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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 |
| 12 |
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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 |
| 15 |
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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 |
| 9 |
> |
* 1. 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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> |
* 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 |
| 14 |
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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 |
| 30 |
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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 |
| 33 |
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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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include <algorithm> |
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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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> |
namespace OpenMD { |
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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, RealType 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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> |
deltaR_ = len_ /(double) nRBins_; |
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> |
deltaCosAngle_ = 2.0 / (double)nAngleBins_; |
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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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|
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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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> |
for (unsigned 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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> |
void GofRAngle::initializeHistogram() { |
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npairs_ = 0; |
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< |
for (int i = 0; i < histogram_.size(); ++i) |
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> |
for (unsigned 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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– |
|
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void GofRAngle::processHistogram() { |
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– |
|
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int nPairs = getNPairs(); |
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RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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RealType pairDensity = nPairs /volume; |
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RealType 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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> |
for(unsigned int i = 0 ; i < histogram_.size(); ++i){ |
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|
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RealType rLower = i * deltaR_; |
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RealType rUpper = rLower + deltaR_; |
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RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
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RealType nIdeal = volSlice * pairConstant; |
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|
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< |
for (int j = 0; j < histogram_[i].size(); ++j){ |
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> |
for (unsigned 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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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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RealType distance = r12.length(); |
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< |
int whichRBin = distance / deltaR_; |
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> |
int whichRBin = int(distance / deltaR_); |
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|
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if (distance <= len_) { |
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+ |
|
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RealType cosAngle = evaluateAngle(sd1, sd2); |
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RealType halfBin = (nAngleBins_ - 1) * 0.5; |
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< |
int whichThetaBin = halfBin * (cosAngle + 1.0); |
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> |
int whichThetaBin = int(halfBin * (cosAngle + 1.0)); |
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++histogram_[whichRBin][whichThetaBin]; |
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|
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++npairs_; |
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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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> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
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RealType 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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> |
for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { |
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RealType 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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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos2 - pos1; |
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< |
|
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> |
|
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if (usePeriodicBoundaryConditions_) |
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currentSnapshot_->wrapVector(r12); |
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|
