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 |
> |
Exclude::createArray(simnfo->n_SRI); |
339 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
340 |
|
simnfo->globalExcludes = new int; |
341 |
|
simnfo->n_exclude = tot_SRI; |
342 |
|
} |
343 |
|
else{ |
344 |
|
|
345 |
< |
the_excludes = new int[2]; |
346 |
< |
the_excludes[0] = 0; |
347 |
< |
the_excludes[1] = 0; |
345 |
> |
Exclude::createArray( 1 ); |
346 |
> |
the_excludes = new Exclude*; |
347 |
> |
the_excludes[0] = new Exclude(0); |
348 |
> |
the_excludes[0]->setPair( 0,0 ); |
349 |
|
simnfo->globalExcludes = new int; |
350 |
|
simnfo->globalExcludes[0] = 0; |
351 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
351 |
> |
simnfo->n_exclude = 0; |
352 |
|
} |
353 |
|
|
354 |
|
// set the arrays into the SimInfo object |
355 |
|
|
356 |
|
simnfo->atoms = the_atoms; |
329 |
– |
simnfo->sr_interactions = the_sris; |
357 |
|
simnfo->nGlobalExcludes = 0; |
358 |
|
simnfo->excludes = the_excludes; |
359 |
|
|
410 |
|
|
411 |
|
the_ff->setSimInfo( simnfo ); |
412 |
|
|
413 |
< |
makeAtoms(); |
413 |
> |
makeMolecules(); |
414 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
415 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
416 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
417 |
|
} |
418 |
|
|
392 |
– |
if( tot_bonds ){ |
393 |
– |
makeBonds(); |
394 |
– |
} |
395 |
– |
|
396 |
– |
if( tot_bends ){ |
397 |
– |
makeBends(); |
398 |
– |
} |
399 |
– |
|
400 |
– |
if( tot_torsions ){ |
401 |
– |
makeTorsions(); |
402 |
– |
} |
403 |
– |
|
404 |
– |
|
419 |
|
if (the_globals->getUseRF() ) { |
420 |
|
simnfo->useReactionField = 1; |
421 |
|
|
652 |
|
|
653 |
|
// new AllLong( simnfo ); |
654 |
|
|
641 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
655 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
656 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
657 |
|
|
683 |
|
#endif // is_mpi |
684 |
|
} |
685 |
|
|
686 |
< |
void SimSetup::makeAtoms( void ){ |
686 |
> |
|
687 |
> |
void SimSetup::makeMolecules( void ){ |
688 |
|
|
689 |
< |
int i, j, k, index; |
690 |
< |
double ux, uy, uz, uSqr, u; |
678 |
< |
AtomStamp* current_atom; |
679 |
< |
|
689 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
690 |
> |
molInit info; |
691 |
|
DirectionalAtom* dAtom; |
692 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
692 |
> |
LinkedAssign* extras; |
693 |
> |
LinkedAssign* current_extra; |
694 |
> |
AtomStamp* currentAtom; |
695 |
> |
BondStamp* currentBond; |
696 |
> |
BendStamp* currentBend; |
697 |
> |
TorsionStamp* currentTorsion; |
698 |
> |
|
699 |
> |
//init the forceField paramters |
700 |
|
|
701 |
< |
lMolIndex = 0; |
684 |
< |
molIndex = 0; |
685 |
< |
index = 0; |
686 |
< |
for( i=0; i<n_components; i++ ){ |
701 |
> |
the_ff->readParams(); |
702 |
|
|
703 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
703 |
> |
|
704 |
> |
// init the molecules |
705 |
|
|
706 |
< |
#ifdef IS_MPI |
707 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
708 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
709 |
< |
#endif // is_mpi |
706 |
> |
atomOffset = 0; |
707 |
> |
excludeOffset = 0; |
708 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
709 |
> |
|
710 |
> |
stampID = the_molecules[i].getStampID(); |
711 |
|
|
712 |
< |
molStart = index; |
713 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
714 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
715 |
< |
|
716 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
700 |
< |
if( current_atom->haveOrientation() ){ |
701 |
< |
|
702 |
< |
dAtom = new DirectionalAtom(index); |
703 |
< |
simnfo->n_oriented++; |
704 |
< |
the_atoms[index] = dAtom; |
705 |
< |
|
706 |
< |
ux = current_atom->getOrntX(); |
707 |
< |
uy = current_atom->getOrntY(); |
708 |
< |
uz = current_atom->getOrntZ(); |
709 |
< |
|
710 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
711 |
< |
|
712 |
< |
u = sqrt( uSqr ); |
713 |
< |
ux = ux / u; |
714 |
< |
uy = uy / u; |
715 |
< |
uz = uz / u; |
716 |
< |
|
717 |
< |
dAtom->setSUx( ux ); |
