| 51 |
|
|
| 52 |
|
P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
| 53 |
|
const string& sele1) |
| 54 |
< |
: StaticAnalyser(info, filename), doVect_(true), |
| 55 |
< |
selectionScript1_(sele1), evaluator1_(info), |
| 56 |
< |
evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
| 54 |
> |
: StaticAnalyser(info, filename), doVect_(true), doOffset_(false), |
| 55 |
> |
selectionScript1_(sele1), evaluator1_(info), |
| 56 |
> |
evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
| 57 |
|
|
| 58 |
|
setOutputName(getPrefix(filename) + ".p2"); |
| 59 |
|
|
| 62 |
|
|
| 63 |
|
P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
| 64 |
|
const string& sele1, const string& sele2) |
| 65 |
< |
: StaticAnalyser(info, filename), doVect_(false), |
| 66 |
< |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), |
| 67 |
< |
evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
| 65 |
> |
: StaticAnalyser(info, filename), doVect_(false), doOffset_(false), |
| 66 |
> |
selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), |
| 67 |
> |
evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
| 68 |
|
|
| 69 |
|
setOutputName(getPrefix(filename) + ".p2"); |
| 70 |
|
|
| 72 |
|
evaluator2_.loadScriptString(sele2); |
| 73 |
|
} |
| 74 |
|
|
| 75 |
+ |
P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename, |
| 76 |
+ |
const string& sele1, int seleOffset) |
| 77 |
+ |
: StaticAnalyser(info, filename), doVect_(false), doOffset_(true), |
| 78 |
+ |
seleOffset_(seleOffset), selectionScript1_(sele1), evaluator1_(info), |
| 79 |
+ |
evaluator2_(info), seleMan1_(info), seleMan2_(info) { |
| 80 |
+ |
|
| 81 |
+ |
setOutputName(getPrefix(filename) + ".p2"); |
| 82 |
+ |
|
| 83 |
+ |
evaluator1_.loadScriptString(sele1); |
| 84 |
+ |
} |
| 85 |
+ |
|
| 86 |
|
void P2OrderParameter::process() { |
| 87 |
|
Molecule* mol; |
| 88 |
|
RigidBody* rb; |
| 113 |
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Mat3x3d orderTensor(0.0); |
| 114 |
|
vecCount = 0; |
| 115 |
|
|
| 116 |
< |
if (evaluator1_.isDynamic()) |
| 106 |
< |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 116 |
> |
seleMan1_.setSelectionSet(evaluator1_.evaluate()); |
| 117 |
|
|
| 118 |
|
if (doVect_) { |
| 119 |
|
|
| 131 |
|
|
| 132 |
|
} else { |
| 133 |
|
|
| 134 |
< |
if (evaluator2_.isDynamic()) |
| 125 |
< |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 126 |
< |
|
| 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)) { |
| 134 |
> |
if (doOffset_) { |
| 135 |
|
|
| 136 |
< |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 136 |
> |
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
| 137 |
> |
sd1 = seleMan1_.nextSelected(ii)) { |
| 138 |
|
|
| 139 |
< |
if (usePeriodicBoundaryConditions_) |
| 140 |
< |
currentSnapshot_->wrapVector(vec); |
| 139 |
> |
// This will require careful rewriting if StaticProps is |
| 140 |
> |
// ever parallelized. For an example, see |
| 141 |
> |
// Thermo::getTaggedAtomPairDistance |
| 142 |
|
|
| 143 |
< |
vec.normalize(); |
| 143 |
> |
int sd2Index = sd1->getGlobalIndex() + seleOffset_; |
| 144 |
> |
sd2 = info_->getIOIndexToIntegrableObject(sd2Index); |
| 145 |
> |
|
| 146 |
> |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 147 |
> |
|
| 148 |
> |
if (usePeriodicBoundaryConditions_) |
| 149 |
> |
currentSnapshot_->wrapVector(vec); |
| 150 |
> |
|
| 151 |
> |
vec.normalize(); |
| 152 |
> |
|
| 153 |
> |
orderTensor +=outProduct(vec, vec); |
| 154 |
> |
vecCount++; |
| 155 |
> |
} |
| 156 |
> |
|
| 157 |
> |
orderTensor /= vecCount; |
| 158 |
> |
} else { |
| 159 |
> |
|
| 160 |
> |
