| 189 |
|
if( currentStamp == NULL ){ |
| 190 |
|
sprintf( painCave.errMsg, |
| 191 |
|
"SimSetup error: Component \"%s\" was not found in the " |
| 192 |
< |
"list of declared molecules\n" |
| 192 |
> |
"list of declared molecules\n", |
| 193 |
|
id ); |
| 194 |
|
painCave.isFatal = 1; |
| 195 |
|
simError(); |
| 238 |
|
|
| 239 |
|
mpiSim = new mpiSimulation( simnfo ); |
| 240 |
|
|
| 241 |
< |
mpiSim->divideLabor(); |
| 241 |
> |
|
| 242 |
> |
|
| 243 |
> |
globalIndex = mpiSim->divideLabor(); |
| 244 |
> |
|
| 245 |
|
|
| 246 |
+ |
|
| 247 |
|
// set up the local variables |
| 248 |
|
|
| 249 |
|
int localMol, allMol; |
| 396 |
|
the_ff->setSimInfo( simnfo ); |
| 397 |
|
|
| 398 |
|
makeAtoms(); |
| 399 |
< |
|
| 399 |
> |
// |
| 400 |
|
if( tot_bonds ){ |
| 401 |
|
makeBonds(); |
| 402 |
|
} |
| 571 |
|
|
| 572 |
|
// new AllLong( simnfo ); |
| 573 |
|
|
| 574 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo ); |
| 574 |
> |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
| 575 |
|
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo ); |
| 576 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo ); |
| 577 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 649 |
|
} |
| 650 |
|
} |
| 651 |
|
|
| 652 |
+ |
#ifdef IS_MPI |
| 653 |
+ |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
| 654 |
+ |
|
| 655 |
+ |
delete[] globalIndex; |
| 656 |
+ |
|
| 657 |
+ |
mpiSim->mpiRefresh(); |
| 658 |
+ |
#endif //IS_MPI |
| 659 |
+ |
|
| 660 |
|
the_ff->initializeAtoms(); |
| 661 |
|
} |
| 662 |
|
|
| 669 |
|
the_bonds = new bond_pair[tot_bonds]; |
| 670 |
|
index = 0; |
| 671 |
|
offset = 0; |
| 672 |
< |
molIndex = 0;g1 |
| 672 |
> |
molIndex = 0; |
| 673 |
|
|
| 674 |
|
for( i=0; i<n_components; i++ ){ |
| 675 |
|
|
| 696 |
|
|
| 697 |
|
#ifdef IS_MPI |
| 698 |
|
} |
| 699 |
< |
#endif is_mpi |
| 699 |
> |
#endif //is_mpi |
| 700 |
|
|
| 701 |
|
molIndex++; |
| 702 |
|
} |
