| 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 |
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*/ |
| 42 |
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|
| 43 |
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#include "applications/staticProps/P2OrderParameter.hpp" |
| 58 |
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setOutputName(getPrefix(filename) + ".p2"); |
| 59 |
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|
| 60 |
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evaluator1_.loadScriptString(sele1); |
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– |
|
| 61 |
– |
if (!evaluator1_.isDynamic()) { |
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– |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 63 |
– |
} |
| 61 |
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} |
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|
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P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
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setOutputName(getPrefix(filename) + ".p2"); |
| 70 |
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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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< |
if (!evaluator1_.isDynamic()) { |
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< |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 79 |
< |
}else { |
| 80 |
< |
sprintf( painCave.errMsg, |
| 81 |
< |
"--sele1 must be static selection\n"); |
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< |
painCave.severity = OPENMD_ERROR; |
| 83 |
< |
painCave.isFatal = 1; |
| 84 |
< |
simError(); |
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< |
} |
| 86 |
< |
|
| 87 |
< |
if (!evaluator2_.isDynamic()) { |
| 88 |
< |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
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< |
}else { |
| 90 |
< |
sprintf( painCave.errMsg, |
| 91 |
< |
"--sele2 must be static selection\n"); |
| 92 |
< |
painCave.severity = OPENMD_ERROR; |
| 93 |
< |
painCave.isFatal = 1; |
| 94 |
< |
simError(); |
| 95 |
< |
} |
| 96 |
< |
|
| 97 |
< |
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
| 98 |
< |
sprintf( painCave.errMsg, |
| 99 |
< |
"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n"); |
| 100 |
< |
painCave.severity = OPENMD_ERROR; |
| 101 |
< |
painCave.isFatal = 1; |
| 102 |
< |
simError(); |
| 103 |
< |
|
| 104 |
< |
} |
| 105 |
< |
|
| 106 |
< |
int i; |
| 107 |
< |
int j; |
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< |
StuntDouble* sd1; |
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< |
StuntDouble* sd2; |
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< |
for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j); |
| 111 |
< |
sd1 != NULL && sd2 != NULL; |
| 112 |
< |
sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) { |
| 113 |
< |
|
| 114 |
< |
sdPairs_.push_back(make_pair(sd1, sd2)); |
| 115 |
< |
} |
| 72 |
> |
evaluator2_.loadScriptString(sele2); |
| 73 |
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} |
| 74 |
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|
| 75 |
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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; |
| 80 |
< |
StuntDouble* sd; |
| 81 |
< |
int i, ii; |
| 82 |
< |
|
| 80 |
> |
StuntDouble* sd1; |
| 81 |
> |
StuntDouble* sd2; |
| 82 |
> |
int ii; |
| 83 |
> |
int jj; |
| 84 |
> |
int vecCount; |
| 85 |
> |
|
| 86 |
|
DumpReader reader(info_, dumpFilename_); |
| 87 |
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int nFrames = reader.getNFrames(); |
| 88 |
|
|
| 100 |
|
} |
| 101 |
|
|
| 102 |
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Mat3x3d orderTensor(0.0); |
| 103 |
+ |
vecCount = 0; |
| 104 |
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|
| 105 |
+ |
if (evaluator1_.isDynamic()) |
| 106 |
+ |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 107 |
+ |
|
| 108 |
|
if (doVect_) { |
| 109 |
|
|
| 110 |
< |
if (evaluator1_.isDynamic()) |
| 111 |
< |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 112 |
< |
|
| 113 |
< |
for (sd = seleMan1_.beginSelected(ii); sd != NULL; |
| 150 |
< |
sd = seleMan1_.nextSelected(ii)) { |
| 151 |
< |
if (sd->isDirectional()) { |
| 152 |
< |
Vector3d vec = sd->getA().getColumn(2); |
| 110 |
> |
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
| 111 |
> |
sd1 = seleMan1_.nextSelected(ii)) { |
| 112 |
> |
if (sd1->isDirectional()) { |
| 113 |
> |
Vector3d vec = sd1->getA().getColumn(2); |
| 114 |
|
vec.normalize(); |
| 115 |
|
orderTensor += outProduct(vec, vec); |
| 116 |
+ |
vecCount++; |
| 117 |
|
} |
| 118 |
|
} |
| 119 |
|
|
| 120 |
< |
orderTensor /= seleMan1_.getSelectionCount(); |
| 120 |
> |
orderTensor /= vecCount; |
| 121 |
|
|
| 122 |
|
} else { |
| 123 |
+ |
|
| 124 |
+ |
if (evaluator2_.isDynamic()) |
