| 53 |
|
setOutputName(getPrefix(filename) + ".gofrz"); |
| 54 |
|
|
| 55 |
|
deltaR_ = len_ / (double) nRBins_; |
| 56 |
< |
deltaZ_ = len_ / (double)nZBins_; |
| 56 |
> |
deltaZ_ = 86.52361692 / (double)nZBins_; // for solvated_NVT.md4 |
| 57 |
> |
|
| 58 |
|
histogram_.resize(nRBins_); |
| 59 |
|
avgGofr_.resize(nRBins_); |
| 60 |
|
for (int i = 0 ; i < nRBins_; ++i) { |
| 61 |
< |
histogram_[i].resize(nZBins_); |
| 62 |
< |
avgGofr_[i].resize(nZBins_); |
| 61 |
> |
histogram_[i].resize(nRBins_); |
| 62 |
> |
avgGofr_[i].resize(nRBins_); |
| 63 |
> |
for (int j = 0 ; j < nZBins_; ++j) { |
| 64 |
> |
histogram_[i][j].resize(nZBins_); |
| 65 |
> |
avgGofr_[i][j].resize(nZBins_); |
| 66 |
|
} |
| 67 |
|
} |
| 68 |
< |
|
| 69 |
< |
|
| 68 |
> |
|
| 69 |
> |
} |
| 70 |
|
void GofRZ::preProcess() { |
| 71 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 72 |
< |
std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
| 71 |
> |
for (int i = 0; i < avgGofr_[i].size(); ++i) { |
| 72 |
> |
avgGofr_[i].resize(nRBins_); |
| 73 |
> |
for (int j = 0; j < avgGofr_[i][j].size(); ++j) { |
| 74 |
> |
std::fill(avgGofr_[i][j].begin(), avgGofr_[i][j].end(), 0); |
| 75 |
> |
} |
| 76 |
|
} |
| 77 |
|
} |
| 78 |
|
|
| 79 |
|
void GofRZ::initalizeHistogram() { |
| 80 |
|
npairs_ = 0; |
| 81 |
< |
for (int i = 0; i < histogram_.size(); ++i){ |
| 82 |
< |
std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
| 81 |
> |
for (int i = 0; i < histogram_[i].size(); ++i){ |
| 82 |
> |
histogram_[i].resize(nRBins_); |
| 83 |
> |
for (int j = 0; j < histogram_[i][j].size(); ++j){ |
| 84 |
> |
std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0); |
| 85 |
> |
} |
| 86 |
|
} |
| 87 |
|
} |
| 88 |
|
|
| 89 |
|
void GofRZ::processHistogram() { |
| 90 |
|
int nPairs = getNPairs(); |
| 91 |
|
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 92 |
< |
RealType pairDensity = nPairs / volume; |
| 92 |
> |
RealType pairDensity = nPairs / volume * 2.0; |
| 93 |
|
|
| 94 |
< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
| 94 |
> |
for(int i = 0 ; i < histogram_[i].size(); ++i){ |
| 95 |
|
|
| 96 |
|
RealType rLower = i * deltaR_; |
| 97 |
|
RealType rUpper = rLower + deltaR_; |
| 98 |
|
RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower )); |
| 99 |
|
RealType nIdeal = volSlice * pairDensity; |
| 100 |
|
|
| 101 |
< |
for (int j = 0; j < histogram_[i].size(); ++j){ |
| 101 |
> |
for (int j = 0; j < histogram_[i][j].size(); ++j){ |
| 102 |
|
avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
| 103 |
|
} |
| 104 |
|
} |
| 122 |
|
|
| 123 |
|
if (distance <= len_) { |
| 124 |
|
|
| 125 |
< |
RealType Z = abs(r12.z()); |
| 125 |
> |
RealType Z = fabs(r12.z()); |
| 126 |
|
|
| 127 |
< |
if (Z <= len_) { |
| 127 |
> |
if (Z <= 86.52361692) { |
| 128 |
|
int whichZBin = Z / deltaZ_; |
| 129 |
+ |
|
| 130 |
|
++histogram_[whichRBin][whichZBin]; |
| 131 |
|
++npairs_; |
| 132 |
|
} |
| 140 |
|
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 141 |
|
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 142 |
|
rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 143 |
< |
rdfStream << "#nZBins =" << nZBins_ << "deltaZ = " << deltaZ_ << "\n"; |
| 144 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 143 |
> |
rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n"; |
| 144 |
> |
for (int i = 0; i < avgGofr_[i].size(); ++i) { |
| 145 |
|
RealType r = deltaR_ * (i + 0.5); |
| 146 |
|
|
| 147 |
< |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
| 147 |
> |
for(int j = 0; j < avgGofr_[i][j].size(); ++j) { |
| 148 |
|
RealType z = deltaZ_ * (j + 0.5); |
| 149 |
|
rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; |
| 150 |
|
} |
