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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 202 by mmeineke, Tue Dec 10 21:41:26 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  
243    // set up the local variables
244    
245 <  int localMol;
245 >  int localMol, allMol;
246    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
247    
248 +  allMol = 0;
249    localMol = 0;
250    local_atoms = 0;
251    local_bonds = 0;
# Line 252 | Line 255 | void SimSetup::createSim( void ){
255  
256      for( j=0; j<components_nmol[i]; j++ ){
257        
258 <      if( mpiSim->getMyMolStart() <= j &&
259 <          j <= mpiSim->getMyMolEnd() ){
258 >      if( mpiSim->getMyMolStart() <= allMol &&
259 >          allMol <= mpiSim->getMyMolEnd() ){
260          
261          local_atoms +=    comp_stamps[i]->getNAtoms();
262          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 261 | Line 264 | void SimSetup::createSim( void ){
264          local_torsions += comp_stamps[i]->getNTorsions();
265          localMol++;
266        }      
267 +      allMol++;
268      }
269    }
270 <
270 >  local_SRI = local_bonds + local_bends + local_torsions;
271    
272  
273    simnfo->n_atoms = mpiSim->getMyNlocal();  
274    
275 +  if( local_atoms != simnfo->n_atoms ){
276 +    sprintf( painCave.errMsg,
277 +             "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
278 +             " localAtom (%d) are note equal.\n",
279 +             simnfo->n_atoms,
280 +             local_atoms );
281 +    painCave.isFatal = 1;
282 +    simError();
283 +  }
284  
285 +  simnfo->n_bonds = local_bonds;
286 +  simnfo->n_bends = local_bends;
287 +  simnfo->n_torsions = local_torsions;
288 +  simnfo->n_SRI = local_SRI;
289 +  simnfo->n_mol = localMol;
290 +
291 +  strcpy( checkPointMsg, "Passed nlocal consistency check." );
292 +  MPIcheckPoint();
293 +  
294 +  
295   #endif // is_mpi
296    
297  
# Line 290 | Line 313 | void SimSetup::createSim( void ){
313    simnfo->sr_interactions = the_sris;
314    simnfo->n_exclude = tot_SRI;
315    simnfo->excludes = the_excludes;
293 –
294 –
295 –  // initialize the arrays
296 –
297 –  the_ff->setSimInfo( simnfo );
298 –
299 –  makeAtoms();
316  
301 –  if( tot_bonds ){
302 –    makeBonds();
303 –  }
317  
305 –  if( tot_bends ){
306 –    makeBends();
307 –  }
308 –
309 –  if( tot_torsions ){
310 –    makeTorsions();
311 –  }
312 –
313 –
318    // get some of the tricky things that may still be in the globals
319  
320    if( simnfo->n_dipoles ){
# Line 383 | Line 387 | void SimSetup::createSim( void ){
387   #endif // is_mpi
388  
389  
390 +  // initialize the arrays
391  
392 < //   if( the_globals->haveInitialConfig() ){
388 < //        InitializeFromFile* fileInit;
389 < //     fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
392 >  the_ff->setSimInfo( simnfo );
393  
394 < //     fileInit->read_xyz( simnfo ); // default velocities on
394 >  makeAtoms();
395  
396 < //     delete fileInit;
397 < //   }
398 < //   else{
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;
416 > #ifdef IS_MPI // is_mpi
417 >     if( worldRank == 0 ){
418 > #endif //is_mpi
419 >   fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
420 > #ifdef IS_MPI
421 >     }else fileInit = new InitializeFromFile( NULL );
422 > #endif
423 >   fileInit->read_xyz( simnfo ); // default velocities on
424  
425 +   delete fileInit;
426 + }
427 + else{
428 +
429   #ifdef IS_MPI
430  
431    // no init from bass
# Line 407 | Line 439 | void SimSetup::createSim( void ){
439  
440    initFromBass();
441  
442 < #endif // is_mpi
443 <
442 >
443 > #endif
444 > }
445 >
446   #ifdef IS_MPI
447    strcpy( checkPointMsg, "Successfully read in the initial configuration" );
448    MPIcheckPoint();
# Line 418 | Line 452 | void SimSetup::createSim( void ){
452    
453  
454    
455 <  //   }
455 >
456    
457   #ifdef IS_MPI
458    if( worldRank == 0 ){
# Line 529 | 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 544 | Line 580 | void SimSetup::makeAtoms( void ){
580    double ux, uy, uz, uSqr, u;
581    AtomStamp* current_atom;
582    DirectionalAtom* dAtom;
583 <  int molIndex, molStart, molEnd, nMemb;
