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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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> |
* [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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#include <algorithm> |
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namespace OpenMD { |
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|
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GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1, |
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< |
const std::string& sele2, RealType len, int nrbins, int nZBins) |
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< |
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nZBins_(nZBins){ |
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> |
const std::string& sele2, RealType len, RealType zlen, int nrbins, int nZBins) |
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> |
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), zLen_(zlen), nRBins_(nrbins), nZBins_(nZBins){ |
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|
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< |
setOutputName(getPrefix(filename) + ".gofrz"); |
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> |
setOutputName(getPrefix(filename) + ".gofrz"); |
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|
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< |
deltaR_ = len_ / (double) nRBins_; |
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< |
deltaZ_ = 86.52361692 / (double)nZBins_; // for solvated_NVT.md4 |
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> |
deltaR_ = len_ / (double) nRBins_; |
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> |
deltaZ_ = zLen_ / (double)nZBins_; // for solvated_NVT.md4 |
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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(nRBins_); |
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< |
avgGofr_[i].resize(nRBins_); |
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< |
for (int j = 0 ; j < nZBins_; ++j) { |
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< |
histogram_[i][j].resize(nZBins_); |
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< |
avgGofr_[i][j].resize(nZBins_); |
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< |
} |
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< |
} |
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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(nZBins_); |
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> |
avgGofr_[i].resize(nZBins_); |
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> |
} |
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} |
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+ |
|
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void GofRZ::preProcess() { |
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< |
for (int i = 0; i < avgGofr_[i].size(); ++i) { |
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< |
avgGofr_[i].resize(nRBins_); |
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< |
for (int j = 0; j < avgGofr_[i][j].size(); ++j) { |
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< |
std::fill(avgGofr_[i][j].begin(), avgGofr_[i][j].end(), 0); |
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< |
} |
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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 GofRZ::initalizeHistogram() { |
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npairs_ = 0; |
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< |
for (int i = 0; i < histogram_[i].size(); ++i){ |
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< |
histogram_[i].resize(nRBins_); |
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< |
for (int j = 0; j < histogram_[i][j].size(); ++j){ |
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< |
std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0); |
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< |
} |
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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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RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
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RealType pairDensity = nPairs / volume * 2.0; |
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|
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< |
for(int i = 0 ; i < histogram_[i].size(); ++i){ |
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> |
for(unsigned int i = 0 ; i < histogram_.size(); ++i){ |
| 86 |
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|
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RealType rLower = i * deltaR_; |
| 88 |
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RealType rUpper = rLower + deltaR_; |
| 89 |
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RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower )); |
| 90 |
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RealType nIdeal = volSlice * pairDensity; |
| 91 |
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|
| 92 |
< |
for (int j = 0; j < histogram_[i][j].size(); ++j){ |
| 93 |
< |
avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
| 92 |
> |
for (unsigned int j = 0; j < histogram_[i].size(); ++j){ |
| 93 |
> |
avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
| 94 |
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} |
| 95 |
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} |
| 96 |
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|
| 115 |
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|
| 116 |
|
RealType Z = fabs(r12.z()); |
| 117 |
|
|
| 118 |
< |
if (Z <= 86.52361692) { |
| 118 |
> |
if (Z <= zLen_) { |
| 119 |
|
int whichZBin = Z / deltaZ_; |
| 120 |
< |
|
| 120 |
> |
|
| 121 |
|
++histogram_[whichRBin][whichZBin]; |
| 122 |
|
++npairs_; |
| 123 |
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} |
| 132 |
|
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 133 |
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rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 134 |
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rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n"; |
| 135 |
< |
for (int i = 0; i < avgGofr_[i].size(); ++i) { |
| 136 |
< |
RealType r = deltaR_ * (i + 0.5); |
| 135 |
> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
| 136 |
> |
RealType r = deltaR_ * (i + 0.5); |
| 137 |
|
|
| 138 |
< |
for(int j = 0; j < avgGofr_[i][j].size(); ++j) { |
| 138 |
> |
for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { |
| 139 |
|
RealType z = deltaZ_ * (j + 0.5); |
| 140 |
< |
rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; |
| 141 |
< |
} |
| 140 |
> |
rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; |
| 141 |
> |
} |
| 142 |
|
|
| 143 |
< |
rdfStream << "\n"; |
| 143 |
> |
rdfStream << "\n"; |
| 144 |
|
} |
| 145 |
|
|
| 146 |
|
} else { |
