| 6 |
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* 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
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|
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|
#include <algorithm> |
| 44 |
|
#include "applications/staticProps/GofXyz.hpp" |
| 45 |
|
#include "utils/simError.h" |
| 46 |
|
#include "primitives/Molecule.hpp" |
| 47 |
< |
namespace oopse { |
| 47 |
> |
namespace OpenMD { |
| 48 |
|
|
| 49 |
< |
GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len, int nrbins) |
| 50 |
< |
: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins) { |
| 51 |
< |
setOutputName(getPrefix(filename) + ".gxyz"); |
| 49 |
> |
GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins) |
| 50 |
> |
: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) { |
| 51 |
> |
setOutputName(getPrefix(filename) + ".gxyz"); |
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|
|
| 53 |
< |
deltaR_ = len_ / nRBins_; |
| 53 |
> |
evaluator3_.loadScriptString(sele3); |
| 54 |
> |
if (!evaluator3_.isDynamic()) { |
| 55 |
> |
seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
| 56 |
> |
} |
| 57 |
> |
|
| 58 |
> |
deltaR_ = len_ / nRBins_; |
| 59 |
|
|
| 60 |
< |
histogram_.resize(nRBins_); |
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< |
for (int i = 0 ; i < nRBins_; ++i) { |
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> |
histogram_.resize(nRBins_); |
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> |
for (int i = 0 ; i < nRBins_; ++i) { |
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|
histogram_[i].resize(nRBins_); |
| 63 |
|
for(int j = 0; j < nRBins_; ++j) { |
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< |
histogram_[i][j].resize(nRBins_); |
| 64 |
> |
histogram_[i][j].resize(nRBins_); |
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|
} |
| 66 |
< |
} |
| 66 |
> |
} |
| 67 |
> |
|
| 68 |
> |
} |
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|
|
| 63 |
– |
//create atom2Mol mapping (should be other class' responsibility) |
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– |
atom2Mol_.insert(atom2Mol_.begin(), info_->getNGlobalAtoms() + info_->getNGlobalRigidBodies(), static_cast<Molecule*>(NULL)); |
| 65 |
– |
|
| 66 |
– |
SimInfo::MoleculeIterator mi; |
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– |
Molecule* mol; |
| 68 |
– |
Molecule::AtomIterator ai; |
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– |
Atom* atom; |
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– |
Molecule::RigidBodyIterator rbIter; |
| 71 |
– |
RigidBody* rb; |
| 72 |
– |
|
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– |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 74 |
– |
|
| 75 |
– |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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– |
atom2Mol_[atom->getGlobalIndex()] = mol; |
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– |
} |
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|
|
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< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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< |
atom2Mol_[rb->getGlobalIndex()] = mol; |
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< |
} |
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< |
|
| 83 |
< |
} |
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< |
} |
| 85 |
< |
|
| 86 |
< |
|
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< |
void GofXyz::preProcess() { |
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> |
void GofXyz::preProcess() { |
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|
for (int i = 0 ; i < nRBins_; ++i) { |
