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 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
339 |
< |
the_excludes = new int[2 * 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 |
|
} |
347 |
|
else{ |
348 |
|
|
349 |
< |
the_excludes = new int[2]; |
350 |
< |
the_excludes[0] = 0; |
351 |
< |
the_excludes[1] = 0; |
349 |
> |
Exclude::createArray( 1 ); |
350 |
> |
the_excludes = new Exclude*; |
351 |
> |
the_excludes[0] = new Exclude(0); |
352 |
> |
the_excludes[0]->setPair( 0,0 ); |
353 |
|
simnfo->globalExcludes = new int; |
354 |
|
simnfo->globalExcludes[0] = 0; |
355 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
355 |
> |
simnfo->n_exclude = 0; |
356 |
|
} |
357 |
|
|
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 |
|
|
365 |
|
|
366 |
|
// get some of the tricky things that may still be in the globals |
367 |
|
|
336 |
– |
if( simnfo->n_dipoles ){ |
337 |
– |
|
338 |
– |
if( !the_globals->haveRRF() ){ |
339 |
– |
sprintf( painCave.errMsg, |
340 |
– |
"SimSetup Error, system has dipoles, but no rRF was set.\n"); |
341 |
– |
painCave.isFatal = 1; |
342 |
– |
simError(); |
343 |
– |
} |
344 |
– |
if( !the_globals->haveDielectric() ){ |
345 |
– |
sprintf( painCave.errMsg, |
346 |
– |
"SimSetup Error, system has dipoles, but no" |
347 |
– |
" dielectric was set.\n" ); |
348 |
– |
painCave.isFatal = 1; |
349 |
– |
simError(); |
350 |
– |
} |
351 |
– |
|
352 |
– |
simnfo->rRF = the_globals->getRRF(); |
353 |
– |
simnfo->dielectric = the_globals->getDielectric(); |
354 |
– |
} |
355 |
– |
|
356 |
– |
#ifdef IS_MPI |
357 |
– |
strcpy( checkPointMsg, "rRf and dielectric check out" ); |
358 |
– |
MPIcheckPoint(); |
359 |
– |
#endif // is_mpi |
368 |
|
|
369 |
|
if( the_globals->haveBox() ){ |
370 |
|
simnfo->box_x = the_globals->getBox(); |
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 |
|
|
424 |
< |
if( tot_bonds ){ |
425 |
< |
makeBonds(); |
426 |
< |
} |
427 |
< |
|
428 |
< |
if( tot_bends ){ |
429 |
< |
makeBends(); |
430 |
< |
} |
431 |
< |
|
432 |
< |
if( tot_torsions ){ |
433 |
< |
makeTorsions(); |
434 |
< |
} |
424 |
> |
if (the_globals->getUseRF() ) { |
425 |
> |
simnfo->useReactionField = 1; |
426 |
> |
|
427 |
> |
if( !the_globals->haveECR() ){ |
428 |
> |
sprintf( painCave.errMsg, |
429 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
430 |
> |
"box length for the electrostaticCutoffRadius.\n" |
431 |
> |
"I hope you have a very fast processor!\n"); |
432 |
> |
painCave.isFatal = 0; |
433 |
> |
simError(); |
434 |
> |
double smallest; |
435 |
> |
smallest = simnfo->box_x; |
436 |
> |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
437 |
> |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
438 |
> |
simnfo->ecr = 0.5 * smallest; |
439 |
> |
} else { |
440 |
> |
simnfo->ecr = the_globals->getECR(); |
441 |
> |
} |
442 |
|
|
443 |
+ |
if( !the_globals->haveEST() ){ |
444 |
+ |
sprintf( painCave.errMsg, |
445 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
446 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
447 |
+ |
); |
448 |
+ |
painCave.isFatal = 0; |
449 |
+ |
simError(); |
450 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
451 |
+ |
} else { |
452 |
+ |
simnfo->est = the_globals->getEST(); |
453 |
+ |
} |
454 |
+ |
|
455 |
+ |
if(!the_globals->haveDielectric() ){ |
456 |
+ |
sprintf( painCave.errMsg, |
457 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
458 |
+ |
"setting a dielectric constant!\n" |
459 |
+ |
); |
460 |
+ |
painCave.isFatal = 1; |
461 |
+ |
simError(); |
462 |
+ |
} |
463 |
+ |
simnfo->dielectric = the_globals->getDielectric(); |
464 |
+ |
} else { |
465 |
+ |
if (simnfo->n_dipoles) { |
466 |
+ |
|
467 |
+ |
if( !the_globals->haveECR() ){ |
468 |
+ |
sprintf( painCave.errMsg, |
469 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest" |
470 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
471 |
+ |
"I hope you have a very fast processor!\n"); |
472 |
+ |
painCave.isFatal = 0; |
473 |
+ |
