# | Line 18 | Line 18 | nanoBuilder::nanoBuilder(int &hasError){ | |
---|---|---|
18 | int Errors; | |
19 | int foundCore,foundShell; | |
20 | int i; | |
21 | + | |
22 | + | |
23 | ||
24 | //Zero variables | |
25 | particleRadius = 0.0; | |
# | Line 214 | Line 216 | int nanoBuilder::buildNanoParticle( void ){ | |
216 | ||
217 | DumpWriter* writer; | |
218 | SimInfo* simnfo; | |
219 | + | SimState* theConfig; |
220 | ||
221 | Lattice *myLattice; | |
222 | MoLocator *coreLocate; | |
# | Line 322 | Line 325 | int nanoBuilder::buildNanoParticle( void ){ | |
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; | |
# | Line 335 | Line 344 | int nanoBuilder::buildNanoParticle( void ){ | |
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 | } | |
# | Line 356 | Line 365 | int nanoBuilder::buildNanoParticle( void ){ | |
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 ); |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |