| 35 |
|
* |
| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
< |
* [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). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <algorithm> |
| 45 |
|
#include "applications/staticProps/GofXyz.hpp" |
| 46 |
|
#include "utils/simError.h" |
| 47 |
|
#include "primitives/Molecule.hpp" |
| 48 |
+ |
#include "types/MultipoleAdapter.hpp" |
| 49 |
+ |
|
| 50 |
|
namespace OpenMD { |
| 51 |
|
|
| 52 |
|
GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins) |
| 81 |
|
} |
| 82 |
|
|
| 83 |
|
|
| 84 |
< |
void GofXyz::initalizeHistogram() { |
| 84 |
> |
void GofXyz::initializeHistogram() { |
| 85 |
|
//calculate the center of mass of the molecule of selected stuntdouble in selection1 |
| 86 |
|
|
| 87 |
|
if (!evaluator3_.isDynamic()) { |
| 103 |
|
StuntDouble* sd3; |
| 104 |
|
|
| 105 |
|
for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); |
| 106 |
< |
sd1 != NULL, sd3 != NULL; |
| 106 |
> |
sd1 != NULL || sd3 != NULL; |
| 107 |
|
sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) { |
| 108 |
|
|
| 109 |
< |
Vector3d r3 =sd3->getPos(); |
| 109 |
> |
Vector3d r3 = sd3->getPos(); |
| 110 |
|
Vector3d r1 = sd1->getPos(); |
| 111 |
|
Vector3d v1 = r3 - r1; |
| 112 |
|
if (usePeriodicBoundaryConditions_) |
| 113 |
|
info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
| 114 |
< |
Vector3d zaxis = sd1->getElectroFrame().getColumn(2); |
| 114 |
> |
|
| 115 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
| 116 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
| 117 |
> |
|
| 118 |
> |
Vector3d zaxis; |
| 119 |
> |
if (ma1.isDipole()) |
| 120 |
> |
zaxis = sd1->getDipole(); |
| 121 |
> |
else |
| 122 |
> |
zaxis = sd1->getA().transpose() * V3Z; |
| 123 |
> |
|
| 124 |
|
Vector3d xaxis = cross(v1, zaxis); |
| 125 |
|
Vector3d yaxis = cross(zaxis, xaxis); |
| 126 |
|
|
| 151 |
|
|
| 152 |
|
Vector3d newR12 = i->second * r12; |
| 153 |
|
// x, y and z's possible values range -halfLen_ to halfLen_ |
| 154 |
< |
int xbin = (newR12.x()+ halfLen_) / deltaR_; |
| 155 |
< |
int ybin = (newR12.y() + halfLen_) / deltaR_; |
| 156 |
< |
int zbin = (newR12.z() + halfLen_) / deltaR_; |
| 154 |
> |
int xbin = int( (newR12.x() + halfLen_) / deltaR_); |
| 155 |
> |
int ybin = int( (newR12.y() + halfLen_) / deltaR_); |
| 156 |
> |
int zbin = int( (newR12.z() + halfLen_) / deltaR_); |
| 157 |
|
|
| 158 |
|
if (xbin < nRBins_ && xbin >=0 && |
| 159 |
|
ybin < nRBins_ && ybin >= 0 && |
| 170 |
|
//rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 171 |
|
//rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 172 |
|
//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) { |
| 166 |
< |
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 |
|
} |
