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 |
< |
|
772 |
< |
the_excludes[index*2] = |
773 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
774 |
< |
the_excludes[index*2 + 1] = |
770 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
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 |
< |
|
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 |
< |
} |
781 |
< |
|
782 |
< |
|
783 |
< |
|
784 |
< |
|
785 |
< |
|
786 |
< |
|
787 |
< |
|
788 |
< |
|
789 |
< |
|
790 |
< |
|
791 |
< |
|
792 |
< |
|
793 |
< |
|
794 |
< |
|
795 |
< |
|
796 |
< |
void SimSetup::makeAtoms( void ){ |
797 |
< |
|
798 |
< |
int i, j, k, index; |
799 |
< |
double ux, uy, uz, uSqr, u; |
800 |
< |
AtomStamp* current_atom; |
801 |
< |
|
802 |
< |
DirectionalAtom* dAtom; |
803 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
780 |
> |
} |
781 |
> |
excludeOffset += info.nBonds; |
782 |
|
|
783 |
< |
lMolIndex = 0; |
784 |
< |
molIndex = 0; |
785 |
< |
index = 0; |
786 |
< |
for( i=0; i<n_components; i++ ){ |
787 |
< |
|
788 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
789 |
< |
|
812 |
< |
#ifdef IS_MPI |
813 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
814 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
815 |
< |
#endif // is_mpi |
816 |
< |
|
817 |
< |
molStart = index; |
818 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
819 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); 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_atom = comp_stamps[i]->getAtom( k ); |
822 |
< |
if( current_atom->haveOrientation() ){ |
791 |
> |
if( currentBend->haveExtras() ){ |
792 |
|
|
793 |
< |
dAtom = new DirectionalAtom(index); |
794 |
< |
simnfo->n_oriented++; |
826 |
< |
the_atoms[index] = dAtom; |
793 |
> |
extras = current_bend->getExtras(); |
794 |
> |
current_extra = extras; |
795 |
|
|
796 |
< |
ux = current_atom->getOrntX(); |
797 |
< |
uy = current_atom->getOrntY(); |
830 |
< |
uz = current_atom->getOrntZ(); |
831 |
< |
|
832 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
833 |
< |
|
834 |
< |
u = sqrt( uSqr ); |
835 |
< |
ux = ux / u; |
836 |
< |
uy = uy / u; |
837 |
< |
uz = uz / u; |
838 |
< |
|
839 |
< |
dAtom->setSUx( ux ); |
840 |
< |
dAtom->setSUy( uy ); |
841 |
< |
dAtom->setSUz( uz ); |
842 |
< |
} |
843 |
< |
else{ |
844 |
< |
the_atoms[index] = new GeneralAtom(index); |
845 |
< |
} |
846 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
847 |
< |
the_atoms[index]->setIndex( index ); |
848 |
< |
|
849 |
< |
// increment the index and repeat; |
850 |
< |
index++; |
851 |
< |
} |
852 |
< |
|
853 |
< |
molEnd = index -1; |
854 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
855 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
856 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
857 |
< |
the_molecules[lMolIndex].setStampID( i ); |
858 |
< |
lMolIndex++; |
859 |
< |
|
860 |
< |
#ifdef IS_MPI |
861 |
< |
} |
862 |
< |
#endif //is_mpi |
863 |
< |
|
864 |
< |
molIndex++; |
865 |
< |
} |
866 |
< |
} |
867 |
< |
|
868 |
< |
#ifdef IS_MPI |
869 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
870 |
< |
|
871 |
< |
delete[] globalIndex; |
872 |
< |
|
873 |
< |
mpiSim->mpiRefresh(); |
874 |
< |
#endif //IS_MPI |
875 |
< |
|
876 |
< |
the_ff->initializeAtoms(); |
877 |
< |
} |
878 |
< |
|
879 |
< |
void SimSetup::makeBonds( void ){ |
880 |
< |
|
881 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
882 |
< |
bond_pair* the_bonds; |
883 |
< |
BondStamp* current_bond; |
884 |
< |
|
885 |
< |
the_bonds = new bond_pair[tot_bonds]; |
886 |
< |
index = 0; |
887 |
< |
offset = 0; |
888 |
< |
molIndex = 0; |
889 |
< |
|
890 |
< |
for( i=0; i<n_components; i++ ){ |
891 |
< |
|
892 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
893 |
< |
|
894 |
< |
#ifdef IS_MPI |
895 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