583 >  int molIndex, molStart, molEnd, nMemb, lMolIndex;
584  
585 <
585 >  lMolIndex = 0;
586    molIndex = 0;
587    index = 0;
588    for( i=0; i<n_components; i++ ){
589  
590      for( j=0; j<components_nmol[i]; j++ ){
591  
592 <      molStart = index;
593 <      nMemb = comp_stamps[i]->getNAtoms();
594 <      for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
592 > #ifdef IS_MPI
593 >      if( mpiSim->getMyMolStart() <= molIndex &&
594 >          molIndex <= mpiSim->getMyMolEnd() ){
595 > #endif // is_mpi        
596  
597 <        current_atom = comp_stamps[i]->getAtom( k );
598 <        if( current_atom->haveOrientation() ){
599 <
600 <          dAtom = new DirectionalAtom(index);
601 <          simnfo->n_oriented++;
602 <          the_atoms[index] = dAtom;
603 <
604 <          ux = current_atom->getOrntX();
605 <          uy = current_atom->getOrntY();
606 <          uz = current_atom->getOrntZ();
607 <
608 <          uSqr = (ux * ux) + (uy * uy) + (uz * uz);
609 <
610 <          u = sqrt( uSqr );
611 <          ux = ux / u;
612 <          uy = uy / u;
613 <          uz = uz / u;
614 <
615 <          dAtom->setSUx( ux );
616 <          dAtom->setSUy( uy );
617 <          dAtom->setSUz( uz );
618 <        }
619 <        else{
620 <          the_atoms[index] = new GeneralAtom(index);
621 <        }
622 <        the_atoms[index]->setType( current_atom->getType() );
623 <        the_atoms[index]->setIndex( index );
624 <
625 <        // increment the index and repeat;
626 <        index++;
627 <      }
597 >        molStart = index;
598 >        nMemb = comp_stamps[i]->getNAtoms();
599 >        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
600 >          
601 >          current_atom = comp_stamps[i]->getAtom( k );
602 >          if( current_atom->haveOrientation() ){
603 >            
604 >            dAtom = new DirectionalAtom(index);
605 >            simnfo->n_oriented++;
606 >            the_atoms[index] = dAtom;
607 >            
608 >            ux = current_atom->getOrntX();
609 >            uy = current_atom->getOrntY();
610 >            uz = current_atom->getOrntZ();
611 >            
612 >            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
613 >            
614 >            u = sqrt( uSqr );
615 >            ux = ux / u;
616 >            uy = uy / u;
617 >            uz = uz / u;
618 >            
619 >            dAtom->setSUx( ux );
620 >            dAtom->setSUy( uy );
621 >            dAtom->setSUz( uz );
622 >          }
623 >          else{
624 >            the_atoms[index] = new GeneralAtom(index);
625 >          }
626 >          the_atoms[index]->setType( current_atom->getType() );
627 >          the_atoms[index]->setIndex( index );
628 >          
629 >          // increment the index and repeat;
630 >          index++;
631 >        }
632 >        
633 >        molEnd = index -1;
634 >        the_molecules[lMolIndex].setNMembers( nMemb );
635 >        the_molecules[lMolIndex].setStartAtom( molStart );
636 >        the_molecules[lMolIndex].setEndAtom( molEnd );
637 >        the_molecules[lMolIndex].setStampID( i );
638 >        lMolIndex++;
639  
640 <      molEnd = index -1;
641 <      the_molecules[molIndex].setNMembers( nMemb );
642 <      the_molecules[molIndex].setStartAtom( molStart );
643 <      the_molecules[molIndex].setEndAtom( molEnd );
596 <      the_molecules[molIndex].setStampID( i );
640 > #ifdef IS_MPI
641 >      }
642 > #endif //is_mpi
643 >      
644        molIndex++;
598 –
645      }
646    }
647  
# Line 604 | Line 650 | void SimSetup::makeBonds( void ){
650  
651   void SimSetup::makeBonds( void ){
652  
653 <  int i, j, k, index, offset;
653 >  int i, j, k, index, offset, molIndex;
654    bond_pair* the_bonds;
655    BondStamp* current_bond;
656  
657    the_bonds = new bond_pair[tot_bonds];
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 <      for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
667 <
668 <        current_bond = comp_stamps[i]->getBond( k );
669 <        the_bonds[index].a = current_bond->getA() + offset;
670 <        the_bonds[index].b = current_bond->getB() + offset;
671 <
672 <        the_excludes[index].i = the_bonds[index].a;
