| 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> |
| 45 |
|
#include "applications/staticProps/GofXyz.hpp" |
| 46 |
|
#include "utils/simError.h" |
| 47 |
|
#include "primitives/Molecule.hpp" |
| 48 |
< |
namespace oopse { |
| 48 |
> |
#include "types/MultipoleAdapter.hpp" |
| 49 |
|
|
| 50 |
< |
GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, double len, int nrbins) |
| 51 |
< |
: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) { |
| 50 |
> |
namespace OpenMD { |
| 51 |
> |
|
| 52 |
> |
GofXyz::GofXyz(SimInfo* info, const std::string& filename, |
| 53 |
> |
const std::string& sele1, const std::string& sele2, |
| 54 |
> |
const std::string& sele3, RealType len, int nrbins) |
| 55 |
> |
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), |
| 56 |
> |
halfLen_(len/2), nRBins_(nrbins), evaluator3_(info), seleMan3_(info) { |
| 57 |
> |
|
| 58 |
|
setOutputName(getPrefix(filename) + ".gxyz"); |
| 59 |
< |
|
| 59 |
> |
|
| 60 |
|
evaluator3_.loadScriptString(sele3); |
| 61 |
|
if (!evaluator3_.isDynamic()) { |
| 62 |
< |
seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
| 62 |
> |
seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
| 63 |
|
} |
| 64 |
< |
|
| 64 |
> |
|
| 65 |
|
deltaR_ = len_ / nRBins_; |
| 66 |
|
|
| 67 |
|
histogram_.resize(nRBins_); |
| 68 |
|
for (int i = 0 ; i < nRBins_; ++i) { |
| 69 |
< |
histogram_[i].resize(nRBins_); |
| 70 |
< |
for(int j = 0; j < nRBins_; ++j) { |
| 71 |
< |
histogram_[i][j].resize(nRBins_); |
| 72 |
< |
} |
| 73 |
< |
} |
| 74 |
< |
|
| 75 |
< |
} |
| 76 |
< |
|
| 70 |
< |
|
| 71 |
< |
void GofXyz::preProcess() { |
| 69 |
> |
histogram_[i].resize(nRBins_); |
| 70 |
> |
for(int j = 0; j < nRBins_; ++j) { |
| 71 |
> |
histogram_[i][j].resize(nRBins_); |
| 72 |
> |
} |
| 73 |
> |
} |
| 74 |
> |
} |
| 75 |
> |
|
| 76 |
> |
void GofXyz::preProcess() { |
| 77 |
|
for (int i = 0 ; i < nRBins_; ++i) { |
| 78 |
< |
histogram_[i].resize(nRBins_); |
| 79 |
< |
for(int j = 0; j < nRBins_; ++j) { |
| 80 |
< |
std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0); |
| 81 |
< |
} |
| 78 |
> |
histogram_[i].resize(nRBins_); |
| 79 |
> |
for(int j = 0; j < nRBins_; ++j) { |
| 80 |
> |
std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0); |
| 81 |
> |
} |
| 82 |
|
} |
| 83 |
< |
} |
| 84 |
< |
|
| 85 |
< |
|
| 86 |
< |
void GofXyz::initalizeHistogram() { |
| 87 |
< |
//calculate the center of mass of the molecule of selected stuntdouble in selection1 |
| 88 |
< |
|
| 83 |
> |
} |
| 84 |
> |
|
| 85 |
> |
|
| 86 |
> |
void GofXyz::initializeHistogram() { |
| 87 |
> |
// Calculate the center of mass of the molecule of selected |
| 88 |
> |
// StuntDouble in selection1 |
| 89 |
> |
|
| 90 |
|
if (!evaluator3_.isDynamic()) { |
| 91 |
< |
seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
| 91 |
> |
seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
| 92 |
|
} |
| 93 |
|
|
| 94 |
|
assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount()); |
