| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 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 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* 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 |
< |
* |
| 18 |
< |
* 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 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* 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 |
+ |
* |
| 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 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <algorithm> |
| 44 |
|
#include <fstream> |
| 45 |
|
#include "applications/staticProps/GofRAngle.hpp" |
| 46 |
+ |
#include "primitives/Atom.hpp" |
| 47 |
+ |
#include "types/MultipoleAdapter.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
|
|
| 50 |
< |
namespace oopse { |
| 50 |
> |
namespace OpenMD { |
| 51 |
|
|
| 52 |
< |
GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
| 53 |
< |
: RadialDistrFunc(info, filename, sele1, sele2){ |
| 52 |
> |
GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, |
| 53 |
> |
const std::string& sele2, RealType len, int nrbins, int nangleBins) |
| 54 |
> |
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){ |
| 55 |
|
|
| 56 |
< |
} |
| 56 |
> |
deltaR_ = len_ /(double) nRBins_; |
| 57 |
> |
deltaCosAngle_ = 2.0 / (double)nAngleBins_; |
| 58 |
> |
histogram_.resize(nRBins_); |
| 59 |
> |
avgGofr_.resize(nRBins_); |
| 60 |
> |
for (int i = 0 ; i < nRBins_; ++i) { |
| 61 |
> |
histogram_[i].resize(nAngleBins_); |
| 62 |
> |
avgGofr_[i].resize(nAngleBins_); |
| 63 |
> |
} |
| 64 |
> |
} |
| 65 |
|
|
| 66 |
|
|
| 67 |
< |
void GofRAngle::preProcess() { |
| 68 |
< |
|
| 69 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 58 |
< |
std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
| 67 |
> |
void GofRAngle::preProcess() { |
| 68 |
> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
| 69 |
> |
std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0); |
| 70 |
|
} |
| 71 |
< |
} |
| 71 |
> |
} |
| 72 |
|
|
| 73 |
< |
void GofRAngle::initalizeHistogram() { |
| 73 |
> |
void GofRAngle::initializeHistogram() { |
| 74 |
|
npairs_ = 0; |
| 75 |
< |
for (int i = 0; i < histogram_.size(); ++i) |
| 76 |
< |
std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
| 77 |
< |
} |
| 75 |
> |
for (unsigned int i = 0; i < histogram_.size(); ++i){ |
| 76 |
> |
std::fill(histogram_[i].begin(), histogram_[i].end(), 0); |
| 77 |
> |
} |
| 78 |
> |
} |
| 79 |
|
|
| 80 |
< |
|
| 69 |
< |
void GofRAngle::processHistogram() { |
| 70 |
< |
|
| 80 |
> |
void GofRAngle::processHistogram() { |
| 81 |
|
int nPairs = getNPairs(); |
| 82 |
< |
double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 83 |
< |
double pairDensity = nPairs /volume; |
| 84 |
< |
double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
| 82 |
> |
RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume(); |
| 83 |
> |
RealType pairDensity = nPairs /volume; |
| 84 |
> |
RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0; |
| 85 |
|
|
| 86 |
< |
for(int i = 0 ; i < histogram_.size(); ++i){ |
| 86 |
> |
for(unsigned int i = 0 ; i < histogram_.size(); ++i){ |
| 87 |
|
|
| 88 |
< |
double rLower = i * deltaR_; |
| 89 |
< |
double rUpper = rLower + deltaR_; |
| 90 |
