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root/group/trunk/mdtools/interface_implementation/SimSetup.cpp
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Comparing trunk/mdtools/interface_implementation/SimSetup.cpp (file contents):
Revision 206 by chuckv, Thu Dec 12 21:21:59 2002 UTC vs.
Revision 249 by chuckv, Mon Jan 27 21:28:19 2003 UTC

# Line 10 | Line 10
10  
11   #ifdef IS_MPI
12   #include "mpiBASS.h"
13 + #include "mpiSimulation.hpp"
14   #include "bassDiag.hpp"
15   #endif
16  
# Line 92 | Line 93 | void SimSetup::createSim( void ){
93    if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
94    else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
95    else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
96 +  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
97    else{
98      sprintf( painCave.errMsg,
99               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 187 | Line 189 | void SimSetup::createSim( void ){
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();
# Line 234 | Line 236 | void SimSetup::createSim( void ){
236  
237    // divide the molecules among processors here.
238    
239 <  mpiSimulation* mpiSim = new mpiSimulation( simnfo );
239 >  mpiSim = new mpiSimulation( simnfo );
240    
241    mpiSim->divideLabor();
242  
# Line 313 | Line 315 | void SimSetup::createSim( void ){
315    simnfo->excludes = the_excludes;
316  
317  
316 –  // initialize the arrays
317 –
318 –  the_ff->setSimInfo( simnfo );
319 –
320 –  makeAtoms();
321 –
322 –  if( tot_bonds ){
323 –    makeBonds();
324 –  }
325 –
326 –  if( tot_bends ){
327 –    makeBends();
328 –  }
329 –
330 –  if( tot_torsions ){
331 –    makeTorsions();
332 –  }
333 –
334 –
318    // get some of the tricky things that may still be in the globals
319  
320    if( simnfo->n_dipoles ){
# Line 402 | Line 385 | void SimSetup::createSim( void ){
385    strcpy( checkPointMsg, "Box size set up" );
386    MPIcheckPoint();
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 558 | 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 );
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 ){
# Line 583 | Line 590 | void SimSetup::makeAtoms( void ){
590      for( j=0; j<components_nmol[i]; j++ ){
591  
592   #ifdef IS_MPI
593 <      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
594 <          molIndex <= simnfo->mpiSim->getMyMolEnd() ){
593 >      if( mpiSim->getMyMolStart() <= molIndex &&
594 >          molIndex <= mpiSim->getMyMolEnd() ){
595   #endif // is_mpi        
596  
597          molStart = index;
# Line 651 | Line 658 | void SimSetup::makeBonds( void ){
658    index = 0;
659    offset = 0;
660    molIndex = 0;
661 +
662    for( i=0; i<n_components; i++ ){
663  
664      for( j=0; j<components_nmol[i]; j++ ){
665  
666   #ifdef IS_MPI
667 <      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
668 <          molIndex <= simnfo->mpiSim->getMyMolEnd() ){
667 >      if( mpiSim->getMyMolStart() <= molIndex &&
668 >          molIndex <= mpiSim->getMyMolEnd() ){
669   #endif // is_mpi        
670          
671          for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
# Line 700 | Line 708 | void SimSetup::makeBends( void ){
708      for( j=0; j<components_nmol[i]; j++ ){
709  
710   #ifdef IS_MPI
711 <      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
712 <          molIndex <= simnfo->mpiSim->getMyMolEnd() ){
711 >      if( mpiSim->getMyMolStart() <= molIndex &&
712 >          molIndex <= mpiSim->getMyMolEnd() ){
713   #endif // is_mpi        
714  
715          for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
# Line 745 | Line 753 | void SimSetup::makeTorsions( void ){
753      for( j=0; j<components_nmol[i]; j++ ){
754  
755   #ifdef IS_MPI
756 <      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
757 <          molIndex <= simnfo->mpiSim->getMyMolEnd() ){
756 >      if( mpiSim->getMyMolStart() <= molIndex &&
757 >          molIndex <= mpiSim->getMyMolEnd() ){
758   #endif // is_mpi        
759  
760        for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){

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