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< |
histogram_[i].resize(nRBins_); |
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< |
for(int j = 0; j < nRBins_; ++j) { |
| 75 |
< |
std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0); |
| 76 |
< |
} |
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> |
histogram_[i].resize(nRBins_); |
| 74 |
> |
for(int j = 0; j < nRBins_; ++j) { |
| 75 |
> |
std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0); |
| 76 |
> |
} |
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|
} |
| 78 |
< |
} |
| 78 |
> |
} |
| 79 |
|
|
| 80 |
|
|
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< |
void GofXyz::initalizeHistogram() { |
| 81 |
> |
void GofXyz::initalizeHistogram() { |
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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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< |
//determine the new coordinate set of selection1 |
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< |
//v1 = Rs1 -Rcom, |
| 86 |
< |
//z = Rs1.dipole |
| 84 |
> |
if (!evaluator3_.isDynamic()) { |
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> |
seleMan3_.setSelectionSet(evaluator3_.evaluate()); |
| 86 |
> |
} |
| 87 |
> |
|
| 88 |
> |
assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount()); |
| 89 |
> |
|
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> |
//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane |
| 91 |
> |
//v1 = s3 -s1, |
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> |
//z = origin.dipole |
| 93 |
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//x = v1 X z |
| 94 |
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//y = z X x |
| 95 |
< |
coorSets_.clear(); |
| 95 |
> |
rotMats_.clear(); |
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|
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|
int i; |
| 98 |
< |
StuntDouble* sd; |
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< |
for (sd = seleMan1_.beginSelected(i); sd != NULL; sd = seleMan1_.nextSelected(i)) { |
| 100 |
< |
Vector3d rcom = getMolCom(sd); |
| 101 |
< |
Vector3d rs1 = sd->getPos(); |
| 102 |
< |
Vector3d v1 = rcom - rs1; |
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< |
CoorSet currCoorSet; |
| 104 |
< |
currCoorSet.zaxis = sd->getElectroFrame().getColumn(2); |
| 105 |
< |
v1.normalize(); |
| 106 |
< |
currCoorSet.zaxis.normalize(); |
| 107 |
< |
currCoorSet.xaxis = cross(v1, currCoorSet.zaxis); |
| 108 |
< |
currCoorSet.yaxis = cross(currCoorSet.zaxis, currCoorSet.xaxis); |
| 109 |
< |
coorSets_.insert(std::map<int, CoorSet>::value_type(sd->getGlobalIndex(), currCoorSet)); |
| 98 |
> |
int j; |
| 99 |
> |
StuntDouble* sd1; |
| 100 |
> |
StuntDouble* sd3; |
| 101 |
> |
|
| 102 |
> |
for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j); |
| 103 |
> |
sd1 != NULL, sd3 != NULL; |
| 104 |
> |
sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) { |
| 105 |
> |
|
| 106 |
> |
Vector3d r3 =sd3->getPos(); |
| 107 |
> |
Vector3d r1 = sd1->getPos(); |
| 108 |
> |
Vector3d v1 = r3 - r1; |
| 109 |
> |
if (usePeriodicBoundaryConditions_) |
| 110 |
> |
info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1); |
| 111 |
> |
Vector3d zaxis = sd1->getElectroFrame().getColumn(2); |
| 112 |
> |
Vector3d xaxis = cross(v1, zaxis); |
| 113 |
> |
Vector3d yaxis = cross(zaxis, xaxis); |
| 114 |
> |
|
| 115 |
> |
xaxis.normalize(); |
| 116 |
> |
yaxis.normalize(); |
| 117 |
> |
zaxis.normalize(); |
| 118 |
> |
|
| 119 |
> |
RotMat3x3d rotMat; |
| 120 |
> |
rotMat.setRow(0, xaxis); |
| 121 |
> |
rotMat.setRow(1, yaxis); |
| 122 |
> |
rotMat.setRow(2, zaxis); |
| 123 |
> |
|
| 124 |
> |
rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat)); |
| 125 |
|
} |
