| 45 |
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#include "applications/staticProps/GofXyz.hpp" |
| 46 |
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#include "utils/simError.h" |
| 47 |
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#include "primitives/Molecule.hpp" |
| 48 |
+ |
#include "types/MultipoleAdapter.hpp" |
| 49 |
+ |
|
| 50 |
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namespace OpenMD { |
| 51 |
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|
| 52 |
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GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins) |
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sd1 != NULL || sd3 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) { |
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|
| 109 |
< |
Vector3d r3 =sd3->getPos(); |
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> |
Vector3d r3 = sd3->getPos(); |
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Vector3d r1 = sd1->getPos(); |
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Vector3d v1 = r3 - r1; |
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if (usePeriodicBoundaryConditions_) |
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info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
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< |
Vector3d zaxis = sd1->getElectroFrame().getColumn(2); |
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> |
|
| 115 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
| 116 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
| 117 |
> |
|
| 118 |
> |
Vector3d zaxis; |
| 119 |
> |
if (ma1.isDipole()) |
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> |
zaxis = sd1->getDipole(); |
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> |
else |
| 122 |
> |
zaxis = sd1->getA().transpose() * V3Z; |
| 123 |
> |
|
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Vector3d xaxis = cross(v1, zaxis); |
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Vector3d yaxis = cross(zaxis, xaxis); |
| 126 |
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|
| 151 |
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|
| 152 |
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Vector3d newR12 = i->second * r12; |
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// x, y and z's possible values range -halfLen_ to halfLen_ |
| 154 |
< |
int xbin = (newR12.x()+ halfLen_) / deltaR_; |
| 154 |
> |
int xbin = (newR12.x() + halfLen_) / deltaR_; |
| 155 |
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int ybin = (newR12.y() + halfLen_) / deltaR_; |
| 156 |
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int zbin = (newR12.z() + halfLen_) / deltaR_; |
| 157 |
|
|
| 170 |
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//rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 171 |
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//rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 172 |
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//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 173 |
< |
for (int i = 0; i < histogram_.size(); ++i) { |
| 174 |
< |
|
| 175 |
< |
for(int j = 0; j < histogram_[i].size(); ++j) { |
| 176 |
< |
|
| 177 |
< |
for(int k = 0;k < histogram_[i][j].size(); ++k) { |
| 167 |
< |
rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] )); |
| 173 |
> |
for (unsigned int i = 0; i < histogram_.size(); ++i) { |
| 174 |
> |
for(unsigned int j = 0; j < histogram_[i].size(); ++j) { |
| 175 |
> |
for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) { |
| 176 |
> |
rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), |
| 177 |
> |
sizeof(histogram_[i][j][k] )); |
| 178 |
|
} |
| 179 |
|
} |
| 180 |
|
} |