simError(); |
474 |
+ |
double smallest; |
475 |
+ |
smallest = simnfo->box_x; |
476 |
+ |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
477 |
+ |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
478 |
+ |
simnfo->ecr = 0.5 * smallest; |
479 |
+ |
} else { |
480 |
+ |
simnfo->ecr = the_globals->getECR(); |
481 |
+ |
} |
482 |
+ |
|
483 |
+ |
if( !the_globals->haveEST() ){ |
484 |
+ |
sprintf( painCave.errMsg, |
485 |
+ |
"SimSetup Warning: using default value of 5% of the" |
486 |
+ |
"electrostaticCutoffRadius for the " |
487 |
+ |
"electrostaticSkinThickness\n" |
488 |
+ |
); |
489 |
+ |
painCave.isFatal = 0; |
490 |
+ |
simError(); |
491 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
492 |
+ |
} else { |
493 |
+ |
simnfo->est = the_globals->getEST(); |
494 |
+ |
} |
495 |
+ |
} |
496 |
+ |
} |
497 |
|
|
498 |
+ |
#ifdef IS_MPI |
499 |
+ |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
500 |
+ |
MPIcheckPoint(); |
501 |
+ |
#endif // is_mpi |
502 |
|
|
430 |
– |
|
431 |
– |
|
432 |
– |
|
503 |
|
if( the_globals->haveInitialConfig() ){ |
504 |
|
|
505 |
|
InitializeFromFile* fileInit; |
657 |
|
|
658 |
|
// new AllLong( simnfo ); |
659 |
|
|
590 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
591 |
– |
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 |
|
|
688 |
|
#endif // is_mpi |
689 |
|
} |
690 |
|
|
623 |
– |
void SimSetup::makeAtoms( void ){ |
691 |
|
|
692 |
< |
int i, j, k, index; |
626 |
< |
double ux, uy, uz, uSqr, u; |
627 |
< |
AtomStamp* current_atom; |
692 |
> |
void SimSetup::makeMolecules( void ){ |
693 |
|
|
694 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
695 |
+ |
molInit info; |
696 |
|
DirectionalAtom* dAtom; |
697 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
697 |
> |
LinkedAssign* extras; |
698 |
> |
LinkedAssign* current_extra; |
699 |
> |
AtomStamp* currentAtom; |
700 |
> |
BondStamp* currentBond; |
701 |
> |
BendStamp* currentBend; |
702 |
> |
TorsionStamp* currentTorsion; |
703 |
|
|
704 |
< |
lMolIndex = 0; |
705 |
< |
molIndex = 0; |
706 |
< |
index = 0; |
635 |
< |
for( i=0; i<n_components; i++ ){ |
704 |
> |
bond_pair* theBonds; |
705 |
> |
bend_set* theBends; |
706 |
> |
torsion_set* theTorsions; |
707 |
|
|
708 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
708 |
> |
|
709 |
> |
//init the forceField paramters |
710 |
|
|
711 |
< |
#ifdef IS_MPI |
640 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
641 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
642 |
< |
#endif // is_mpi |
711 |
> |
the_ff->readParams(); |
712 |
|
|
713 |
< |
molStart = index; |
714 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
646 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
647 |
< |
|
648 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
649 |
< |
if( current_atom->haveOrientation() ){ |
650 |
< |
|
651 |
< |
dAtom = new DirectionalAtom(index); |
652 |
< |
simnfo->n_oriented++; |
653 |
< |
the_atoms[index] = dAtom; |
654 |
< |
|
655 |
< |
ux = current_atom->getOrntX(); |
656 |
< |
uy = current_atom->getOrntY(); |
657 |
< |
uz = current_atom->getOrntZ(); |
658 |
< |
|
659 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
660 |
< |
|
661 |
< |
u = sqrt( uSqr ); |
662 |
< |
ux = ux / u; |
663 |
< |
uy = uy / u; |
664 |
< |
uz = uz / u; |
665 |
< |
|
666 |
< |
dAtom->setSUx( ux ); |
667 |
< |
dAtom->setSUy( uy ); |
668 |
< |
dAtom->setSUz( uz ); |
669 |
< |
} |
670 |
< |
else{ |
671 |
< |
the_atoms[index] = new GeneralAtom(index); |
672 |
< |
} |
673 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
674 |
< |
the_atoms[index]->setIndex( index ); |
675 |
< |
|
676 |
< |
// increment the index and repeat; |
677 |
< |
index++; |
678 |
< |
} |
679 |
< |
|
680 |
< |
molEnd = index -1; |
681 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
682 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
683 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
684 |
< |
the_molecules[lMolIndex].setStampID( i ); |
