| 35 |
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* |
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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). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [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 <fstream> |
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#include "applications/staticProps/GofRAngle.hpp" |
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+ |
#include "primitives/Atom.hpp" |
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+ |
#include "types/MultipoleAdapter.hpp" |
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#include "utils/simError.h" |
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namespace OpenMD { |
| 65 |
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| 66 |
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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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|
| 86 |
< |
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; |
| 92 |
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|
| 93 |
< |
for (int j = 0; j < histogram_[i].size(); ++j){ |
| 93 |
> |
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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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_); |
| 113 |
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if (distance <= len_) { |
| 115 |
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RealType cosAngle = evaluateAngle(sd1, sd2); |
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RealType halfBin = (nAngleBins_ - 1) * 0.5; |
| 118 |
< |
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"; |
| 131 |
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rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 132 |
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rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; |
| 133 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 134 |
< |
RealType r = deltaR_ * (i + 0.5); |
| 133 |
> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
| 134 |
> |
// RealType r = deltaR_ * (i + 0.5); |
| 135 |
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|
| 136 |
< |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
| 137 |
< |
RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 136 |
> |
for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { |
| 137 |
> |
// RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 138 |
|
rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; |
| 139 |
|
} |
| 140 |
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|
| 159 |
|
currentSnapshot_->wrapVector(r12); |
| 160 |
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|
| 161 |
|
r12.normalize(); |
| 162 |
< |
Vector3d dipole = sd1->getElectroFrame().getColumn(2); |
| 163 |
< |
dipole.normalize(); |
| 164 |
< |
return dot(r12, dipole); |
| 162 |
> |
|
| 163 |
> |
Vector3d vec; |
| 164 |
> |
|
| 165 |
> |
if (sd1->isAtom()) { |
| 166 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
| 167 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
| 168 |
> |
|
| 169 |
> |
if (ma1.isDipole() ) |
| 170 |
> |
vec = sd1->getDipole(); |
| 171 |
> |
else |
| 172 |
> |
vec = sd1->getA().transpose() * V3Z; |
| 173 |
> |
} else { |
| 174 |
> |
vec = sd1->getA().transpose() * V3Z; |
| 175 |
> |
} |
| 176 |
> |
|
| 177 |
> |
vec.normalize(); |
| 178 |
> |
|
| 179 |
> |
return dot(r12, vec); |
| 180 |
|
} |
| 181 |
|
|
| 182 |
|
RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
| 183 |
< |
Vector3d v1 = sd1->getElectroFrame().getColumn(2); |
| 184 |
< |
Vector3d v2 = sd2->getElectroFrame().getColumn(2); |
| 183 |
> |
Vector3d v1, v2; |
| 184 |
> |
|
| 185 |
> |
if (sd1->isAtom()){ |
| 186 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
| 187 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
| 188 |
> |
if (ma1.isDipole() ) |
| 189 |
> |
v1 = sd1->getDipole(); |
| 190 |
> |
else |
| 191 |
> |
v1 = sd1->getA().transpose() * V3Z; |
| 192 |
> |
} else { |
| 193 |
> |
v1 = sd1->getA().transpose() * V3Z; |
| 194 |
> |
} |
| 195 |
> |
|
| 196 |
> |
if (sd2->isAtom()) { |
| 197 |
> |
AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType(); |
| 198 |
> |
MultipoleAdapter ma2 = MultipoleAdapter(atype2); |
| 199 |
> |
|
| 200 |
> |
if (ma2.isDipole() ) |
| 201 |
> |
v2 = sd2->getDipole(); |
| 202 |
> |
else |
| 203 |
> |
v2 = sd2->getA().transpose() * V3Z; |
| 204 |
> |
} else { |
| 205 |
> |
v2 = sd2->getA().transpose() * V3Z; |
| 206 |
> |
} |
| 207 |
> |
|
| 208 |
|
v1.normalize(); |
| 209 |
|
v2.normalize(); |
| 210 |
|
return dot(v1, v2); |
