# | Line 313 | Line 313 | void SimSetup::createSim( void ){ | |
---|---|---|
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 ); |
321 | – | |
322 | – | makeAtoms(); |
323 | – | |
324 | – | if( tot_bonds ){ |
325 | – | makeBonds(); |
326 | – | } |
327 | – | |
328 | – | if( tot_bends ){ |
329 | – | makeBends(); |
330 | – | } |
316 | ||
332 | – | if( tot_torsions ){ |
333 | – | makeTorsions(); |
334 | – | } |
317 | ||
336 | – | |
318 | // get some of the tricky things that may still be in the globals | |
319 | ||
320 | if( simnfo->n_dipoles ){ | |
# | Line 406 | Line 387 | void SimSetup::createSim( void ){ | |
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; | |
# | Line 560 | Line 563 | void SimSetup::createSim( void ){ | |
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 ); | |
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 ){ |
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