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root/group/trunk/OOPSE_old/src/mdtools/libmdCode/SimSetup.cpp
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Comparing trunk/OOPSE_old/src/mdtools/libmdCode/SimSetup.cpp (file contents):
Revision 311 by mmeineke, Tue Mar 11 16:27:34 2003 UTC vs.
Revision 368 by chuckv, Thu Mar 20 00:02:39 2003 UTC

# Line 308 | Line 308 | void SimSetup::createSim( void ){
308  
309    if( simnfo->n_SRI ){
310      the_sris = new SRI*[simnfo->n_SRI];
311 <    the_excludes = new ex_pair[simnfo->n_SRI];
311 >    the_excludes = new int[2 * simnfo->n_SRI];
312 >    simnfo->globalExcludes = new int;
313 >    simnfo->n_exclude = tot_SRI;
314 >  }
315 >  else{
316 >    
317 >    the_excludes = new int[2];
318 >    the_excludes[0] = 0;
319 >    the_excludes[1] = 0;
320 >    simnfo->globalExcludes = new int;
321 >    simnfo->globalExcludes[0] = 0;
322 >
323 >    simnfo->n_exclude = 1;
324    }
325  
326    // set the arrays into the SimInfo object
327  
328    simnfo->atoms = the_atoms;
329    simnfo->sr_interactions = the_sris;
330 <  simnfo->n_exclude = tot_SRI;
330 >  simnfo->nGlobalExcludes = 0;
331    simnfo->excludes = the_excludes;
332  
333  
# Line 396 | Line 408 | void SimSetup::createSim( void ){
408    the_ff->setSimInfo( simnfo );
409  
410    makeAtoms();
411 <  //
411 >  simnfo->identArray = new int[simnfo->n_atoms];
412 >  for(i=0; i<simnfo->n_atoms; i++){
413 >    simnfo->identArray[i] = the_atoms[i]->getIdent();
414 >  }
415 >  
416    if( tot_bonds ){
417      makeBonds();
418    }
# Line 576 | Line 592 | void SimSetup::createSim( void ){
592    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
594  
595 +
596 +
597 +  // initialize the Fortran
598 +  
599 +  simnfo->refreshSim();
600 +  
601 +  if( !strcmp( simnfo->mixingRule, "standard") ){
602 +    the_ff->initForceField( LB_MIXING_RULE );
603 +  }
604 +  else if( !strcmp( simnfo->mixingRule, "explicit") ){
605 +    the_ff->initForceField( EXPLICIT_MIXING_RULE );
606 +  }
607 +  else{
608 +    sprintf( painCave.errMsg,
609 +             "SimSetup Error: unknown mixing rule -> \"%s\"\n",
610 +             simnfo->mixingRule );
611 +    painCave.isFatal = 1;
612 +    simError();
613 +  }
614 +
615 +
616 + #ifdef IS_MPI
617 +  strcpy( checkPointMsg,
618 +          "Successfully intialized the mixingRule for Fortran." );
619 +  MPIcheckPoint();
620 + #endif // is_mpi
621   }
622  
623   void SimSetup::makeAtoms( void ){
# Line 583 | Line 625 | void SimSetup::makeAtoms( void ){
625    int i, j, k, index;
626    double ux, uy, uz, uSqr, u;
627    AtomStamp* current_atom;
628 +
629    DirectionalAtom* dAtom;
630    int molIndex, molStart, molEnd, nMemb, lMolIndex;
631  
# Line 662 | Line 705 | void SimSetup::makeBonds( void ){
705  
706   void SimSetup::makeBonds( void ){
707  
708 <  int i, j, k, index, offset, molIndex;
708 >  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709    bond_pair* the_bonds;
710    BondStamp* current_bond;
711  
# Line 685 | Line 728 | void SimSetup::makeBonds( void ){
728            current_bond = comp_stamps[i]->getBond( k );
729            the_bonds[index].a = current_bond->getA() + offset;
730            the_bonds[index].b = current_bond->getB() + offset;
731 +
732 +          exI = the_bonds[index].a;
733 +          exJ = the_bonds[index].b;
734 +
735 +          // exclude_I must always be the smaller of the pair
736 +          if( exI > exJ ){
737 +            tempEx = exI;
738 +            exI = exJ;
739 +            exJ = tempEx;
740 +          }
741 +
742            
743 <          the_excludes[index].i = the_bonds[index].a;
744 <          the_excludes[index].j = the_bonds[index].b;
743 > #ifdef IS_MPI
744 >
745 >          the_excludes[index*2] =    
746 >            the_atoms[exI]->getGlobalIndex() + 1;
747 >          the_excludes[index*2 + 1] =
748 >            the_atoms[exJ]->getGlobalIndex() + 1;
749 >
750 > #else  // isn't MPI
751 >          
752 >          the_excludes[index*2] =     exI + 1;
753 >          the_excludes[index*2 + 1] = exJ + 1;
754 >          // fortran index from 1 (hence the +1 in the indexing)
755 > #endif  //is_mpi
756            
757            // increment the index and repeat;
