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 |
674 |
|
|
675 |
|
void SimSetup::makeMolecules( void ){ |
676 |
|
|
677 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset; |
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; |
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(); |
701 |
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
702 |
|
info.nBends = comp_stamps[stampID]->getNBends(); |
703 |
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
704 |
< |
|
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]; |
752 |
|
} |
753 |
|
|
754 |
|
// make the bonds |
755 |
< |
for(j=0; j<nBonds; j++){ |
755 |
> |
for(j=0; j<info.nBonds; j++){ |
756 |
|
|
757 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
758 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
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[index*2] = |
768 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
769 |
< |
the_excludes[index*2 + 1] = |
770 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
771 |
< |
|
776 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
777 |
|
#else // isn't MPI |
778 |
< |
|
774 |
< |
the_excludes[index*2] = exI + 1; |
775 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
776 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
777 |
< |
|
778 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
779 |
|
#endif //is_mpi |
780 |
< |
|
781 |
< |
} |
780 |
> |
} |
781 |
> |
excludeOffset += info.nBonds; |
782 |
|
|
783 |
< |
|
784 |
< |
|
785 |
< |
|
786 |
< |
|
787 |
< |
|
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 |
|
|
901 |
|
|
902 |
|
|