| 47 |
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* @version 1.0 |
| 48 |
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*/ |
| 49 |
|
|
| 50 |
+ |
#ifdef IS_MPI |
| 51 |
+ |
#include <mpi.h> |
| 52 |
+ |
#endif |
| 53 |
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#include <algorithm> |
| 54 |
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#include <set> |
| 55 |
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#include <map> |
| 64 |
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#include "io/ForceFieldOptions.hpp" |
| 65 |
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#include "brains/ForceField.hpp" |
| 66 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 64 |
– |
#ifdef IS_MPI |
| 65 |
– |
#include <mpi.h> |
| 66 |
– |
#endif |
| 67 |
|
|
| 68 |
|
using namespace std; |
| 69 |
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namespace OpenMD { |
| 372 |
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|
| 373 |
|
void SimInfo::addInteractionPairs(Molecule* mol) { |
| 374 |
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ForceFieldOptions& options_ = forceField_->getForceFieldOptions(); |
| 375 |
+ |
vector<Atom*>::iterator atomIter; |
| 376 |
|
vector<Bond*>::iterator bondIter; |
| 377 |
|
vector<Bend*>::iterator bendIter; |
| 378 |
|
vector<Torsion*>::iterator torsionIter; |
| 379 |
|
vector<Inversion*>::iterator inversionIter; |
| 380 |
+ |
Atom* atom; |
| 381 |
|
Bond* bond; |
| 382 |
|
Bend* bend; |
| 383 |
|
Torsion* torsion; |
| 420 |
|
atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
| 421 |
|
} |
| 422 |
|
} |
| 423 |
+ |
|
| 424 |
|
|
| 425 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; |
| 426 |
|
bond = mol->nextBond(bondIter)) { |
| 941 |
|
} |
| 942 |
|
} |
| 943 |
|
|
| 944 |
< |
// Build the identArray_ |
| 944 |
> |
// Build the identArray_ and regions_ |
| 945 |
|
|
| 946 |
|
identArray_.clear(); |
| 947 |
< |
identArray_.reserve(getNAtoms()); |
| 948 |
< |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 947 |
> |
identArray_.reserve(getNAtoms()); |
| 948 |
> |
regions_.clear(); |
| 949 |
> |
regions_.reserve(getNAtoms()); |
| 950 |
> |
|
| 951 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 952 |
> |
int reg = mol->getRegion(); |
| 953 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 954 |
|
identArray_.push_back(atom->getIdent()); |
| 955 |
+ |
regions_.push_back(reg); |
| 956 |
|
} |
| 957 |
|
} |
| 958 |
< |
|
| 958 |
> |
|
| 959 |
|
topologyDone_ = true; |
| 960 |
|
} |
| 961 |
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|
