--- trunk/src/applications/staticProps/BondOrderParameter.cpp 2006/09/21 18:04:52 1044 +++ trunk/src/applications/staticProps/BondOrderParameter.cpp 2011/08/12 14:37:25 1610 @@ -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. @@ -37,28 +28,34 @@ * 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 $Id$ + * */ - - -/* 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/SphericalHarmonic.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) + ".bo"); @@ -69,35 +66,80 @@ 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); // Q can take values from 0 to 1 MinQ_ = 0.0; - MaxQ_ = 1.0; + MaxQ_ = 1.1; deltaQ_ = (MaxQ_ - MinQ_) / nbins; - Q_histogram_.resize(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: - MinW_ = -0.18; - MaxW_ = 0.18; + MinW_ = -1.1; + MaxW_ = 1.1; deltaW_ = (MaxW_ - MinW_) / nbins; - W_histogram_.resize(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() { @@ -114,28 +156,35 @@ namespace oopse { RealType phi; RealType r; RealType dist; - std::map QBar_lm; - RealType QSq_l; - RealType Q_l; - ComplexType W_l; - ComplexType W_l_hat; - int nBonds; + 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; - // Make arrays for Wigner3jm - double* THRCOF = new double[mSize_]; - // Variables for Wigner routine - double l_ = (double)lNumber_; - double m1Pass, m2Min, m2Max; - int error, m1, m2, m3; - // Set the l for the spherical harmonic, it doesn't change - sphericalHarmonic.setL(lNumber_); - 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_++; @@ -153,21 +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)) { myIndex = sd->getGlobalIndex(); - - // For this central atom, zero out nBonds and QBar_lm - 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: @@ -180,7 +228,9 @@ namespace oopse { if (atom->getGlobalIndex() != myIndex) { vec = sd->getPos() - atom->getPos(); - currentSnapshot_->wrapVector(vec); + + if (usePeriodicBoundaryConditions_) + currentSnapshot_->wrapVector(vec); // Calculate "bonds" and build Q_lm(r) where // Q_lm = Y_lm(theta(r),phi(r)) @@ -194,10 +244,14 @@ namespace oopse { if (r < rCut_) { costheta = vec.z() / r; phi = atan2(vec.y(), vec.x()); - - for(int m = -lNumber_; m <= lNumber_; m++){ - sphericalHarmonic.setM(m); - QBar_lm[m] += sphericalHarmonic.getValueAt(costheta,phi); + + 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++; } @@ -205,107 +259,142 @@ namespace oopse { } } - // Normalize Qbar2 - for (int m = -lNumber_;m <= lNumber_; m++){ - QBar_lm[m] /= nBonds; - std::cout << "m = " << m << " QBLM = " << QBar_lm[m] << "\n"; - } + + 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; - // Find second order invariant Q_l - - QSq_l = 0.0; - for (int m = -lNumber_; m <= lNumber_; m++){ - QSq_l += norm(QBar_lm[m]); + q2[l] += norm(q[std::make_pair(l,m)]); + } + q_l[l] = sqrt(q2[l] * 4.0 * NumericConstant::PI / (RealType)(2*l + 1)); } - std::cout << "qsq_l = " << QSq_l << "\n"; - Q_l = sqrt(QSq_l * 4.0 * NumericConstant::PI / - (2.0*(RealType)lNumber_ + 1.0)); - - // Find Third Order Invariant W_l - 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; + // 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)]; + } } - // Get Wigner coefficients - m1Pass = (double)m1; - Wigner3jm(&l_, &l_, &l_, &m1Pass, &m2Min, &m2Max, THRCOF, &mSize_, &error); - for (int m_index = 1; m_index < (int)(m2Max - m2Min-1.0); m_index++) { - m2 = floor(m2Min) + m_index - 1; - m3 = -m1-m2; - W_l += THRCOF[m_index]*QBar_lm[m1]*QBar_lm[m2]*QBar_lm[m3]; - } + + w_hat[l] = w[l] / pow(q2[l], 1.5); } - - W_l_hat = W_l / pow(QSq_l, 1.5); - - // accumulate histogram data for Q_l and W_l_hat: - std::cout << "Ql = " << Q_l << " Wl = " << W_l_hat << "\n"; - collectHistogram(Q_l, real(W_l_hat)); - + collectHistogram(q_l, w_hat); + + 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)]; + } + } } } + + // Normalize Qbar2 + for (int l = 0; l <= lMax_; l++) { + for (int m = -l; m <= l; m++){ + QBar[std::make_pair(l,m)] /= Nbonds; + } + } - writeOrderParameter(); + // 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)); + } + + // 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::collectHistogram(std::vector q, + std::vector what) { - void BondOrderParameter::collectHistogram(RealType Q_l, RealType W_l_hat) { - - if (Q_l >= MinQ_ && Q_l < MaxQ_) { - int qbin = (Q_l - MinQ_) / deltaQ_; - Q_histogram_[qbin] += 1; - Qcount_++; - sumQ_ += Q_l; - sumQ2_ += Q_l * Q_l; - } else { - sprintf( painCave.errMsg, - "Q_l value outside reasonable range\n"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); + 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(); + } } - if (W_l_hat >= MinW_ && W_l_hat < MaxW_) { - int wbin = (W_l_hat - MinW_) / deltaW_; - W_histogram_[wbin] += 1; - Wcount_++; - sumW_ += W_l_hat; - sumW2_ += W_l_hat*W_l_hat; - } else { - sprintf( painCave.errMsg, - "W_l_hat value outside reasonable range\n"); - painCave.severity = OOPSE_ERROR; - painCave.isFatal = 1; - simError(); + 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::writeOrderParameter() { + void BondOrderParameter::writeOrderParameter(std::vector Q, + std::vector What) { + std::ofstream osq((getOutputFileName() + "q").c_str()); if (osq.is_open()) { - - RealType qAvg = sumQ_ / (RealType) Qcount_; - RealType qStdDev = sumQ2_ / (RealType) Qcount_ - qAvg*qAvg; - osq << "# Bond Order Parameter Q_" << lNumber_ << "\n"; + osq << "# Bond Order Parameters\n"; osq << "# selection: (" << selectionScript_ << ")\n"; - osq << "# : " << qAvg << "\n"; - osq << "# std. dev.: " << qStdDev << "\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 < Q_histogram_.size(); ++i) { - RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; - osq << Qval << "\t" << Q_histogram_[i] / frameCounter_ << "\n"; + for (int i = 0; i < nBins_; ++i) { + RealType Qval = MinQ_ + (i + 0.5) * deltaQ_; + osq << Qval; + for (int l = 0; l <= lMax_; l++) { + + osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; + } + osq << "\n"; } - + osq.close(); + } else { sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", (getOutputFileName() + "q").c_str()); @@ -316,21 +405,23 @@ namespace oopse { std::ofstream osw((getOutputFileName() + "w").c_str()); if (osw.is_open()) { - - RealType wAvg = sumW_ / (RealType) Wcount_; - RealType wStdDev = sumW2_ / (RealType) Wcount_ - wAvg*wAvg; - - osw << "# Bond Order Parameter W_" << lNumber_ << "\n"; + osw << "# Bond Order Parameters\n"; osw << "# selection: (" << selectionScript_ << ")\n"; - osw << "# : " << wAvg << "\n"; - osw << "# std. dev.: " << wStdDev << "\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 < W_histogram_.size(); ++i) { - RealType Wval = MinW_ + (i + 0.5) * deltaW_; - osw << Wval << "\t" << W_histogram_[i] / frameCounter_ << "\n"; + 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", @@ -338,5 +429,6 @@ namespace oopse { painCave.isFatal = 1; simError(); } + } }