< |
double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 91 |
< |
double nIdeal = volSlice * pairConstant; |
| 88 |
> |
RealType rLower = i * deltaR_; |
| 89 |
> |
RealType rUpper = rLower + deltaR_; |
| 90 |
> |
RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower ); |
| 91 |
> |
RealType nIdeal = volSlice * pairConstant; |
| 92 |
|
|
| 93 |
< |
for (int j = 0; j < histogram_[i].size(); ++j){ |
| 94 |
< |
avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
| 95 |
< |
} |
| 93 |
> |
for (unsigned int j = 0; j < histogram_[i].size(); ++j){ |
| 94 |
> |
avgGofr_[i][j] += histogram_[i][j] / nIdeal; |
| 95 |
> |
} |
| 96 |
|
} |
| 97 |
|
|
| 98 |
< |
} |
| 98 |
> |
} |
| 99 |
|
|
| 100 |
< |
void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 100 |
> |
void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 101 |
|
|
| 102 |
|
if (sd1 == sd2) { |
| 103 |
< |
return; |
| 103 |
> |
return; |
| 104 |
|
} |
| 95 |
– |
|
| 105 |
|
Vector3d pos1 = sd1->getPos(); |
| 106 |
|
Vector3d pos2 = sd2->getPos(); |
| 107 |
< |
Vector3d r12 = pos1 - pos2; |
| 108 |
< |
currentSnapshot_->wrapVector(r12); |
| 107 |
> |
Vector3d r12 = pos2 - pos1; |
| 108 |
> |
if (usePeriodicBoundaryConditions_) |
| 109 |
> |
currentSnapshot_->wrapVector(r12); |
| 110 |
|
|
| 111 |
< |
double distance = r12.length(); |
| 112 |
< |
int whichRBin = distance / deltaR_; |
| 111 |
> |
RealType distance = r12.length(); |
| 112 |
> |
int whichRBin = int(distance / deltaR_); |
| 113 |
|
|
| 114 |
|
if (distance <= len_) { |
| 115 |
< |
double cosAngle = evaluateAngle(sd1, sd2); |
| 116 |
< |
double halfBin = (nAngleBins_ - 1) * 0.5; |
| 117 |
< |
int whichThetaBin = halfBin * (cosAngle + 1.0); |
| 118 |
< |
++histogram_[whichRBin][whichThetaBin]; |
| 115 |
> |
|
| 116 |
> |
RealType cosAngle = evaluateAngle(sd1, sd2); |
| 117 |
> |
RealType halfBin = (nAngleBins_ - 1) * 0.5; |
| 118 |
> |
int whichThetaBin = int(halfBin * (cosAngle + 1.0)); |
| 119 |
> |
++histogram_[whichRBin][whichThetaBin]; |
| 120 |
|
|
| 121 |
< |
++npairs_; |
| 121 |
> |
++npairs_; |
| 122 |
|
} |
| 123 |
< |
} |
| 123 |
> |
} |
| 124 |
|
|
| 125 |
< |
void GofRAngle::writeRdf() { |
| 125 |
> |
void GofRAngle::writeRdf() { |
| 126 |
|
std::ofstream rdfStream(outputFilename_.c_str()); |
| 127 |
|
if (rdfStream.is_open()) { |
| 128 |
< |
rdfStream << "#radial distribution function\n"; |
| 129 |
< |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 130 |
< |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 131 |
< |
rdfStream << "#r\tcorrValue\n"; |
| 132 |
< |
for (int i = 0; i < avgGofr_.size(); ++i) { |
| 133 |
< |
double r = deltaR_ * (i + 0.5); |
| 128 |
> |
rdfStream << "#radial distribution function\n"; |
| 129 |
> |
rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 130 |
> |
rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 131 |
> |
rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 132 |
> |
rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n"; |
| 133 |
> |
for (unsigned int i = 0; i < avgGofr_.size(); ++i) { |
| 134 |
> |
// RealType r = deltaR_ * (i + 0.5); |
| 135 |
|
|
| 136 |
< |
for(int j = 0; j < avgGofr_[i].size(); ++j) { |
| 137 |
< |
double cosAngle = -1.0 + (i + 0.5)*deltaCosAngle_; |
| 138 |
< |
