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 |
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 |
– |
} |
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 |
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 |
|
|
668 |
|
strcpy( checkPointMsg, |
669 |
|
"Successfully intialized the mixingRule for Fortran." ); |
670 |
|
MPIcheckPoint(); |
671 |
+ |
#endif // is_mpi |
672 |
+ |
} |
673 |
+ |
|
674 |
+ |
|
675 |
+ |
void SimSetup::makeMolecules( void ){ |
676 |
+ |
|
677 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
678 |
+ |
molInit info; |
679 |
+ |
DirectionalAtom* dAtom; |
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 |
+ |
the_ff->readParams(); |
690 |
+ |
|
691 |
+ |
|
692 |
+ |
// init the molecules |
693 |
+ |
|
694 |
+ |
atomOffset = 0; |
695 |
+ |
excludeOffset = 0; |
696 |
+ |
for(i=0; i<simnfo->n_mol; i++){ |
697 |
+ |
|
698 |
+ |
stampID = the_molecules[i].getStampID(); |
699 |
+ |
|
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 |
+ |
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 |
+ |
theBonds = new bond_pair[info.nBonds]; |
713 |
+ |
theBends = new bend_set[info.nBends]; |
714 |
+ |
theTorsions = new torsion_set[info.nTorsions]; |
715 |
+ |
|
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 |
+ |
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 |
+ |
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 |
+ |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
779 |
+ |
#endif //is_mpi |
780 |
+ |
} |
781 |
+ |
excludeOffset += info.nBonds; |
782 |
+ |
|
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 |
+ |
if( currentBend->haveExtras() ){ |
792 |
+ |
|
793 |
+ |
extras = current_bend->getExtras(); |
794 |
+ |
current_extra = extras; |
795 |
+ |
|
796 |
+ |
while( current_extra != NULL ){ |
797 |
+ |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
798 |
+ |
|
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 1: |
808 |
+ |
theBends[j].ghost = |
809 |
+ |
(int)current_extra->getDouble() + atomOffset; |
810 |
+ |
theBends[j].isGhost = 1; |
811 |
+ |
break; |
812 |
+ |
|
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 |
+ |
|
824 |
+ |
else{ |
825 |
+ |
|
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 |
+ |
current_extra = current_extra->getNext(); |
836 |
+ |
} |
837 |
+ |
} |
838 |
+ |
|
839 |
+ |
if( !theBends[j].isGhost ){ |
840 |
+ |
|
841 |
+ |
exI = theBends[j].a; |
842 |
+ |
exJ = theBends[j].c; |
843 |
+ |
} |
844 |
+ |
else{ |
845 |
+ |
|
846 |
+ |
exI = theBends[j].a; |
847 |
+ |
exJ = theBends[j].b; |
848 |
+ |
} |
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 |
+ |
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 |
+ |
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 |
+ |
|
900 |
+ |
// send the arrays off to the forceField for init. |
901 |
+ |
|
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 |
+ |
|
907 |
+ |
|
908 |
+ |
the_molecules[i].initialize( info ); |
909 |
+ |
atomOffset += info.nAtoms; |
910 |
+ |
} |
911 |
+ |
|
912 |
+ |
// clean up the forcefield |
913 |
+ |
|
914 |
+ |
the_ff->cleanMe(); |
915 |
|
} |
916 |
+ |
|
917 |
+ |
|
918 |
|
|
919 |
|
void SimSetup::makeAtoms( void ){ |
920 |
|
|