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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 |
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* program. An acceptable form of acknowledgement is citation of |
| 12 |
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* the article in which the program was described (Matthew |
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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 |
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* Parallel Simulation Engine for Molecular Dynamics," |
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< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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< |
* |
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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 |
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|
* notice, this list of conditions and the following disclaimer. |
| 11 |
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* |
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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 |
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* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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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 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
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+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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+ |
* [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). |
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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 "applications/staticProps/GofXyz.hpp" |
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#include "utils/simError.h" |
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#include "primitives/Molecule.hpp" |
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namespace oopse { |
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> |
#include "types/MultipoleAdapter.hpp" |
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|
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GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, double len, int nrbins) |
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namespace OpenMD { |
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> |
|
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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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: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) { |
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setOutputName(getPrefix(filename) + ".gxyz"); |
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|
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} |
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|
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|
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void GofXyz::initalizeHistogram() { |
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> |
void GofXyz::initializeHistogram() { |
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//calculate the center of mass of the molecule of selected stuntdouble in selection1 |
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|
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if (!evaluator3_.isDynamic()) { |
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StuntDouble* sd3; |
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|
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for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); |
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sd1 != NULL, sd3 != NULL; |
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> |
sd1 != NULL || sd3 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) { |
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|
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< |
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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info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
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Vector3d zaxis = sd1->getElectroFrame().getColumn(2); |
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> |
if (usePeriodicBoundaryConditions_) |
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> |
info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
| 114 |
> |
|
| 115 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
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> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
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> |
|
| 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); |
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|
| 143 |
|
Vector3d pos1 = sd1->getPos(); |
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Vector3d pos2 = sd2->getPos(); |
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Vector3d r12 = pos2 - pos1; |
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< |
currentSnapshot_->wrapVector(r12); |
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> |
if (usePeriodicBoundaryConditions_) |
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> |
currentSnapshot_->wrapVector(r12); |
| 148 |
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|
| 149 |
|
std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex()); |
| 150 |
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assert(i != rotMats_.end()); |
| 151 |
|
|
| 152 |
|
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_; |
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< |
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 |
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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) { |
| 164 |
< |
rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] )); |
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> |
for (unsigned int i = 0; i < histogram_.size(); ++i) { |
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> |
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 |
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} |
| 179 |
|
} |
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} |
