307 |
|
|
308 |
|
|
309 |
|
if( simnfo->n_SRI ){ |
310 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
311 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
310 |
> |
Exclude::createArray(simnfo->n_SRI); |
311 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
312 |
|
simnfo->globalExcludes = new int; |
313 |
|
simnfo->n_exclude = tot_SRI; |
314 |
|
} |
315 |
|
else{ |
316 |
|
|
317 |
< |
the_excludes = new int[2]; |
318 |
< |
the_excludes[0] = 0; |
319 |
< |
the_excludes[1] = 0; |
317 |
> |
Exclude::createArray( 1 ); |
318 |
> |
the_excludes = new Exclude*; |
319 |
> |
the_excludes[0] = new Exclude(0); |
320 |
> |
the_excludes[0]->setPair( 0,0 ); |
321 |
|
simnfo->globalExcludes = new int; |
322 |
|
simnfo->globalExcludes[0] = 0; |
323 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
323 |
> |
simnfo->n_exclude = 0; |
324 |
|
} |
325 |
|
|
326 |
|
// set the arrays into the SimInfo object |
332 |
|
|
333 |
|
|
334 |
|
// get some of the tricky things that may still be in the globals |
335 |
– |
|
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 |
– |
} |
335 |
|
|
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 |
336 |
|
|
337 |
|
if( the_globals->haveBox() ){ |
338 |
|
simnfo->box_x = the_globals->getBox(); |
402 |
|
} |
403 |
|
|
404 |
|
|
405 |
< |
|
405 |
> |
if (the_globals->getUseRF() ) { |
406 |
> |
simnfo->useReactionField = 1; |
407 |
> |
|
408 |
> |
if( !the_globals->haveECR() ){ |
409 |
> |
sprintf( painCave.errMsg, |
410 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
411 |
> |
"box length for the electrostaticCutoffRadius.\n" |
412 |
> |
"I hope you have a very fast processor!\n"); |
413 |
> |
painCave.isFatal = 0; |
414 |
> |
simError(); |
415 |
> |
double smallest; |
416 |
> |
smallest = simnfo->box_x; |
417 |
> |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
418 |
> |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
419 |
> |
simnfo->ecr = 0.5 * smallest; |
420 |
> |
} else { |
421 |
> |
simnfo->ecr = the_globals->getECR(); |
422 |
> |
} |
423 |
|
|
424 |
+ |
if( !the_globals->haveEST() ){ |
425 |
+ |
sprintf( painCave.errMsg, |
426 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
427 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
428 |
+ |
); |
429 |
+ |
painCave.isFatal = 0; |
430 |
+ |
simError(); |
431 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
432 |
+ |
} else { |
433 |
+ |
simnfo->est = the_globals->getEST(); |
434 |
+ |
} |
435 |
+ |
|
436 |
+ |
if(!the_globals->haveDielectric() ){ |
437 |
+ |
sprintf( painCave.errMsg, |
438 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
439 |
+ |
"setting a dielectric constant!\n" |
440 |
+ |
); |
441 |
+ |
painCave.isFatal = 1; |
442 |
+ |
simError(); |
443 |
+ |
} |
444 |
+ |
simnfo->dielectric = the_globals->getDielectric(); |
445 |
+ |
} else { |
446 |
+ |
if (simnfo->n_dipoles) { |
447 |
+ |
|
448 |
+ |
if( !the_globals->haveECR() ){ |
449 |
+ |
sprintf( painCave.errMsg, |
450 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest" |
451 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
452 |
+ |
"I hope you have a very fast processor!\n"); |
453 |
+ |
painCave.isFatal = 0; |
454 |
+ |
simError(); |
455 |
+ |
double smallest; |
456 |
+ |
smallest = simnfo->box_x; |
457 |
+ |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
458 |
+ |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
459 |
+ |
simnfo->ecr = 0.5 * smallest; |
460 |
+ |
} else { |
461 |
+ |
simnfo->ecr = the_globals->getECR(); |
462 |
+ |
} |
463 |
+ |
|
464 |
+ |
if( !the_globals->haveEST() ){ |
465 |
+ |
sprintf( painCave.errMsg, |
466 |
+ |
"SimSetup Warning: using default value of 5% of the" |