| 95 |
|
|
| 96 |
< |
//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane |
| 97 |
< |
//v1 = s3 -s1, |
| 98 |
< |
//z = origin.dipole |
| 99 |
< |
//x = v1 X z |
| 100 |
< |
//y = z X x |
| 96 |
> |
// The Dipole direction of selection3 and position of selection3 will |
| 97 |
> |
// be used to determine the y-z plane |
| 98 |
> |
// v1 = s3 -s1, |
| 99 |
> |
// z = origin.dipole |
| 100 |
> |
// x = v1 X z |
| 101 |
> |
// y = z X x |
| 102 |
|
rotMats_.clear(); |
| 103 |
|
|
| 104 |
|
int i; |
| 107 |
|
StuntDouble* sd3; |
| 108 |
|
|
| 109 |
|
for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); |
| 110 |
< |
sd1 != NULL, sd3 != NULL; |
| 111 |
< |
sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) { |
| 110 |
> |
sd1 != NULL || sd3 != NULL; |
| 111 |
> |
sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) { |
| 112 |
|
|
| 113 |
< |
Vector3d r3 =sd3->getPos(); |
| 114 |
< |
Vector3d r1 = sd1->getPos(); |
| 115 |
< |
Vector3d v1 = r3 - r1; |
| 113 |
> |
Vector3d r3 = sd3->getPos(); |
| 114 |
> |
Vector3d r1 = sd1->getPos(); |
| 115 |
> |
Vector3d v1 = r3 - r1; |
| 116 |
> |
if (usePeriodicBoundaryConditions_) |
| 117 |
|
info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
| 110 |
– |
Vector3d zaxis = sd1->getElectroFrame().getColumn(2); |
| 111 |
– |
Vector3d xaxis = cross(v1, zaxis); |
| 112 |
– |
Vector3d yaxis = cross(zaxis, xaxis); |
| 118 |
|
|
| 119 |
< |
xaxis.normalize(); |
| 120 |
< |
yaxis.normalize(); |
| 116 |
< |
zaxis.normalize(); |
| 119 |
> |
AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType(); |
| 120 |
> |
MultipoleAdapter ma1 = MultipoleAdapter(atype1); |
| 121 |
|
|
| 122 |
< |
RotMat3x3d rotMat; |
| 123 |
< |
rotMat.setRow(0, xaxis); |
| 124 |
< |
rotMat.setRow(1, yaxis); |
| 125 |
< |
rotMat.setRow(2, zaxis); |
| 122 |
> |
Vector3d zaxis; |
| 123 |
> |
if (ma1.isDipole()) |
| 124 |
> |
zaxis = sd1->getDipole(); |
| 125 |
> |
else |
| 126 |
> |
zaxis = sd1->getA().transpose() * V3Z; |
| 127 |
> |
|
| 128 |
> |
Vector3d xaxis = cross(v1, zaxis); |
| 129 |
> |
Vector3d yaxis = cross(zaxis, xaxis); |
| 130 |
> |
|
| 131 |
> |
xaxis.normalize(); |
| 132 |
> |
yaxis.normalize(); |
| 133 |
> |
zaxis.normalize(); |
| 134 |
> |
|
| 135 |
> |
RotMat3x3d rotMat; |
| 136 |
> |
rotMat.setRow(0, xaxis); |
| 137 |
> |
rotMat.setRow(1, yaxis); |
| 138 |
> |
rotMat.setRow(2, zaxis); |
| 139 |
|
|
| 140 |
< |
rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat)); |
| 140 |
> |
rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat)); |
| 141 |
|
} |
| 142 |
|
|
| 143 |
< |
} |
| 143 |
> |
} |
| 144 |
|
|
| 145 |
< |
void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 145 |
> |
void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 146 |
|
|
| 147 |
|
Vector3d pos1 = sd1->getPos(); |
| 148 |
|
Vector3d pos2 = sd2->getPos(); |
| 149 |
|
Vector3d r12 = pos2 - pos1; |
| 150 |
< |
currentSnapshot_->wrapVector(r12); |
| 150 |
> |