685 |
< |
lMolIndex++; |
713 |
> |
|
714 |
> |
// init the atoms |
715 |
|
|
716 |
< |
#ifdef IS_MPI |
717 |
< |
} |
718 |
< |
#endif //is_mpi |
719 |
< |
|
720 |
< |
molIndex++; |
692 |
< |
} |
693 |
< |
} |
694 |
< |
|
695 |
< |
#ifdef IS_MPI |
696 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
716 |
> |
double ux, uy, uz, u, uSqr; |
717 |
> |
|
718 |
> |
atomOffset = 0; |
719 |
> |
excludeOffset = 0; |
720 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
721 |
|
|
722 |
< |
delete[] globalIndex; |
722 |
> |
stampID = the_molecules[i].getStampID(); |
723 |
|
|
724 |
< |
mpiSim->mpiRefresh(); |
725 |
< |
#endif //IS_MPI |
726 |
< |
|
727 |
< |
the_ff->initializeAtoms(); |
728 |
< |
} |
724 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
725 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
726 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
727 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
728 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
729 |
|
|
730 |
< |
void SimSetup::makeBonds( void ){ |
730 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
731 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
732 |
> |
info.myBonds = new Bond*[info.nBonds]; |
733 |
> |
info.myBends = new Bend*[info.nBends]; |
734 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
735 |
|
|
736 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
737 |
< |
bond_pair* the_bonds; |
738 |
< |
BondStamp* current_bond; |
739 |
< |
|
740 |
< |
the_bonds = new bond_pair[tot_bonds]; |
741 |
< |
index = 0; |
742 |
< |
offset = 0; |
743 |
< |
molIndex = 0; |
744 |
< |
|
745 |
< |
for( i=0; i<n_components; i++ ){ |
718 |
< |
|
719 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
720 |
< |
|
721 |
< |
#ifdef IS_MPI |
722 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
723 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
724 |
< |
#endif // is_mpi |
736 |
> |
theBonds = new bond_pair[info.nBonds]; |
737 |
> |
theBends = new bend_set[info.nBends]; |
738 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
739 |
> |
|
740 |
> |
// make the Atoms |
741 |
> |
|
742 |
> |
for(j=0; j<info.nAtoms; j++){ |
743 |
> |
|
744 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
745 |
> |
if( currentAtom->haveOrientation() ){ |
746 |
|
|
747 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
748 |
< |
|
749 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
750 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
751 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
752 |
< |
|
753 |
< |
exI = the_bonds[index].a; |
754 |
< |
exJ = the_bonds[index].b; |
755 |
< |
|
756 |
< |
// exclude_I must always be the smaller of the pair |
757 |
< |
if( exI > exJ ){ |
758 |
< |
tempEx = exI; |
759 |
< |
exI = exJ; |
760 |
< |
exJ = tempEx; |
761 |
< |
} |
762 |
< |
|
763 |
< |
|
747 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
748 |
> |
simnfo->n_oriented++; |
749 |
> |
info.myAtoms[j] = dAtom; |
750 |
> |
|
751 |
> |
ux = currentAtom->getOrntX(); |
752 |
> |
uy = currentAtom->getOrntY(); |
753 |
> |
uz = currentAtom->getOrntZ(); |
754 |
> |
|
755 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
756 |
> |
|
757 |
> |
u = sqrt( uSqr ); |
758 |
> |
ux = ux / u; |
759 |
> |
uy = uy / u; |
760 |
> |
uz = uz / u; |
761 |
> |
|
762 |
> |
dAtom->setSUx( ux ); |
763 |
> |
dAtom->setSUy( uy ); |
764 |
> |
dAtom->setSUz( uz ); |
765 |
> |
} |
766 |
> |
else{ |
767 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
768 |
> |
} |
769 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
770 |
> |
|
771 |
|
#ifdef IS_MPI |
772 |
< |
|
773 |
< |
the_excludes[index*2] = |
746 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
747 |
< |
the_excludes[index*2 + 1] = |
748 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
749 |
< |
|
750 |
< |
#else // isn't MPI |
751 |
< |
|
752 |
< |
the_excludes[index*2] = exI + 1; |
753 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
