| 191 |
|
simnfo->n_bends = tot_bends; |
| 192 |
|
simnfo->n_torsions = tot_torsions; |
| 193 |
|
simnfo->n_SRI = tot_SRI; |
| 194 |
+ |
simnfo->n_mol = tot_nmol; |
| 195 |
|
|
| 196 |
+ |
|
| 197 |
+ |
#ifdef IS_MPI |
| 198 |
+ |
|
| 199 |
|
// divide the molecules among processors here. |
| 200 |
+ |
|
| 201 |
+ |
new mpiSimulation( simnfo ); |
| 202 |
+ |
|
| 203 |
+ |
simnfo->mpiSim->divideLabor( n_components, comp_stamps, components_nmol ); |
| 204 |
|
|
| 205 |
+ |
#endif // is_mpi |
| 206 |
+ |
|
| 207 |
|
|
| 208 |
|
// create the atom and short range interaction arrays |
| 209 |
|
|
| 210 |
< |
Atom::createArrays(tot_atoms); |
| 211 |
< |
the_atoms = new Atom*[tot_atoms]; |
| 212 |
< |
the_molecules = new Molecule[tot_nmol]; |
| 210 |
> |
Atom::createArrays(simnfo->n_atoms); |
| 211 |
> |
the_atoms = new Atom*[simnfo->n_atoms]; |
| 212 |
> |
the_molecules = new Molecule[simnfo->n_mol]; |
| 213 |
|
|
| 214 |
|
|
| 215 |
< |
if( tot_SRI ){ |
| 216 |
< |
the_sris = new SRI*[tot_SRI]; |
| 217 |
< |
the_excludes = new ex_pair[tot_SRI]; |
| 215 |
> |
if( simnfo->n_SRI ){ |
| 216 |
> |
the_sris = new SRI*[simnfo->n_SRI]; |
| 217 |
> |
the_excludes = new ex_pair[simnfo->n_SRI]; |
| 218 |
|
} |
| 219 |
|
|
| 220 |
|
// set the arrays into the SimInfo object |
| 243 |
|
makeTorsions(); |
| 244 |
|
} |
| 245 |
|
|
| 236 |
– |
// makeMolecules(); |
| 246 |
|
|
| 247 |
|
// get some of the tricky things that may still be in the globals |
| 248 |
|
|
| 326 |
|
// delete fileInit; |
| 327 |
|
// } |
| 328 |
|
// else{ |
| 329 |
+ |
|
| 330 |
+ |
#ifdef IS_MPI |
| 331 |
+ |
|
| 332 |
+ |
// no init from bass |
| 333 |
+ |
|
| 334 |
+ |
sprintf( painCave.errMsg, |
| 335 |
+ |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
| 336 |
+ |
painCave.isFatal; |
| 337 |
+ |
simError(); |
| 338 |
+ |
|
| 339 |
+ |
#else |
| 340 |
|
|
| 341 |
|
initFromBass(); |
| 342 |
+ |
|
| 343 |
+ |
#endif // is_mpi |
| 344 |
|
|
| 345 |
|
#ifdef IS_MPI |
| 346 |
< |
strcpy( checkPointMsg, "initFromBass successfully created the lattice" ); |
| 346 |
> |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
| 347 |
|
MPIcheckPoint(); |
| 348 |
|
#endif // is_mpi |
| 349 |
|
|
