--- trunk/src/applications/staticProps/GofRAngle.cpp 2005/02/17 16:21:07 360 +++ trunk/src/applications/staticProps/GofRAngle.cpp 2014/10/02 14:35:14 2023 @@ -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. @@ -37,138 +28,407 @@ * 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, + RealType len, int nrbins, int nangleBins) + : RadialDistrFunc(info, filename, sele1, sele2), len_(len), + nRBins_(nrbins), nAngleBins_(nangleBins), evaluator3_(info), + seleMan3_(info), doSele3_(false) { + + 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_); + } + } + + GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, + const std::string& sele1, + const std::string& sele2, + const std::string& sele3, + RealType len, int nrbins, int nangleBins) + : RadialDistrFunc(info, filename, sele1, sele2), len_(len), + nRBins_(nrbins), nAngleBins_(nangleBins), selectionScript3_(sele3), + evaluator3_(info), seleMan3_(info), doSele3_(true) { -GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, - const std::string& sele2, double 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) { - histogram_[i].resize(nAngleBins_); - avgGofr_[i].resize(nAngleBins_); + histogram_[i].resize(nAngleBins_); + avgGofr_[i].resize(nAngleBins_); } -} + evaluator3_.loadScriptString(sele3); + if (!evaluator3_.isDynamic()) { + seleMan3_.setSelectionSet(evaluator3_.evaluate()); + } -void GofRAngle::preProcess() { + } + + void GofRAngle::processNonOverlapping( SelectionManager& sman1, + SelectionManager& sman2) { + StuntDouble* sd1; + StuntDouble* sd2; + StuntDouble* sd3; + int i; + int j; + int k; + + // This is the same as a non-overlapping pairwise loop structure: + // for (int i = 0; i < ni ; ++i ) { + // for (int j = 0; j < nj; ++j) {} + // } - for (int i = 0; i < avgGofr_.size(); ++i) { - std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); + if (doSele3_) { + if (evaluator3_.isDynamic()) { + seleMan3_.setSelectionSet(evaluator3_.evaluate()); + } + if (sman1.getSelectionCount() != seleMan3_.getSelectionCount() ) { + RadialDistrFunc::processNonOverlapping( sman1, sman2 ); + } + + for (sd1 = sman1.beginSelected(i), sd3 = seleMan3_.beginSelected(k); + sd1 != NULL && sd3 != NULL; + sd1 = sman1.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) { + for (sd2 = sman2.beginSelected(j); sd2 != NULL; + sd2 = sman2.nextSelected(j)) { + collectHistogram(sd1, sd2, sd3); + } + } + } else { + RadialDistrFunc::processNonOverlapping( sman1, sman2 ); } -} + } -void GofRAngle::initalizeHistogram() { - npairs_ = 0; - for (int i = 0; i < histogram_.size(); ++i) - std::fill(histogram_[i].begin(), histogram_[i].end(), 0); -} + void GofRAngle::processOverlapping( SelectionManager& sman) { + StuntDouble* sd1; + StuntDouble* sd2; + StuntDouble* sd3; + int i; + int j; + int k; + // This is the same as a pairwise loop structure: + // for (int i = 0; i < n-1 ; ++i ) { + // for (int j = i + 1; j < n; ++j) {} + // } + + if (doSele3_) { + if (evaluator3_.isDynamic()) { + seleMan3_.setSelectionSet(evaluator3_.evaluate()); + } + if (sman.getSelectionCount() != seleMan3_.getSelectionCount() ) { + RadialDistrFunc::processOverlapping( sman); + } + for (sd1 = sman.beginSelected(i), sd3 = seleMan3_.beginSelected(k); + sd1 != NULL && sd3 != NULL; + sd1 = sman.nextSelected(i), sd3 = seleMan3_.nextSelected(k)) { + for (j = i, sd2 = sman.nextSelected(j); sd2 != NULL; + sd2 = sman.nextSelected(j)) { + collectHistogram(sd1, sd2, sd3); + } + } + } else { + RadialDistrFunc::processOverlapping( sman); + } + } + -void GofRAngle::processHistogram() { + void GofRAngle::preProcess() { + for (unsigned int i = 0; i < avgGofr_.size(); ++i) { + std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); + } + } + void GofRAngle::initializeHistogram() { + npairs_ = 0; + 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){ - 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 = pos1 - pos2; - currentSnapshot_->wrapVector(r12); + Vector3d r12 = pos2 - pos1; + 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() { - 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); - - for(int j = 0; j < avgGofr_[i].size(); ++j) { - double cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; - rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; - } + void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2, + StuntDouble* sd3) { - rdfStream << "\n"; - } + if (sd1 == sd2) { + return; + } + + Vector3d p1 = sd1->getPos(); + Vector3d p3 = sd3->getPos(); + + Vector3d c = 0.5 * (p1 + p3); + Vector3d r13 = p3 - p1; + + Vector3d r12 = sd2->getPos() - c; + + if (usePeriodicBoundaryConditions_) { + currentSnapshot_->wrapVector(r12); + currentSnapshot_->wrapVector(r13); + } + + RealType distance = r12.length(); + int whichRBin = int(distance / deltaR_); + + if (distance <= len_) { + + RealType cosAngle = evaluateAngle(sd1, sd2, sd3); + RealType halfBin = (nAngleBins_ - 1) * 0.5; + int whichThetaBin = int(halfBin * (cosAngle + 1.0)); + ++histogram_[whichRBin][whichThetaBin]; + ++npairs_; + } + } + + 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_ << ")"; + if (doSele3_) { + rdfStream << "\tselection3: (" << selectionScript3_ << ")\n"; + } else { + rdfStream << "\n"; + } + rdfStream << "#nRBins = " << nRBins_ << "\tmaxLen = " + << len_ << "\tdeltaR = " << deltaR_ <<"\n"; + rdfStream << "#nAngleBins =" << nAngleBins_ << "\tdeltaCosAngle = " + << deltaCosAngle_ << "\n"; + for (unsigned int i = 0; i < avgGofr_.size(); ++i) { + // RealType r = deltaR_ * (i + 0.5); + + 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"; + } + } 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 = pos1 - pos2; - currentSnapshot_->wrapVector(r12); + Vector3d r12 = pos2 - pos1; + + 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 = sd1->getElectroFrame().getColumn(2); + Vector3d vec; + + if (!sd1->isDirectional()) { + sprintf(painCave.errMsg, + "GofRTheta: attempted to use a non-directional object: %s\n", + sd1->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + + 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 GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, + StuntDouble* sd3) { + Vector3d p1 = sd1->getPos(); + Vector3d p3 = sd3->getPos(); + + Vector3d c = 0.5 * (p1 + p3); + Vector3d r13 = p3 - p1; + + Vector3d r12 = sd2->getPos() - c; + + if (usePeriodicBoundaryConditions_) { + currentSnapshot_->wrapVector(r12); + currentSnapshot_->wrapVector(r13); + } + + r12.normalize(); + r13.normalize(); + + return dot(r12, r13); + } + + RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { + Vector3d v1, v2; + + if (!sd1->isDirectional()) { + sprintf(painCave.errMsg, + "GofROmega: attempted to use a non-directional object: %s\n", + sd1->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + + 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->isDirectional()) { + sprintf(painCave.errMsg, + "GofROmega attempted to use a non-directional object: %s\n", + sd2->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + + 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); -} + } + RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2, + StuntDouble* sd3) { + Vector3d v1; + Vector3d v2; + + v1 = sd3->getPos() - sd1->getPos(); + if (usePeriodicBoundaryConditions_) + currentSnapshot_->wrapVector(v1); + + if (!sd2->isDirectional()) { + sprintf(painCave.errMsg, + "GofROmega: attempted to use a non-directional object: %s\n", + sd2->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + + 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); + } }