# | Line 231 | Line 231 | namespace OpenMD { | |
---|---|---|
231 | vector<Atom*>::iterator k; | |
232 | ||
233 | Molecule* mol; | |
234 | < | StuntDouble* integrableObject; |
234 | > | StuntDouble* sd; |
235 | Atom* atom; | |
236 | ||
237 | ndf_local = 0; | |
238 | nfq_local = 0; | |
239 | ||
240 | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { | |
241 | < | for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
242 | < | integrableObject = mol->nextIntegrableObject(j)) { |
241 | > | |
242 | > | for (sd = mol->beginIntegrableObject(j); sd != NULL; |
243 | > | sd = mol->nextIntegrableObject(j)) { |
244 | ||
245 | ndf_local += 3; | |
246 | ||
247 | < | if (integrableObject->isDirectional()) { |
248 | < | if (integrableObject->isLinear()) { |
247 | > | if (sd->isDirectional()) { |
248 | > | if (sd->isLinear()) { |
249 | ndf_local += 2; | |
250 | } else { | |
251 | ndf_local += 3; | |
252 | } | |
253 | } | |
254 | } | |
255 | + | |
256 | for (atom = mol->beginFluctuatingCharge(k); atom != NULL; | |
257 | atom = mol->nextFluctuatingCharge(k)) { | |
258 | if (atom->isFluctuatingCharge()) { | |
# | Line 312 | Line 314 | namespace OpenMD { | |
314 | MoleculeIterator i; | |
315 | vector<StuntDouble*>::iterator j; | |
316 | Molecule* mol; | |
317 | < | StuntDouble* integrableObject; |
317 | > | StuntDouble* sd; |
318 | ||
319 | // Raw degrees of freedom that we have to set | |
320 | ndfRaw_local = 0; | |
321 | ||
322 | for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { | |
321 | – | for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
322 | – | integrableObject = mol->nextIntegrableObject(j)) { |
323 | ||
324 | + | for (sd = mol->beginIntegrableObject(j); sd != NULL; |
325 | + | sd = mol->nextIntegrableObject(j)) { |
326 | + | |
327 | ndfRaw_local += 3; | |
328 | ||
329 | < | if (integrableObject->isDirectional()) { |
330 | < | if (integrableObject->isLinear()) { |
329 | > | if (sd->isDirectional()) { |
330 | > | if (sd->isLinear()) { |
331 | ndfRaw_local += 2; | |
332 | } else { | |
333 | ndfRaw_local += 3; | |
# | Line 384 | Line 387 | namespace OpenMD { | |
387 | Molecule::RigidBodyIterator rbIter; | |
388 | RigidBody* rb; | |
389 | Molecule::IntegrableObjectIterator ii; | |
390 | < | StuntDouble* integrableObject; |
390 | > | StuntDouble* sd; |
391 | ||
392 | < | for (integrableObject = mol->beginIntegrableObject(ii); |
393 | < | integrableObject != NULL; |
391 | < | integrableObject = mol->nextIntegrableObject(ii)) { |
392 | > | for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
393 | > | sd = mol->nextIntegrableObject(ii)) { |
394 | ||
395 | < | if (integrableObject->isRigidBody()) { |
396 | < | rb = static_cast<RigidBody*>(integrableObject); |
395 | > | if (sd->isRigidBody()) { |
396 | > | rb = static_cast<RigidBody*>(sd); |
397 | vector<Atom*> atoms = rb->getAtoms(); | |
398 | set<int> rigidAtoms; | |
399 | for (int i = 0; i < static_cast<int>(atoms.size()); ++i) { | |
# | Line 402 | Line 404 | namespace OpenMD { | |
404 | } | |
405 | } else { | |
406 | set<int> oneAtomSet; | |
407 | < | oneAtomSet.insert(integrableObject->getGlobalIndex()); |
408 | < | atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
407 | > | oneAtomSet.insert(sd->getGlobalIndex()); |
408 | > | atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
409 | } | |
410 | } | |
411 | ||
# | Line 537 | Line 539 | namespace OpenMD { | |
539 | Molecule::RigidBodyIterator rbIter; | |
540 | RigidBody* rb; | |
541 | Molecule::IntegrableObjectIterator ii; | |
542 | < | StuntDouble* integrableObject; |
542 | > | StuntDouble* sd; |
543 | ||
544 | < | for (integrableObject = mol->beginIntegrableObject(ii); |
545 | < | integrableObject != NULL; |
544 | < | integrableObject = mol->nextIntegrableObject(ii)) { |
544 | > | for (sd = mol->beginIntegrableObject(ii); sd != NULL; |
545 | > | sd = mol->nextIntegrableObject(ii)) { |
546 | ||
547 | < | if (integrableObject->isRigidBody()) { |
548 | < | rb = static_cast<RigidBody*>(integrableObject); |
547 | > | if (sd->isRigidBody()) { |
548 | > | rb = static_cast<RigidBody*>(sd); |
549 | vector<Atom*> atoms = rb->getAtoms(); | |
550 | set<int> rigidAtoms; | |
551 | for (int i = 0; i < static_cast<int>(atoms.size()); ++i) { | |
# | Line 555 | Line 556 | namespace OpenMD { | |
556 | } | |
557 | } else { | |
558 | set<int> oneAtomSet; | |
559 | < | oneAtomSet.insert(integrableObject->getGlobalIndex()); |
560 | < | atomGroups.insert(map<int, set<int> >::value_type(integrableObject->getGlobalIndex(), oneAtomSet)); |
559 | > | oneAtomSet.insert(sd->getGlobalIndex()); |
560 | > | atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
561 | } | |
562 | } | |
563 |
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