| 61 |
|
if (!evaluator1_.isDynamic()) { |
| 62 |
|
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 63 |
|
} |
| 64 |
– |
|
| 64 |
|
} |
| 65 |
|
|
| 66 |
|
P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
| 121 |
|
SimInfo::MoleculeIterator mi; |
| 122 |
|
Molecule::RigidBodyIterator rbIter; |
| 123 |
|
StuntDouble* sd; |
| 124 |
< |
int i; |
| 126 |
< |
|
| 124 |
> |
int i, ii; |
| 125 |
|
|
| 126 |
|
DumpReader reader(info_, dumpFilename_); |
| 127 |
|
int nFrames = reader.getNFrames(); |
| 129 |
|
for (int i = 0; i < nFrames; i += step_) { |
| 130 |
|
reader.readFrame(i); |
| 131 |
|
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 132 |
< |
|
| 132 |
> |
|
| 133 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 134 |
|
mol = info_->nextMolecule(mi)) { |
| 135 |
|
//change the positions of atoms which belong to the rigidbodies |
| 146 |
|
if (evaluator1_.isDynamic()) |
| 147 |
|
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 148 |
|
|
| 149 |
< |
for (sd = seleMan1_.beginSelected(i); sd != NULL; |
| 150 |
< |
sd = seleMan1_.nextSelected(i)) { |
| 149 |
> |
for (sd = seleMan1_.beginSelected(ii); sd != NULL; |
| 150 |
> |
sd = seleMan1_.nextSelected(ii)) { |
| 151 |
|
if (sd->isDirectional()) { |
| 152 |
|
Vector3d vec = sd->getA().getColumn(2); |
| 153 |
|
vec.normalize(); |
| 171 |
|
orderTensor /= sdPairs_.size(); |
| 172 |
|
} |
| 173 |
|
|
| 174 |
+ |
|
| 175 |
|
orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 176 |
|
|
| 177 |
|
Vector3d eigenvalues; |
| 178 |
|
Mat3x3d eigenvectors; |
| 179 |
+ |
|
| 180 |
|
Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors); |
| 181 |
|
|
| 182 |
|
int which; |
| 196 |
|
} |
| 197 |
|
|
| 198 |
|
RealType angle = 0.0; |
| 199 |
< |
|
| 199 |
> |
RealType p4 = 0.0; |
| 200 |
|
|
| 201 |
|
if (doVect_) { |
| 202 |
< |
for (sd = seleMan1_.beginSelected(i); sd != NULL; |
| 203 |
< |
sd = seleMan1_.nextSelected(i)) { |
| 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)); |
| 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; |
| 210 |
|
} |
| 211 |
|
} |
| 212 |
|
angle = angle/(seleMan1_.getSelectionCount()*NumericConstant::PI)*180.0; |
| 213 |
< |
|
| 213 |
> |
p4 /= (seleMan1_.getSelectionCount()); |
| 214 |
|
} else { |
| 215 |
|
for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 216 |
|
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 217 |
|
if (usePeriodicBoundaryConditions_) |
| 218 |
|
currentSnapshot_->wrapVector(vec); |
| 219 |
< |
vec.normalize(); |
| 220 |
< |
|
| 221 |
< |
angle += acos(dot(vec, director)) ; |
| 219 |
> |
vec.normalize(); |
| 220 |
> |
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; |
| 223 |
|
} |
| 224 |
|
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
| 225 |
+ |
p4 /= (seleMan1_.getSelectionCount()); |
| 226 |
|
} |
| 227 |
|
|
| 228 |
|
OrderParam param; |
| 229 |
|
param.p2 = p2; |
| 230 |
|
param.director = director; |
| 231 |
|
param.angle = angle; |
| 232 |
+ |
param.p4 = p4; |
| 233 |
|
|
| 234 |
|
orderParams_.push_back(param); |
| 235 |
|
|
| 247 |
|
if (!doVect_) { |
| 248 |
|
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 249 |
|
} |
| 250 |
< |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
| 250 |
> |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\t<p4>\n"; |
| 251 |
|
|
| 252 |
|
for (size_t i = 0; i < orderParams_.size(); ++i) { |
| 253 |
|
os << orderParams_[i].p2 << "\t" |
| 254 |
|
<< orderParams_[i].director[0] << "\t" |
| 255 |
|
<< orderParams_[i].director[1] << "\t" |
| 256 |
|
<< orderParams_[i].director[2] << "\t" |
| 257 |
< |
<< orderParams_[i].angle << "\n"; |
| 257 |
> |
<< orderParams_[i].angle << "\t" |
| 258 |
> |
<< orderParams_[i].p4 << "\n"; |
| 259 |
|
|
| 260 |
|
} |
| 261 |
|
|