467 |
+ |
"electrostaticCutoffRadius for the " |
468 |
+ |
"electrostaticSkinThickness\n" |
469 |
+ |
); |
470 |
+ |
painCave.isFatal = 0; |
471 |
+ |
simError(); |
472 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
473 |
+ |
} else { |
474 |
+ |
simnfo->est = the_globals->getEST(); |
475 |
+ |
} |
476 |
+ |
} |
477 |
+ |
} |
478 |
|
|
479 |
+ |
#ifdef IS_MPI |
480 |
+ |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
481 |
+ |
MPIcheckPoint(); |
482 |
+ |
#endif // is_mpi |
483 |
|
|
484 |
|
if( the_globals->haveInitialConfig() ){ |
485 |
|
|
671 |
|
#endif // is_mpi |
672 |
|
} |
673 |
|
|
623 |
– |
void SimSetup::makeAtoms( void ){ |
674 |
|
|
675 |
< |
int i, j, k, index; |
626 |
< |
double ux, uy, uz, uSqr, u; |
627 |
< |
AtomStamp* current_atom; |
675 |
> |
void SimSetup::makeMolecules( void ){ |
676 |
|
|
677 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
678 |
+ |
molInit info; |
679 |
|
DirectionalAtom* dAtom; |
680 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
680 |
> |
LinkedAssign* extras; |
681 |
> |
LinkedAssign* current_extra; |
682 |
> |
AtomStamp* currentAtom; |
683 |
> |
BondStamp* currentBond; |
684 |
> |
BendStamp* currentBend; |
685 |
> |
TorsionStamp* currentTorsion; |
686 |
> |
|
687 |
> |
//init the forceField paramters |
688 |
|
|
689 |
< |
lMolIndex = 0; |
633 |
< |
molIndex = 0; |
634 |
< |
index = 0; |
635 |
< |
for( i=0; i<n_components; i++ ){ |
689 |
> |
the_ff->readParams(); |
690 |
|
|
691 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
691 |
> |
|
692 |
> |
// init the molecules |
693 |
|
|
694 |
< |
#ifdef IS_MPI |
695 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
696 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
697 |
< |
#endif // is_mpi |
694 |
> |
atomOffset = 0; |
695 |
> |
excludeOffset = 0; |
696 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
697 |
> |
|
698 |
> |
stampID = the_molecules[i].getStampID(); |
699 |
|
|
700 |
< |
molStart = index; |
701 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
702 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
703 |
< |
|
704 |
< |
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++; |
700 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
701 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
702 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
703 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
704 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
705 |
|
|
706 |
< |
#ifdef IS_MPI |
707 |
< |
} |
708 |
< |
#endif //is_mpi |
709 |
< |
|
710 |
< |
molIndex++; |
692 |
< |
} |
693 |
< |
} |
706 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
707 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
708 |
> |
info.myBonds = new Bond*[info.nBonds]; |
709 |
> |
info.myBends = new Bend*[info.nBends]; |
710 |
> |
info.myTorsions = new Torsions*[info.nTorsions]; |
711 |
|
|
712 |
< |
#ifdef IS_MPI |
713 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
712 |
> |
theBonds = new bond_pair[info.nBonds]; |
713 |
> |
theBends = new bend_set[info.nBends]; |
714 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
715 |
|
|
716 |
< |
delete[] globalIndex; |
717 |
< |
|
718 |
< |
mpiSim->mpiRefresh(); |
719 |
< |
#endif //IS_MPI |
720 |
< |
|
721 |
< |
the_ff->initializeAtoms(); |
704 |
< |
} |
705 |
< |
|
706 |
< |
void SimSetup::makeBonds( void ){ |
707 |
< |
|
708 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
709 |
< |
bond_pair* the_bonds; |
710 |
< |
BondStamp* current_bond; |
711 |
< |
|
712 |
< |
the_bonds = new bond_pair[tot_bonds]; |
713 |
< |
index = 0; |
714 |
< |
offset = 0; |
715 |
< |
