| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 50 |
+ |
#ifdef IS_MPI |
| 51 |
+ |
#include <mpi.h> |
| 52 |
+ |
#endif |
| 53 |
|
#include <algorithm> |
| 54 |
|
#include <set> |
| 55 |
|
#include <map> |
| 64 |
|
#include "io/ForceFieldOptions.hpp" |
| 65 |
|
#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 |
|
namespace OpenMD { |
| 91 |
|
for (vector<Component*>::iterator i = components.begin(); |
| 92 |
|
i !=components.end(); ++i) { |
| 93 |
|
molStamp = (*i)->getMoleculeStamp(); |
| 94 |
+ |
if ( (*i)->haveRegion() ) { |
| 95 |
+ |
molStamp->setRegion( (*i)->getRegion() ); |
| 96 |
+ |
} else { |
| 97 |
+ |
// set the region to a disallowed value: |
| 98 |
+ |
molStamp->setRegion( -1 ); |
| 99 |
+ |
} |
| 100 |
+ |
|
| 101 |
|
nMolWithSameStamp = (*i)->getNMol(); |
| 102 |
|
|
| 103 |
|
addMoleculeStamp(molStamp, nMolWithSameStamp); |
| 418 |
|
atomGroups.insert(map<int, set<int> >::value_type(sd->getGlobalIndex(), oneAtomSet)); |
| 419 |
|
} |
| 420 |
|
} |
| 421 |
+ |
|
| 422 |
|
|
| 423 |
|
for (bond= mol->beginBond(bondIter); bond != NULL; |
| 424 |
|
bond = mol->nextBond(bondIter)) { |
| 939 |
|
} |
| 940 |
|
} |
| 941 |
|
|
| 942 |
< |
// Build the identArray_ |
| 942 |
> |
// Build the identArray_ and regions_ |
| 943 |
|
|
| 944 |
|
identArray_.clear(); |
| 945 |
< |
identArray_.reserve(getNAtoms()); |
| 946 |
< |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 945 |
> |
identArray_.reserve(getNAtoms()); |
| 946 |
> |
regions_.clear(); |
| 947 |
> |
regions_.reserve(getNAtoms()); |
| 948 |
> |
|
| 949 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 950 |
> |
int reg = mol->getRegion(); |
| 951 |
|
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 952 |
|
identArray_.push_back(atom->getIdent()); |
| 953 |
+ |
regions_.push_back(reg); |
| 954 |
|
} |
| 955 |
|
} |
| 956 |
< |
|
| 956 |
> |
|
| 957 |
|
topologyDone_ = true; |
| 958 |
|
} |
| 959 |
|
|
