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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
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* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
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< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
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* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
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+ |
* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
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* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
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* [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/GofAngle2.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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|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
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GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, |
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const std::string& sele2, int nangleBins) |
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|
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void GofAngle2::preProcess() { |
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|
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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 GofAngle2::initalizeHistogram() { |
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> |
void GofAngle2::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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Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos1 - pos2; |
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currentSnapshot_->wrapVector(r12); |
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Vector3d dipole1 = sd1->getElectroFrame().getColumn(2); |
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< |
Vector3d dipole2 = sd2->getElectroFrame().getColumn(2); |
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> |
if (usePeriodicBoundaryConditions_) |
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> |
currentSnapshot_->wrapVector(r12); |
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> |
|
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> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
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> |
AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType(); |
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> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
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> |
MultipoleAdapter ma2 = MultipoleAdapter(atype2); |
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> |
|
| 107 |
> |
Vector3d dipole1, dipole2; |
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> |
if (ma1.isDipole()) |
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> |
dipole1 = sd1->getDipole(); |
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> |
else |
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> |
dipole1 = sd1->getA().transpose() * V3Z; |
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> |
|
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> |
if (ma2.isDipole()) |
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> |
dipole2 = sd2->getDipole(); |
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> |
else |
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> |
dipole2 = sd2->getA().transpose() * V3Z; |
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|
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|
r12.normalize(); |
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dipole1.normalize(); |
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dipole2.normalize(); |
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|
| 122 |
|
|
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< |
double cosAngle1 = dot(r12, dipole1); |
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< |
double cosAngle2 = dot(dipole1, dipole2); |
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> |
RealType cosAngle1 = dot(r12, dipole1); |
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> |
RealType cosAngle2 = dot(dipole1, dipole2); |
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|
|
| 126 |
< |
double halfBin = (nAngleBins_ - 1) * 0.5; |
| 127 |
< |
int angleBin1 = halfBin * (cosAngle1 + 1.0); |
| 128 |
< |
int angleBin2 = halfBin * (cosAngle1 + 1.0); |
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> |
RealType halfBin = (nAngleBins_ - 1) * 0.5; |
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> |
int angleBin1 = int(halfBin * (cosAngle1 + 1.0)); |
| 128 |
> |
int angleBin2 = int(halfBin * (cosAngle2 + 1.0)); |
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|
|
| 130 |
< |
++histogram_[angleBin1][angleBin1]; |
| 130 |
> |
++histogram_[angleBin1][angleBin2]; |
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|
++npairs_; |
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|
} |
| 133 |
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|
| 138 |
|
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 140 |
|
rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; |
| 141 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 142 |
< |
double cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; |
| 143 |
< |
|
| 144 |
< |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
| 145 |
< |
double 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) { |
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> |
// RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 146 |
|
rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t"; |
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|
} |
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|