molIndex = 0; |
716 |
< |
|
717 |
< |
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 |
716 |
> |
// make the Atoms |
717 |
> |
|
718 |
> |
for(j=0; j<info.nAtoms; j++){ |
719 |
> |
|
720 |
> |
currentAtom = theComponents[stampID]->getAtom( j ); |
721 |
> |
if( currentAtom->haveOrientation() ){ |
722 |
|
|
723 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
724 |
< |
|
725 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
726 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
727 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
728 |
< |
|
729 |
< |
exI = the_bonds[index].a; |
730 |
< |
exJ = the_bonds[index].b; |
731 |
< |
|
732 |
< |
// exclude_I must always be the smaller of the pair |
733 |
< |
if( exI > exJ ){ |
734 |
< |
tempEx = exI; |
735 |
< |
exI = exJ; |
736 |
< |
exJ = tempEx; |
737 |
< |
} |
738 |
< |
|
739 |
< |
|
723 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
724 |
> |
simnfo->n_oriented++; |
725 |
> |
info.myAtoms[j] = dAtom; |
726 |
> |
|
727 |
> |
ux = currentAtom->getOrntX(); |
728 |
> |
uy = currentAtom->getOrntY(); |
729 |
> |
uz = currentAtom->getOrntZ(); |
730 |
> |
|
731 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
732 |
> |
|
733 |
> |
u = sqrt( uSqr ); |
734 |
> |
ux = ux / u; |
735 |
> |
uy = uy / u; |
736 |
> |
uz = uz / u; |
737 |
> |
|
738 |
> |
dAtom->setSUx( ux ); |
739 |
> |
dAtom->setSUy( uy ); |
740 |
> |
dAtom->setSUz( uz ); |
741 |
> |
} |
742 |
> |
else{ |
743 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
744 |
> |
} |
745 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
746 |
> |
|
747 |
|
#ifdef IS_MPI |
748 |
+ |
|
749 |
+ |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
750 |
+ |
|
751 |
+ |
#endif // is_mpi |
752 |
+ |
} |
753 |
+ |
|
754 |
+ |
// make the bonds |
755 |
+ |
for(j=0; j<info.nBonds; j++){ |
756 |
+ |
|
757 |
+ |
currentBond = comp_stamps[stampID]->getBond( j ); |
758 |
+ |
theBonds[j].a = currentBond->getA() + atomOffset; |
759 |
+ |
theBonds[j].b = currentBond->getB() + atomOffset; |
760 |
|
|
761 |
< |
the_excludes[index*2] = |
762 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
747 |
< |
the_excludes[index*2 + 1] = |
748 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
761 |
> |
exI = theBonds[i].a; |
762 |
> |
exJ = theBonds[i].b; |
763 |
|
|
764 |
+ |
// exclude_I must always be the smaller of the pair |
765 |
+ |
if( exI > exJ ){ |
766 |
+ |
tempEx = exI; |
767 |
+ |
exI = exJ; |
768 |
+ |
exJ = tempEx; |
769 |
+ |
} |
770 |
+ |
#ifdef IS_MPI |
771 |
+ |
tempEx = exI; |
772 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
773 |
+ |
tempEx = exJ; |
774 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
775 |
+ |
|
776 |
+ |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
777 |
|
#else // isn't MPI |
778 |
< |
|
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) |
778 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
779 |
|
#endif //is_mpi |
780 |
< |
|
781 |
< |
// increment the index and repeat; |
758 |
< |
index++; |
759 |
< |
} |
760 |
< |
offset += comp_stamps[i]->getNAtoms(); |
761 |
< |
|
762 |
< |
#ifdef IS_MPI |
763 |
< |
} |
764 |
< |
#endif //is_mpi |
765 |
< |
|
766 |
< |
molIndex++; |
767 |
< |
} |
768 |
< |
} |
780 |
> |
} |
781 |
> |
excludeOffset += info.nBonds; |
782 |
|
|
783 |
< |
the_ff->initializeBonds( the_bonds ); |
784 |
< |
} |
785 |
< |
|
786 |
< |
void SimSetup::makeBends( void ){ |
787 |
< |
|
788 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
789 |
< |
bend_set* the_bends; |
777 |
< |
BendStamp* current_bend; |
778 |
< |
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 |
< |
|
790 |
< |
