--- trunk/src/applications/staticProps/BondOrderParameter.cpp 2006/09/19 21:14:11 1039 +++ trunk/src/applications/staticProps/BondOrderParameter.cpp 2009/11/25 20:02:06 1390 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,32 +28,36 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Vardeman & Gezelter, in progress (2009). + * + * Created by J. Daniel Gezelter on 09/26/06. + * @author J. Daniel Gezelter + * @version $Id: BondOrderParameter.cpp,v 1.23 2009-11-25 20:01:59 gezelter Exp $ + * */ - - -/* Creates orientational bond order parameters as outlined by - * Bond-orientaional order in liquids and glasses, Steinhart,Nelson,Ronchetti - * Phys Rev B, 28,784,1983 - * - */ #include "applications/staticProps/BondOrderParameter.hpp" #include "utils/simError.h" #include "io/DumpReader.hpp" #include "primitives/Molecule.hpp" #include "utils/NumericConstant.hpp" -#include "math/RealSphericalHarmonic.hpp" -namespace oopse { +namespace OpenMD { 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 nbins) : StaticAnalyser(info, filename), selectionScript_(sele), evaluator_(info), seleMan_(info){ - setOutputName(getPrefix(filename) + ".obo"); + setOutputName(getPrefix(filename) + ".bo"); evaluator_.loadScriptString(sele); if (!evaluator_.isDynamic()) { @@ -71,53 +66,128 @@ namespace oopse { // Set up cutoff radius and order of the Legendre Polynomial: - lNumber_ = lNumber; rCut_ = rCut; - mSize_ = 2*lNumber_+1; + nBins_ = nbins; + Qcount_.resize(lMax_+1); + Wcount_.resize(lMax_+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_ = 1.1; + deltaQ_ = (MaxQ_ - MinQ_) / 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); - W_histogram_.resize(nbins); + MinW_ = -1.1; + MaxW_ = 1.1; + deltaW_ = (MaxW_ - MinW_) / nbins; - } + // Make arrays for Wigner3jm + double* THRCOF = new double[2*lMax_+1]; + // Variables for Wigner routine + double lPass, m1Pass, m2m, m2M; + int error, mSize; + mSize = 2*lMax_+1; + for (int l = 0; l <= lMax_; l++) { + lPass = (double)l; + for (int m1 = -l; m1 <= l; m1++) { + m1Pass = (double)m1; + + std::pair lm = std::make_pair(l, m1); + + // Zero work array + for (int ii = 0; ii < 2*l + 1; ii++){ + THRCOF[ii] = 0.0; + } + + // Get Wigner coefficients + Wigner3jm(&lPass, &lPass, &lPass, + &m1Pass, &m2m, &m2M, + THRCOF, &mSize, &error); + + m2Min[lm] = (int)floor(m2m); + m2Max[lm] = (int)floor(m2M); + + for (int mmm = 0; mmm <= (int)(m2M - m2m); mmm++) { + w3j[lm].push_back(THRCOF[mmm]); + } + } + } + delete [] THRCOF; + THRCOF = NULL; + } + + BondOrderParameter::~BondOrderParameter() { + Q_histogram_.clear(); + W_histogram_.clear(); + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++) { + w3j[std::make_pair(l,m)].clear(); + } + } + w3j.clear(); + m2Min.clear(); + m2Max.clear(); + } + void BondOrderParameter::initalizeHistogram() { - std::fill(Q_histogram_.begin(), Q_histogram_.end(), 0); - std::fill(W_histogram_.begin(), W_histogram_.end(), 0); + for (int bin = 0; bin < nBins_; bin++) { + for (int l = 0; l <= lMax_; l++) { + Q_histogram_[std::make_pair(bin,l)] = 0; + W_histogram_[std::make_pair(bin,l)] = 0; + } + } } void BondOrderParameter::process() { 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; - RealType QSq_l; - RealType Q_l; - int nBonds; - RealSphericalHarmonic sphericalHarmonic; + std::map,ComplexType> q; + std::vector q_l; + std::vector q2; + std::vector w; + std::vector