+ |
} else { |
299 |
+ |
sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", |
300 |
+ |
getOutputFileName().c_str()); |
301 |
+ |
painCave.isFatal = 1; |
302 |
+ |
simError(); |
303 |
+ |
} |
304 |
+ |
} |
305 |
|
} |