rdfStream << r << "\t" << cosAngle << "\t" << avgGofr_[i][j]/nProcessed_ << "\n"; |
| 139 |
< |
} |
| 140 |
< |
} |
| 136 |
> |
for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) { |
| 137 |
> |
// RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_; |
| 138 |
> |
rdfStream << avgGofr_[i][j]/nProcessed_ << "\t"; |
| 139 |
> |
} |
| 140 |
> |
|
| 141 |
> |
rdfStream << "\n"; |
| 142 |
> |
} |
| 143 |
|
|
| 144 |
|
} else { |
| 145 |
< |
|
| 146 |
< |
|
| 145 |
> |
sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str()); |
| 146 |
> |
painCave.isFatal = 1; |
| 147 |
> |
simError(); |
| 148 |
|
} |
| 149 |
|
|
| 150 |
|
rdfStream.close(); |
| 151 |
< |
} |
| 151 |
> |
} |
| 152 |
|
|
| 153 |
< |
double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
| 153 |
> |
RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
| 154 |
|
Vector3d pos1 = sd1->getPos(); |
| 155 |
|
Vector3d pos2 = sd2->getPos(); |
| 156 |
< |
Vector3d r12 = pos1 - pos2; |
| 157 |
< |
currentSnapshot_->wrapVector(r12); |
| 156 |
> |
Vector3d r12 = pos2 - pos1; |
| 157 |
> |
|
| 158 |
> |
if (usePeriodicBoundaryConditions_) |
| 159 |
> |
currentSnapshot_->wrapVector(r12); |
| 160 |
> |
|
| 161 |
|
r12.normalize(); |
| 144 |
– |
Vector3d dipole = sd1->getElectroFrame().getColumn(2); |
| 145 |
– |
dipole.normalize(); |
| 146 |
– |
return dot(r12, dipole); |
| 147 |
– |
} |
| 162 |
|
|
| 163 |
< |
double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
| 164 |
< |
Vector3d v1 = sd1->getElectroFrame().getColumn(2); |
| 165 |
< |
Vector3d v2 = sd1->getElectroFrame().getColumn(2); |
| 163 |
> |
Vector3d vec; |
| 164 |
> |
|
| 165 |
> |
if (sd1->isAtom()) { |
| 166 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
| 167 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
| 168 |
> |
|
| 169 |
> |
if (ma1.isDipole() ) |
| 170 |
> |
vec = sd1->getDipole(); |
| 171 |
> |
else |
| 172 |
> |
vec = sd1->getA().transpose() * V3Z; |
| 173 |
> |
} else { |
| 174 |
> |
vec = sd1->getA().transpose() * V3Z; |
| 175 |
> |
} |
| 176 |
> |
|
| 177 |
> |
vec.normalize(); |
| 178 |
> |
|
| 179 |
> |
return dot(r12, vec); |
| 180 |
> |
} |
| 181 |
> |
|
| 182 |
> |
RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) { |
| 183 |
> |
Vector3d v1, v2; |
| 184 |
> |
|
| 185 |
> |
if (sd1->isAtom()){ |
| 186 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
| 187 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
| 188 |
> |
if (ma1.isDipole() ) |
| 189 |
> |
v1 = sd1->getDipole(); |
| 190 |
> |
else |
| 191 |
> |
v1 = sd1->getA().transpose() * V3Z; |
| 192 |
> |
} else { |
| 193 |
> |
v1 = sd1->getA().transpose() * V3Z; |
| 194 |
> |
} |
| 195 |
> |
|
| 196 |
> |
if (sd2->isAtom()) { |
| 197 |
> |
AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType(); |
| 198 |
> |
MultipoleAdapter ma2 = MultipoleAdapter(atype2); |
| 199 |
> |
|
| 200 |
> |
if (ma2.isDipole() ) |
| 201 |
> |
v2 = sd2->getDipole(); |
| 202 |
> |
else |
| 203 |
> |
v2 = sd2->getA().transpose() * V3Z; |
| 204 |
> |
} else { |
| 205 |
> |
v2 = sd2->getA().transpose() * V3Z; |
| 206 |
> |
} |
| 207 |
> |
|
| 208 |
|
v1.normalize(); |
| 209 |
|
v2.normalize(); |
| 210 |
|
return dot(v1, v2); |
| 211 |
< |
} |
| 211 |
> |
} |
| 212 |
|
|
| 213 |
|
|
| 214 |
|
} |