| 125 |
+ |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 126 |
|
|
| 127 |
< |
for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); |
| 128 |
< |
j != sdPairs_.end(); ++j) { |
| 129 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 127 |
> |
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
| 128 |
> |
sprintf( painCave.errMsg, |
| 129 |
> |
"In frame %d, the number of selected StuntDoubles are not\n" |
| 130 |
> |
"\tthe same in --sele1 and sele2\n", i); |
| 131 |
> |
painCave.severity = OPENMD_INFO; |
| 132 |
> |
painCave.isFatal = 0; |
| 133 |
> |
simError(); |
| 134 |
> |
} |
| 135 |
> |
|
| 136 |
> |
for (sd1 = seleMan1_.beginSelected(ii), |
| 137 |
> |
sd2 = seleMan2_.beginSelected(jj); |
| 138 |
> |
sd1 != NULL && sd2 != NULL; |
| 139 |
> |
sd1 = seleMan1_.nextSelected(ii), |
| 140 |
> |
sd2 = seleMan2_.nextSelected(jj)) { |
| 141 |
> |
|
| 142 |
> |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 143 |
> |
|
| 144 |
|
if (usePeriodicBoundaryConditions_) |
| 145 |
|
currentSnapshot_->wrapVector(vec); |
| 146 |
+ |
|
| 147 |
|
vec.normalize(); |
| 148 |
+ |
|
| 149 |
|
orderTensor +=outProduct(vec, vec); |
| 150 |
+ |
vecCount++; |
| 151 |
|
} |
| 152 |
|
|
| 153 |
< |
orderTensor /= sdPairs_.size(); |
| 153 |
> |
orderTensor /= vecCount; |
| 154 |
|
} |
| 155 |
|
|
| 156 |
+ |
if (vecCount == 0) { |
| 157 |
+ |
sprintf( painCave.errMsg, |
| 158 |
+ |
"In frame %d, the number of selected vectors was zero.\n" |
| 159 |
+ |
"\tThis will not give a meaningful order parameter.", i); |
| 160 |
+ |
painCave.severity = OPENMD_ERROR; |
| 161 |
+ |
painCave.isFatal = 1; |
| 162 |
+ |
simError(); |
| 163 |
+ |
} |
| 164 |
|
|
| 165 |
|
orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity(); |
| 166 |
|
|
| 186 |
|
} |
| 187 |
|
|
| 188 |
|
RealType angle = 0.0; |
| 189 |
< |
RealType p4 = 0.0; |
| 189 |
> |
vecCount = 0; |
| 190 |
|
|
| 191 |
|
if (doVect_) { |
| 192 |
< |
for (sd = seleMan1_.beginSelected(ii); sd != NULL; |
| 193 |
< |
sd = seleMan1_.nextSelected(ii)) { |
| 194 |
< |
if (sd->isDirectional()) { |
| 195 |
< |
Vector3d vec = sd->getA().getColumn(2); |
| 192 |
> |
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
| 193 |
> |
sd1 = seleMan1_.nextSelected(ii)) { |
| 194 |
> |
if (sd1->isDirectional()) { |
| 195 |
> |
Vector3d vec = sd1->getA().getColumn(2); |
| 196 |
|
vec.normalize(); |
| 197 |
< |
RealType myDot = dot(vec, director); |
| 198 |
< |
angle += acos(myDot); |
| 209 |
< |
p4 += (35.0 * pow(myDot, 4) - 30.0 * pow(myDot, 2) + 3.0) / 8.0; |
| 197 |
> |
angle += acos(dot(vec, director)); |
| 198 |
> |
vecCount++; |
| 199 |
|
} |
| 200 |
|
} |
| 201 |
< |
angle = angle/(seleMan1_.getSelectionCount()*NumericConstant::PI)*180.0; |
| 202 |
< |
p4 /= (seleMan1_.getSelectionCount()); |
| 201 |
> |
angle = angle/(vecCount*NumericConstant::PI)*180.0; |
| 202 |
> |
|
| 203 |
|
} else { |
| 204 |
< |
for (vector<pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) { |
| 205 |
< |
Vector3d vec = j->first->getPos() - j->second->getPos(); |
| 204 |
> |
for (sd1 = seleMan1_.beginSelected(ii), |
| 205 |
> |
sd2 = seleMan2_.beginSelected(jj); |
| 206 |
> |
sd1 != NULL && sd2 != NULL; |
| 207 |
> |
sd1 = seleMan1_.nextSelected(ii), |
| 208 |
> |
sd2 = seleMan2_.nextSelected(jj)) { |
| 209 |
> |
|
| 210 |
> |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 211 |
|
if (usePeriodicBoundaryConditions_) |
| 212 |
|
currentSnapshot_->wrapVector(vec); |
| 213 |
|
vec.normalize(); |
| 214 |
< |
RealType myDot = dot(vec, director); |
| 215 |
< |
angle += acos(myDot); |
| 222 |
< |
p4 += (35.0 * pow(myDot, 4) - 30.0 * pow(myDot, 2) + 3.0) / 8.0; |
| 214 |
> |
angle += acos(dot(vec, director)) ; |
| 215 |
> |
vecCount++; |
| 216 |
|
} |
| 217 |
< |
angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0; |
| 225 |
< |
p4 /= (seleMan1_.getSelectionCount()); |
| 217 |
> |
angle = angle / (vecCount * NumericConstant::PI) * 180.0; |
| 218 |
|
} |
| 219 |
|
|
| 220 |
|
OrderParam param; |
| 221 |
|
param.p2 = p2; |
| 222 |
|
param.director = director; |
| 223 |
|
param.angle = angle; |
| 232 |
– |
param.p4 = p4; |
| 224 |
|
|
| 225 |
|
orderParams_.push_back(param); |
| 226 |
|
|
| 238 |
|
if (!doVect_) { |
| 239 |
|
os << "selection2: (" << selectionScript2_ << ")\n"; |
| 240 |
|
} |
| 241 |
< |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\t<p4>\n"; |
| 241 |
> |
os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n"; |
| 242 |
|
|
| 243 |
|
for (size_t i = 0; i < orderParams_.size(); ++i) { |
| 244 |
|
os << orderParams_[i].p2 << "\t" |
| 245 |
|
<< orderParams_[i].director[0] << "\t" |
| 246 |
|
<< orderParams_[i].director[1] << "\t" |
| 247 |
|
<< orderParams_[i].director[2] << "\t" |
| 248 |
< |
<< orderParams_[i].angle << "\t" |
| 258 |
< |
<< orderParams_[i].p4 << "\n"; |
| 248 |
> |
<< orderParams_[i].angle << "\n"; |
| 249 |
|
|
| 250 |
|
} |
| 251 |
|
|