#ifdef IS_MPI |
791 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
792 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
793 |
< |
#endif // is_mpi |
794 |
< |
|
795 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
783 |
> |
//make the bends |
784 |
> |
for(j=0; j<info.nBends; j++){ |
785 |
> |
|
786 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
787 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
788 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
789 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
790 |
|
|
791 |
< |
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() ){ |
791 |
> |
if( currentBend->haveExtras() ){ |
792 |
|
|
793 |
< |
extras = current_bend->getExtras(); |
794 |
< |
current_extra = extras; |
793 |
> |
extras = current_bend->getExtras(); |
794 |
> |
current_extra = extras; |
795 |
|
|
796 |
< |
while( current_extra != NULL ){ |
797 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
796 |
> |
while( current_extra != NULL ){ |
797 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
798 |
|
|
799 |
< |
switch( current_extra->getType() ){ |
799 |
> |
switch( current_extra->getType() ){ |
800 |
> |
|
801 |
> |
case 0: |
802 |
> |
theBends[j].ghost = |
803 |
> |
current_extra->getInt() + atomOffset; |
804 |
> |
theBends[j].isGhost = 1; |
805 |
> |
break; |
806 |
|
|
807 |
< |
case 0: |
808 |
< |
the_bends[index].ghost = |
809 |
< |
current_extra->getInt() + offset; |
810 |
< |
the_bends[index].isGhost = 1; |
811 |
< |
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 |
< |
} |
807 |
> |
case 1: |
808 |
> |
theBends[j].ghost = |
809 |
> |
(int)current_extra->getDouble() + atomOffset; |
810 |
> |
theBends[j].isGhost = 1; |
811 |
> |
break; |
812 |
|
|
813 |
< |
else{ |
814 |
< |
|
815 |
< |
sprintf( painCave.errMsg, |
816 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
817 |
< |
" -->%s in Bend[%d] in %s\n", |
818 |
< |
current_extra->getlhs(), |
819 |
< |
k, comp_stamps[i]->getID() ); |
820 |
< |
painCave.isFatal = 1; |
843 |
< |
simError(); |
844 |
< |
} |
845 |
< |
|
846 |
< |
current_extra = current_extra->getNext(); |
813 |
> |
default: |
814 |
> |
sprintf( painCave.errMsg, |
815 |
> |
"SimSetup Error: ghostVectorSource was neiter a " |
816 |
> |
"double nor an int.\n" |
817 |
> |
"-->Bend[%d] in %s\n", |
818 |
> |
j, comp_stamps[stampID]->getID() ); |
819 |
> |
painCave.isFatal = 1; |
820 |
> |
simError(); |
821 |
|
} |
822 |
|
} |
823 |
|
|
850 |
– |
if( !the_bends[index].isGhost ){ |
851 |
– |
|
852 |
– |
exI = the_bends[index].a; |
853 |
– |
exJ = the_bends[index].c; |
854 |
– |
} |
824 |
|
else{ |
825 |
|
|
826 |
< |
exI = the_bends[index].a; |
827 |
< |
exJ = the_bends[index].b; |
826 |
> |
sprintf( painCave.errMsg, |
827 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
828 |
> |
" -->%s in Bend[%d] in %s\n", |
829 |
> |
current_extra->getlhs(), |
830 |
> |
j, comp_stamps[stampID]->getID() ); |
831 |
> |
painCave.isFatal = 1; |
832 |
> |
simError(); |
833 |
|
} |
834 |
|
|
835 |
< |
// exclude_I must always be the smaller of the pair |
836 |
< |
if( exI > exJ ){ |
837 |
< |
tempEx = exI; |
864 |
< |
exI = exJ; |
865 |
< |
exJ = tempEx; |
866 |
< |
} |
867 |
< |
|
868 |
< |
|
869 |
< |
#ifdef IS_MPI |
870 |
< |
|
871 |
< |
the_excludes[(index + tot_bonds)*2] = |
872 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
873 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
874 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
875 |
< |
|
876 |
< |
#else // isn't MPI |
877 |
< |
|
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) |
881 |
< |
#endif //is_mpi |
882 |
< |
|
835 |
> |