| 126 |
|
|
| 127 |
< |
} |
| 127 |
> |
} |
| 128 |
|
|
| 129 |
< |
void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 129 |
> |
void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) { |
| 130 |
|
|
| 131 |
|
Vector3d pos1 = sd1->getPos(); |
| 132 |
|
Vector3d pos2 = sd2->getPos(); |
| 133 |
|
Vector3d r12 = pos2 - pos1; |
| 134 |
< |
currentSnapshot_->wrapVector(r12); |
| 134 |
> |
if (usePeriodicBoundaryConditions_) |
| 135 |
> |
currentSnapshot_->wrapVector(r12); |
| 136 |
|
|
| 137 |
< |
std::map<int, CoorSet>::iterator i = coorSets_.find(sd1->getGlobalIndex()); |
| 138 |
< |
assert(i != coorSets_.end()); |
| 137 |
> |
std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex()); |
| 138 |
> |
assert(i != rotMats_.end()); |
| 139 |
|
|
| 140 |
< |
double x = dot(r12, i->second.xaxis); |
| 141 |
< |
double y = dot(r12, i->second.yaxis); |
| 142 |
< |
double z = dot(r12, i->second.zaxis); |
| 140 |
> |
Vector3d newR12 = i->second * r12; |
| 141 |
> |
// x, y and z's possible values range -halfLen_ to halfLen_ |
| 142 |
> |
int xbin = (newR12.x()+ halfLen_) / deltaR_; |
| 143 |
> |
int ybin = (newR12.y() + halfLen_) / deltaR_; |
| 144 |
> |
int zbin = (newR12.z() + halfLen_) / deltaR_; |
| 145 |
|
|
| 146 |
< |
int xbin = x / deltaR_; |
| 147 |
< |
int ybin = y / deltaR_; |
| 148 |
< |
int zbin = z / deltaR_; |
| 149 |
< |
|
| 142 |
< |
if (xbin < nRBins_ && ybin < nRBins_ && zbin < nRBins_) { |
| 143 |
< |
++histogram_[x][y][z]; |
| 146 |
> |
if (xbin < nRBins_ && xbin >=0 && |
| 147 |
> |
ybin < nRBins_ && ybin >= 0 && |
| 148 |
> |
zbin < nRBins_ && zbin >=0 ) { |
| 149 |
> |
++histogram_[xbin][ybin][zbin]; |
| 150 |
|
} |
| 151 |
|
|
| 152 |
< |
} |
| 152 |
> |
} |
| 153 |
|
|
| 154 |
< |
void GofXyz::writeRdf() { |
| 154 |
> |
void GofXyz::writeRdf() { |
| 155 |
|
std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary); |
| 156 |
|
if (rdfStream.is_open()) { |
| 157 |
< |
//rdfStream << "#g(x, y, z)\n"; |
| 158 |
< |
//rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 159 |
< |
//rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 160 |
< |
//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 161 |
< |
for (int i = 0; i < histogram_.size(); ++i) { |
| 157 |
> |
//rdfStream << "#g(x, y, z)\n"; |
| 158 |
> |
//rdfStream << "#selection1: (" << selectionScript1_ << ")\t"; |
| 159 |
> |
//rdfStream << "selection2: (" << selectionScript2_ << ")\n"; |
| 160 |
> |
//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n"; |
| 161 |
> |
for (int i = 0; i < histogram_.size(); ++i) { |
| 162 |
|
|
| 163 |
< |
for(int j = 0; j < histogram_[i].size(); ++j) { |
| 163 |
> |
for(int j = 0; j < histogram_[i].size(); ++j) { |
| 164 |
|
|
| 165 |
< |
for(int k = 0;k < histogram_[i].size(); ++k) { |
| 166 |
< |
rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] )); |
| 167 |
< |
} |
| 168 |
< |
} |
| 169 |
< |
} |
| 165 |
> |
for(int k = 0;k < histogram_[i][j].size(); ++k) { |
| 166 |
> |
rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ), sizeof(histogram_[i][j][k] )); |
| 167 |
> |
} |
| 168 |
> |
} |
| 169 |
> |
} |
| 170 |
|
|
| 171 |
|
} else { |
| 172 |
|
|
| 173 |
< |
sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str()); |
| 174 |
< |
painCave.isFatal = 1; |
| 175 |
< |
simError(); |
| 173 |
> |
sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str()); |
| 174 |
> |
painCave.isFatal = 1; |
| 175 |
> |
simError(); |
| 176 |
|
} |
| 177 |
|
|
| 178 |
|
rdfStream.close(); |
| 179 |
< |
} |
| 179 |
> |
} |
| 180 |
|
|
| 175 |
– |
Vector3d GofXyz::getMolCom(StuntDouble* sd){ |
| 176 |
– |
Molecule* mol = atom2Mol_[sd->getGlobalIndex()]; |
| 177 |
– |
assert(mol); |
| 178 |
– |
return mol->getCom(); |
| 181 |
|
} |
| 180 |
– |
|
| 181 |
– |
} |