896 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
897 |
< |
#endif // is_mpi |
898 |
< |
|
899 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
900 |
< |
|
901 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
902 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
903 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
904 |
< |
|
905 |
< |
exI = the_bonds[index].a; |
906 |
< |
exJ = the_bonds[index].b; |
907 |
< |
|
908 |
< |
// exclude_I must always be the smaller of the pair |
909 |
< |
if( exI > exJ ){ |
910 |
< |
tempEx = exI; |
911 |
< |
exI = exJ; |
912 |
< |
exJ = tempEx; |
913 |
< |
} |
914 |
< |
|
915 |
< |
|
916 |
< |
#ifdef IS_MPI |
917 |
< |
|
918 |
< |
the_excludes[index*2] = |
919 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
920 |
< |
the_excludes[index*2 + 1] = |
921 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
922 |
< |
|
923 |
< |
#else // isn't MPI |
924 |
< |
|
925 |
< |
the_excludes[index*2] = exI + 1; |
926 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
927 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
928 |
< |
#endif //is_mpi |
929 |
< |
|
930 |
< |
// increment the index and repeat; |
931 |
< |
index++; |
932 |
< |
} |
933 |
< |
offset += comp_stamps[i]->getNAtoms(); |
934 |
< |
|
935 |
< |
#ifdef IS_MPI |
936 |
< |
} |
937 |
< |
#endif //is_mpi |
938 |
< |
|
939 |
< |
molIndex++; |
940 |
< |
} |
941 |
< |
} |
942 |
< |
|
943 |
< |
the_ff->initializeBonds( the_bonds ); |
944 |
< |
} |
945 |
< |
|
946 |
< |
void SimSetup::makeBends( void ){ |
947 |
< |
|
948 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
949 |
< |
bend_set* the_bends; |
950 |
< |
BendStamp* current_bend; |
951 |
< |
LinkedAssign* extras; |
952 |
< |
LinkedAssign* current_extra; |
953 |
< |
|
954 |
< |
|
955 |
< |
the_bends = new bend_set[tot_bends]; |
956 |
< |
index = 0; |
957 |
< |
offset = 0; |
958 |
< |
molIndex = 0; |
959 |
< |
for( i=0; i<n_components; i++ ){ |
960 |
< |
|
961 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
962 |
< |
|
963 |
< |
#ifdef IS_MPI |
964 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
965 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
966 |
< |
#endif // is_mpi |
967 |
< |
|
968 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
969 |
< |
|
970 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
971 |
< |
the_bends[index].a = current_bend->getA() + offset; |
972 |
< |
the_bends[index].b = current_bend->getB() + offset; |
973 |
< |
the_bends[index].c = current_bend->getC() + offset; |
974 |
< |
|
975 |
< |
if( current_bend->haveExtras() ){ |
976 |
< |
|
977 |
< |
extras = current_bend->getExtras(); |
978 |
< |
current_extra = extras; |
979 |
< |
|
980 |
< |
while( current_extra != NULL ){ |
981 |
< |
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; |
990 |
< |
|
991 |
< |
case 1: |
992 |
< |
the_bends[index].ghost = |
993 |
< |
(int)current_extra->getDouble() + offset; |
994 |
< |
the_bends[index].isGhost = 1; |
995 |
< |
break; |
996 |
< |
|
997 |
< |
default: |
998 |
< |
sprintf( painCave.errMsg, |
999 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
1000 |
< |
"double nor an int.\n" |
1001 |
< |
"-->Bend[%d] in %s\n", |
1002 |
< |
k, comp_stamps[i]->getID() ); |
1003 |
< |
painCave.isFatal = 1; |
1004 |
< |
simError(); |
1005 |
< |
} |
1006 |
< |
} |
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; |
1016 |
< |
simError(); |
1017 |
< |
} |
1018 |
< |
|
1019 |
< |
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 |
|
|
1023 |
– |
if( !the_bends[index].isGhost ){ |
1024 |
– |
|
1025 |
– |
exI = the_bends[index].a; |
1026 |
– |
exJ = the_bends[index].c; |
1027 |
– |
} |
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 |
1035 |
< |
if( exI > exJ ){ |
1036 |
< |
tempEx = exI; |
1037 |
< |
exI = exJ; |
1038 |
< |
exJ = tempEx; |
1039 |