current_extra = current_extra->getNext(); |
836 |
> |
} |
837 |
> |
} |
838 |
|
|
839 |
< |
// increment the index and repeat; |
840 |
< |
index++; |
841 |
< |
} |
842 |
< |
offset += comp_stamps[i]->getNAtoms(); |
839 |
> |
if( !theBends[j].isGhost ){ |
840 |
> |
|
841 |
> |
exI = theBends[j].a; |
842 |
> |
exJ = theBends[j].c; |
843 |
> |
} |
844 |
> |
else{ |
845 |
|
|
846 |
< |
#ifdef IS_MPI |
846 |
> |
exI = theBends[j].a; |
847 |
> |
exJ = theBends[j].b; |
848 |
|
} |
849 |
< |
#endif //is_mpi |
850 |
< |
|
851 |
< |
molIndex++; |
849 |
> |
|
850 |
> |
// exclude_I must always be the smaller of the pair |
851 |
> |
if( exI > exJ ){ |
852 |
> |
tempEx = exI; |
853 |
> |
exI = exJ; |
854 |
> |
exJ = tempEx; |
855 |
> |
} |
856 |
> |
#ifdef IS_MPI |
857 |
> |
tempEx = exI; |
858 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
859 |
> |
tempEx = exJ; |
860 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
861 |
> |
|
862 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
863 |
> |
#else // isn't MPI |
864 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
865 |
> |
#endif //is_mpi |
866 |
|
} |
867 |
< |
} |
867 |
> |
excludeOffset += info.nBends; |
868 |
|
|
869 |
+ |
for(j=0; j<info.nTorsions; j++){ |
870 |
+ |
|
871 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
872 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
873 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
874 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
875 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
876 |
+ |
|
877 |
+ |
exI = theTorsions[j].a; |
878 |
+ |
exJ = theTorsions[j].d; |
879 |
+ |
|
880 |
+ |
// exclude_I must always be the smaller of the pair |
881 |
+ |
if( exI > exJ ){ |
882 |
+ |
tempEx = exI; |
883 |
+ |
exI = exJ; |
884 |
+ |
exJ = tempEx; |
885 |
+ |
} |
886 |
|
#ifdef IS_MPI |
887 |
< |
sprintf( checkPointMsg, |
888 |
< |
"Successfully created the bends list.\n" ); |
889 |
< |
MPIcheckPoint(); |
890 |
< |
#endif // is_mpi |
891 |
< |
|
887 |
> |
tempEx = exI; |
888 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
889 |
> |
tempEx = exJ; |
890 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
891 |
> |
|
892 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
893 |
> |
#else // isn't MPI |
894 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
895 |
> |
#endif //is_mpi |
896 |
> |
} |
897 |
> |
excludeOffset += info.nTorsions; |
898 |
|
|
899 |
< |
the_ff->initializeBends( the_bends ); |
900 |
< |
} |
906 |
< |
|
907 |
< |
void SimSetup::makeTorsions( void ){ |
899 |
> |
|
900 |
> |
// send the arrays off to the forceField for init. |
901 |
|
|
902 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
903 |
< |
torsion_set* the_torsions; |
904 |
< |
TorsionStamp* current_torsion; |
902 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
903 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
904 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
905 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
906 |
|
|
913 |
– |
the_torsions = new torsion_set[tot_torsions]; |
914 |
– |
index = 0; |
915 |
– |
offset = 0; |
916 |
– |
molIndex = 0; |
917 |
– |
for( i=0; i<n_components; i++ ){ |
907 |
|
|
908 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
909 |
< |
|
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 |
< |
} |
908 |
> |
the_molecules[i].initialize( info ); |
909 |
> |
atomOffset += info.nAtoms; |
910 |
|
} |
911 |
|
|
912 |
< |
the_ff->initializeTorsions( the_torsions ); |
912 |
> |
// clean up the forcefield |
913 |
> |
the_ff->calcRcut(); |
914 |
> |
the_ff->cleanMe(); |
915 |
|
} |
916 |
|
|
917 |
|
void SimSetup::initFromBass( void ){ |