--- trunk/src/applications/staticProps/GofRAngle.cpp 2005/02/21 16:57:22 373 +++ trunk/src/applications/staticProps/GofRAngle.cpp 2014/02/20 16:27:30 1968 @@ -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. @@ -37,136 +28,187 @@ * 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, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include #include #include "applications/staticProps/GofRAngle.hpp" +#include "primitives/Atom.hpp" +#include "types/MultipoleAdapter.hpp" #include "utils/simError.h" -namespace oopse { +namespace OpenMD { -GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, - const std::string& sele2, double len, int nrbins, int nangleBins) + GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, + const std::string& sele2, RealType len, int nrbins, int nangleBins) : RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){ - deltaR_ = len_ /nRBins_; - deltaCosAngle_ = 2.0 / nAngleBins_; - - histogram_.resize(nRBins_); - avgGofr_.resize(nRBins_); - for (int i = 0 ; i < nRBins_; ++i) { + deltaR_ = len_ /(double) nRBins_; + deltaCosAngle_ = 2.0 / (double)nAngleBins_; + histogram_.resize(nRBins_); + avgGofr_.resize(nRBins_); + for (int i = 0 ; i < nRBins_; ++i) { histogram_[i].resize(nAngleBins_); avgGofr_[i].resize(nAngleBins_); + } } -} -void GofRAngle::preProcess() { - - for (int i = 0; i < avgGofr_.size(); ++i) { - std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); + void GofRAngle::preProcess() { + for (unsigned int i = 0; i < avgGofr_.size(); ++i) { + std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); } -} + } -void GofRAngle::initalizeHistogram() { + void GofRAngle::initializeHistogram() { npairs_ = 0; - for (int i = 0; i < histogram_.size(); ++i) - std::fill(histogram_[i].begin(), histogram_[i].end(), 0); -} + for (unsigned int i = 0; i < histogram_.size(); ++i){ + std::fill(histogram_[i].begin(), histogram_[i].end(), 0); + } + } - -void GofRAngle::processHistogram() { - + void GofRAngle::processHistogram() { int nPairs = getNPairs(); - double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); - double pairDensity = nPairs /volume; - double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; + RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); + RealType pairDensity = nPairs /volume; + RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; - for(int i = 0 ; i < histogram_.size(); ++i){ + for(unsigned int i = 0 ; i < histogram_.size(); ++i){ - double rLower = i * deltaR_; - double rUpper = rLower + deltaR_; - double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); - double nIdeal = volSlice * pairConstant; + RealType rLower = i * deltaR_; + RealType rUpper = rLower + deltaR_; + RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); + RealType nIdeal = volSlice * pairConstant; - for (int j = 0; j < histogram_[i].size(); ++j){ - avgGofr_[i][j] += histogram_[i][j] / nIdeal; - } + for (unsigned int j = 0; j < histogram_[i].size(); ++j){ + avgGofr_[i][j] += histogram_[i][j] / nIdeal; + } } -} + } -void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { + void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { if (sd1 == sd2) { - return; + return; } - Vector3d pos1 = sd1->getPos(); Vector3d pos2 = sd2->getPos(); Vector3d r12 = pos2 - pos1; - currentSnapshot_->wrapVector(r12); + if (usePeriodicBoundaryConditions_) + currentSnapshot_->wrapVector(r12); - double distance = r12.length(); - int whichRBin = distance / deltaR_; + RealType distance = r12.length(); + int whichRBin = int(distance / deltaR_); if (distance <= len_) { - double cosAngle = evaluateAngle(sd1, sd2); - double halfBin = (nAngleBins_ - 1) * 0.5; - int whichThetaBin = halfBin * (cosAngle + 1.0); - ++histogram_[whichRBin][whichThetaBin]; + + RealType cosAngle = evaluateAngle(sd1, sd2); + RealType halfBin = (nAngleBins_ - 1) * 0.5; + int whichThetaBin = int(halfBin * (cosAngle + 1.0)); + ++histogram_[whichRBin][whichThetaBin]; - ++npairs_; + ++npairs_; } -} + } -void GofRAngle::writeRdf() { + void GofRAngle::writeRdf() { std::ofstream rdfStream(outputFilename_.c_str()); if (rdfStream.is_open()) { - rdfStream << "#radial distribution function\n"; - rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; - rdfStream << "selection2: (" << selectionScript2_ << ")\n"; - rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; - rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; - for (int i = 0; i < avgGofr_.size(); ++i) { - double r = deltaR_ * (i + 0.5); + rdfStream << "#radial distribution function\n"; + rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; + rdfStream << "selection2: (" << selectionScript2_ << ")\n"; + rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; + rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; + for (unsigned int i = 0; i < avgGofr_.size(); ++i) { + // RealType r = deltaR_ * (i + 0.5); - for(int j = 0; j < avgGofr_[i].size(); ++j) { - double cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; - rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; - } + for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { + // RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; + rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; + } - rdfStream << "\n"; - } + rdfStream << "\n"; + } } else { - sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str()); - painCave.isFatal = 1; - simError(); + sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str()); + painCave.isFatal = 1; + simError(); } rdfStream.close(); -} + } -double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { + RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { Vector3d pos1 = sd1->getPos(); Vector3d pos2 = sd2->getPos(); Vector3d r12 = pos2 - pos1; - currentSnapshot_->wrapVector(r12); + + if (usePeriodicBoundaryConditions_) + currentSnapshot_->wrapVector(r12); + r12.normalize(); - Vector3d dipole = sd1->getElectroFrame().getColumn(2); - dipole.normalize(); - return dot(r12, dipole); -} -double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { - Vector3d v1 = sd1->getElectroFrame().getColumn(2); - Vector3d v2 = sd2->getElectroFrame().getColumn(2); + Vector3d vec; + + if (sd1->isAtom()) { + AtomType* atype1 = static_cast(sd1)->getAtomType(); + MultipoleAdapter ma1 = MultipoleAdapter(atype1); + + if (ma1.isDipole() ) + vec = sd1->getDipole(); + else + vec = sd1->getA().transpose() * V3Z; + } else { + vec = sd1->getA().transpose() * V3Z; + } + + vec.normalize(); + + return dot(r12, vec); + } + + RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { + Vector3d v1, v2; + + if (sd1->isAtom()){ + AtomType* atype1 = static_cast(sd1)->getAtomType(); + MultipoleAdapter ma1 = MultipoleAdapter(atype1); + if (ma1.isDipole() ) + v1 = sd1->getDipole(); + else + v1 = sd1->getA().transpose() * V3Z; + } else { + v1 = sd1->getA().transpose() * V3Z; + } + + if (sd2->isAtom()) { + AtomType* atype2 = static_cast(sd2)->getAtomType(); + MultipoleAdapter ma2 = MultipoleAdapter(atype2); + + if (ma2.isDipole() ) + v2 = sd2->getDipole(); + else + v2 = sd2->getA().transpose() * V3Z; + } else { + v2 = sd2->getA().transpose() * V3Z; + } + v1.normalize(); v2.normalize(); return dot(v1, v2); -} + } }