| 161 |
|
#endif // is_mpi |
| 162 |
|
|
| 163 |
|
// make an array of molecule stamps that match the components used. |
| 164 |
+ |
// also extract the used stamps out into a separate linked list |
| 165 |
|
|
| 166 |
+ |
simnfo->nComponents = n_components; |
| 167 |
+ |
simnfo->componentsNmol = components_nmol; |
| 168 |
+ |
simnfo->compStamps = comp_stamps; |
| 169 |
+ |
simnfo->headStamp = new LinkedMolStamp(); |
| 170 |
+ |
|
| 171 |
+ |
char* id; |
| 172 |
+ |
LinkedMolStamp* headStamp = simnfo->headStamp; |
| 173 |
+ |
LinkedMolStamp* currentStamp = NULL; |
| 174 |
|
for( i=0; i<n_components; i++ ){ |
| 175 |
|
|
| 176 |
< |
comp_stamps[i] = |
| 177 |
< |
the_stamps->getMolecule( the_components[i]->getType() ); |
| 176 |
> |
id = the_components[i]->getType(); |
| 177 |
> |
comp_stamps[i] = NULL; |
| 178 |
> |
|
| 179 |
> |
// check to make sure the component isn't already in the list |
| 180 |
> |
|
| 181 |
> |
comp_stamps[i] = headStamp->match( id ); |
| 182 |
> |
if( comp_stamps[i] == NULL ){ |
| 183 |
> |
|
| 184 |
> |
// extract the component from the list; |
| 185 |
> |
|
| 186 |
> |
currentStamp = the_stamps->extractMolStamp( id ); |
| 187 |
> |
if( currentStamp == NULL ){ |
| 188 |
> |
sprintf( painCave.errMsg, |
| 189 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
| 190 |
> |
"list of declared molecules\n" |
| 191 |
> |
id ); |
| 192 |
> |
painCave.isFatal = 1; |
| 193 |
> |
simError(); |
| 194 |
> |
} |
| 195 |
> |
|
| 196 |
> |
headStamp->add( currentStamp ); |
| 197 |
> |
comp_stamps[i] = headStamp->match( id ); |
| 198 |
> |
} |
| 199 |
|
} |
| 200 |
|
|
| 201 |
+ |
#ifdef IS_MPI |
| 202 |
+ |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
| 203 |
+ |
MPIcheckPoint(); |
| 204 |
+ |
#endif // is_mpi |
| 205 |
+ |
|
| 206 |
|
|
| 207 |
|
|
| 208 |
+ |
|
| 209 |
|
// caclulate the number of atoms, bonds, bends and torsions |
| 210 |
|
|
| 211 |
|
tot_atoms = 0; |
| 227 |
|
simnfo->n_bends = tot_bends; |
| 228 |
|
simnfo->n_torsions = tot_torsions; |
| 229 |
|
simnfo->n_SRI = tot_SRI; |
| 230 |
+ |
simnfo->n_mol = tot_nmol; |
| 231 |
|
|
| 232 |
+ |
|
| 233 |
+ |
#ifdef IS_MPI |
| 234 |
+ |
|
| 235 |
+ |
// divide the molecules among processors here. |
| 236 |
+ |
|
| 237 |
+ |
new mpiSimulation( simnfo ); |
| 238 |
+ |
|
| 239 |
+ |
simnfo->mpiSim->divideLabor( n_components, comp_stamps, components_nmol ); |
| 240 |
+ |
|
| 241 |
+ |
#endif // is_mpi |
| 242 |
+ |
|
| 243 |
+ |
|
| 244 |
|
// create the atom and short range interaction arrays |
| 245 |
|
|
| 246 |
< |
Atom::createArrays(tot_atoms); |
| 247 |
< |
the_atoms = new Atom*[tot_atoms]; |
| 248 |
< |
the_molecules = new Molecule[tot_nmol]; |
| 246 |
> |
Atom::createArrays(simnfo->n_atoms); |
| 247 |
> |
the_atoms = new Atom*[simnfo->n_atoms]; |
| 248 |
> |
the_molecules = new Molecule[simnfo->n_mol]; |
| 249 |
|
|
| 250 |
|
|
| 251 |
< |
if( tot_SRI ){ |
| 252 |
< |
the_sris = new SRI*[tot_SRI]; |
| 253 |
< |
the_excludes = new ex_pair[tot_SRI]; |
| 251 |
> |
if( simnfo->n_SRI ){ |
| 252 |
> |
the_sris = new SRI*[simnfo->n_SRI]; |
| 253 |
> |
the_excludes = new ex_pair[simnfo->n_SRI]; |
| 254 |
|
} |
| 255 |
|
|
| 256 |
|
// set the arrays into the SimInfo object |
| 279 |
|
makeTorsions(); |
| 280 |
|
} |
| 281 |
|
|
| 233 |
– |
// makeMolecules(); |
| 282 |
|
|
| 283 |
|
// get some of the tricky things that may still be in the globals |
| 284 |
|
|
| 363 |
|
// } |
| 364 |
|
// else{ |
| 365 |
|
|
| 366 |
+ |
#ifdef IS_MPI |
| 367 |
+ |
|
| 368 |
+ |
// no init from bass |
| 369 |
+ |
|
| 370 |
+ |
sprintf( painCave.errMsg, |
| 371 |
+ |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
| 372 |
+ |
painCave.isFatal; |
| 373 |
+ |
simError(); |
| 374 |
+ |
|
| 375 |
+ |
#else |
| 376 |
+ |
|
| 377 |
|
initFromBass(); |
| 378 |
+ |
|
| 379 |
+ |
#endif // is_mpi |
| 380 |
|
|
| 381 |
|
#ifdef IS_MPI |
| 382 |
< |
strcpy( checkPointMsg, "initFromBass successfully created the lattice" ); |
| 382 |
> |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
| 383 |
|
MPIcheckPoint(); |
| 384 |
|
#endif // is_mpi |
| 385 |
|
|
