--- trunk/src/applications/staticProps/GofAngle2.cpp 2005/02/17 16:21:07 360 +++ trunk/src/applications/staticProps/GofAngle2.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. @@ -37,108 +28,304 @@ * 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/GofAngle2.hpp" +#include "primitives/Atom.hpp" +#include "types/MultipoleAdapter.hpp" #include "utils/simError.h" -namespace oopse { +namespace OpenMD { -GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, - const std::string& sele2, int nangleBins) - : RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) { + GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, + const std::string& sele1, + const std::string& sele2, int nangleBins) + : RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins), + evaluator3_(info), + seleMan3_(info), doSele3_(false) { + + setOutputName(getPrefix(filename) + ".gto"); + + deltaCosAngle_ = 2.0 / nAngleBins_; + + histogram_.resize(nAngleBins_); + avgGofr_.resize(nAngleBins_); + for (int i = 0 ; i < nAngleBins_; ++i) { + histogram_[i].resize(nAngleBins_); + avgGofr_[i].resize(nAngleBins_); + } + } + GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, + const std::string& sele1, + const std::string& sele2, + const std::string& sele3, int nangleBins) + : RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins), + evaluator3_(info), selectionScript3_(sele3), + seleMan3_(info), doSele3_(true) { + setOutputName(getPrefix(filename) + ".gto"); deltaCosAngle_ = 2.0 / nAngleBins_; - + histogram_.resize(nAngleBins_); avgGofr_.resize(nAngleBins_); for (int i = 0 ; i < nAngleBins_; ++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 GofAngle2::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) {} + // } + if (doSele3_) { + if (evaluator3_.isDynamic()) { + seleMan3_.setSelectionSet(evaluator3_.evaluate()); + } + if (sman1.getSelectionCount() != seleMan3_.getSelectionCount() ) { + RadialDistrFunc::processNonOverlapping( sman1, sman2 ); + } -void GofAngle2::preProcess() { + 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 ); + } + } - for (int i = 0; i < avgGofr_.size(); ++i) { - std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); + void GofAngle2::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 GofAngle2::preProcess() { + + for (unsigned int i = 0; i < avgGofr_.size(); ++i) { + std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); } -} + } -void GofAngle2::initalizeHistogram() { + void GofAngle2::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 GofAngle2::processHistogram() { + void GofAngle2::processHistogram() { //std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus>) -} + } -void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { + void GofAngle2::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 dipole1 = sd1->getElectroFrame().getColumn(2); - Vector3d dipole2 = sd2->getElectroFrame().getColumn(2); + if (usePeriodicBoundaryConditions_) + currentSnapshot_->wrapVector(r12); + + AtomType* atype1 = static_cast(sd1)->getAtomType(); + AtomType* atype2 = static_cast(sd2)->getAtomType(); + MultipoleAdapter ma1 = MultipoleAdapter(atype1); + MultipoleAdapter ma2 = MultipoleAdapter(atype2); + + if (!sd1->isDirectional()) { + sprintf(painCave.errMsg, + "GofAngle2: attempted to use a non-directional object: %s\n", + sd1->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + + if (!sd2->isDirectional()) { + sprintf(painCave.errMsg, + "GofAngle2: attempted to use a non-directional object: %s\n", + sd2->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + + Vector3d dipole1, dipole2; + if (ma1.isDipole()) + dipole1 = sd1->getDipole(); + else + dipole1 = sd1->getA().transpose() * V3Z; + + if (ma2.isDipole()) + dipole2 = sd2->getDipole(); + else + dipole2 = sd2->getA().transpose() * V3Z; r12.normalize(); dipole1.normalize(); dipole2.normalize(); - double cosAngle1 = dot(r12, dipole1); - double cosAngle2 = dot(dipole1, dipole2); + RealType cosAngle1 = dot(r12, dipole1); + RealType cosAngle2 = dot(dipole1, dipole2); - double halfBin = (nAngleBins_ - 1) * 0.5; - int angleBin1 = halfBin * (cosAngle1 + 1.0); - int angleBin2 = halfBin * (cosAngle1 + 1.0); + RealType halfBin = (nAngleBins_ - 1) * 0.5; + int angleBin1 = int(halfBin * (cosAngle1 + 1.0)); + int angleBin2 = int(halfBin * (cosAngle2 + 1.0)); - ++histogram_[angleBin1][angleBin1]; + ++histogram_[angleBin1][angleBin2]; ++npairs_; -} + } -void GofAngle2::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 << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; - for (int i = 0; i < avgGofr_.size(); ++i) { - double cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; + void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2, + StuntDouble* sd3) { - for(int j = 0; j < avgGofr_[i].size(); ++j) { - double cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; - rdfStream <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(); + + if (!sd2->isDirectional()) { + sprintf(painCave.errMsg, + "GofAngle2: attempted to use a non-directional object: %s\n", + sd2->getType().c_str()); + painCave.isFatal = 1; + simError(); + } + + AtomType* atype2 = static_cast(sd2)->getAtomType(); + MultipoleAdapter ma2 = MultipoleAdapter(atype2); + + Vector3d dipole2; + if (ma2.isDipole()) + dipole2 = sd2->getDipole(); + else + dipole2 = sd2->getA().transpose() * V3Z; + + dipole2.normalize(); + + RealType cosAngle1 = dot(r12, r13); + RealType cosAngle2 = dot(r13, dipole2); + + RealType halfBin = (nAngleBins_ - 1) * 0.5; + int angleBin1 = int(halfBin * (cosAngle1 + 1.0)); + int angleBin2 = int(halfBin * (cosAngle2 + 1.0)); + + ++histogram_[angleBin1][angleBin2]; + ++npairs_; + + } + + void GofAngle2::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 << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " + << deltaCosAngle_ << "\n"; + for (unsigned int i = 0; i < avgGofr_.size(); ++i) { + // RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; + for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { + // RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; + rdfStream <