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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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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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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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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|
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#include <algorithm> |
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#include <fstream> |
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#include "applications/staticProps/GofRAngle.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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|
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GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, double len, int nrbins, int nangleBins) |
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: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){ |
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|
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deltaR_ = len_ /nRBins_; |
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deltaCosAngle_ = 2.0 / nAngleBins_; |
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|
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histogram_.resize(nRBins_); |
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avgGofr_.resize(nRBins_); |
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for (int i = 0 ; i < nRBins_; ++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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void GofRAngle::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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} |
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} |
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|
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void GofRAngle::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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|
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|
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void GofRAngle::processHistogram() { |
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|
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int nPairs = getNPairs(); |
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double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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double pairDensity = nPairs /volume; |
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double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
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|
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for(int i = 0 ; i < histogram_.size(); ++i){ |
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|
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double rLower = i * deltaR_; |
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double rUpper = rLower + deltaR_; |
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double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
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double nIdeal = volSlice * pairConstant; |
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|
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for (int j = 0; j < histogram_[i].size(); ++j){ |
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avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
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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 GofRAngle::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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} |
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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 = pos2 - pos1; |
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currentSnapshot_->wrapVector(r12); |
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|
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double distance = r12.length(); |
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int whichRBin = distance / deltaR_; |
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|
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if (distance <= len_) { |
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double cosAngle = evaluateAngle(sd1, sd2); |
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double halfBin = (nAngleBins_ - 1) * 0.5; |
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int whichThetaBin = halfBin * (cosAngle + 1.0); |
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++histogram_[whichRBin][whichThetaBin]; |
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|
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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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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 << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\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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double r = deltaR_ * (i + 0.5); |
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|
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for(int j = 0; j < avgGofr_[i].size(); ++j) { |
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double cosAngle = -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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sprintf(painCave.errMsg, "GofRAngle: 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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double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos2 - pos1; |
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currentSnapshot_->wrapVector(r12); |
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r12.normalize(); |
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Vector3d dipole = sd1->getElectroFrame().getColumn(2); |
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dipole.normalize(); |
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return dot(r12, dipole); |
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} |
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|
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double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
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Vector3d v1 = sd1->getElectroFrame().getColumn(2); |
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Vector3d v2 = sd2->getElectroFrame().getColumn(2); |
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v1.normalize(); |
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v2.normalize(); |
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return dot(v1, v2); |
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} |
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|
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|
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} |
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|
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|
