| 35 |
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* |
| 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> |
| 44 |
|
#include <fstream> |
| 45 |
|
#include "applications/staticProps/GofAngle2.hpp" |
| 46 |
+ |
#include "primitives/Atom.hpp" |
| 47 |
+ |
#include "types/MultipoleAdapter.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
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|
| 50 |
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namespace OpenMD { |
| 69 |
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|
| 70 |
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void GofAngle2::preProcess() { |
| 71 |
|
|
| 72 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 72 |
> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
| 73 |
|
std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
| 74 |
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} |
| 75 |
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} |
| 76 |
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|
| 77 |
< |
void GofAngle2::initalizeHistogram() { |
| 77 |
> |
void GofAngle2::initializeHistogram() { |
| 78 |
|
npairs_ = 0; |
| 79 |
< |
for (int i = 0; i < histogram_.size(); ++i) |
| 79 |
> |
for (unsigned int i = 0; i < histogram_.size(); ++i) |
| 80 |
|
std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
| 81 |
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} |
| 82 |
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|
| 98 |
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Vector3d r12 = pos1 - pos2; |
| 99 |
|
if (usePeriodicBoundaryConditions_) |
| 100 |
|
currentSnapshot_->wrapVector(r12); |
| 101 |
< |
Vector3d dipole1 = sd1->getElectroFrame().getColumn(2); |
| 102 |
< |
Vector3d dipole2 = sd2->getElectroFrame().getColumn(2); |
| 101 |
> |
|
| 102 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
| 103 |
> |
AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType(); |
| 104 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
| 105 |
> |
MultipoleAdapter ma2 = MultipoleAdapter(atype2); |
| 106 |
> |
|
| 107 |
> |
Vector3d dipole1, dipole2; |
| 108 |
> |
if (ma1.isDipole()) |
| 109 |
> |
dipole1 = sd1->getDipole(); |
| 110 |
> |
else |
| 111 |
> |
dipole1 = sd1->getA().transpose() * V3Z; |
| 112 |
> |
|
| 113 |
> |
if (ma2.isDipole()) |
| 114 |
> |
dipole2 = sd2->getDipole(); |
| 115 |
> |
else |
| 116 |
> |
dipole2 = sd2->getA().transpose() * V3Z; |
| 117 |
|
|
| 118 |
|
r12.normalize(); |
| 119 |
|
dipole1.normalize(); |
| 124 |
|
RealType cosAngle2 = dot(dipole1, dipole2); |
| 125 |
|
|
| 126 |
|
RealType halfBin = (nAngleBins_ - 1) * 0.5; |
| 127 |
< |
int angleBin1 = halfBin * (cosAngle1 + 1.0); |
| 128 |
< |
int angleBin2 = halfBin * (cosAngle2 + 1.0); |
| 127 |
> |
int angleBin1 = int(halfBin * (cosAngle1 + 1.0)); |
| 128 |
> |
int angleBin2 = int(halfBin * (cosAngle2 + 1.0)); |
| 129 |
|
|
| 130 |
|
++histogram_[angleBin1][angleBin2]; |
| 131 |
|
++npairs_; |
| 138 |
|
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 139 |
|
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 140 |
|
rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; |
| 141 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 142 |
< |
RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; |
| 143 |
< |
|
| 144 |
< |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
| 145 |
< |
RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 141 |
> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
| 142 |
> |
// RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; |
| 143 |
> |
|
| 144 |
> |
for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { |
| 145 |
> |
// RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 146 |
|
rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t"; |
| 147 |
|
} |
| 148 |
|
|
