| 128 |
|
// create the atom and short range interaction arrays |
| 129 |
|
|
| 130 |
|
the_atoms = new Atom*[tot_atoms]; |
| 131 |
< |
// the_molecules = new Molecule[tot_nmol]; |
| 131 |
> |
the_molecules = new Molecule[tot_nmol]; |
| 132 |
|
|
| 133 |
|
|
| 134 |
|
if( tot_SRI ){ |
| 142 |
|
simnfo->sr_interactions = the_sris; |
| 143 |
|
simnfo->n_exclude = tot_SRI; |
| 144 |
|
simnfo->excludes = the_excludes; |
| 145 |
+ |
|
| 146 |
|
|
| 147 |
|
// initialize the arrays |
| 148 |
|
|
| 343 |
|
double ux, uy, uz, uSqr, u; |
| 344 |
|
AtomStamp* current_atom; |
| 345 |
|
DirectionalAtom* dAtom; |
| 346 |
+ |
int molIndex, molStart, molEnd, nMemb; |
| 347 |
+ |
|
| 348 |
|
|
| 349 |
+ |
molIndex = 0; |
| 350 |
|
index = 0; |
| 351 |
|
for( i=0; i<n_components; i++ ){ |
| 352 |
|
|
| 353 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 354 |
|
|
| 355 |
+ |
molStart = index; |
| 356 |
+ |
nMemb = comp_stamps[i]->getNAtoms(); |
| 357 |
|
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
| 358 |
|
|
| 359 |
|
current_atom = comp_stamps[i]->getAtom( k ); |
| 387 |
|
// increment the index and repeat; |
| 388 |
|
index++; |
| 389 |
|
} |
| 390 |
+ |
|
| 391 |
+ |
molEnd = index -1; |
| 392 |
+ |
the_molecules[molIndex].setNMembers( nMemb ); |
| 393 |
+ |
the_molecules[molIndex].setStartAtom( molStart ); |
| 394 |
+ |
the_molecules[molIndex].setEndAtom( molEnd ); |
| 395 |
+ |
molIndex++; |
| 396 |
+ |
|
| 397 |
|
} |
| 398 |
|
} |
| 399 |
|
|
| 499 |
|
the_ff->initializeTorsions( the_torsions ); |
| 500 |
|
} |
| 501 |
|
|
| 489 |
– |
void SimSetup::makeMolecules( void ){ |
| 490 |
– |
|
| 491 |
– |
//empy for now |
| 492 |
– |
} |
| 493 |
– |
|
| 502 |
|
void SimSetup::initFromBass( void ){ |
| 503 |
|
|
| 504 |
|
int i, j, k; |
