| 189 |
|
if( currentStamp == NULL ){ |
| 190 |
|
sprintf( painCave.errMsg, |
| 191 |
|
"SimSetup error: Component \"%s\" was not found in the " |
| 192 |
< |
"list of declared molecules\n" |
| 192 |
> |
"list of declared molecules\n", |
| 193 |
|
id ); |
| 194 |
|
painCave.isFatal = 1; |
| 195 |
|
simError(); |
| 238 |
|
|
| 239 |
|
mpiSim = new mpiSimulation( simnfo ); |
| 240 |
|
|
| 241 |
< |
mpiSim->divideLabor(); |
| 241 |
> |
globalIndex = mpiSim->divideLabor(); |
| 242 |
|
|
| 243 |
|
// set up the local variables |
| 244 |
|
|
| 313 |
|
simnfo->sr_interactions = the_sris; |
| 314 |
|
simnfo->n_exclude = tot_SRI; |
| 315 |
|
simnfo->excludes = the_excludes; |
| 316 |
– |
|
| 317 |
– |
|
| 318 |
– |
// initialize the arrays |
| 319 |
– |
|
| 320 |
– |
the_ff->setSimInfo( simnfo ); |
| 316 |
|
|
| 322 |
– |
makeAtoms(); |
| 317 |
|
|
| 324 |
– |
if( tot_bonds ){ |
| 325 |
– |
makeBonds(); |
| 326 |
– |
} |
| 327 |
– |
|
| 328 |
– |
if( tot_bends ){ |
| 329 |
– |
makeBends(); |
| 330 |
– |
} |
| 331 |
– |
|
| 332 |
– |
if( tot_torsions ){ |
| 333 |
– |
makeTorsions(); |
| 334 |
– |
} |
| 335 |
– |
|
| 336 |
– |
|
| 318 |
|
// get some of the tricky things that may still be in the globals |
| 319 |
|
|
| 320 |
|
if( simnfo->n_dipoles ){ |
| 387 |
|
#endif // is_mpi |
| 388 |
|
|
| 389 |
|
|
| 390 |
+ |
// initialize the arrays |
| 391 |
|
|
| 392 |
+ |
the_ff->setSimInfo( simnfo ); |
| 393 |
+ |
|
| 394 |
+ |
makeAtoms(); |
| 395 |
+ |
|
| 396 |
+ |
if( tot_bonds ){ |
| 397 |
+ |
makeBonds(); |
| 398 |
+ |
} |
| 399 |
+ |
|
| 400 |
+ |
if( tot_bends ){ |
| 401 |
+ |
makeBends(); |
| 402 |
+ |
} |
| 403 |
+ |
|
| 404 |
+ |
if( tot_torsions ){ |
| 405 |
+ |
makeTorsions(); |
| 406 |
+ |
} |
| 407 |
+ |
|
| 408 |
+ |
|
| 409 |
+ |
|
| 410 |
+ |
|
| 411 |
+ |
|
| 412 |
+ |
|
| 413 |
|
if( the_globals->haveInitialConfig() ){ |
| 414 |
|
|
| 415 |
|
InitializeFromFile* fileInit; |
| 563 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
| 564 |
|
|
| 565 |
|
|
| 566 |
< |
// make the longe range forces and the integrator |
| 566 |
> |
// // make the longe range forces and the integrator |
| 567 |
|
|
| 568 |
< |
new AllLong( simnfo ); |
| 568 |
> |
// new AllLong( simnfo ); |
| 569 |
|
|
| 570 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo ); |
| 570 |
> |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
| 571 |
|
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo ); |
| 572 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo ); |
| 573 |
+ |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 574 |
+ |
|
| 575 |
|
} |
| 576 |
|
|
| 577 |
|
void SimSetup::makeAtoms( void ){ |
| 645 |
|
} |
| 646 |
|
} |
| 647 |
|
|
| 648 |
+ |
#ifdef IS_MPI |
| 649 |
+ |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
| 650 |
+ |
|
| 651 |
+ |
delete[] globalIndex; |
| 652 |
+ |
#endif IS_MPI |
| 653 |
+ |
|
| 654 |
|
the_ff->initializeAtoms(); |
| 655 |
|
} |
| 656 |
|
|
| 663 |
|
the_bonds = new bond_pair[tot_bonds]; |
| 664 |
|
index = 0; |
| 665 |
|
offset = 0; |
| 666 |
< |
molIndex = 0;g1 |
| 666 |
> |
molIndex = 0; |
| 667 |
|
|
| 668 |
|
for( i=0; i<n_components; i++ ){ |
| 669 |
|
|