< |
} |
1040 |
< |
|
1041 |
< |
|
1042 |
< |
#ifdef IS_MPI |
1043 |
< |
|
1044 |
< |
the_excludes[(index + tot_bonds)*2] = |
1045 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1046 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
1047 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1048 |
< |
|
1049 |
< |
#else // isn't MPI |
1050 |
< |
|
1051 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
1052 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1053 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
1054 |
< |
#endif //is_mpi |
1055 |
< |
|
1056 |
< |
|
1057 |
< |
// increment the index and repeat; |
1058 |
< |
index++; |
835 |
> |
current_extra = current_extra->getNext(); |
836 |
|
} |
837 |
< |
offset += comp_stamps[i]->getNAtoms(); |
837 |
> |
} |
838 |
> |
|
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++; |
852 |
< |
} |
853 |
< |
} |
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 |
< |
#ifdef IS_MPI |
870 |
< |
sprintf( checkPointMsg, |
871 |
< |
"Successfully created the bends list.\n" ); |
872 |
< |
MPIcheckPoint(); |
873 |
< |
#endif // is_mpi |
874 |
< |
|
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 |
< |
the_ff->initializeBends( the_bends ); |
881 |
< |
} |
882 |
< |
|
883 |
< |
void SimSetup::makeTorsions( void ){ |
884 |
< |
|
885 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1083 |
< |
torsion_set* the_torsions; |
1084 |
< |
TorsionStamp* current_torsion; |
1085 |
< |
|
1086 |
< |
the_torsions = new torsion_set[tot_torsions]; |
1087 |
< |
index = 0; |
1088 |
< |
offset = 0; |
1089 |
< |
molIndex = 0; |
1090 |
< |
for( i=0; i<n_components; i++ ){ |
1091 |
< |
|
1092 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1093 |
< |
|
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 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
888 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
889 |
< |
#endif // is_mpi |
890 |
< |
|
891 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
892 |
< |
|
1101 |
< |
current_torsion = comp_stamps[i]->getTorsion( k ); |
1102 |
< |
the_torsions[index].a = current_torsion->getA() + offset; |
1103 |
< |
the_torsions[index].b = current_torsion->getB() + offset; |
1104 |
< |
the_torsions[index].c = current_torsion->getC() + offset; |
1105 |
< |
the_torsions[index].d = current_torsion->getD() + offset; |
1106 |
< |
|
1107 |
< |
exI = the_torsions[index].a; |
1108 |
< |
exJ = the_torsions[index].d; |
1109 |
< |
|
1110 |
< |
|
1111 |
< |
// exclude_I must always be the smaller of the pair |
1112 |
< |
if( exI > exJ ){ |
1113 |
< |
tempEx = exI; |
1114 |
< |
exI = exJ; |
1115 |
< |
exJ = tempEx; |
1116 |
< |
} |
1117 |
< |
|
1118 |
< |
|
1119 |
< |
#ifdef IS_MPI |
1120 |
< |
|
1121 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
1122 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1123 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1124 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1125 |
< |
|
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 |
< |
|
1128 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1129 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1130 |
< |
// fortran indexes from 1 (hence the +1 in the indexing) |
894 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
895 |
|
#endif //is_mpi |
896 |
< |
|
896 |
> |
} |
897 |
> |
excludeOffset += info.nTorsions; |
898 |
|
|
899 |
< |
// increment the index and repeat; |
900 |
< |
index++; |
1136 |
< |
} |
1137 |
< |
offset += comp_stamps[i]->getNAtoms(); |
899 |
> |
|
900 |
> |
// send the arrays off to the forceField for init. |
901 |
|
|
902 |
< |
#ifdef IS_MPI |
903 |
< |
} |
904 |
< |
#endif //is_mpi |
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 |
< |
molIndex++; |
908 |
< |
} |
907 |
> |
|
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 ){ |