--- trunk/src/applications/staticProps/GofRAngle.cpp 2005/04/15 22:04:00 507 +++ trunk/src/applications/staticProps/GofRAngle.cpp 2012/08/22 02:28:28 1782 @@ -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. @@ -37,6 +28,16 @@ * 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -44,15 +45,14 @@ #include "applications/staticProps/GofRAngle.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) + 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_; - + deltaR_ = len_ /(double) nRBins_; + deltaCosAngle_ = 2.0 / (double)nAngleBins_; histogram_.resize(nRBins_); avgGofr_.resize(nRBins_); for (int i = 0 ; i < nRBins_; ++i) { @@ -63,34 +63,32 @@ namespace oopse { void GofRAngle::preProcess() { - - for (int i = 0; i < avgGofr_.size(); ++i) { + for (unsigned int i = 0; i < avgGofr_.size(); ++i) { std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); } } void GofRAngle::initalizeHistogram() { npairs_ = 0; - for (int i = 0; i < histogram_.size(); ++i) + for (unsigned int i = 0; i < histogram_.size(); ++i){ std::fill(histogram_[i].begin(), histogram_[i].end(), 0); + } } - 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){ + for (unsigned int j = 0; j < histogram_[i].size(); ++j){ avgGofr_[i][j] += histogram_[i][j] / nIdeal; } } @@ -102,18 +100,19 @@ namespace oopse { if (sd1 == sd2) { 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(); + RealType distance = r12.length(); int whichRBin = distance / deltaR_; if (distance <= len_) { - double cosAngle = evaluateAngle(sd1, sd2); - double halfBin = (nAngleBins_ - 1) * 0.5; + + RealType cosAngle = evaluateAngle(sd1, sd2); + RealType halfBin = (nAngleBins_ - 1) * 0.5; int whichThetaBin = halfBin * (cosAngle + 1.0); ++histogram_[whichRBin][whichThetaBin]; @@ -129,11 +128,11 @@ namespace oopse { 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); + 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_; + for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { + RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; } @@ -149,18 +148,21 @@ namespace oopse { 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) { + RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { Vector3d v1 = sd1->getElectroFrame().getColumn(2); Vector3d v2 = sd2->getElectroFrame().getColumn(2); v1.normalize();