718 |
< |
dAtom->setSUy( uy ); |
719 |
< |
dAtom->setSUz( uz ); |
720 |
< |
} |
721 |
< |
else{ |
722 |
< |
the_atoms[index] = new GeneralAtom(index); |
723 |
< |
} |
724 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
725 |
< |
the_atoms[index]->setIndex( index ); |
726 |
< |
|
727 |
< |
// increment the index and repeat; |
728 |
< |
index++; |
729 |
< |
} |
730 |
< |
|
731 |
< |
molEnd = index -1; |
732 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
733 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
734 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
735 |
< |
the_molecules[lMolIndex].setStampID( i ); |
736 |
< |
lMolIndex++; |
737 |
< |
|
738 |
< |
#ifdef IS_MPI |
739 |
< |
} |
740 |
< |
#endif //is_mpi |
741 |
< |
|
742 |
< |
molIndex++; |
743 |
< |
} |
744 |
< |
} |
712 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
713 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
714 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
715 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
716 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
717 |
|
|
718 |
< |
#ifdef IS_MPI |
719 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
720 |
< |
|
721 |
< |
delete[] globalIndex; |
718 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
719 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
720 |
> |
info.myBonds = new Bond*[info.nBonds]; |
721 |
> |
info.myBends = new Bend*[info.nBends]; |
722 |
> |
info.myTorsions = new Torsions*[info.nTorsions]; |
723 |
|
|
724 |
< |
mpiSim->mpiRefresh(); |
725 |
< |
#endif //IS_MPI |
726 |
< |
|
727 |
< |
the_ff->initializeAtoms(); |
728 |
< |
} |
729 |
< |
|
730 |
< |
void SimSetup::makeBonds( void ){ |
731 |
< |
|
732 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
733 |
< |
bond_pair* the_bonds; |
761 |
< |
BondStamp* current_bond; |
762 |
< |
|
763 |
< |
the_bonds = new bond_pair[tot_bonds]; |
764 |
< |
index = 0; |
765 |
< |
offset = 0; |
766 |
< |
molIndex = 0; |
767 |
< |
|
768 |
< |
for( i=0; i<n_components; i++ ){ |
769 |
< |
|
770 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
771 |
< |
|
772 |
< |
#ifdef IS_MPI |
773 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
774 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
775 |
< |
#endif // is_mpi |
724 |
> |
theBonds = new bond_pair[info.nBonds]; |
725 |
> |
theBends = new bend_set[info.nBends]; |
726 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
727 |
> |
|
728 |
> |
// make the Atoms |
729 |
> |
|
730 |
> |
for(j=0; j<info.nAtoms; j++){ |
731 |
> |
|
732 |
> |
currentAtom = theComponents[stampID]->getAtom( j ); |
733 |
> |
if( currentAtom->haveOrientation() ){ |
734 |
|
|
735 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
736 |
< |
|
737 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
780 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
781 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
782 |
< |
|
783 |
< |
exI = the_bonds[index].a; |
784 |
< |
exJ = the_bonds[index].b; |
785 |
< |
|
786 |
< |
// exclude_I must always be the smaller of the pair |
787 |
< |
if( exI > exJ ){ |
788 |
< |
tempEx = exI; |
789 |
< |
exI = exJ; |
790 |
< |
exJ = tempEx; |
791 |
< |
} |
792 |
< |
|
793 |
< |
|
794 |
< |
#ifdef IS_MPI |
795 |
< |
|
796 |
< |
the_excludes[index*2] = |
797 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
798 |
< |
the_excludes[index*2 + 1] = |
799 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
800 |
< |
|
801 |
< |
#else // isn't MPI |
802 |
< |
|
803 |
< |
the_excludes[index*2] = exI + 1; |
804 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
805 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
806 |
< |
#endif //is_mpi |
807 |
< |
|
808 |
< |
// increment the index and repeat; |
809 |
< |
index++; |
810 |
< |
} |
811 |
< |
offset += comp_stamps[i]->getNAtoms(); |
735 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
736 |
> |
simnfo->n_oriented++; |
737 |
> |
info.myAtoms[j] = dAtom; |
738 |
|
|
739 |
< |
#ifdef IS_MPI |
739 |
> |
