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 |
|
|
490 |
– |
void SimSetup::makeMolecules( void ){ |
491 |
– |
|
492 |
– |
int i,j,k; |
493 |
– |
|
494 |
– |
for( i=0; i<n_components; i++ ){ |
495 |
– |
|
496 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
497 |
– |
|
498 |
– |
|
499 |
– |
|
500 |
– |
} |
501 |
– |
|
502 |
|
void SimSetup::initFromBass( void ){ |
503 |
|
|
504 |
|
int i, j, k; |