w_hat; + std::map,ComplexType> QBar; + std::vector Q2; + std::vector Q; + std::vector W; + std::vector W_hat; + int nBonds, Nbonds; + SphericalHarmonic sphericalHarmonic; int i, j; - - + DumpReader reader(info_, dumpFilename_); int nFrames = reader.getNFrames(); + frameCounter_ = 0; + q_l.resize(lMax_+1); + q2.resize(lMax_+1); + w.resize(lMax_+1); + w_hat.resize(lMax_+1); + Q2.resize(lMax_+1); + Q.resize(lMax_+1); + W.resize(lMax_+1); + W_hat.resize(lMax_+1); + Nbonds = 0; + for (int istep = 0; istep < nFrames; istep += step_) { reader.readFrame(istep); + frameCounter_++; currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); if (evaluator_.isDynamic()) { @@ -132,19 +202,20 @@ namespace oopse { rb = mol->nextRigidBody(rbIter)) { rb->updateAtoms(); } - } - + } + // outer loop is over the selected StuntDoubles: for (sd = seleMan_.beginSelected(i); sd != NULL; sd = seleMan_.nextSelected(i)) { - // For this central atom, zero out nBonds and QBar_lm - + myIndex = sd->getGlobalIndex(); nBonds = 0; - - for (int m = -lNumber_; m <= lNumber_; m++) { - QBar_lm[m] = 0.0; + + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++) { + q[std::make_pair(l,m)] = 0.0; + } } // inner loop is over all other atoms in the system: @@ -154,139 +225,208 @@ 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(); + + if (usePeriodicBoundaryConditions_) + 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 l = 0; l <= lMax_; l++) { + sphericalHarmonic.setL(l); + for(int m = -l; m <= l; m++){ + sphericalHarmonic.setM(m); + q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); + } + } + nBonds++; + } + } } } - // Normalize Qbar - for (int m = -lNumber_;m <= lNumber_; m++){ - QBar_lm[m] /= nBonds; + + for (int l = 0; l <= lMax_; l++) { + q2[l] = 0.0; + for (int m = -l; m <= l; m++){ + q[std::make_pair(l,m)] /= (RealType)nBonds; + q2[l] += norm(q[std::make_pair(l,m)]); + } + q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); } - - // Find second order invariant Q_l - - QSq_l = 0.0; - for (int m = -lNumber_; m <= lNumber_; m++){ - QSq_l += pow(QBar_lm[m], 2); - } - Q_l = sqrt(QSq_l*(4.0 * NumericConstant::PI / (2.0*(RealType)lNumber_ + 1))); - + // Find Third Order Invariant W_l + + for (int l = 0; l <= lMax_; l++) { + w[l] = 0.0; + for (int m1 = -l; m1 <= l; m1++) { + std::pair lm = std::make_pair(l, m1); + for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { + int m2 = m2Min[lm] + mmm; + int m3 = -m1-m2; + w[l] += w3j[lm][mmm] * q[lm] * + q[std::make_pair(l,m2)] * q[std::make_pair(l,m3)]; + } + } + + w_hat[l] = w[l] / pow(q2[l], 1.5); + } - // 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; + collectHistogram(q_l, w_hat); - W_l_ = 0.0; - for (int m1 = -lNumber_; m1 <= lNumber_; m1++) { - // Zero work array - for (int ii = 0; ii < mSize_; ii+){ - THRCOF[i] = 0.0; + Nbonds += nBonds; + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++) { + QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)]; } - // 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++) { - 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_hat = W_l_ / pow(QSq_l, 1.5); - - // accumulate histogram data for Q_l and W_l_hat: - - collectHistogram(Q_l, W_l_hat); - } } + + // Normalize Qbar2 + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++){ + QBar[std::make_pair(l,m)] /= Nbonds; + } + } - // Normalize by number of frames - for (int m = -lNumber_; m <= lNumber_; m++){ - QBar_lm[m] /= nFrames; + // Find second order invariant Q_l + + for (int l = 0; l <= lMax_; l++) { + Q2[l] = 0.0; + for (int m = -l; m <= l; m++){ + Q2[l] += norm(QBar[std::make_pair(l,m)]); + } + Q[l] = sqrt(Q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); } - - - - - writeOrderParameter(); + // Find Third Order Invariant W_l + for (int l = 0; l <= lMax_; l++) { + W[l] = 0.0; + for (int m1 = -l; m1 <= l; m1++) { + std::pair lm = std::make_pair(l, m1); + for (int mmm = 0; mmm <= (m2Max[lm] - m2Min[lm]); mmm++) { + int m2 = m2Min[lm] + mmm; + int m3 = -m1-m2; + W[l] += w3j[lm][mmm] * QBar[lm] * + QBar[std::make_pair(l,m2)] * QBar[std::make_pair(l,m3)]; + } + } + + W_hat[l] = W[l] / pow(Q2[l], 1.5); + } + + writeOrderParameter(Q, W_hat); } - - 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; + void BondOrderParameter::collectHistogram(std::vector q, + std::vector what) { - for(int i = 0 ; i < histogram_.size(); ++i){ + for (int l = 0; l <= lMax_; l++) { + if (q[l] >= MinQ_ && q[l] < MaxQ_) { + int qbin = (q[l] - MinQ_) / deltaQ_; + Q_histogram_[std::make_pair(qbin,l)] += 1; + Qcount_[l]++; + } else { + sprintf( painCave.errMsg, + "q_l value outside reasonable range\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } - 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; + for (int l = 0; l <= lMax_; l++) { + if (real(what[l]) >= MinW_ && real(what[l]) < MaxW_) { + int wbin = (real(what[l]) - MinW_) / deltaW_; + W_histogram_[std::make_pair(wbin,l)] += 1; + Wcount_[l]++; + } else { + sprintf( painCave.errMsg, + "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); + painCave.severity = OPENMD_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 < Max_W) { - int whichBin = W_l_hat / deltaW_; - W_histogram_[whichBin] += 1; - } - } - + void BondOrderParameter::writeOrderParameter(std::vector Q, + std::vector What) { + + std::ofstream osq((getOutputFileName() + "q").c_str()); - void BondOrderParameter::writeOrderParameter() { + if (osq.is_open()) { + + osq << "# Bond Order Parameters\n"; + osq << "# selection: (" << selectionScript_ << ")\n"; + osq << "# \n"; + for (int l = 0; l <= lMax_; l++) { + osq << "# : " << Q[l] << "\n"; + } + // Normalize by number of frames and write it out: + for (int i = 0; i < nBins_; ++i) { + RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; + osq << Qval; + for (int l = 0; l <= lMax_; l++) { - std::ofstream os(getOutputFileName().c_str()); - os << "#Bond Order Parameter\n"; - os << "#selection: (" << selectionScript_ << ")\n"; + osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; + } + osq << "\n"; + } - 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"; + 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()) { + osw << "# Bond Order Parameters\n"; + osw << "# selection: (" << selectionScript_ << ")\n"; + osw << "# \n"; + for (int l = 0; l <= lMax_; l++) { + osw << "# : " << real(What[l]) << "\t" << imag(What[l]) << "\n"; + } + // Normalize by number of frames and write it out: + for (int i = 0; i < nBins_; ++i) { + RealType Wval = MinW_ + (i + 0.5) * deltaW_; + osw << Wval; + for (int l = 0; l <= lMax_; l++) { + osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; + } + osw << "\n"; + } + + osw.close(); + } else { + sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", + (getOutputFileName() + "w").c_str()); + painCave.isFatal = 1; + simError(); + } + + } }