ux = currentAtom->getOrntX(); |
740 |
> |
uy = currentAtom->getOrntY(); |
741 |
> |
uz = currentAtom->getOrntZ(); |
742 |
> |
|
743 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
744 |
> |
|
745 |
> |
u = sqrt( uSqr ); |
746 |
> |
ux = ux / u; |
747 |
> |
uy = uy / u; |
748 |
> |
uz = uz / u; |
749 |
> |
|
750 |
> |
dAtom->setSUx( ux ); |
751 |
> |
dAtom->setSUy( uy ); |
752 |
> |
dAtom->setSUz( uz ); |
753 |
|
} |
754 |
< |
#endif //is_mpi |
754 |
> |
else{ |
755 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
756 |
> |
} |
757 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
758 |
> |
|
759 |
> |
#ifdef IS_MPI |
760 |
|
|
761 |
< |
molIndex++; |
762 |
< |
} |
763 |
< |
} |
761 |
> |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
762 |
> |
|
763 |
> |
#endif // is_mpi |
764 |
> |
} |
765 |
> |
|
766 |
> |
// make the bonds |
767 |
> |
for(j=0; j<info.nBonds; j++){ |
768 |
> |
|
769 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
770 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
771 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
772 |
|
|
773 |
< |
the_ff->initializeBonds( the_bonds ); |
774 |
< |
} |
773 |
> |
exI = theBonds[i].a; |
774 |
> |
exJ = theBonds[i].b; |
775 |
|
|
776 |
< |
void SimSetup::makeBends( void ){ |
777 |
< |
|
778 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
779 |
< |
bend_set* the_bends; |
780 |
< |
BendStamp* current_bend; |
781 |
< |
LinkedAssign* extras; |
782 |
< |
LinkedAssign* current_extra; |
783 |
< |
|
784 |
< |
|
785 |
< |
the_bends = new bend_set[tot_bends]; |
786 |
< |
index = 0; |
787 |
< |
offset = 0; |
788 |
< |
molIndex = 0; |
789 |
< |
for( i=0; i<n_components; i++ ){ |
790 |
< |
|
791 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
792 |
< |
|
793 |
< |
#ifdef IS_MPI |
842 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
843 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
844 |
< |
#endif // is_mpi |
776 |
> |
// exclude_I must always be the smaller of the pair |
777 |
> |
if( exI > exJ ){ |
778 |
> |
tempEx = exI; |
779 |
> |
exI = exJ; |
780 |
> |
exJ = tempEx; |
781 |
> |
} |
782 |
> |
#ifdef IS_MPI |
783 |
> |
tempEx = exI; |
784 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
785 |
> |
tempEx = exJ; |
786 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
787 |
> |
|
788 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
789 |
> |
#else // isn't MPI |
790 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
791 |
> |
#endif //is_mpi |
792 |
> |
} |
793 |
> |
excludeOffset += info.nBonds; |
794 |
|
|
795 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
795 |
> |
//make the bends |
796 |
> |
for(j=0; j<info.nBends; j++){ |
797 |
> |
|
798 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
799 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
800 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
801 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
802 |
|
|
803 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
849 |
< |
the_bends[index].a = current_bend->getA() + offset; |
850 |
< |
the_bends[index].b = current_bend->getB() + offset; |
851 |
< |
the_bends[index].c = current_bend->getC() + offset; |
852 |
< |
|
853 |
< |
if( current_bend->haveExtras() ){ |
803 |
> |
if( currentBend->haveExtras() ){ |
804 |
|
|
805 |
< |
extras = current_bend->getExtras(); |
806 |
< |
current_extra = extras; |
805 |
> |
extras = current_bend->getExtras(); |
806 |
> |
current_extra = extras; |
807 |
|
|
808 |
< |
while( current_extra != NULL ){ |
809 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
808 |
> |
while( current_extra != NULL ){ |
809 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
810 |
|
|
811 |
< |
switch( current_extra->getType() ){ |
811 |
> |
switch( current_extra->getType() ){ |
812 |
> |
|
813 |
> |
case 0: |
814 |
> |
theBends[j].ghost = |
815 |
> |
current_extra->getInt() + atomOffset; |
816 |
> |
theBends[j].isGhost = 1; |
817 |
> |
break; |
818 |
|
|
819 |
< |
case 0: |
820 |
< |
the_bends[index].ghost = |
821 |
< |
