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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC

# Line 307 | Line 307 | void SimSetup::createSim( void ){
307  
308  
309    if( simnfo->n_SRI ){
310 <    the_sris = new SRI*[simnfo->n_SRI];
311 <    the_excludes = new int[2 * simnfo->n_SRI];
310 >    Exclude::createArray(simnfo->n_SRI);
311 >    the_excludes = new Exclude*[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;
317 >    Exclude::createArray( 1 );
318 >    the_excludes = new Exclude*;
319 >    the_excludes[0] = new Exclude(0);
320 >    the_excludes[0]->setPair( 0,0 );
321      simnfo->globalExcludes = new int;
322      simnfo->globalExcludes[0] = 0;
323 <
323 <    simnfo->n_exclude = 1;
323 >    simnfo->n_exclude = 0;
324    }
325  
326    // set the arrays into the SimInfo object
# Line 674 | Line 674 | void SimSetup::makeMolecules( void ){
674  
675   void SimSetup::makeMolecules( void ){
676  
677 <  int i, j, exI, exJ, tempEx, stampID, atomOffset;
677 >  int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
678    molInit info;
679    DirectionalAtom* dAtom;
680 +  LinkedAssign* extras;
681 +  LinkedAssign* current_extra;
682    AtomStamp* currentAtom;
683    BondStamp* currentBond;
684    BendStamp* currentBend;
# Line 690 | Line 692 | void SimSetup::makeMolecules( void ){
692    // init the molecules
693  
694    atomOffset = 0;
695 +  excludeOffset = 0;
696    for(i=0; i<simnfo->n_mol; i++){
697      
698      stampID = the_molecules[i].getStampID();
# Line 698 | Line 701 | void SimSetup::makeMolecules( void ){
701      info.nBonds    = comp_stamps[stampID]->getNBonds();
702      info.nBends    = comp_stamps[stampID]->getNBends();
703      info.nTorsions = comp_stamps[stampID]->getNTorsions();
704 <    
704 >    info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
705 >
706      info.myAtoms = &the_atoms[atomOffset];
707 +    info.myExcludes = &the_excludes[excludeOffset];
708      info.myBonds = new Bond*[info.nBonds];
709      info.myBends = new Bend*[info.nBends];
710      info.myTorsions = new Torsions*[info.nTorsions];
# Line 747 | Line 752 | void SimSetup::makeMolecules( void ){
752      }
753      
754      // make the bonds
755 <    for(j=0; j<nBonds; j++){
755 >    for(j=0; j<info.nBonds; j++){
756        
757        currentBond = comp_stamps[stampID]->getBond( j );
758        theBonds[j].a = currentBond->getA() + atomOffset;
# Line 763 | Line 768 | void SimSetup::makeMolecules( void ){
768          exJ = tempEx;
769        }
770   #ifdef IS_MPI
771 +      tempEx = exI;
772 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
773 +      tempEx = exJ;
774 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
775        
776 <      the_excludes[index*2] =    
768 <        the_atoms[exI]->getGlobalIndex() + 1;
769 <      the_excludes[index*2 + 1] =
770 <        the_atoms[exJ]->getGlobalIndex() + 1;
771 <      
776 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
777   #else  // isn't MPI
778 <      
774 <      the_excludes[index*2] =     exI + 1;
775 <      the_excludes[index*2 + 1] = exJ + 1;
776 <      // fortran index from 1 (hence the +1 in the indexing)
777 <
778 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
779   #endif  //is_mpi
780 <    
781 <  }
780 >    }
781 >    excludeOffset += info.nBonds;
782  
783 <
784 <
785 <
786 <
787 <
783 >    //make the bends
784 >    for(j=0; j<info.nBends; j++){
785 >      
786 >      currentBend = comp_stamps[stampID]->getBend( j );
787 >      theBends[j].a = currentBend->getA() + atomOffset;
788 >      theBends[j].b = currentBend->getB() + atomOffset;
789 >      theBends[j].c = currentBend->getC() + atomOffset;
790 >          
791 >      if( currentBend->haveExtras() ){
792 >            
793 >        extras = current_bend->getExtras();
794 >        current_extra = extras;
795 >            
796 >        while( current_extra != NULL ){
797 >          if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
798 >                
799 >            switch( current_extra->getType() ){
800 >              
801 >            case 0:
802 >              theBends[j].ghost =
803 >                current_extra->getInt() + atomOffset;
804 >              theBends[j].isGhost = 1;
805 >              break;
806 >                  
807 >            case 1:
808 >              theBends[j].ghost =
809 >                (int)current_extra->getDouble() + atomOffset;
810 >              theBends[j].isGhost = 1;
811 >              break;
812 >              
813 >            default:
814 >              sprintf( painCave.errMsg,
815 >                       "SimSetup Error: ghostVectorSource was neiter a "
816 >                       "double nor an int.\n"
817 >                       "-->Bend[%d] in %s\n",
818 >                       j, comp_stamps[stampID]->getID() );
819 >              painCave.isFatal = 1;
820 >              simError();
821 >            }
822 >          }
823 >          
824 >          else{
825 >            
826 >            sprintf( painCave.errMsg,
827 >                     "SimSetup Error: unhandled bend assignment:\n"
828 >                     "    -->%s in Bend[%d] in %s\n",
829 >                     current_extra->getlhs(),
830 >                     j, comp_stamps[stampID]->getID() );
831 >            painCave.isFatal = 1;
832 >            simError();
833 >          }
834 >          
835 >          current_extra = current_extra->getNext();
836 >        }
837 >      }
838 >          
839 >      if( !theBends[j].isGhost ){
840 >            
841 >        exI = theBends[j].a;
842 >        exJ = theBends[j].c;
843 >      }
844 >      else{
845 >        
846 >        exI = theBends[j].a;
847 >        exJ = theBends[j].b;
848 >      }
849 >      
850 >      // exclude_I must always be the smaller of the pair
851 >      if( exI > exJ ){
852 >        tempEx = exI;
853 >        exI = exJ;
854 >        exJ = tempEx;
855 >      }
856 > #ifdef IS_MPI
857 >      tempEx = exI;
858 >      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
859 >      tempEx = exJ;
860 >      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
861 >      
862 >      the_excludes[j+excludeOffset]->setPair( exI, exJ );
863 > #else  // isn't MPI
864 >      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
865 > #endif  //is_mpi
866 >    }
867 >    excludeOffset += info.nBends;
868  
869 +    for(j=0; j<info.nTorsions; j++){
870 +      
871 +      currentTorsion = comp_stamps[stampID]->getTorsion( j );
872 +      theTorsions[j].a = currentTorsion->getA() + atomOffset;
873 +      theTorsions[j].b = currentTorsion->getB() + atomOffset;
874 +      theTorsions[j].c = currentTorsion->getC() + atomOffset;
875 +      theTorsions[j].d = currentTorsion->getD() + atomOffset;
876 +      
877 +      exI = theTorsions[j].a;
878 +      exJ = theTorsions[j].d;
879  
880 +      // exclude_I must always be the smaller of the pair
881 +      if( exI > exJ ){
882 +        tempEx = exI;
883 +        exI = exJ;
884 +        exJ = tempEx;
885 +      }
886 + #ifdef IS_MPI
887 +      tempEx = exI;
888 +      exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889 +      tempEx = exJ;
890 +      exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891 +      
892 +      the_excludes[j+excludeOffset]->setPair( exI, exJ );
893 + #else  // isn't MPI
894 +      the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
895 + #endif  //is_mpi
896 +    }
897 +    excludeOffset += info.nTorsions;
898  
899 +    
900  
901  
902  

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