| 36 |
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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 |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
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#include "applications/staticProps/P2OrderParameter.hpp" |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/NumericConstant.hpp" |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
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const string& sele1) |
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: StaticAnalyser(info, filename), doVect_(true), |
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selectionScript1_(sele1), evaluator1_(info), |
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evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
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|
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setOutputName(getPrefix(filename) + ".p2"); |
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|
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evaluator1_.loadScriptString(sele1); |
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|
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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} |
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} |
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|
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P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2) |
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: StaticAnalyser(info, filename), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info), |
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seleMan1_(info), seleMan2_(info){ |
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|
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P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
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const string& sele1, const string& sele2) |
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: StaticAnalyser(info, filename), doVect_(false), |
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selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), |
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evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
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|
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setOutputName(getPrefix(filename) + ".p2"); |
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|
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> |
|
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evaluator1_.loadScriptString(sele1); |
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evaluator2_.loadScriptString(sele2); |
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|
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|
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if (!evaluator1_.isDynamic()) { |
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seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
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}else { |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (!evaluator2_.isDynamic()) { |
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seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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}else { |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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> |
|
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if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
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sprintf( painCave.errMsg, |
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"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n"); |
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painCave.severity = OPENMD_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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|
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|
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} |
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|
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int i; |
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int j; |
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StuntDouble* sd1; |
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sd1 != NULL && sd2 != NULL; |
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sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
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|
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sdPairs_.push_back(std::make_pair(sd1, sd2)); |
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} |
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|
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sdPairs_.push_back(make_pair(sd1, sd2)); |
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} |
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} |
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|
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void P2OrderParameter::process() { |
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RigidBody* rb; |
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SimInfo::MoleculeIterator mi; |
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Molecule::RigidBodyIterator rbIter; |
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StuntDouble* sd; |
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int ii; |
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|
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DumpReader reader(info_, dumpFilename_); |
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int nFrames = reader.getNFrames(); |
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for (int i = 0; i < nFrames; i += step_) { |
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reader.readFrame(i); |
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currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
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< |
|
| 134 |
< |
|
| 135 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
| 133 |
> |
|
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> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
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> |
mol = info_->nextMolecule(mi)) { |
| 136 |
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//change the positions of atoms which belong to the rigidbodies |
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< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
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> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
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> |
rb = mol->nextRigidBody(rbIter)) { |
| 139 |
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rb->updateAtoms(); |
| 140 |
< |
} |
| 122 |
< |
|
| 140 |
> |
} |
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} |
| 142 |
|
|
| 143 |
|
Mat3x3d orderTensor(0.0); |
| 144 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
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< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 146 |
< |
if (usePeriodicBoundaryConditions_) |
| 147 |
< |
currentSnapshot_->wrapVector(vec); |
| 148 |
< |
vec.normalize(); |
| 149 |
< |
orderTensor +=outProduct(vec, vec); |
| 144 |
> |
|
| 145 |
> |
if (doVect_) { |
| 146 |
> |
|
| 147 |
> |
if (evaluator1_.isDynamic()) |
| 148 |
> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 149 |
> |
|
| 150 |
> |
for (sd = seleMan1_.beginSelected(ii); sd != NULL; |
| 151 |
> |
sd = seleMan1_.nextSelected(ii)) { |
| 152 |
> |
if (sd->isDirectional()) { |
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> |
Vector3d vec = sd->getA().getColumn(2); |
| 154 |
> |
vec.normalize(); |
| 155 |
> |
orderTensor += outProduct(vec, vec); |
| 156 |
> |
} |
| 157 |
> |
} |
| 158 |
> |
|
| 159 |
> |
orderTensor /= seleMan1_.getSelectionCount(); |
| 160 |
> |
|
| 161 |
> |
} else { |
| 162 |
> |
|
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> |
for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); |
| 164 |
> |
j != sdPairs_.end(); ++j) { |
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> |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
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> |
if (usePeriodicBoundaryConditions_) |
| 167 |
> |
currentSnapshot_->wrapVector(vec); |
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> |
vec.normalize(); |
| 169 |
> |
orderTensor +=outProduct(vec, vec); |
| 170 |
> |
} |
| 171 |
> |
|
| 172 |
> |
orderTensor /= sdPairs_.size(); |
| 173 |
|
} |
| 174 |
|
|
| 175 |
< |
orderTensor /= sdPairs_.size(); |
| 175 |
> |
|
| 176 |
|
orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 177 |
|
|
| 178 |
|
Vector3d eigenvalues; |
| 179 |
|
Mat3x3d eigenvectors; |
| 180 |
+ |
|
| 181 |
|
Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
| 182 |
|
|
| 183 |
|
int which; |
| 197 |
|
} |
| 198 |
|
|
| 199 |
|
RealType angle = 0.0; |
| 200 |
< |
for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 201 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 202 |
< |
if (usePeriodicBoundaryConditions_) |
| 203 |
< |
currentSnapshot_->wrapVector(vec); |
| 204 |
< |
vec.normalize(); |
| 205 |
< |
|
| 206 |
< |
angle += acos(dot(vec, director)) ; |
| 200 |
> |
|
| 201 |
> |
if (doVect_) { |
| 202 |
> |
for (sd = seleMan1_.beginSelected(ii); sd != NULL; |
| 203 |
> |
sd = seleMan1_.nextSelected(ii)) { |
| 204 |
> |
if (sd->isDirectional()) { |
| 205 |
> |
Vector3d vec = sd->getA().getColumn(2); |
| 206 |
> |
vec.normalize(); |
| 207 |
> |
angle += acos(dot(vec, director)); |
| 208 |
> |
} |
| 209 |
> |
} |
| 210 |
> |
angle = angle/(seleMan1_.getSelectionCount()*NumericConstant::PI)*180.0; |
| 211 |
> |
|
| 212 |
> |
} else { |
| 213 |
> |
for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 214 |
> |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 215 |
> |
if (usePeriodicBoundaryConditions_) |
| 216 |
> |
currentSnapshot_->wrapVector(vec); |
| 217 |
> |
vec.normalize(); |
| 218 |
> |
angle += acos(dot(vec, director)) ; |
| 219 |
> |
} |
| 220 |
> |
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
| 221 |
|
} |
| 166 |
– |
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
| 222 |
|
|
| 223 |
|
OrderParam param; |
| 224 |
|
param.p2 = p2; |
| 228 |
|
orderParams_.push_back(param); |
| 229 |
|
|
| 230 |
|
} |
| 231 |
< |
|
| 231 |
> |
|
| 232 |
|
writeP2(); |
| 233 |
< |
|
| 233 |
> |
|
| 234 |
|
} |
| 235 |
|
|
| 236 |
|
void P2OrderParameter::writeP2() { |
| 237 |
|
|
| 238 |
< |
std::ofstream os(getOutputFileName().c_str()); |
| 238 |
> |
ofstream os(getOutputFileName().c_str()); |
| 239 |
|
os << "#radial distribution function\n"; |
| 240 |
|
os<< "#selection1: (" << selectionScript1_ << ")\t"; |
| 241 |
< |
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 241 |
> |
if (!doVect_) { |
| 242 |
> |
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 243 |
> |
} |
| 244 |
|
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
| 245 |
|
|
| 246 |
< |
for (std::size_t i = 0; i < orderParams_.size(); ++i) { |
| 246 |
> |
for (size_t i = 0; i < orderParams_.size(); ++i) { |
| 247 |
|
os << orderParams_[i].p2 << "\t" |
| 248 |
|
<< orderParams_[i].director[0] << "\t" |
| 249 |
|
<< orderParams_[i].director[1] << "\t" |
