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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
| 11 |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/GofRAngle2.hpp" |
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#include "applications/staticProps/GofAngle2.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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namespace OpenMD { |
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|
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GofRAngle2::GofRAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: RadialDistrFunc(info, filename, sele1, sele2){ |
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GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, int nangleBins) |
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: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) { |
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|
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} |
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setOutputName(getPrefix(filename) + ".gto"); |
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|
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deltaCosAngle_ = 2.0 / nAngleBins_; |
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|
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void GofRAngle2::preProcess() { |
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> |
histogram_.resize(nAngleBins_); |
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> |
avgGofr_.resize(nAngleBins_); |
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for (int i = 0 ; i < nAngleBins_; ++i) { |
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histogram_[i].resize(nAngleBins_); |
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avgGofr_[i].resize(nAngleBins_); |
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} |
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|
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} |
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|
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|
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void GofAngle2::preProcess() { |
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|
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for (int i = 0; i < avgGofr_.size(); ++i) { |
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std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
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std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
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} |
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} |
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} |
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|
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void GofRAngle2::initalizeHistogram() { |
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> |
void GofAngle2::initalizeHistogram() { |
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npairs_ = 0; |
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for (int i = 0; i < histogram_.size(); ++i) |
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std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
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} |
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std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
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} |
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|
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|
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< |
void GofRAngle2::processHistogram() { |
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> |
void GofAngle2::processHistogram() { |
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|
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//std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>) |
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|
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} |
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} |
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|
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void GofRAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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> |
void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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|
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if (sd1 == sd2) { |
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return; |
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return; |
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} |
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|
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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos1 - pos2; |
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currentSnapshot_->wrapVector(r12); |
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(r12); |
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Vector3d dipole1 = sd1->getElectroFrame().getColumn(2); |
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Vector3d dipole2 = sd2->getElectroFrame().getColumn(2); |
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|
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dipole2.normalize(); |
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|
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|
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double cosAngle1 = dot(r12, dipole1); |
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double cosAngle2 = dot(dipole1, dipole2); |
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RealType cosAngle1 = dot(r12, dipole1); |
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RealType cosAngle2 = dot(dipole1, dipole2); |
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|
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double halfBin = (nAngleBins_ - 1) * 0.5; |
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RealType halfBin = (nAngleBins_ - 1) * 0.5; |
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int angleBin1 = halfBin * (cosAngle1 + 1.0); |
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int angleBin2 = halfBin * (cosAngle1 + 1.0); |
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int angleBin2 = halfBin * (cosAngle2 + 1.0); |
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|
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++histogram_[angleBin1][angleBin1]; |
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++histogram_[angleBin1][angleBin2]; |
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++npairs_; |
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} |
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} |
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|
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void GofRAngle::writeRdf() { |
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> |
void GofAngle2::writeRdf() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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if (rdfStream.is_open()) { |
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rdfStream << "#radial distribution function\n"; |
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rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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rdfStream << "#r\tcorrValue\n"; |
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for (int i = 0; i < avgGofr_.size(); ++i) { |
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double cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; |
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rdfStream << "#radial distribution function\n"; |
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rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; |
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for (int i = 0; i < avgGofr_.size(); ++i) { |
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RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; |
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|
|
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< |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
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double cosAngle2 = -1.0 + (i + 0.5)*deltaCosAngle_; |
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rdfStream << cosAngle1 << "\t" << cosAngle2 << "\t" << avgGofr_[i][j]/nProcessed_ << "\n"; |
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} |
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< |
} |
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> |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
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RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; |
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> |
rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t"; |
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} |
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> |
|
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rdfStream << "\n"; |
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} |
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|
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} else { |
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|
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< |
|
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> |
sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str()); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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} |
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|
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rdfStream.close(); |
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< |
} |
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> |
} |
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|
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} |