754 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
755 |
< |
#endif //is_mpi |
756 |
< |
|
757 |
< |
// increment the index and repeat; |
758 |
< |
index++; |
759 |
< |
} |
760 |
< |
offset += comp_stamps[i]->getNAtoms(); |
761 |
< |
|
762 |
< |
#ifdef IS_MPI |
763 |
< |
} |
764 |
< |
#endif //is_mpi |
772 |
> |
|
773 |
> |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
774 |
|
|
775 |
< |
molIndex++; |
776 |
< |
} |
777 |
< |
} |
775 |
> |
#endif // is_mpi |
776 |
> |
} |
777 |
> |
|
778 |
> |
// make the bonds |
779 |
> |
for(j=0; j<info.nBonds; j++){ |
780 |
> |
|
781 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
782 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
783 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
784 |
|
|
785 |
< |
the_ff->initializeBonds( the_bonds ); |
786 |
< |
} |
785 |
> |
exI = theBonds[i].a; |
786 |
> |
exJ = theBonds[i].b; |
787 |
|
|
788 |
< |
void SimSetup::makeBends( void ){ |
789 |
< |
|
790 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
791 |
< |
bend_set* the_bends; |
792 |
< |
BendStamp* current_bend; |
793 |
< |
LinkedAssign* extras; |
779 |
< |
LinkedAssign* current_extra; |
780 |
< |
|
781 |
< |
|
782 |
< |
the_bends = new bend_set[tot_bends]; |
783 |
< |
index = 0; |
784 |
< |
offset = 0; |
785 |
< |
molIndex = 0; |
786 |
< |
for( i=0; i<n_components; i++ ){ |
787 |
< |
|
788 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
789 |
< |
|
788 |
> |
// exclude_I must always be the smaller of the pair |
789 |
> |
if( exI > exJ ){ |
790 |
> |
tempEx = exI; |
791 |
> |
exI = exJ; |
792 |
> |
exJ = tempEx; |
793 |
> |
} |
794 |
|
#ifdef IS_MPI |
795 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
796 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
797 |
< |
#endif // is_mpi |
795 |
> |
tempEx = exI; |
796 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
797 |
> |
tempEx = exJ; |
798 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
799 |
> |
|
800 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
801 |
> |
#else // isn't MPI |
802 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
803 |
> |
#endif //is_mpi |
804 |
> |
} |
805 |
> |
excludeOffset += info.nBonds; |
806 |
|
|
807 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
807 |
> |
//make the bends |
808 |
> |
for(j=0; j<info.nBends; j++){ |
809 |
> |
|
810 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
811 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
812 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
813 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
814 |
|
|
815 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
798 |
< |
the_bends[index].a = current_bend->getA() + offset; |
799 |
< |
the_bends[index].b = current_bend->getB() + offset; |
800 |
< |
the_bends[index].c = current_bend->getC() + offset; |
801 |
< |
|
802 |
< |
if( current_bend->haveExtras() ){ |
815 |
> |
if( currentBend->haveExtras() ){ |
816 |
|
|
817 |
< |
extras = current_bend->getExtras(); |
818 |
< |
current_extra = extras; |
817 |
> |
extras = currentBend->getExtras(); |
818 |
> |
current_extra = extras; |
819 |
|
|
820 |
< |
while( current_extra != NULL ){ |
821 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
820 |
> |
while( current_extra != NULL ){ |
821 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
822 |
|
|
823 |
< |
switch( current_extra->getType() ){ |
823 |
> |
switch( current_extra->getType() ){ |
824 |
> |
|
825 |
> |
case 0: |
826 |
> |
theBends[j].ghost = |
827 |
> |
current_extra->getInt() + atomOffset; |
828 |
> |
theBends[j].isGhost = 1; |
829 |
> |
break; |
830 |
|
|
831 |
< |
case 0: |
832 |
< |
the_bends[index].ghost = |
833 |
< |
current_extra->getInt() + offset; |
834 |
< |
the_bends[index].isGhost = 1; |
835 |
< |
break; |
817 |
< |
|
818 |
< |
case 1: |
819 |
< |
the_bends[index].ghost = |
820 |
< |
(int)current_extra->getDouble() + offset; |
821 |
< |
the_bends[index].isGhost = 1; |
822 |
< |
