240 |
|
|
241 |
|
globalIndex = mpiSim->divideLabor(); |
242 |
|
|
243 |
– |
|
244 |
– |
|
243 |
|
// set up the local variables |
244 |
|
|
245 |
|
int localMol, allMol; |
314 |
|
|
315 |
|
if(mol2proc[i] == worldRank ){ |
316 |
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
317 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
318 |
|
molIndex++; |
319 |
|
} |
320 |
|
} |
325 |
|
for(i=0; i<n_components; i++){ |
326 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
327 |
|
the_molecules[molIndex].setStampID( i ); |
328 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
329 |
|
molIndex++; |
330 |
|
} |
331 |
|
} |
335 |
|
|
336 |
|
|
337 |
|
if( simnfo->n_SRI ){ |
338 |
+ |
|
339 |
+ |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
340 |
+ |
|
341 |
|
Exclude::createArray(simnfo->n_SRI); |
342 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
343 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
344 |
|
simnfo->globalExcludes = new int; |
345 |
< |
simnfo->n_exclude = tot_SRI; |
345 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
346 |
|
} |
347 |
|
else{ |
348 |
|
|
358 |
|
// set the arrays into the SimInfo object |
359 |
|
|
360 |
|
simnfo->atoms = the_atoms; |
361 |
+ |
simnfo->molecules = the_molecules; |
362 |
|
simnfo->nGlobalExcludes = 0; |
363 |
|
simnfo->excludes = the_excludes; |
364 |
|
|
660 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
661 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
662 |
|
|
663 |
< |
|
663 |
> |
#ifdef IS_MPI |
664 |
> |
mpiSim->mpiRefresh(); |
665 |
> |
#endif |
666 |
|
|
667 |
|
// initialize the Fortran |
668 |
< |
|
668 |
> |
|
669 |
> |
|
670 |
|
simnfo->refreshSim(); |
671 |
|
|
672 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
703 |
|
BondStamp* currentBond; |
704 |
|
BendStamp* currentBend; |
705 |
|
TorsionStamp* currentTorsion; |
706 |
+ |
|
707 |
+ |
bond_pair* theBonds; |
708 |
+ |
bend_set* theBends; |
709 |
+ |
torsion_set* theTorsions; |
710 |
+ |
|
711 |
|
|
712 |
|
//init the forceField paramters |
713 |
|
|
714 |
|
the_ff->readParams(); |
715 |
|
|
716 |
|
|
717 |
< |
// init the molecules |
717 |
> |
// init the atoms |
718 |
|
|
719 |
+ |
double ux, uy, uz, u, uSqr; |
720 |
+ |
|
721 |
|
atomOffset = 0; |
722 |
|
excludeOffset = 0; |
723 |
|
for(i=0; i<simnfo->n_mol; i++){ |
734 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
735 |
|
info.myBonds = new Bond*[info.nBonds]; |
736 |
|
info.myBends = new Bend*[info.nBends]; |
737 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
737 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
738 |
|
|
739 |
|
theBonds = new bond_pair[info.nBonds]; |
740 |
|
theBends = new bend_set[info.nBends]; |
744 |
|
|
745 |
|
for(j=0; j<info.nAtoms; j++){ |
746 |
|
|
747 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
747 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
748 |
|
if( currentAtom->haveOrientation() ){ |
749 |
|
|
750 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
785 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
786 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
787 |
|
|
788 |
< |
exI = theBonds[i].a; |
789 |
< |
exJ = theBonds[i].b; |
788 |
> |
exI = theBonds[j].a; |
789 |
> |
exJ = theBonds[j].b; |
790 |
|
|
791 |
|
// exclude_I must always be the smaller of the pair |
792 |
|
if( exI > exJ ){ |
802 |
|
|
803 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
804 |
|
#else // isn't MPI |
805 |
+ |
|
806 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
807 |
|
#endif //is_mpi |
808 |
|
} |
818 |
|
|
819 |
|
if( currentBend->haveExtras() ){ |
820 |
|
|
821 |
< |
extras = current_bend->getExtras(); |
821 |
> |
extras = currentBend->getExtras(); |
822 |
|
current_extra = extras; |
823 |
|
|
824 |
|
while( current_extra != NULL ){ |
840 |
|
|
841 |
|
default: |
842 |
|
sprintf( painCave.errMsg, |
843 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
843 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
844 |
|
"double nor an int.\n" |
845 |
|
"-->Bend[%d] in %s\n", |
846 |
|
j, comp_stamps[stampID]->getID() ); |
934 |
|
|
935 |
|
|
936 |
|
the_molecules[i].initialize( info ); |
937 |
+ |
|
938 |
+ |
|
939 |
|
atomOffset += info.nAtoms; |
940 |
+ |
delete[] theBonds; |
941 |
+ |
delete[] theBends; |
942 |
+ |
delete[] theTorsions; |
943 |
|
} |
944 |
|
|
945 |
+ |
#ifdef IS_MPI |
946 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
947 |
+ |
MPIcheckPoint(); |
948 |
+ |
#endif // is_mpi |
949 |
+ |
|
950 |
|
// clean up the forcefield |
951 |
|
the_ff->calcRcut(); |
952 |
|
the_ff->cleanMe(); |
953 |
+ |
|
954 |
|
} |
955 |
|
|
956 |
|
void SimSetup::initFromBass( void ){ |