| 310 |
|
the_sris = new SRI*[simnfo->n_SRI]; |
| 311 |
|
the_excludes = new int[2 * simnfo->n_SRI]; |
| 312 |
|
simnfo->globalExcludes = new int; |
| 313 |
+ |
simnfo->n_exclude = tot_SRI; |
| 314 |
|
} |
| 315 |
|
else{ |
| 316 |
< |
the_excludes = new int; |
| 316 |
> |
|
| 317 |
> |
the_excludes = new int[2]; |
| 318 |
> |
the_excludes[0] = 0; |
| 319 |
> |
the_excludes[1] = 0; |
| 320 |
|
simnfo->globalExcludes = new int; |
| 321 |
+ |
simnfo->globalExcludes[0] = 0; |
| 322 |
+ |
|
| 323 |
+ |
simnfo->n_exclude = 1; |
| 324 |
|
} |
| 325 |
|
|
| 326 |
|
// set the arrays into the SimInfo object |
| 327 |
|
|
| 328 |
|
simnfo->atoms = the_atoms; |
| 329 |
|
simnfo->sr_interactions = the_sris; |
| 323 |
– |
simnfo->n_exclude = tot_SRI; |
| 330 |
|
simnfo->nGlobalExcludes = 0; |
| 331 |
|
simnfo->excludes = the_excludes; |
| 332 |
|
|
| 598 |
|
|
| 599 |
|
simnfo->refreshSim(); |
| 600 |
|
|
| 601 |
< |
if( !stcmp( simnfo->mixingRule, "standard") ){ |
| 601 |
> |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
| 602 |
|
the_ff->initForceField( LB_MIXING_RULE ); |
| 603 |
|
} |
| 604 |
< |
else if( !stcmp( simnfo->mixingRule, "explicit") ){ |
| 604 |
> |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
| 605 |
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
| 606 |
|
} |
| 607 |
|
else{ |
| 705 |
|
|
| 706 |
|
void SimSetup::makeBonds( void ){ |
| 707 |
|
|
| 708 |
< |
int i, j, k, index, offset, molIndex; |
| 708 |
> |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 709 |
|
bond_pair* the_bonds; |
| 710 |
|
BondStamp* current_bond; |
| 711 |
|
|
| 772 |
|
|
| 773 |
|
void SimSetup::makeBends( void ){ |
| 774 |
|
|
| 775 |
< |
int i, j, k, index, offset, molIndex, exI, exJ; |
| 775 |
> |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 776 |
|
bend_set* the_bends; |
| 777 |
|
BendStamp* current_bend; |
| 778 |
|
LinkedAssign* extras; |
