18 |
|
int Errors; |
19 |
|
int foundCore,foundShell; |
20 |
|
int i; |
21 |
+ |
|
22 |
+ |
|
23 |
|
|
24 |
|
//Zero variables |
25 |
|
particleRadius = 0.0; |
216 |
|
|
217 |
|
DumpWriter* writer; |
218 |
|
SimInfo* simnfo; |
219 |
+ |
SimState* theConfig; |
220 |
|
|
221 |
|
Lattice *myLattice; |
222 |
|
MoLocator *coreLocate; |
325 |
|
} |
326 |
|
|
327 |
|
|
328 |
< |
Atom::createArrays( nAtoms ); |
326 |
< |
atoms = new Atom*[nAtoms]; |
328 |
> |
// set up the SimInfo object |
329 |
|
|
330 |
+ |
simnfo = new SimInfo(); |
331 |
+ |
simnfo->n_atoms = nAtoms; |
332 |
+ |
|
333 |
+ |
theConfig = simnfo->getConfiguration(); |
334 |
+ |
theConfig->createArrays( nAtoms ); |
335 |
+ |
simnfo->atoms = new Atom*[nAtoms]; |
336 |
+ |
atoms = simnfo->atoms; |
337 |
|
|
338 |
|
|
339 |
|
shesActualSizetoMe = 0; |
344 |
|
orientationMunger( A ); |
345 |
|
if( moleculeVector[i].isCore){ |
346 |
|
nCoreAtomCounter += nCoreModelAtoms; |
347 |
< |
coreLocate->placeMol(moleculeVector[i].pos,A,atoms,nShellAtomCounter); |
347 |
> |
coreLocate->placeMol(moleculeVector[i].pos,A,atoms,nShellAtomCounter, theConfig); |
348 |
|
} |
349 |
|
else { |
350 |
|
nShellAtomCounter += nShellModelAtoms; |
351 |
< |
shellLocate->placeMol(moleculeVector[i].pos,A,atoms,nCoreAtomCounter); |
351 |
> |
shellLocate->placeMol(moleculeVector[i].pos,A,atoms,nCoreAtomCounter, theConfig); |
352 |
|
} |
353 |
|
shesActualSizetoMe++; |
354 |
|
} |
365 |
|
simnfo->Hmat[1][1] = 1.0; |
366 |
|
simnfo->Hmat[2][2] = 1.0; |
367 |
|
|
359 |
– |
// set up the SimInfo object |
368 |
|
|
361 |
– |
simnfo = new SimInfo(); |
362 |
– |
simnfo->n_atoms = nAtoms; |
369 |
|
|
370 |
|
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
371 |
|
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
372 |
|
|
367 |
– |
simnfo->atoms = atoms; |
368 |
– |
|
373 |
|
// set up the writer and write out |
374 |
|
|
375 |
|
writer = new DumpWriter( simnfo ); |