| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
|
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
/** |
| 61 |
|
#include "io/ForceFieldOptions.hpp" |
| 62 |
|
#include "UseTheForce/ForceField.hpp" |
| 63 |
|
#include "nonbonded/SwitchingFunction.hpp" |
| 64 |
+ |
#ifdef IS_MPI |
| 65 |
+ |
#include <mpi.h> |
| 66 |
+ |
#endif |
| 67 |
|
|
| 68 |
|
using namespace std; |
| 69 |
|
namespace OpenMD { |
| 823 |
|
|
| 824 |
|
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 825 |
|
GlobalAtomIndices[atom->getLocalIndex()] = atom->getGlobalIndex(); |
| 822 |
– |
cerr << "LI = " << atom->getLocalIndex() << "GAI = " << GlobalAtomIndices[atom->getLocalIndex()] << "\n"; |
| 826 |
|
} |
| 827 |
|
} |
| 828 |
|
return GlobalAtomIndices; |
| 844 |
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 845 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 846 |
|
GlobalGroupIndices.push_back(cg->getGlobalIndex()); |
| 844 |
– |
cerr << "LI, GGI = " << GlobalGroupIndices.size() << " " << cg->getGlobalIndex() << "\n"; |
| 847 |
|
} |
| 848 |
|
} |
| 849 |
|
return GlobalGroupIndices; |