current_extra->getInt() + offset; |
822 |
< |
the_bends[index].isGhost = 1; |
823 |
< |
break; |
868 |
< |
|
869 |
< |
case 1: |
870 |
< |
the_bends[index].ghost = |
871 |
< |
(int)current_extra->getDouble() + offset; |
872 |
< |
the_bends[index].isGhost = 1; |
873 |
< |
break; |
874 |
< |
|
875 |
< |
default: |
876 |
< |
sprintf( painCave.errMsg, |
877 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
878 |
< |
"double nor an int.\n" |
879 |
< |
"-->Bend[%d] in %s\n", |
880 |
< |
k, comp_stamps[i]->getID() ); |
881 |
< |
painCave.isFatal = 1; |
882 |
< |
simError(); |
883 |
< |
} |
884 |
< |
} |
819 |
> |
case 1: |
820 |
> |
theBends[j].ghost = |
821 |
> |
(int)current_extra->getDouble() + atomOffset; |
822 |
> |
theBends[j].isGhost = 1; |
823 |
> |
break; |
824 |
|
|
825 |
< |
else{ |
826 |
< |
|
827 |
< |
sprintf( painCave.errMsg, |
828 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
829 |
< |
" -->%s in Bend[%d] in %s\n", |
830 |
< |
current_extra->getlhs(), |
831 |
< |
k, comp_stamps[i]->getID() ); |
832 |
< |
painCave.isFatal = 1; |
894 |
< |
simError(); |
895 |
< |
} |
896 |
< |
|
897 |
< |
current_extra = current_extra->getNext(); |
825 |
> |
default: |
826 |
> |
sprintf( painCave.errMsg, |
827 |
> |
"SimSetup Error: ghostVectorSource was neiter a " |
828 |
> |
"double nor an int.\n" |
829 |
> |
"-->Bend[%d] in %s\n", |
830 |
> |
j, comp_stamps[stampID]->getID() ); |
831 |
> |
painCave.isFatal = 1; |
832 |
> |
simError(); |
833 |
|
} |
834 |
|
} |
835 |
|
|
901 |
– |
if( !the_bends[index].isGhost ){ |
902 |
– |
|
903 |
– |
exI = the_bends[index].a; |
904 |
– |
exJ = the_bends[index].c; |
905 |
– |
} |
836 |
|
else{ |
837 |
|
|
838 |
< |
exI = the_bends[index].a; |
839 |
< |
exJ = the_bends[index].b; |
838 |
> |
sprintf( painCave.errMsg, |
839 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
840 |
> |
" -->%s in Bend[%d] in %s\n", |
841 |
> |
current_extra->getlhs(), |
842 |
> |
j, comp_stamps[stampID]->getID() ); |
843 |
> |
painCave.isFatal = 1; |
844 |
> |
simError(); |
845 |
|
} |
846 |
|
|
847 |
< |
// exclude_I must always be the smaller of the pair |
913 |
< |
if( exI > exJ ){ |
914 |
< |
tempEx = exI; |
915 |
< |
exI = exJ; |
916 |
< |
exJ = tempEx; |
917 |
< |
} |
918 |
< |
|
919 |
< |
|
920 |
< |
#ifdef IS_MPI |
921 |
< |
|
922 |
< |
the_excludes[(index + tot_bonds)*2] = |
923 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
924 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
925 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
926 |
< |
|
927 |
< |
#else // isn't MPI |
928 |
< |
|
929 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
930 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
931 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
932 |
< |
#endif //is_mpi |
933 |
< |
|
934 |
< |
|
935 |
< |
// increment the index and repeat; |
936 |
< |
index++; |
847 |
> |
current_extra = current_extra->getNext(); |
848 |
|
} |
938 |
– |
offset += comp_stamps[i]->getNAtoms(); |
939 |
– |
|
940 |
– |
#ifdef IS_MPI |
849 |
|
} |
850 |
< |
#endif //is_mpi |
851 |
< |
|
852 |
< |
molIndex++; |
853 |
< |
} |
854 |
< |
} |
855 |
< |
|
850 |
> |
|
851 |
> |
if( !theBends[j].isGhost ){ |
852 |
> |
|
853 |
> |
exI = theBends[j].a; |
854 |
> |
exJ = theBends[j].c; |
855 |
> |
} |
856 |
> |
else{ |
857 |
> |
|
858 |
> |
exI = theBends[j].a; |
859 |
> |
exJ = theBends[j].b; |
860 |
> |
} |
861 |
> |
|
862 |
> |
// exclude_I must always be the smaller of the pair |
863 |
> |
if( exI > exJ ){ |
864 |
> |
tempEx = exI; |
865 |
> |
exI = exJ; |
866 |
> |
exJ = tempEx; |
867 |
> |
} |
868 |
|
#ifdef IS_MPI |
869 |
< |
sprintf( checkPointMsg, |
870 |
< |
"Successfully created the bends list.\n" ); |
871 |
< |
MPIcheckPoint(); |
872 |
< |
#endif // is_mpi |
873 |
< |
|
869 |
> |
tempEx = exI; |
870 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
871 |
> |
tempEx = exJ; |
872 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
873 |
> |
|
874 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
875 |
> |
#else // isn't MPI |