seleMan2_.setSelectionSet(evaluator2_.evaluate()); |
| 161 |
> |
|
| 162 |
> |
if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) { |
| 163 |
> |
sprintf( painCave.errMsg, |
| 164 |
> |
"In frame %d, the number of selected StuntDoubles are\n" |
| 165 |
> |
"\tnot the same in --sele1 and sele2\n", i); |
| 166 |
> |
painCave.severity = OPENMD_INFO; |
| 167 |
> |
painCave.isFatal = 0; |
| 168 |
> |
simError(); |
| 169 |
> |
} |
| 170 |
> |
|
| 171 |
> |
for (sd1 = seleMan1_.beginSelected(ii), |
| 172 |
> |
sd2 = seleMan2_.beginSelected(jj); |
| 173 |
> |
sd1 != NULL && sd2 != NULL; |
| 174 |
> |
sd1 = seleMan1_.nextSelected(ii), |
| 175 |
> |
sd2 = seleMan2_.nextSelected(jj)) { |
| 176 |
> |
|
| 177 |
> |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 178 |
> |
|
| 179 |
> |
if (usePeriodicBoundaryConditions_) |
| 180 |
> |
currentSnapshot_->wrapVector(vec); |
| 181 |
|
|
| 182 |
< |
orderTensor +=outProduct(vec, vec); |
| 183 |
< |
vecCount++; |
| 182 |
> |
vec.normalize(); |
| 183 |
> |
|
| 184 |
> |
orderTensor +=outProduct(vec, vec); |
| 185 |
> |
vecCount++; |
| 186 |
> |
} |
| 187 |
> |
|
| 188 |
> |
orderTensor /= vecCount; |
| 189 |
|
} |
| 152 |
– |
|
| 153 |
– |
orderTensor /= vecCount; |
| 190 |
|
} |
| 191 |
|
|
| 192 |
|
if (vecCount == 0) { |
| 237 |
|
angle = angle/(vecCount*NumericConstant::PI)*180.0; |
| 238 |
|
|
| 239 |
|
} else { |
| 240 |
< |
for (sd1 = seleMan1_.beginSelected(ii), |
| 241 |
< |
sd2 = seleMan2_.beginSelected(jj); |
| 242 |
< |
sd1 != NULL && sd2 != NULL; |
| 243 |
< |
sd1 = seleMan1_.nextSelected(ii), |
| 244 |
< |
sd2 = seleMan2_.nextSelected(jj)) { |
| 245 |
< |
|
| 246 |
< |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 247 |
< |
if (usePeriodicBoundaryConditions_) |
| 248 |
< |
currentSnapshot_->wrapVector(vec); |
| 249 |
< |
vec.normalize(); |
| 250 |
< |
angle += acos(dot(vec, director)) ; |
| 251 |
< |
vecCount++; |
| 240 |
> |
if (doOffset_) { |
| 241 |
> |
|
| 242 |
> |
for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL; |
| 243 |
> |
sd1 = seleMan1_.nextSelected(ii)) { |
| 244 |
> |
|
| 245 |
> |
// This will require careful rewriting if StaticProps is |
| 246 |
> |
// ever parallelized. For an example, see |
| 247 |
> |
// Thermo::getTaggedAtomPairDistance |
| 248 |
> |
|
| 249 |
> |
int sd2Index = sd1->getGlobalIndex() + seleOffset_; |
| 250 |
> |
sd2 = info_->getIOIndexToIntegrableObject(sd2Index); |
| 251 |
> |
|
| 252 |
> |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 253 |
> |
if (usePeriodicBoundaryConditions_) |
| 254 |
> |
currentSnapshot_->wrapVector(vec); |
| 255 |
> |
vec.normalize(); |
| 256 |
> |
angle += acos(dot(vec, director)) ; |
| 257 |
> |
vecCount++; |
| 258 |
> |
} |
| 259 |
> |
angle = angle / (vecCount * NumericConstant::PI) * 180.0; |
| 260 |
> |
|
| 261 |
> |
} else { |
| 262 |
> |
|
| 263 |
> |
for (sd1 = seleMan1_.beginSelected(ii), |
| 264 |
> |
sd2 = seleMan2_.beginSelected(jj); |
| 265 |
> |
sd1 != NULL && sd2 != NULL; |
| 266 |
> |
sd1 = seleMan1_.nextSelected(ii), |
| 267 |
> |
sd2 = seleMan2_.nextSelected(jj)) { |
| 268 |
> |
|
| 269 |
> |
Vector3d vec = sd1->getPos() - sd2->getPos(); |
| 270 |
> |
if (usePeriodicBoundaryConditions_) |
| 271 |
> |
currentSnapshot_->wrapVector(vec); |
| 272 |
> |
vec.normalize(); |
| 273 |
> |
angle += acos(dot(vec, director)) ; |
| 274 |
> |
vecCount++; |
| 275 |
> |
} |
| 276 |
> |
angle = angle / (vecCount * NumericConstant::PI) * 180.0; |
| 277 |
|
} |
| 217 |
– |
angle = angle / (vecCount * NumericConstant::PI) * 180.0; |
| 278 |
|
} |
| 279 |
|
|
| 280 |
|
OrderParam param; |