break; |
823 |
< |
|
824 |
< |
default: |
825 |
< |
sprintf( painCave.errMsg, |
826 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
827 |
< |
"double nor an int.\n" |
828 |
< |
"-->Bend[%d] in %s\n", |
829 |
< |
k, comp_stamps[i]->getID() ); |
830 |
< |
painCave.isFatal = 1; |
831 |
< |
simError(); |
832 |
< |
} |
833 |
< |
} |
831 |
> |
case 1: |
832 |
> |
theBends[j].ghost = |
833 |
> |
(int)current_extra->getDouble() + atomOffset; |
834 |
> |
theBends[j].isGhost = 1; |
835 |
> |
break; |
836 |
|
|
837 |
< |
else{ |
838 |
< |
|
839 |
< |
sprintf( painCave.errMsg, |
840 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
841 |
< |
" -->%s in Bend[%d] in %s\n", |
842 |
< |
current_extra->getlhs(), |
843 |
< |
k, comp_stamps[i]->getID() ); |
844 |
< |
painCave.isFatal = 1; |
843 |
< |
simError(); |
844 |
< |
} |
845 |
< |
|
846 |
< |
current_extra = current_extra->getNext(); |
837 |
> |
default: |
838 |
> |
sprintf( painCave.errMsg, |
839 |
> |
"SimSetup Error: ghostVectorSource was neiter a " |
840 |
> |
"double nor an int.\n" |
841 |
> |
"-->Bend[%d] in %s\n", |
842 |
> |
j, comp_stamps[stampID]->getID() ); |
843 |
> |
painCave.isFatal = 1; |
844 |
> |
simError(); |
845 |
|
} |
846 |
|
} |
847 |
|
|
850 |
– |
if( !the_bends[index].isGhost ){ |
851 |
– |
|
852 |
– |
exI = the_bends[index].a; |
853 |
– |
exJ = the_bends[index].c; |
854 |
– |
} |
848 |
|
else{ |
849 |
|
|
850 |
< |
exI = the_bends[index].a; |
851 |
< |
exJ = the_bends[index].b; |
850 |
> |
sprintf( painCave.errMsg, |
851 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
852 |
> |
" -->%s in Bend[%d] in %s\n", |
853 |
> |
current_extra->getlhs(), |
854 |
> |
j, comp_stamps[stampID]->getID() ); |
855 |
> |
painCave.isFatal = 1; |
856 |
> |
simError(); |
857 |
|
} |
858 |
|
|
859 |
< |
// exclude_I must always be the smaller of the pair |
860 |
< |
if( exI > exJ ){ |
861 |
< |
tempEx = exI; |
862 |
< |
exI = exJ; |
863 |
< |
exJ = tempEx; |
864 |
< |
} |
859 |
> |
current_extra = current_extra->getNext(); |
860 |
> |
} |
861 |
> |
} |
862 |
> |
|
863 |
> |
if( !theBends[j].isGhost ){ |
864 |
> |
|
865 |
> |
exI = theBends[j].a; |
866 |
> |
exJ = theBends[j].c; |
867 |
> |
} |
868 |
> |
else{ |
869 |
> |
|
870 |
> |
exI = theBends[j].a; |
871 |
> |
exJ = theBends[j].b; |
872 |
> |
} |
873 |
> |
|
874 |
> |
// exclude_I must always be the smaller of the pair |
875 |
> |
if( exI > exJ ){ |
876 |
> |
tempEx = exI; |
877 |
> |
exI = exJ; |
878 |
> |
exJ = tempEx; |
879 |
> |
} |
880 |
> |
#ifdef IS_MPI |
881 |
> |
tempEx = exI; |
882 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
883 |
> |
tempEx = exJ; |
884 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
885 |
> |
|
886 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
887 |
> |
#else // isn't MPI |
888 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
889 |
> |
#endif //is_mpi |
890 |
> |
} |
891 |
> |
excludeOffset += info.nBends; |
892 |
|
|
893 |
+ |
for(j=0; j<info.nTorsions; j++){ |
894 |
+ |
|
895 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
896 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
897 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
898 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
899 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
900 |
+ |
|
901 |
+ |
exI = theTorsions[j].a; |
902 |
+ |
exJ = theTorsions[j].d; |
903 |
|
|
904 |
+ |
// exclude_I must always be the smaller of the pair |
905 |
+ |
if( exI > exJ ){ |
906 |
+ |
tempEx = exI; |
907 |
+ |
exI = exJ; |
908 |
+ |
exJ = tempEx; |
909 |
+ |
} |
910 |
|
#ifdef IS_MPI |
911 |
< |
|
912 |
< |
the_excludes[(index + tot_bonds)*2] = |
913 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
914 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
915 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
916 |
< |
|
911 |
> |
tempEx = exI; |
912 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
913 |
> |
tempEx = exJ; |
914 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
