| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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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). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
| 42 |
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|
| 43 |
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#include <algorithm> |
| 63 |
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|
| 64 |
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|
| 65 |
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void GofRAngle::preProcess() { |
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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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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){ |
| 91 |
> |
for (unsigned int j = 0; j < histogram_[i].size(); ++j){ |
| 92 |
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avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
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} |
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} |
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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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|
| 112 |
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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"; |
| 130 |
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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 r = deltaR_ * (i + 0.5); |
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> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
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> |
// RealType r = deltaR_ * (i + 0.5); |
| 133 |
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|
| 134 |
< |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
| 135 |
< |
RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 134 |
> |
for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { |
| 135 |
> |
// RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 136 |
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rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; |
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} |
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|