758            index++;
# Line 707 | Line 772 | void SimSetup::makeBends( void ){
772  
773   void SimSetup::makeBends( void ){
774  
775 <  int i, j, k, index, offset, molIndex;
775 >  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
776    bend_set* the_bends;
777    BendStamp* current_bend;
778    LinkedAssign* extras;
# Line 734 | Line 799 | void SimSetup::makeBends( void ){
799            the_bends[index].b = current_bend->getB() + offset;
800            the_bends[index].c = current_bend->getC() + offset;
801            
802 <          if( current_bend->haveExtras ){
802 >          if( current_bend->haveExtras() ){
803              
804              extras = current_bend->getExtras();
805              current_extra = extras;
# Line 778 | Line 843 | void SimSetup::makeBends( void ){
843                  simError();
844                }
845                
846 <              current_extra = current_extra->next;
846 >              current_extra = current_extra->getNext();
847              }
848            }
849            
850            if( !the_bends[index].isGhost ){
851              
852 <            the_excludes[index + tot_bonds].i = the_bends[index].a;
853 <            the_excludes[index + tot_bonds].j = the_bends[index].c;
852 >            exI = the_bends[index].a;
853 >            exJ = the_bends[index].c;
854            }
855            else{
856              
857 <            the_excludes[index + tot_bonds].i = the_bends[index].a;
858 <            the_excludes[index + tot_bonds].j = the_bends[index].b;
857 >            exI = the_bends[index].a;
858 >            exJ = the_bends[index].b;
859            }
860 +          
861 +          // exclude_I must always be the smaller of the pair
862 +          if( exI > exJ ){
863 +            tempEx = exI;
864 +            exI = exJ;
865 +            exJ = tempEx;
866 +          }
867 +
868 +
869 + #ifdef IS_MPI
870 +
871 +          the_excludes[(index + tot_bonds)*2] =    
872 +            the_atoms[exI]->getGlobalIndex() + 1;
873 +          the_excludes[(index + tot_bonds)*2 + 1] =
874 +            the_atoms[exJ]->getGlobalIndex() + 1;
875 +          
876 + #else  // isn't MPI
877 +          
878 +          the_excludes[(index + tot_bonds)*2] =     exI + 1;
879 +          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880 +          // fortran index from 1 (hence the +1 in the indexing)
881 + #endif  //is_mpi
882            
883 +          
884            // increment the index and repeat;
885            index++;
886          }
# Line 818 | Line 906 | void SimSetup::makeTorsions( void ){
906  
907   void SimSetup::makeTorsions( void ){
908  
909 <  int i, j, k, index, offset, molIndex;
909 >  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
910    torsion_set* the_torsions;
911    TorsionStamp* current_torsion;
912  
# Line 843 | Line 931 | void SimSetup::makeTorsions( void ){
931          the_torsions[index].c = current_torsion->getC() + offset;
932          the_torsions[index].d = current_torsion->getD() + offset;
933  
934 <        the_excludes[index + tot_bonds + tot_bends].i = the_torsions[index].a;
935 <        the_excludes[index + tot_bonds + tot_bends].j = the_torsions[index].d;
934 >        exI = the_torsions[index].a;
935 >        exJ = the_torsions[index].d;
936 >
937 >        
938 >        // exclude_I must always be the smaller of the pair
939 >        if( exI > exJ ){
940 >          tempEx = exI;
941 >          exI = exJ;
942 >          exJ = tempEx;
943 >        }
944  
945 +
946 + #ifdef IS_MPI
947 +        
948 +        the_excludes[(index + tot_bonds + tot_bends)*2] =    
949 +          the_atoms[exI]->getGlobalIndex() + 1;
950 +        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951 +          the_atoms[exJ]->getGlobalIndex() + 1;
952 +        
953 + #else  // isn't MPI
954 +        
955 +        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956 +        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957 +        // fortran indexes from 1 (hence the +1 in the indexing)
958 + #endif  //is_mpi
959 +        
960 +
961          // increment the index and repeat;
962          index++;
963        }

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