| 88 |
|
|
| 89 |
|
vector<Component*> components = simParams->getComponents(); |
| 90 |
|
|
| 91 |
< |
for (vector<Component*>::iterator i = components.begin(); i !=components.end(); ++i) { |
| 91 |
> |
for (vector<Component*>::iterator i = components.begin(); |
| 92 |
> |
i !=components.end(); ++i) { |
| 93 |
|
molStamp = (*i)->getMoleculeStamp(); |
| 94 |
|
nMolWithSameStamp = (*i)->getNMol(); |
| 95 |
|
|
| 782 |
|
|
| 783 |
|
void SimInfo::setupSimVariables() { |
| 784 |
|
useAtomicVirial_ = simParams_->getUseAtomicVirial(); |
| 785 |
< |
// we only call setAccumulateBoxDipole if the accumulateBoxDipole parameter is true |
| 785 |
> |
// we only call setAccumulateBoxDipole if the accumulateBoxDipole |
| 786 |
> |
// parameter is true |
| 787 |
|
calcBoxDipole_ = false; |
| 788 |
|
if ( simParams_->haveAccumulateBoxDipole() ) |
| 789 |
|
if ( simParams_->getAccumulateBoxDipole() ) { |
| 981 |
|
|
| 982 |
|
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 983 |
|
|
| 984 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
| 984 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; |
| 985 |
> |
atom = mol->nextAtom(atomIter)) { |
| 986 |
|
atom->setSnapshotManager(sman_); |
| 987 |
|
} |
| 988 |
|
|
| 989 |
< |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 989 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 990 |
> |
rb = mol->nextRigidBody(rbIter)) { |
| 991 |
|
rb->setSnapshotManager(sman_); |
| 992 |
|
} |
| 993 |
|
|
| 994 |
< |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; cg = mol->nextCutoffGroup(cgIter)) { |
| 994 |
> |
for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; |
| 995 |
> |
cg = mol->nextCutoffGroup(cgIter)) { |
| 996 |
|
cg->setSnapshotManager(sman_); |
| 997 |
|
} |
| 998 |
|
} |
| 1007 |
|
|
| 1008 |
|
|
| 1009 |
|
StuntDouble* SimInfo::getIOIndexToIntegrableObject(int index) { |
| 1010 |
< |
return IOIndexToIntegrableObject.at(index); |
| 1010 |
> |
if (index >= IOIndexToIntegrableObject.size()) { |
| 1011 |
> |
sprintf(painCave.errMsg, |
| 1012 |
> |
"SimInfo::getIOIndexToIntegrableObject Error: Integrable Object\n" |
| 1013 |
> |
"\tindex exceeds number of known objects!\n"); |
| 1014 |
> |
painCave.isFatal = 1; |
| 1015 |
> |
simError(); |
| 1016 |
> |
return NULL; |
| 1017 |
> |
} else |
| 1018 |
> |
return IOIndexToIntegrableObject.at(index); |
| 1019 |
|
} |
| 1020 |
|
|
| 1021 |
|
void SimInfo::setIOIndexToIntegrableObject(const vector<StuntDouble*>& v) { |
| 1022 |
|
IOIndexToIntegrableObject= v; |
| 1023 |
|
} |
| 1011 |
– |
/* |
| 1012 |
– |
void SimInfo::setStuntDoubleFromGlobalIndex(vector<StuntDouble*> v) { |
| 1013 |
– |
assert( v.size() == nAtoms_ + nRigidBodies_); |
| 1014 |
– |
sdByGlobalIndex_ = v; |
| 1015 |
– |
} |
| 1024 |
|
|
| 1017 |
– |
StuntDouble* SimInfo::getStuntDoubleFromGlobalIndex(int index) { |
| 1018 |
– |
//assert(index < nAtoms_ + nRigidBodies_); |
| 1019 |
– |
return sdByGlobalIndex_.at(index); |
| 1020 |
– |
} |
| 1021 |
– |
*/ |
| 1025 |
|
int SimInfo::getNGlobalConstraints() { |
| 1026 |
|
int nGlobalConstraints; |
| 1027 |
|
#ifdef IS_MPI |
