--- trunk/src/applications/staticProps/BondOrderParameter.cpp 2006/09/25 22:08:33 1051 +++ 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. @@ -37,14 +28,21 @@ * 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" @@ -52,12 +50,12 @@ #include "primitives/Molecule.hpp" #include "utils/NumericConstant.hpp" -namespace oopse { +namespace OpenMD { BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, const std::string& sele, - double rCut, int lMax, 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"); @@ -68,7 +66,6 @@ namespace oopse { // Set up cutoff radius and order of the Legendre Polynomial: - lMax_ = lMax; rCut_ = rCut; nBins_ = nbins; Qcount_.resize(lMax_+1); @@ -83,16 +80,59 @@ namespace oopse { // 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; - } + // 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() { for (int bin = 0; bin < nBins_; bin++) { for (int l = 0; l <= lMax_; l++) { @@ -118,6 +158,9 @@ namespace oopse { RealType dist; 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; @@ -126,22 +169,21 @@ namespace oopse { int nBonds, Nbonds; SphericalHarmonic sphericalHarmonic; int i, j; - // Make arrays for Wigner3jm - double* THRCOF = new double[2*lMax_+1]; - // Variables for Wigner routine - double lPass, m1Pass, m2Min, m2Max; - int error, m1, m2, m3, mSize; - mSize = 2*lMax_+1; 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); @@ -186,7 +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)) @@ -206,6 +250,7 @@ namespace oopse { for(int m = -l; m <= l; m++){ sphericalHarmonic.setM(m); q[std::make_pair(l,m)] += sphericalHarmonic.getValueAt(costheta, phi); + } } nBonds++; @@ -215,20 +260,39 @@ namespace oopse { } - for (int l = 0; l <= lMax_; l++) { - q_l[l] = 0.0; - for(int m = -l; m <= l; m++) { - q_l[l] += norm(q[std::make_pair(l,m)]); - } - q_l[l] *= 4.0*NumericConstant::PI/(RealType)(2*l + 1); - q_l[l] = sqrt(q_l[l])/(RealType)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)); } - collectHistogram(q_l); + + // 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); + } + + 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)] += q[std::make_pair(l,m)]; + QBar[std::make_pair(l,m)] += (RealType)nBonds*q[std::make_pair(l,m)]; } } } @@ -251,33 +315,18 @@ namespace oopse { 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; - lPass = (double)l; for (int m1 = -l; m1 <= l; m1++) { - // Zero work array - for (int ii = 0; ii < 2*l + 1; ii++){ - THRCOF[ii] = 0.0; + 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)]; } - // Get Wigner coefficients - m1Pass = (double)m1; - - Wigner3jm(&lPass, &lPass, &lPass, - &m1Pass, &m2Min, &m2Max, - THRCOF, &mSize, &error); - - for (int mmm = 0; mmm < (int)(m2Max - m2Min); mmm++) { - m2 = (int)floor(m2Min) + mmm; - m3 = -m1-m2; - W[l] += THRCOF[mmm] * - QBar[std::make_pair(l,m1)] * - QBar[std::make_pair(l,m2)] * - QBar[std::make_pair(l,m3)]; - } } W_hat[l] = W[l] / pow(Q2[l], 1.5); @@ -286,7 +335,8 @@ namespace oopse { writeOrderParameter(Q, W_hat); } - void BondOrderParameter::collectHistogram(std::vector q) { + void BondOrderParameter::collectHistogram(std::vector q, + std::vector what) { for (int l = 0; l <= lMax_; l++) { if (q[l] >= MinQ_ && q[l] < MaxQ_) { @@ -296,45 +346,89 @@ namespace oopse { } else { sprintf( painCave.errMsg, "q_l value outside reasonable range\n"); - painCave.severity = OOPSE_ERROR; + painCave.severity = OPENMD_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(std::vector Q, std::vector What) { + void BondOrderParameter::writeOrderParameter(std::vector Q, + std::vector What) { - std::ofstream os(getOutputFileName().c_str()); - - if (os.is_open()) { + std::ofstream osq((getOutputFileName() + "q").c_str()); + + if (osq.is_open()) { - os << "# Bond Order Parameters\n"; - os << "# selection: (" << selectionScript_ << ")\n"; + osq << "# Bond Order Parameters\n"; + osq << "# selection: (" << selectionScript_ << ")\n"; + osq << "# \n"; for (int l = 0; l <= lMax_; l++) { - os << "# \n"; - os << "# : " << Q[l] << "\n"; - os << "# : " << real(What[l]) << "\n"; + 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_; - os << Qval; + osq << Qval; for (int l = 0; l <= lMax_; l++) { - os << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)] / (RealType)Qcount_[l]; + + osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; } - os << "\n"; + osq << "\n"; } - os.close(); + osq.close(); } else { sprintf(painCave.errMsg, "BondOrderParameter: unable to open %s\n", - getOutputFileName().c_str()); + (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(); + } + } }