| 328 |
|
|
| 329 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 330 |
|
|
| 331 |
< |
if( mol2proc[j] == worldRank ){ |
| 331 |
> |
if( mol2proc[allMol] == worldRank ){ |
| 332 |
|
|
| 333 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 334 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 385 |
|
if(mol2proc[i] == worldRank ){ |
| 386 |
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 387 |
|
the_molecules[molIndex].setMyIndex( molIndex ); |
| 388 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
| 389 |
|
molIndex++; |
| 390 |
|
} |
| 391 |
|
} |
| 397 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
| 398 |
|
the_molecules[molIndex].setStampID( i ); |
| 399 |
|
the_molecules[molIndex].setMyIndex( molIndex ); |
| 400 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
| 401 |
|
molIndex++; |
| 402 |
|
} |
| 403 |
|
} |
| 487 |
|
|
| 488 |
|
makeMolecules(); |
| 489 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 490 |
+ |
simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
| 491 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 492 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 493 |
+ |
} |
| 494 |
+ |
for(i=0; i< simnfo->n_mol; i++) { |
| 495 |
+ |
the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
| 496 |
|
} |
| 497 |
|
|
| 498 |
|
if (the_globals->getUseRF() ) { |
| 734 |
|
|
| 735 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
| 736 |
|
new Symplectic(simnfo, the_ff, the_extendedsystem); |
| 731 |
– |
std::cerr << "called new Symplecic\n"; |
| 732 |
– |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
| 737 |
|
} |
| 738 |
|
else if( !strcmp( force_field, "LJ" ) ){ |
| 739 |
|
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
| 736 |
– |
std::cerr << "called new Verlet\n"; |
| 737 |
– |
fprintf( stderr, "called new Verlet. stderr\n" ); |
| 740 |
|
} |
| 741 |
|
else { |
| 742 |
|
std::cerr << "I'm a bug.\n"; |
