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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)) |
| 17 |
< |
* |
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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 |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 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 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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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 |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
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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). |
| 39 |
+ |
* [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/GofR.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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GofR::GofR(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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GofR::GofR(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins) |
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: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){ |
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|
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deltaR_ = len_ /nRBins_; |
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> |
deltaR_ = len_ /nRBins_; |
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|
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histogram_.resize(nRBins_); |
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avgGofr_.resize(nRBins_); |
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> |
histogram_.resize(nRBins_); |
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> |
avgGofr_.resize(nRBins_); |
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|
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setOutputName(getPrefix(filename) + ".gr"); |
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} |
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> |
setOutputName(getPrefix(filename) + ".gofr"); |
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} |
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|
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|
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void GofR::preProcess() { |
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> |
void GofR::preProcess() { |
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std::fill(avgGofr_.begin(), avgGofr_.end(), 0.0); |
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} |
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> |
} |
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|
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void GofR::initalizeHistogram() { |
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npairs_ = 0; |
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> |
void GofR::initializeHistogram() { |
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std::fill(histogram_.begin(), histogram_.end(), 0); |
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} |
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> |
} |
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|
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|
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void GofR::processHistogram() { |
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> |
void GofR::processHistogram() { |
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|
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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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> |
int nPairs = getNPairs(); |
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> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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> |
RealType pairDensity = nPairs /volume * 2.0; |
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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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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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> |
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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avgGofr_[i] += histogram_[i] / nIdeal; |
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> |
avgGofr_[i] += histogram_[i] / 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 GofR::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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> |
void GofR::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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> |
Vector3d r12 = pos2 - pos1; |
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> |
if (usePeriodicBoundaryConditions_) |
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> |
currentSnapshot_->wrapVector(r12); |
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|
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double distance = r12.length(); |
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> |
RealType distance = r12.length(); |
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|
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< |
int whichBin = distance / deltaR_; |
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< |
++histogram_[whichBin]; |
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++npairs_; |
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< |
} |
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> |
if (distance < len_) { |
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> |
int whichBin = distance / deltaR_; |
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> |
histogram_[whichBin] += 2; |
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> |
} |
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} |
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|
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|
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< |
void GofR::writeRdf() { |
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> |
void GofR::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 r = deltaR_ * (i + 0.5); |
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rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n"; |
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} |
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|
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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 (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
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> |
RealType r = deltaR_ * (i + 0.5); |
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> |
rdfStream << r << "\t" << avgGofr_[i]/nProcessed_ << "\n"; |
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> |
} |
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} else { |
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|
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< |
|
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> |
sprintf(painCave.errMsg, "GofR: unable to open %s\n", outputFilename_.c_str()); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
| 127 |
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} |
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|
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rdfStream.close(); |
| 130 |
< |
} |
| 130 |
> |
} |
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|
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} |
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|
