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* @version 1.0 |
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*/ |
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| 50 |
+ |
#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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#include <algorithm> |
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#include <set> |
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#include <map> |
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#include "io/ForceFieldOptions.hpp" |
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#include "brains/ForceField.hpp" |
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#include "nonbonded/SwitchingFunction.hpp" |
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– |
#ifdef IS_MPI |
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– |
#include <mpi.h> |
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– |
#endif |
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using namespace std; |
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namespace OpenMD { |
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forceField_(ff), simParams_(simParams), |
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ndf_(0), fdf_local(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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< |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), nGlobalFluctuatingCharges_(0), |
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< |
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nInversions_(0), |
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< |
nRigidBodies_(0), nIntegrableObjects_(0), nCutoffGroups_(0), |
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< |
nConstraints_(0), nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false), |
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> |
nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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> |
nGlobalFluctuatingCharges_(0), nGlobalBonds_(0), nGlobalBends_(0), |
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> |
nGlobalTorsions_(0), nGlobalInversions_(0), nAtoms_(0), nBonds_(0), |
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> |
nBends_(0), nTorsions_(0), nInversions_(0), nRigidBodies_(0), |
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> |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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> |
nFluctuatingCharges_(0), sman_(NULL), topologyDone_(false), |
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calcBoxDipole_(false), useAtomicVirial_(true) { |
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|
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MoleculeStamp* molStamp; |
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addMoleculeStamp(molStamp, nMolWithSameStamp); |
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|
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//calculate atoms in molecules |
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< |
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
| 108 |
> |
nGlobalAtoms_ += molStamp->getNAtoms() * nMolWithSameStamp; |
| 109 |
> |
nGlobalBonds_ += molStamp->getNBonds() * nMolWithSameStamp; |
| 110 |
> |
nGlobalBends_ += molStamp->getNBends() * nMolWithSameStamp; |
| 111 |
> |
nGlobalTorsions_ += molStamp->getNTorsions() * nMolWithSameStamp; |
| 112 |
> |
nGlobalInversions_ += molStamp->getNInversions() * nMolWithSameStamp; |
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|
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//calculate atoms in cutoff groups |
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int nAtomsInGroups = 0; |
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atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
| 425 |
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} |
| 426 |
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} |
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+ |
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| 428 |
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for (bond= mol->beginBond(bondIter); bond != NULL; |
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bond = mol->nextBond(bondIter)) { |
| 945 |
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} |
| 946 |
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} |
| 947 |
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|
| 948 |
< |
// Build the identArray_ |
| 948 |
> |
// Build the identArray_ and regions_ |
| 949 |
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| 950 |
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identArray_.clear(); |
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< |
identArray_.reserve(getNAtoms()); |
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< |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 951 |
> |
identArray_.reserve(getNAtoms()); |
| 952 |
> |
regions_.clear(); |
| 953 |
> |
regions_.reserve(getNAtoms()); |
| 954 |
> |
|
| 955 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 956 |
> |
int reg = mol->getRegion(); |
| 957 |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 958 |
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identArray_.push_back(atom->getIdent()); |
| 959 |
+ |
regions_.push_back(reg); |
| 960 |
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} |
| 961 |
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} |
| 962 |
< |
|
| 962 |
> |
|
| 963 |
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topologyDone_ = true; |
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} |
| 965 |
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|
| 994 |
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delete sman_; |
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sman_ = sman; |
| 996 |
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|
| 985 |
– |
Molecule* mol; |
| 986 |
– |
RigidBody* rb; |
| 987 |
– |
Atom* atom; |
| 988 |
– |
CutoffGroup* cg; |
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SimInfo::MoleculeIterator mi; |
| 998 |
+ |
Molecule::AtomIterator ai; |
| 999 |
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Molecule::RigidBodyIterator rbIter; |
| 991 |
– |
Molecule::AtomIterator atomIter; |
| 1000 |
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Molecule::CutoffGroupIterator cgIter; |
| 1001 |
+ |
Molecule::BondIterator bondIter; |
| 1002 |
+ |
Molecule::BendIterator bendIter; |
| 1003 |
+ |
Molecule::TorsionIterator torsionIter; |
| 1004 |
+ |
Molecule::InversionIterator inversionIter; |
| 1005 |
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|
| 1006 |
+ |
Molecule* mol; |
| 1007 |
+ |
Atom* atom; |
| 1008 |
+ |
RigidBody* rb; |
| 1009 |
+ |
CutoffGroup* cg; |
| 1010 |
+ |
Bond* bond; |
| 1011 |
+ |
Bend* bend; |
| 1012 |
+ |
Torsion* torsion; |
| 1013 |
+ |
Inversion* inversion; |
| 1014 |
+ |
|
| 1015 |
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for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 1016 |
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|
| 1017 |
< |
for (atom = mol->beginAtom(atomIter); atom != NULL; |
| 1018 |
< |
atom = mol->nextAtom(atomIter)) { |
| 1017 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; |
| 1018 |
> |
atom = mol->nextAtom(ai)) { |
| 1019 |
|
atom->setSnapshotManager(sman_); |
| 1020 |
< |
} |
| 1000 |
< |
|
| 1020 |
> |
} |
| 1021 |
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for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 1022 |
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rb = mol->nextRigidBody(rbIter)) { |
| 1023 |
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rb->setSnapshotManager(sman_); |
| 1024 |
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} |
| 1005 |
– |
|
| 1025 |
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for (cg = mol->beginCutoffGroup(cgIter); cg != NULL; |
| 1026 |
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cg = mol->nextCutoffGroup(cgIter)) { |
| 1027 |
|
cg->setSnapshotManager(sman_); |
| 1028 |
|
} |
| 1029 |
< |
} |
| 1030 |
< |
|
| 1029 |
> |
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 1030 |
> |
bond = mol->nextBond(bondIter)) { |
| 1031 |
> |
bond->setSnapshotManager(sman_); |
| 1032 |
> |
} |
| 1033 |
> |
for (bend = mol->beginBend(bendIter); bend != NULL; |
| 1034 |
> |
bend = mol->nextBend(bendIter)) { |
| 1035 |
> |
bend->setSnapshotManager(sman_); |
| 1036 |
> |
} |
| 1037 |
> |
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 1038 |
> |
torsion = mol->nextTorsion(torsionIter)) { |
| 1039 |
> |
torsion->setSnapshotManager(sman_); |
| 1040 |
> |
} |
| 1041 |
> |
for (inversion = mol->beginInversion(inversionIter); inversion != NULL; |
| 1042 |
> |
inversion = mol->nextInversion(inversionIter)) { |
| 1043 |
> |
inversion->setSnapshotManager(sman_); |
| 1044 |
> |
} |
| 1045 |
> |
} |
| 1046 |
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} |
| 1047 |
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| 1048 |
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