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"; |