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 ){ |
336 |
– |
|
337 |
– |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
338 |
|
|
339 |
|
Exclude::createArray(simnfo->n_SRI); |
340 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
341 |
|
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
342 |
|
simnfo->globalExcludes = new int; |
343 |
< |
simnfo->n_exclude = tot_SRI; |
343 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
344 |
|
} |
345 |
|
else{ |
346 |
|
|
783 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
784 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
785 |
|
|
786 |
< |
exI = theBonds[i].a; |
787 |
< |
exJ = theBonds[i].b; |
786 |
> |
exI = theBonds[j].a; |
787 |
> |
exJ = theBonds[j].b; |
788 |
|
|
789 |
|
// exclude_I must always be the smaller of the pair |
790 |
|
if( exI > exJ ){ |
800 |
|
|
801 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
802 |
|
#else // isn't MPI |
803 |
+ |
|
804 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
805 |
|
#endif //is_mpi |
806 |
|
} |
932 |
|
|
933 |
|
|
934 |
|
the_molecules[i].initialize( info ); |
935 |
+ |
|
936 |
+ |
|
937 |
|
atomOffset += info.nAtoms; |
938 |
|
delete[] theBonds; |
939 |
|
delete[] theBends; |