88 |
|
|
89 |
|
|
90 |
|
|
91 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
92 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
93 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
91 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
92 |
|
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
93 |
|
else{ |
94 |
|
sprintf( painCave.errMsg, |
246 |
|
|
247 |
|
int localMol, allMol; |
248 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
249 |
+ |
|
250 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
251 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
252 |
|
|
253 |
|
allMol = 0; |
254 |
|
localMol = 0; |
260 |
|
|
261 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
262 |
|
|
263 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
263 |
> |
if( mol2proc[j] == worldRank ){ |
264 |
|
|
265 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
266 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
279 |
|
if( local_atoms != simnfo->n_atoms ){ |
280 |
|
sprintf( painCave.errMsg, |
281 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
282 |
< |
" localAtom (%d) are note equal.\n", |
282 |
> |
" localAtom (%d) are not equal.\n", |
283 |
|
simnfo->n_atoms, |
284 |
|
local_atoms ); |
285 |
|
painCave.isFatal = 1; |
304 |
|
Atom::createArrays(simnfo->n_atoms); |
305 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
306 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
307 |
+ |
int molIndex; |
308 |
|
|
309 |
+ |
// initialize the molecule's stampID's |
310 |
|
|
311 |
+ |
#ifdef IS_MPI |
312 |
+ |
|
313 |
+ |
|
314 |
+ |
molIndex = 0; |
315 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
316 |
+ |
|
317 |
+ |
if(mol2proc[i] == worldRank ){ |
318 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
319 |
+ |
molIndex++; |
320 |
+ |
} |
321 |
+ |
} |
322 |
+ |
|
323 |
+ |
#else // is_mpi |
324 |
+ |
|
325 |
+ |
molIndex = 0; |
326 |
+ |
for(i=0; i<n_components; i++){ |
327 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
328 |
+ |
the_molecules[molIndex].setStampID( i ); |
329 |
+ |
molIndex++; |
330 |
+ |
} |
331 |
+ |
} |
332 |
+ |
|
333 |
+ |
|
334 |
+ |
#endif // is_mpi |
335 |
+ |
|
336 |
+ |
|
337 |
|
if( simnfo->n_SRI ){ |
338 |
+ |
|
339 |
+ |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
340 |
+ |
|
341 |
|
Exclude::createArray(simnfo->n_SRI); |
342 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
343 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
344 |
|
simnfo->globalExcludes = new int; |
345 |
|
simnfo->n_exclude = tot_SRI; |
346 |
|
} |
358 |
|
// set the arrays into the SimInfo object |
359 |
|
|
360 |
|
simnfo->atoms = the_atoms; |
361 |
< |
simnfo->sr_interactions = the_sris; |
361 |
> |
simnfo->molecules = the_molecules; |
362 |
|
simnfo->nGlobalExcludes = 0; |
363 |
|
simnfo->excludes = the_excludes; |
364 |
|
|
415 |
|
|
416 |
|
the_ff->setSimInfo( simnfo ); |
417 |
|
|
418 |
< |
makeAtoms(); |
418 |
> |
makeMolecules(); |
419 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
420 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
421 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
422 |
|
} |
423 |
|
|
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 |
– |
|
424 |
|
if (the_globals->getUseRF() ) { |
425 |
|
simnfo->useReactionField = 1; |
426 |
|
|
657 |
|
|
658 |
|
// new AllLong( simnfo ); |
659 |
|
|
641 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
660 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
661 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
662 |
|
|
700 |
|
BondStamp* currentBond; |
701 |
|
BendStamp* currentBend; |
702 |
|
TorsionStamp* currentTorsion; |
703 |
+ |
|
704 |
+ |
bond_pair* theBonds; |
705 |
+ |
bend_set* theBends; |
706 |
+ |
torsion_set* theTorsions; |
707 |
+ |
|
708 |
|
|
709 |
|
//init the forceField paramters |
710 |
|
|
711 |
|
the_ff->readParams(); |
712 |
|
|
713 |
|
|
714 |
< |
// init the molecules |
714 |
> |
// init the atoms |
715 |
|
|
716 |
+ |
double ux, uy, uz, u, uSqr; |
717 |
+ |
|
718 |
|
atomOffset = 0; |
719 |
|
excludeOffset = 0; |
720 |
|
for(i=0; i<simnfo->n_mol; i++){ |
731 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
732 |
|
info.myBonds = new Bond*[info.nBonds]; |
733 |
|
info.myBends = new Bend*[info.nBends]; |
734 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
734 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
735 |
|
|
736 |
|
theBonds = new bond_pair[info.nBonds]; |
737 |
|
theBends = new bend_set[info.nBends]; |
741 |
|
|
742 |
|
for(j=0; j<info.nAtoms; j++){ |
743 |
|
|
744 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
744 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
745 |
|
if( currentAtom->haveOrientation() ){ |
746 |
|
|
747 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
814 |
|
|
815 |
|
if( currentBend->haveExtras() ){ |
816 |
|
|
817 |
< |
extras = current_bend->getExtras(); |
817 |
> |
extras = currentBend->getExtras(); |
818 |
|
current_extra = extras; |
819 |
|
|
820 |
|
while( current_extra != NULL ){ |
931 |
|
|
932 |
|
the_molecules[i].initialize( info ); |
933 |
|
atomOffset += info.nAtoms; |
934 |
+ |
delete[] theBonds; |
935 |
+ |
delete[] theBends; |
936 |
+ |
delete[] theTorsions; |
937 |
|
} |
938 |
|
|
939 |
|
// clean up the forcefield |