876 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
877 |
> |
#endif //is_mpi |
878 |
> |
} |
879 |
> |
excludeOffset += info.nBends; |
880 |
|
|
881 |
< |
the_ff->initializeBends( the_bends ); |
882 |
< |
} |
881 |
> |
for(j=0; j<info.nTorsions; j++){ |
882 |
> |
|
883 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
884 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
885 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
886 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
887 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
888 |
> |
|
889 |
> |
exI = theTorsions[j].a; |
890 |
> |
exJ = theTorsions[j].d; |
891 |
|
|
892 |
< |
void SimSetup::makeTorsions( void ){ |
893 |
< |
|
894 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
895 |
< |
torsion_set* the_torsions; |
896 |
< |
TorsionStamp* current_torsion; |
897 |
< |
|
964 |
< |
the_torsions = new torsion_set[tot_torsions]; |
965 |
< |
index = 0; |
966 |
< |
offset = 0; |
967 |
< |
molIndex = 0; |
968 |
< |
for( i=0; i<n_components; i++ ){ |
969 |
< |
|
970 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
971 |
< |
|
892 |
> |
// exclude_I must always be the smaller of the pair |
893 |
> |
if( exI > exJ ){ |
894 |
> |
tempEx = exI; |
895 |
> |
exI = exJ; |
896 |
> |
exJ = tempEx; |
897 |
> |
} |
898 |
|
#ifdef IS_MPI |
899 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
900 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
901 |
< |
#endif // is_mpi |
902 |
< |
|
903 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
904 |
< |
|
979 |
< |
current_torsion = comp_stamps[i]->getTorsion( k ); |
980 |
< |
the_torsions[index].a = current_torsion->getA() + offset; |
981 |
< |
the_torsions[index].b = current_torsion->getB() + offset; |
982 |
< |
the_torsions[index].c = current_torsion->getC() + offset; |
983 |
< |
the_torsions[index].d = current_torsion->getD() + offset; |
984 |
< |
|
985 |
< |
exI = the_torsions[index].a; |
986 |
< |
exJ = the_torsions[index].d; |
987 |
< |
|
988 |
< |
|
989 |
< |
// exclude_I must always be the smaller of the pair |
990 |
< |
if( exI > exJ ){ |
991 |
< |
tempEx = exI; |
992 |
< |
exI = exJ; |
993 |
< |
exJ = tempEx; |
994 |
< |
} |
995 |
< |
|
996 |
< |
|
997 |
< |
#ifdef IS_MPI |
998 |
< |
|
999 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
1000 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1001 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1002 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1003 |
< |
|
899 |
> |
tempEx = exI; |
900 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
901 |
> |
tempEx = exJ; |
902 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
903 |
> |
|
904 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
905 |
|
#else // isn't MPI |
906 |
< |
|
1006 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1007 |
< |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1008 |
< |
// fortran indexes from 1 (hence the +1 in the indexing) |
906 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
907 |
|
#endif //is_mpi |
908 |
< |
|
908 |
> |
} |
909 |
> |
excludeOffset += info.nTorsions; |
910 |
|
|
911 |
< |
// increment the index and repeat; |
912 |
< |
index++; |
1014 |
< |
} |
1015 |
< |
offset += comp_stamps[i]->getNAtoms(); |
911 |
> |
|
912 |
> |
// send the arrays off to the forceField for init. |
913 |
|
|
914 |
< |
#ifdef IS_MPI |
915 |
< |
} |
916 |
< |
#endif //is_mpi |
914 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
915 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
916 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
917 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
918 |
|
|
919 |
< |
molIndex++; |
920 |
< |
} |
919 |
> |
|
920 |
> |
the_molecules[i].initialize( info ); |
921 |
> |
atomOffset += info.nAtoms; |
922 |
|
} |
923 |
|
|
924 |
< |
the_ff->initializeTorsions( the_torsions ); |
924 |
> |
// clean up the forcefield |
925 |
> |
the_ff->calcRcut(); |
926 |
> |
the_ff->cleanMe(); |
927 |
|
} |
928 |
|
|
929 |
|
void SimSetup::initFromBass( void ){ |