67 |
|
MakeStamps *the_stamps; |
68 |
|
Globals* the_globals; |
69 |
|
ExtendedSystem* the_extendedsystem; |
70 |
< |
int i, j; |
70 |
> |
int i, j, k, globalAtomIndex; |
71 |
|
|
72 |
|
// get the stamps and globals; |
73 |
|
the_stamps = stamps; |
298 |
|
simnfo->n_torsions = tot_torsions; |
299 |
|
simnfo->n_SRI = tot_SRI; |
300 |
|
simnfo->n_mol = tot_nmol; |
301 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
302 |
|
|
302 |
– |
|
303 |
|
#ifdef IS_MPI |
304 |
|
|
305 |
|
// divide the molecules among processors here. |
306 |
|
|
307 |
|
mpiSim = new mpiSimulation( simnfo ); |
308 |
|
|
309 |
– |
|
310 |
– |
|
309 |
|
globalIndex = mpiSim->divideLabor(); |
310 |
|
|
311 |
|
// set up the local variables |
322 |
|
local_bonds = 0; |
323 |
|
local_bends = 0; |
324 |
|
local_torsions = 0; |
325 |
+ |
globalAtomIndex = 0; |
326 |
+ |
|
327 |
+ |
|
328 |
|
for( i=0; i<n_components; i++ ){ |
329 |
|
|
330 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
331 |
|
|
332 |
< |
if( mol2proc[j] == worldRank ){ |
332 |
> |
if( mol2proc[allMol] == worldRank ){ |
333 |
|
|
334 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
335 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
337 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
338 |
|
localMol++; |
339 |
|
} |
340 |
< |
allMol++; |
340 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
341 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
342 |
> |
globalAtomIndex++; |
343 |
> |
} |
344 |
> |
|
345 |
> |
allMol++; |
346 |
|
} |
347 |
|
} |
348 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
349 |
|
|
350 |
+ |
if (worldRank != 0) { |
351 |
+ |
for (i =0; i < tot_atoms; i++){ |
352 |
+ |
std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n"; |
353 |
+ |
} |
354 |
+ |
} |
355 |
|
|
356 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
357 |
|
|
396 |
|
if(mol2proc[i] == worldRank ){ |
397 |
|
the_molecules[molIndex].setStampID( molCompType[i] ); |
398 |
|
the_molecules[molIndex].setMyIndex( molIndex ); |
399 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
400 |
|
molIndex++; |
401 |
|
} |
402 |
|
} |
404 |
|
#else // is_mpi |
405 |
|
|
406 |
|
molIndex = 0; |
407 |
+ |
globalAtomIndex = 0; |
408 |
|
for(i=0; i<n_components; i++){ |
409 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
410 |
|
the_molecules[molIndex].setStampID( i ); |
411 |
|
the_molecules[molIndex].setMyIndex( molIndex ); |
412 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
413 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
414 |
+ |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
415 |
+ |
globalAtomIndex++; |
416 |
+ |
} |
417 |
|
molIndex++; |
418 |
|
} |
419 |
|
} |
746 |
|
|
747 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
748 |
|
new Symplectic(simnfo, the_ff, the_extendedsystem); |
731 |
– |
std::cerr << "called new Symplecic\n"; |
732 |
– |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
749 |
|
} |
750 |
|
else if( !strcmp( force_field, "LJ" ) ){ |
751 |
|
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
736 |
– |
std::cerr << "called new Verlet\n"; |
737 |
– |
fprintf( stderr, "called new Verlet. stderr\n" ); |
752 |
|
} |
753 |
|
else { |
754 |
|
std::cerr << "I'm a bug.\n"; |