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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 348 by mmeineke, Fri Mar 14 21:33:10 2003 UTC vs.
Revision 362 by mmeineke, Tue Mar 18 21:25:45 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 >  }
314 >  else{
315 >    the_excludes = new int;
316 >    simnfo->globalExcludes = new int;
317    }
318  
319    // set the arrays into the SimInfo object
# Line 316 | Line 321 | void SimSetup::createSim( void ){
321    simnfo->atoms = the_atoms;
322    simnfo->sr_interactions = the_sris;
323    simnfo->n_exclude = tot_SRI;
324 +  simnfo->nGlobalExcludes = 0;
325    simnfo->excludes = the_excludes;
326  
327  
# Line 396 | Line 402 | void SimSetup::createSim( void ){
402    the_ff->setSimInfo( simnfo );
403  
404    makeAtoms();
405 <  //
405 >  simnfo->identArray = new int[simnfo->n_atoms];
406 >  for(i=0; i<simnfo->n_atoms; i++){
407 >    simnfo->identArray[i] = the_atoms[i]->getIdent();
408 >  }
409 >  
410    if( tot_bonds ){
411      makeBonds();
412    }
# Line 575 | Line 585 | void SimSetup::createSim( void ){
585    if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
586    if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
587    if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
588 +
589 +
590 +
591 +  // initialize the Fortran
592 +  
593 +  simnfo->refreshSim();
594 +  
595 +  if( !stcmp( simnfo->mixingRule, "standard") ){
596 +    the_ff->initForceField( LB_MIXING_RULE );
597 +  }
598 +  else if( !stcmp( simnfo->mixingRule, "explicit") ){
599 +    the_ff->initForceField( EXPLICIT_MIXING_RULE );
600 +  }
601 +  else{
602 +    sprintf( painCave.errMsg,
603 +             "SimSetup Error: unknown mixing rule -> \"%s\"\n",
604 +             simnfo->mixingRule );
605 +    painCave.isFatal = 1;
606 +    simError();
607 +  }
608  
609 +
610 + #ifdef IS_MPI
611 +  strcpy( checkPointMsg,
612 +          "Successfully intialized the mixingRule for Fortran." );
613 +  MPIcheckPoint();
614 + #endif // is_mpi
615   }
616  
617   void SimSetup::makeAtoms( void ){
# Line 685 | Line 721 | void SimSetup::makeBonds( void ){
721            current_bond = comp_stamps[i]->getBond( k );
722            the_bonds[index].a = current_bond->getA() + offset;
723            the_bonds[index].b = current_bond->getB() + offset;
724 +
725 +          exI = the_bonds[index].a;
726 +          exJ = the_bonds[index].b;
727 +
728 +          // exclude_I must always be the smaller of the pair
729 +          if( exI > exJ ){
730 +            tempEx = exI;
731 +            exI = exJ;
732 +            exJ = tempEx;
733 +          }
734 +
735            
736 <          the_excludes[index].i = the_bonds[index].a;
737 <          the_excludes[index].j = the_bonds[index].b;
736 > #ifdef IS_MPI
737 >
738 >          the_excludes[index*2] =    
739 >            the_atoms[exI]->getGlobalIndex() + 1;
740 >          the_excludes[index*2 + 1] =
741 >            the_atoms[exJ]->getGlobalIndex() + 1;
742 >
743 > #else  // isn't MPI
744            
745 +          the_excludes[index*2] =     exI + 1;
746 +          the_excludes[index*2 + 1] = exJ + 1;
747 +          // fortran index from 1 (hence the +1 in the indexing)
748 + #endif  //is_mpi
749 +          
750            // increment the index and repeat;
751            index++;
752          }
# Line 707 | Line 765 | void SimSetup::makeBends( void ){
765  
766   void SimSetup::makeBends( void ){
767  
768 <  int i, j, k, index, offset, molIndex;
768 >  int i, j, k, index, offset, molIndex, exI, exJ;
769    bend_set* the_bends;
770    BendStamp* current_bend;
771    LinkedAssign* extras;
# Line 784 | Line 842 | void SimSetup::makeBends( void ){
842            
843            if( !the_bends[index].isGhost ){
844              
845 <            the_excludes[index + tot_bonds].i = the_bends[index].a;
846 <            the_excludes[index + tot_bonds].j = the_bends[index].c;
845 >            exI = the_bends[index].a;
846 >            exJ = the_bends[index].c;
847            }
848            else{
849              
850 <            the_excludes[index + tot_bonds].i = the_bends[index].a;
851 <            the_excludes[index + tot_bonds].j = the_bends[index].b;
850 >            exI = the_bends[index].a;
851 >            exJ = the_bends[index].b;
852            }
853            
854 +          // exclude_I must always be the smaller of the pair
855 +          if( exI > exJ ){
856 +            tempEx = exI;
857 +            exI = exJ;
858 +            exJ = tempEx;
859 +          }
860 +
861 +
862 + #ifdef IS_MPI
863 +
864 +          the_excludes[(index + tot_bonds)*2] =    
865 +            the_atoms[exI]->getGlobalIndex() + 1;
866 +          the_excludes[(index + tot_bonds)*2 + 1] =
867 +            the_atoms[exJ]->getGlobalIndex() + 1;
868 +          
869 + #else  // isn't MPI
870 +          
871 +          the_excludes[(index + tot_bonds)*2] =     exI + 1;
872 +          the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
873 +          // fortran index from 1 (hence the +1 in the indexing)
874 + #endif  //is_mpi
875 +          
876 +          
877            // increment the index and repeat;
878            index++;
879          }
# Line 818 | Line 899 | void SimSetup::makeTorsions( void ){
899  
900   void SimSetup::makeTorsions( void ){
901  
902 <  int i, j, k, index, offset, molIndex;
902 >  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
903    torsion_set* the_torsions;
904    TorsionStamp* current_torsion;
905  
# Line 843 | Line 924 | void SimSetup::makeTorsions( void ){
924          the_torsions[index].c = current_torsion->getC() + offset;
925          the_torsions[index].d = current_torsion->getD() + offset;
926  
927 <        the_excludes[index + tot_bonds + tot_bends].i = the_torsions[index].a;
928 <        the_excludes[index + tot_bonds + tot_bends].j = the_torsions[index].d;
927 >        exI = the_torsions[index].a;
928 >        exJ = the_torsions[index].d;
929  
930 +        
931 +        // exclude_I must always be the smaller of the pair
932 +        if( exI > exJ ){
933 +          tempEx = exI;
934 +          exI = exJ;
935 +          exJ = tempEx;
936 +        }
937 +
938 +
939 + #ifdef IS_MPI
940 +        
941 +        the_excludes[(index + tot_bonds + tot_bends)*2] =    
942 +          the_atoms[exI]->getGlobalIndex() + 1;
943 +        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
944 +          the_atoms[exJ]->getGlobalIndex() + 1;
945 +        
946 + #else  // isn't MPI
947 +        
948 +        the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
949 +        the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
950 +        // fortran indexes from 1 (hence the +1 in the indexing)
951 + #endif  //is_mpi
952 +        
953 +
954          // increment the index and repeat;
955          index++;
956        }

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