673 <        the_excludes[index].j = the_bonds[index].b;
674 <
675 <        // increment the index and repeat;
676 <        index++;
666 > #ifdef IS_MPI
667 >      if( mpiSim->getMyMolStart() <= molIndex &&
668 >          molIndex <= mpiSim->getMyMolEnd() ){
669 > #endif // is_mpi        
670 >        
671 >        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
672 >          
673 >          current_bond = comp_stamps[i]->getBond( k );
674 >          the_bonds[index].a = current_bond->getA() + offset;
675 >          the_bonds[index].b = current_bond->getB() + offset;
676 >          
677 >          the_excludes[index].i = the_bonds[index].a;
678 >          the_excludes[index].j = the_bonds[index].b;
679 >          
680 >          // increment the index and repeat;
681 >          index++;
682 >        }
683 >        offset += comp_stamps[i]->getNAtoms();
684 >        
685 > #ifdef IS_MPI
686        }
687 <      offset += comp_stamps[i]->getNAtoms();
688 <    }
687 > #endif is_mpi
688 >      
689 >      molIndex++;
690 >    }      
691    }
692  
693    the_ff->initializeBonds( the_bonds );
# Line 636 | Line 695 | void SimSetup::makeBends( void ){
695  
696   void SimSetup::makeBends( void ){
697  
698 <  int i, j, k, index, offset;
698 >  int i, j, k, index, offset, molIndex;
699    bend_set* the_bends;
700    BendStamp* current_bend;
701  
702    the_bends = new bend_set[tot_bends];
703    index = 0;
704    offset = 0;
705 +  molIndex = 0;
706    for( i=0; i<n_components; i++ ){
707  
708      for( j=0; j<components_nmol[i]; j++ ){
709  
710 <      for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
710 > #ifdef IS_MPI
711 >      if( mpiSim->getMyMolStart() <= molIndex &&
712 >          molIndex <= mpiSim->getMyMolEnd() ){
713 > #endif // is_mpi        
714  
715 <        current_bend = comp_stamps[i]->getBend( k );
716 <        the_bends[index].a = current_bend->getA() + offset;
717 <        the_bends[index].b = current_bend->getB() + offset;
718 <        the_bends[index].c = current_bend->getC() + offset;
719 <
720 <        the_excludes[index + tot_bonds].i = the_bends[index].a;
721 <        the_excludes[index + tot_bonds].j = the_bends[index].c;
722 <
723 <        // increment the index and repeat;
724 <        index++;
715 >        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
716 >          
717 >          current_bend = comp_stamps[i]->getBend( k );
718 >          the_bends[index].a = current_bend->getA() + offset;
719 >          the_bends[index].b = current_bend->getB() + offset;
720 >          the_bends[index].c = current_bend->getC() + offset;
721 >          
722 >          the_excludes[index + tot_bonds].i = the_bends[index].a;
723 >          the_excludes[index + tot_bonds].j = the_bends[index].c;
724 >          
725 >          // increment the index and repeat;
726 >          index++;
727 >        }
728 >        offset += comp_stamps[i]->getNAtoms();
729 >        
730 > #ifdef IS_MPI
731        }
732 <      offset += comp_stamps[i]->getNAtoms();
732 > #endif //is_mpi
733 >
734 >      molIndex++;
735      }
736    }
737  
# Line 669 | Line 740 | void SimSetup::makeTorsions( void ){
740  
741   void SimSetup::makeTorsions( void ){
742  
743 <  int i, j, k, index, offset;
743 >  int i, j, k, index, offset, molIndex;
744    torsion_set* the_torsions;
745    TorsionStamp* current_torsion;
746  
747    the_torsions = new torsion_set[tot_torsions];
748    index = 0;
749    offset = 0;
750 +  molIndex = 0;
751    for( i=0; i<n_components; i++ ){
752  
753      for( j=0; j<components_nmol[i]; j++ ){
754  
755 + #ifdef IS_MPI
756 +      if( mpiSim->getMyMolStart() <= molIndex &&
757 +          molIndex <= mpiSim->getMyMolEnd() ){
758 + #endif // is_mpi        
759 +
760        for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
761  
762          current_torsion = comp_stamps[i]->getTorsion( k );
# Line 695 | Line 772 | void SimSetup::makeTorsions( void ){
772          index++;
773        }
774        offset += comp_stamps[i]->getNAtoms();
775 +
776 + #ifdef IS_MPI
777 +      }
778 + #endif //is_mpi      
779 +
780 +      molIndex++;
781      }
782    }
783  

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