| 485 |
|
|
| 486 |
|
makeMolecules(); |
| 487 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 488 |
+ |
simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
| 489 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 490 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 491 |
+ |
} |
| 492 |
+ |
for(i=0; i< simnfo->n_mol; i++) { |
| 493 |
+ |
the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
| 494 |
|
} |
| 495 |
|
|
| 496 |
|
if (the_globals->getUseRF() ) { |
| 732 |
|
|
| 733 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
| 734 |
|
new Symplectic(simnfo, the_ff, the_extendedsystem); |
| 731 |
– |
std::cerr << "called new Symplecic\n"; |
| 732 |
– |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
| 735 |
|
} |
| 736 |
|
else if( !strcmp( force_field, "LJ" ) ){ |
| 737 |
|
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
| 736 |
– |
std::cerr << "called new Verlet\n"; |
| 737 |
– |
fprintf( stderr, "called new Verlet. stderr\n" ); |
| 738 |
|
} |
| 739 |
|
else { |
| 740 |
|
std::cerr << "I'm a bug.\n"; |
