| 240 |
|
|
| 241 |
|
globalIndex = mpiSim->divideLabor(); |
| 242 |
|
|
| 243 |
– |
|
| 244 |
– |
|
| 243 |
|
// set up the local variables |
| 244 |
|
|
| 245 |
|
int localMol, allMol; |
| 333 |
|
|
| 334 |
|
|
| 335 |
|
if( simnfo->n_SRI ){ |
| 336 |
+ |
|
| 337 |
+ |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
| 338 |
+ |
|
| 339 |
|
Exclude::createArray(simnfo->n_SRI); |
| 340 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 341 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
| 342 |
|
simnfo->globalExcludes = new int; |
| 343 |
|
simnfo->n_exclude = tot_SRI; |
| 344 |
|
} |
| 356 |
|
// set the arrays into the SimInfo object |
| 357 |
|
|
| 358 |
|
simnfo->atoms = the_atoms; |
| 359 |
+ |
simnfo->molecules = the_molecules; |
| 360 |
|
simnfo->nGlobalExcludes = 0; |
| 361 |
|
simnfo->excludes = the_excludes; |
| 362 |
|
|
| 658 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
| 659 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 660 |
|
|
| 661 |
+ |
#ifdef IS_MPI |
| 662 |
+ |
mpiSim->mpiRefresh(); |
| 663 |
+ |
#endif |
| 664 |
|
|
| 659 |
– |
|
| 665 |
|
// initialize the Fortran |
| 666 |
< |
|
| 666 |
> |
|
| 667 |
> |
|
| 668 |
|
simnfo->refreshSim(); |
| 669 |
|
|
| 670 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
