| 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 |
> |
globalIndex = mpiSim->divideLabor(); |
| 242 |
|
|
| 243 |
|
// set up the local variables |
| 244 |
|
|
| 567 |
|
|
| 568 |
|
// new AllLong( simnfo ); |
| 569 |
|
|
| 570 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo ); |
| 570 |
> |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
| 571 |
|
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo ); |
| 572 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo ); |
| 573 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 645 |
|
} |
| 646 |
|
} |
| 647 |
|
|
| 648 |
+ |
#ifdef IS_MPI |
| 649 |
+ |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
| 650 |
+ |
|
| 651 |
+ |
delete[] globalIndex; |
| 652 |
+ |
#endif IS_MPI |
| 653 |
+ |
|
| 654 |
|
the_ff->initializeAtoms(); |
| 655 |
|
} |
| 656 |
|
|
| 663 |
|
the_bonds = new bond_pair[tot_bonds]; |
| 664 |
|
index = 0; |
| 665 |
|
offset = 0; |
| 666 |
< |
molIndex = 0;g1 |
| 666 |
> |
molIndex = 0; |
| 667 |
|
|
| 668 |
|
for( i=0; i<n_components; i++ ){ |
| 669 |
|
|
