| 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). |
| 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 "applications/staticProps/P2OrderParameter.hpp" |
| 122 |
|
SimInfo::MoleculeIterator mi; |
| 123 |
|
Molecule::RigidBodyIterator rbIter; |
| 124 |
|
StuntDouble* sd; |
| 125 |
< |
int i, ii; |
| 125 |
> |
int ii; |
| 126 |
|
|
| 127 |
|
DumpReader reader(info_, dumpFilename_); |
| 128 |
|
int nFrames = reader.getNFrames(); |
| 197 |
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} |
| 198 |
|
|
| 199 |
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RealType angle = 0.0; |
| 199 |
– |
RealType p4 = 0.0; |
| 200 |
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|
| 201 |
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if (doVect_) { |
| 202 |
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for (sd = seleMan1_.beginSelected(ii); sd != NULL; |
| 204 |
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if (sd->isDirectional()) { |
| 205 |
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Vector3d vec = sd->getA().getColumn(2); |
| 206 |
|
vec.normalize(); |
| 207 |
< |
RealType myDot = dot(vec, director); |
| 208 |
< |
angle += acos(myDot); |
| 209 |
< |
p4 += (35.0 * pow(myDot, 4) - 30.0 * pow(myDot, 2) + 3.0) / 8.0; |
| 207 |
> |
angle += acos(dot(vec, director)); |
| 208 |
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} |
| 209 |
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} |
| 210 |
|
angle = angle/(seleMan1_.getSelectionCount()*NumericConstant::PI)*180.0; |
| 211 |
< |
p4 /= (seleMan1_.getSelectionCount()); |
| 211 |
> |
|
| 212 |
|
} else { |
| 213 |
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for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 214 |
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Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 215 |
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if (usePeriodicBoundaryConditions_) |
| 216 |
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currentSnapshot_->wrapVector(vec); |
| 217 |
|
vec.normalize(); |
| 218 |
< |
RealType myDot = dot(vec, director); |
| 221 |
< |
angle += acos(myDot); |
| 222 |
< |
p4 += (35.0 * pow(myDot, 4) - 30.0 * pow(myDot, 2) + 3.0) / 8.0; |
| 218 |
> |
angle += acos(dot(vec, director)) ; |
| 219 |
|
} |
| 220 |
|
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
| 225 |
– |
p4 /= (seleMan1_.getSelectionCount()); |
| 221 |
|
} |
| 222 |
|
|
| 223 |
|
OrderParam param; |
| 224 |
|
param.p2 = p2; |
| 225 |
|
param.director = director; |
| 226 |
|
param.angle = angle; |
| 232 |
– |
param.p4 = p4; |
| 227 |
|
|
| 228 |
|
orderParams_.push_back(param); |
| 229 |
|
|
| 241 |
|
if (!doVect_) { |
| 242 |
|
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 243 |
|
} |
| 244 |
< |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\t<p4>\n"; |
| 244 |
> |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
| 245 |
|
|
| 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" |
| 250 |
|
<< orderParams_[i].director[2] << "\t" |
| 251 |
< |
<< orderParams_[i].angle << "\t" |
| 258 |
< |
<< orderParams_[i].p4 << "\n"; |
| 251 |
> |
<< orderParams_[i].angle << "\n"; |
| 252 |
|
|
| 253 |
|
} |
| 254 |
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|
