--- trunk/src/applications/staticProps/BondOrderParameter.cpp 2006/09/26 14:33:56 1053 +++ 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" @@ -52,7 +50,7 @@ #include "primitives/Molecule.hpp" #include "utils/NumericConstant.hpp" -namespace oopse { +namespace OpenMD { BondOrderParameter::BondOrderParameter(SimInfo* info, const std::string& filename, @@ -82,8 +80,8 @@ 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_ = -0.25; - MaxW_ = 0.25; + MinW_ = -1.1; + MaxW_ = 1.1; deltaW_ = (MaxW_ - MinW_) / nbins; // Make arrays for Wigner3jm @@ -104,27 +102,37 @@ namespace oopse { 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++) { + 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++) { @@ -175,6 +183,7 @@ namespace oopse { 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); @@ -219,7 +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)) @@ -239,6 +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++; @@ -248,33 +260,23 @@ 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; - } - - // Find second order invariant Q_l - 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))/(RealType)nBonds; + q_l[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++) { + 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] * @@ -290,7 +292,7 @@ namespace oopse { 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)]; } } } @@ -319,7 +321,7 @@ namespace oopse { 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++) { + 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] * @@ -344,7 +346,7 @@ 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(); } @@ -357,8 +359,8 @@ namespace oopse { Wcount_[l]++; } else { sprintf( painCave.errMsg, - "Re[w_hat] value outside reasonable range\n"); - painCave.severity = OOPSE_ERROR; + "Re[w_hat] value (%lf) outside reasonable range\n", real(what[l])); + painCave.severity = OPENMD_ERROR; painCave.isFatal = 1; simError(); } @@ -385,7 +387,8 @@ namespace oopse { 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]; + + osq << "\t" << (RealType)Q_histogram_[std::make_pair(i,l)]/(RealType)Qcount_[l]/deltaQ_; } osq << "\n"; } @@ -406,14 +409,15 @@ namespace oopse { osw << "# selection: (" << selectionScript_ << ")\n"; osw << "# \n"; for (int l = 0; l <= lMax_; l++) { - osw << "# : " << real(What[l]) << "\n"; + 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]; + + osw << "\t" << (RealType)W_histogram_[std::make_pair(i,l)]/(RealType)Wcount_[l]/deltaW_; } osw << "\n"; }