if (usePeriodicBoundaryConditions_) |
| 151 |
> |
currentSnapshot_->wrapVector(r12); |
| 152 |
|
|
| 153 |
|
std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex()); |
| 154 |
|
assert(i != rotMats_.end()); |
| 155 |
|
|
| 156 |
|
Vector3d newR12 = i->second * r12; |
| 157 |
|
// x, y and z's possible values range -halfLen_ to halfLen_ |
| 158 |
< |
int xbin = (newR12.x()+ halfLen_) / deltaR_; |
| 159 |
< |
int ybin = (newR12.y() + halfLen_) / deltaR_; |
| 160 |
< |
int zbin = (newR12.z() + halfLen_) / deltaR_; |
| 158 |
> |
int xbin = int( (newR12.x() + halfLen_) / deltaR_); |
| 159 |
> |
int ybin = int( (newR12.y() + halfLen_) / deltaR_); |
| 160 |
> |
int zbin = int( (newR12.z() + halfLen_) / deltaR_); |
| 161 |
|
|
| 162 |
|
if (xbin < nRBins_ && xbin >=0 && |
| 163 |
|
ybin < nRBins_ && ybin >= 0 && |
| 164 |
|
zbin < nRBins_ && zbin >=0 ) { |
| 165 |
< |
++histogram_[xbin][ybin][zbin]; |
| 165 |
> |
++histogram_[xbin][ybin][zbin]; |
| 166 |
|
} |
| 167 |
|
|
| 168 |
< |
} |
| 168 |
> |
} |
| 169 |
|
|
| 170 |
< |
void GofXyz::writeRdf() { |
| 170 |
> |
void GofXyz::writeRdf() { |
| 171 |
|
std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary); |
| 172 |
|
if (rdfStream.is_open()) { |
| 173 |
< |
//rdfStream << "#g(x, y, z)\n"; |
| 174 |
< |
//rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 175 |
< |
//rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 176 |
< |
//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 177 |
< |
for (int i = 0; i < histogram_.size(); ++i) { |
| 178 |
< |
|
| 179 |
< |
for(int j = 0; j < histogram_[i].size(); ++j) { |
| 180 |
< |
|
| 181 |
< |
for(int k = 0;k < histogram_[i][j].size(); ++k) { |
| 182 |
< |
rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] )); |
| 183 |
< |
} |
| 184 |
< |
} |
| 185 |
< |
} |
| 173 |
> |
//rdfStream << "#g(x, y, z)\n"; |
| 174 |
> |
//rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 175 |
> |
//rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 176 |
> |
//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " |
| 177 |
> |
// << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 178 |
> |
for (unsigned int i = 0; i < histogram_.size(); ++i) { |
| 179 |
> |
for(unsigned int j = 0; j < histogram_[i].size(); ++j) { |
| 180 |
> |
for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) { |
| 181 |
> |
rdfStream.write(reinterpret_cast<char *>( &histogram_[i][j][k] ), |
| 182 |
> |
sizeof( histogram_[i][j][k] )); |
| 183 |
> |
} |
| 184 |
> |
} |
| 185 |
> |
} |
| 186 |
|
|
| 187 |
|
} else { |
| 188 |
|
|
| 189 |
< |
sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str()); |
| 190 |
< |
painCave.isFatal = 1; |
| 191 |
< |
simError(); |
| 189 |
> |
sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", |
| 190 |
> |
outputFilename_.c_str()); |
| 191 |
> |
painCave.isFatal = 1; |
| 192 |
> |
simError(); |
| 193 |
|
} |
| 194 |
|
|
| 195 |
|
rdfStream.close(); |
| 196 |
< |
} |
| 196 |
> |
} |
| 197 |
|
|
| 198 |
|
} |
