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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 |
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* 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 |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
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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 |
| 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. |
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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 |
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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). |
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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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> |
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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: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) { |
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|
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setOutputName(getPrefix(filename) + ".gto"); |
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> |
setOutputName(getPrefix(filename) + ".gto"); |
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|
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deltaCosAngle_ = 2.0 / nAngleBins_; |
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> |
deltaCosAngle_ = 2.0 / nAngleBins_; |
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|
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< |
histogram_.resize(nAngleBins_); |
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avgGofr_.resize(nAngleBins_); |
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for (int i = 0 ; i < nAngleBins_; ++i) { |
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> |
histogram_.resize(nAngleBins_); |
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> |
avgGofr_.resize(nAngleBins_); |
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> |
for (int i = 0 ; i < nAngleBins_; ++i) { |
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histogram_[i].resize(nAngleBins_); |
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avgGofr_[i].resize(nAngleBins_); |
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} |
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> |
} |
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|
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< |
} |
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> |
} |
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|
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|
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< |
void GofAngle2::preProcess() { |
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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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std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
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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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|
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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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std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
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< |
} |
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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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|
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< |
void GofAngle2::processHistogram() { |
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> |
void GofAngle2::processHistogram() { |
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|
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//std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>) |
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|
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< |
} |
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> |
} |
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|
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< |
void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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> |
void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
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|
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if (sd1 == sd2) { |
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< |
return; |
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> |
return; |
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} |
| 95 |
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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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> |
|
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> |
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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|
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|
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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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|
|
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< |
double halfBin = (nAngleBins_ - 1) * 0.5; |
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< |
int angleBin1 = halfBin * (cosAngle1 + 1.0); |
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< |
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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|
|
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< |
++histogram_[angleBin1][angleBin1]; |
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> |
++histogram_[angleBin1][angleBin2]; |
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++npairs_; |
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< |
} |
| 132 |
> |
} |
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|
|
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< |
void GofAngle2::writeRdf() { |
| 134 |
> |
void GofAngle2::writeRdf() { |
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std::ofstream rdfStream(outputFilename_.c_str()); |
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if (rdfStream.is_open()) { |
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< |
rdfStream << "#radial distribution function\n"; |
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< |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
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< |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
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< |
rdfStream << "#r\tcorrValue\n"; |
| 141 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
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< |
double cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; |
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> |
rdfStream << "#radial distribution function\n"; |
| 138 |
> |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 139 |
> |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 140 |
> |
rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; |
| 141 |
> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
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> |
// RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_; |
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> |
|
| 144 |
> |
for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { |
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> |
// RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; |
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> |
rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t"; |
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> |
} |
| 148 |
|
|
| 149 |
< |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
| 150 |
< |
double cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 128 |
< |
rdfStream << cosAngle1 << "\t" << cosAngle2 << "\t" << avgGofr_[i][j]/nProcessed_ << "\n"; |
| 129 |
< |
} |
| 130 |
< |
} |
| 149 |
> |
rdfStream << "\n"; |
| 150 |
> |
} |
| 151 |
|
|
| 152 |
|
} else { |
| 153 |
|
|
| 154 |
< |
|
| 154 |
> |
sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str()); |
| 155 |
> |
painCave.isFatal = 1; |
| 156 |
> |
simError(); |
| 157 |
|
} |
| 158 |
|
|
| 159 |
|
rdfStream.close(); |
| 160 |
< |
} |
| 160 |
> |
} |
| 161 |
|
|
| 162 |
|
} |
