# | Line 248 | Line 248 | void SimSetup::createSim( void ){ | |
---|---|---|
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; | |
# | Line 259 | Line 262 | void SimSetup::createSim( void ){ | |
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(); | |
# | Line 279 | Line 281 | void SimSetup::createSim( void ){ | |
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; | |
# | Line 304 | Line 306 | void SimSetup::createSim( void ){ | |
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]; | |
# | Line 326 | Line 356 | void SimSetup::createSim( void ){ | |
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 | ||
# | Line 383 | Line 412 | void SimSetup::createSim( void ){ | |
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 |
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