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"; |