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, |
240 |
|
|
241 |
|
globalIndex = mpiSim->divideLabor(); |
242 |
|
|
245 |
– |
|
246 |
– |
|
243 |
|
// set up the local variables |
244 |
|
|
245 |
|
int localMol, allMol; |
246 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
247 |
+ |
|
248 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
249 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
250 |
|
|
251 |
|
allMol = 0; |
252 |
|
localMol = 0; |
258 |
|
|
259 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
260 |
|
|
261 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
261 |
> |
if( mol2proc[j] == worldRank ){ |
262 |
|
|
263 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
264 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
277 |
|
if( local_atoms != simnfo->n_atoms ){ |
278 |
|
sprintf( painCave.errMsg, |
279 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
280 |
< |
" localAtom (%d) are note equal.\n", |
280 |
> |
" localAtom (%d) are not equal.\n", |
281 |
|
simnfo->n_atoms, |
282 |
|
local_atoms ); |
283 |
|
painCave.isFatal = 1; |
302 |
|
Atom::createArrays(simnfo->n_atoms); |
303 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
304 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
305 |
+ |
int molIndex; |
306 |
|
|
307 |
+ |
// initialize the molecule's stampID's |
308 |
|
|
309 |
+ |
#ifdef IS_MPI |
310 |
+ |
|
311 |
+ |
|
312 |
+ |
molIndex = 0; |
313 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
314 |
+ |
|
315 |
+ |
if(mol2proc[i] == worldRank ){ |
316 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
317 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
318 |
+ |
molIndex++; |
319 |
+ |
} |
320 |
+ |
} |
321 |
+ |
|
322 |
+ |
#else // is_mpi |
323 |
+ |
|
324 |
+ |
molIndex = 0; |
325 |
+ |
for(i=0; i<n_components; i++){ |
326 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
327 |
+ |
the_molecules[molIndex].setStampID( i ); |
328 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
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; |
345 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
346 |
|
} |
347 |
|
else{ |
348 |
|
|
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 |
|
|
663 |
< |
|
663 |
> |
#ifdef IS_MPI |
664 |
> |
mpiSim->mpiRefresh(); |
665 |
> |
#endif |
666 |
|
|
667 |
|
// initialize the Fortran |
668 |
< |
|
668 |
> |
|
669 |
> |
|
670 |
|
simnfo->refreshSim(); |
671 |
|
|
672 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
703 |
|
BondStamp* currentBond; |
704 |
|
BendStamp* currentBend; |
705 |
|
TorsionStamp* currentTorsion; |
706 |
+ |
|
707 |
+ |
bond_pair* theBonds; |
708 |
+ |
bend_set* theBends; |
709 |
+ |
torsion_set* theTorsions; |
710 |
+ |
|
711 |
|
|
712 |
|
//init the forceField paramters |
713 |
|
|
714 |
|
the_ff->readParams(); |
715 |
|
|
716 |
|
|
717 |
< |
// init the molecules |
717 |
> |
// init the atoms |
718 |
|
|
719 |
+ |
double ux, uy, uz, u, uSqr; |
720 |
+ |
|
721 |
|
atomOffset = 0; |
722 |
|
excludeOffset = 0; |
723 |
|
for(i=0; i<simnfo->n_mol; i++){ |
734 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
735 |
|
info.myBonds = new Bond*[info.nBonds]; |
736 |
|
info.myBends = new Bend*[info.nBends]; |
737 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
737 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
738 |
|
|
739 |
|
theBonds = new bond_pair[info.nBonds]; |
740 |
|
theBends = new bend_set[info.nBends]; |
744 |
|
|
745 |
|
for(j=0; j<info.nAtoms; j++){ |
746 |
|
|
747 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
747 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
748 |
|
if( currentAtom->haveOrientation() ){ |
749 |
|
|
750 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
785 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
786 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
787 |
|
|
788 |
< |
exI = theBonds[i].a; |
789 |
< |
exJ = theBonds[i].b; |
788 |
> |
exI = theBonds[j].a; |
789 |
> |
exJ = theBonds[j].b; |
790 |
|
|
791 |
|
// exclude_I must always be the smaller of the pair |
792 |
|
if( exI > exJ ){ |
802 |
|
|
803 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
804 |
|
#else // isn't MPI |
805 |
+ |
|
806 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
807 |
|
#endif //is_mpi |
808 |
|
} |
818 |
|
|
819 |
|
if( currentBend->haveExtras() ){ |
820 |
|
|
821 |
< |
extras = current_bend->getExtras(); |
821 |
> |
extras = currentBend->getExtras(); |
822 |
|
current_extra = extras; |
823 |
|
|
824 |
|
while( current_extra != NULL ){ |
840 |
|
|
841 |
|
default: |
842 |
|
sprintf( painCave.errMsg, |
843 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
843 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
844 |
|
"double nor an int.\n" |
845 |
|
"-->Bend[%d] in %s\n", |
846 |
|
j, comp_stamps[stampID]->getID() ); |
934 |
|
|
935 |
|
|
936 |
|
the_molecules[i].initialize( info ); |
937 |
+ |
|
938 |
+ |
|
939 |
|
atomOffset += info.nAtoms; |
940 |
+ |
delete[] theBonds; |
941 |
+ |
delete[] theBends; |
942 |
+ |
delete[] theTorsions; |
943 |
|
} |
944 |
|
|
945 |
+ |
#ifdef IS_MPI |
946 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
947 |
+ |
MPIcheckPoint(); |
948 |
+ |
#endif // is_mpi |
949 |
+ |
|
950 |
|
// clean up the forcefield |
951 |
|
the_ff->calcRcut(); |
952 |
|
the_ff->cleanMe(); |
953 |
+ |
|
954 |
|
} |
955 |
|
|
956 |
|
void SimSetup::initFromBass( void ){ |