915 |
> |
|
916 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
917 |
|
#else // isn't MPI |
918 |
< |
|
878 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
879 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
880 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
918 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
919 |
|
#endif //is_mpi |
882 |
– |
|
883 |
– |
|
884 |
– |
// increment the index and repeat; |
885 |
– |
index++; |
886 |
– |
} |
887 |
– |
offset += comp_stamps[i]->getNAtoms(); |
888 |
– |
|
889 |
– |
#ifdef IS_MPI |
890 |
– |
} |
891 |
– |
#endif //is_mpi |
892 |
– |
|
893 |
– |
molIndex++; |
920 |
|
} |
921 |
< |
} |
921 |
> |
excludeOffset += info.nTorsions; |
922 |
|
|
923 |
< |
#ifdef IS_MPI |
924 |
< |
sprintf( checkPointMsg, |
899 |
< |
"Successfully created the bends list.\n" ); |
900 |
< |
MPIcheckPoint(); |
901 |
< |
#endif // is_mpi |
902 |
< |
|
923 |
> |
|
924 |
> |
// send the arrays off to the forceField for init. |
925 |
|
|
926 |
< |
the_ff->initializeBends( the_bends ); |
927 |
< |
} |
926 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
927 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
928 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
929 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
930 |
|
|
907 |
– |
void SimSetup::makeTorsions( void ){ |
931 |
|
|
932 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
933 |
< |
torsion_set* the_torsions; |
934 |
< |
TorsionStamp* current_torsion; |
935 |
< |
|
936 |
< |
the_torsions = new torsion_set[tot_torsions]; |
914 |
< |
index = 0; |
915 |
< |
offset = 0; |
916 |
< |
molIndex = 0; |
917 |
< |
for( i=0; i<n_components; i++ ){ |
918 |
< |
|
919 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
920 |
< |
|
921 |
< |
#ifdef IS_MPI |
922 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
923 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
924 |
< |
#endif // is_mpi |
925 |
< |
|
926 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
927 |
< |
|
928 |
< |
current_torsion = comp_stamps[i]->getTorsion( k ); |
929 |
< |
the_torsions[index].a = current_torsion->getA() + offset; |
930 |
< |
the_torsions[index].b = current_torsion->getB() + offset; |
931 |
< |
the_torsions[index].c = current_torsion->getC() + offset; |
932 |
< |
the_torsions[index].d = current_torsion->getD() + offset; |
933 |
< |
|
934 |
< |
exI = the_torsions[index].a; |
935 |
< |
exJ = the_torsions[index].d; |
936 |
< |
|
937 |
< |
|
938 |
< |
// exclude_I must always be the smaller of the pair |
939 |
< |
if( exI > exJ ){ |
940 |
< |
tempEx = exI; |
941 |
< |
exI = exJ; |
942 |
< |
exJ = tempEx; |
943 |
< |
} |
944 |
< |
|
945 |
< |
|
946 |
< |
#ifdef IS_MPI |
947 |
< |
|
948 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
949 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
950 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
951 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
952 |
< |
|
953 |
< |
#else // isn't MPI |
954 |
< |
|
955 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
956 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
957 |
< |
// fortran indexes from 1 (hence the +1 in the indexing) |
958 |
< |
#endif //is_mpi |
959 |
< |
|
960 |
< |
|
961 |
< |
// increment the index and repeat; |
962 |
< |
index++; |
963 |
< |
} |
964 |
< |
offset += comp_stamps[i]->getNAtoms(); |
965 |
< |
|
966 |
< |
#ifdef IS_MPI |
967 |
< |
} |
968 |
< |
#endif //is_mpi |
969 |
< |
|
970 |
< |
molIndex++; |
971 |
< |
} |
932 |
> |
the_molecules[i].initialize( info ); |
933 |
> |
atomOffset += info.nAtoms; |
934 |
> |
delete[] theBonds; |
935 |
> |
delete[] theBends; |
936 |
> |
delete[] theTorsions; |
937 |
|
} |
938 |
|
|
939 |
< |
the_ff->initializeTorsions( the_torsions ); |
939 |
> |
// clean up the forcefield |
940 |
> |
the_ff->calcRcut(); |
941 |
> |
the_ff->cleanMe(); |
942 |
|
} |
943 |
|
|
944 |
|
void SimSetup::initFromBass( void ){ |