| 248 |
|
|
| 249 |
|
int localMol, allMol; |
| 250 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 251 |
+ |
|
| 252 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
| 253 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
| 254 |
|
|
| 255 |
|
allMol = 0; |
| 256 |
|
localMol = 0; |
| 262 |
|
|
| 263 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 264 |
|
|
| 265 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
| 263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
| 265 |
> |
if( mol2proc[j] == worldRank ){ |
| 266 |
|
|
| 267 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 268 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 281 |
|
if( local_atoms != simnfo->n_atoms ){ |
| 282 |
|
sprintf( painCave.errMsg, |
| 283 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
| 284 |
< |
" localAtom (%d) are note equal.\n", |
| 284 |
> |
" localAtom (%d) are not equal.\n", |
| 285 |
|
simnfo->n_atoms, |
| 286 |
|
local_atoms ); |
| 287 |
|
painCave.isFatal = 1; |
| 306 |
|
Atom::createArrays(simnfo->n_atoms); |
| 307 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
| 308 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
| 309 |
+ |
int molIndex; |
| 310 |
+ |
|
| 311 |
+ |
// initialize the molecule's stampID's |
| 312 |
+ |
|
| 313 |
+ |
#ifdef IS_MPI |
| 314 |
+ |
|
| 315 |
+ |
|
| 316 |
+ |
molIndex = 0; |
| 317 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
| 318 |
+ |
|
| 319 |
+ |
if(mol2proc[i] == worldRank ){ |
| 320 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 321 |
+ |
molIndex++; |
| 322 |
+ |
} |
| 323 |
+ |
} |
| 324 |
+ |
|
| 325 |
+ |
#else // is_mpi |
| 326 |
+ |
|
| 327 |
+ |
molIndex = 0; |
| 328 |
+ |
for(i=0; i<n_components; i++){ |
| 329 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
| 330 |
+ |
the_molecules[molIndex].setStampID( i ); |
| 331 |
+ |
molIndex++; |
| 332 |
+ |
} |
| 333 |
+ |
} |
| 334 |
+ |
|
| 335 |
|
|
| 336 |
+ |
#endif // is_mpi |
| 337 |
|
|
| 338 |
+ |
|
| 339 |
|
if( simnfo->n_SRI ){ |
| 340 |
|
Exclude::createArray(simnfo->n_SRI); |
| 341 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 356 |
|
// set the arrays into the SimInfo object |
| 357 |
|
|
| 358 |
|
simnfo->atoms = the_atoms; |
| 329 |
– |
simnfo->sr_interactions = the_sris; |
| 359 |
|
simnfo->nGlobalExcludes = 0; |
| 360 |
|
simnfo->excludes = the_excludes; |
| 361 |
|
|
| 412 |
|
|
| 413 |
|
the_ff->setSimInfo( simnfo ); |
| 414 |
|
|
| 415 |
< |
makeAtoms(); |
| 415 |
> |
makeMolecules(); |
| 416 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 417 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 418 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 419 |
|
} |
| 420 |
|
|
| 392 |
– |
if( tot_bonds ){ |
| 393 |
– |
makeBonds(); |
| 394 |
– |
} |
| 395 |
– |
|
| 396 |
– |
if( tot_bends ){ |
| 397 |
– |
makeBends(); |
| 398 |
– |
} |
| 399 |
– |
|
| 400 |
– |
if( tot_torsions ){ |
| 401 |
– |
makeTorsions(); |
| 402 |
– |
} |
| 403 |
– |
|
| 404 |
– |
|
| 421 |
|
if (the_globals->getUseRF() ) { |
| 422 |
|
simnfo->useReactionField = 1; |
| 423 |
|
|
