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root/group/trunk/OOPSE-1.0/utils/sysbuilder/randomBilayer.cpp
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Comparing trunk/OOPSE-1.0/utils/sysbuilder/randomBilayer.cpp (file contents):
Revision 1334 by gezelter, Fri Jul 16 18:58:03 2004 UTC vs.
Revision 1417 by tim, Tue Jul 27 15:41:17 2004 UTC

# Line 513 | Line 513 | int buildRandomBilayer( double waterCell,
513    theConfig = testInfo->getConfiguration();
514    theConfig->createArrays( lipidNatoms );
515    testInfo->atoms = new Atom*[lipidNatoms];
516 +  for (i=0; i < lipidNatoms; i++) {
517 +          testInfo->atoms[i] = new Atom(i, theConfig);
518 +          testInfo->atoms[i]->setCoords();
519 +  }
520    atoms = testInfo->atoms;
521  
522    // create the test box for initial water displacement
# Line 675 | Line 679 | int buildRandomBilayer( double waterCell,
679    theConfig = testInfo2->getConfiguration();
680    theConfig->createArrays( nAtoms );
681    testInfo2->atoms = new Atom*[nAtoms];
682 +  for (i=0; i < nAtoms; i++) {
683 +          testInfo2->atoms[i] = new Atom(i, theConfig);
684 +          testInfo2->atoms[i]->setCoords();
685 +  }
686    atoms = testInfo2->atoms;
687  
688    rCutSqr = lipid_spaceing * lipid_spaceing;
# Line 851 | Line 859 | int buildRandomBilayer( double waterCell,
859      nAtoms += waterNatoms;
860    }
861    
862 +  std::cerr << "Flag-1\n";
863    theConfig = mainInfo->getConfiguration();
864 +  mainInfo->n_atoms = nAtoms;
865    theConfig->createArrays( nAtoms );
866    mainInfo->atoms = new Atom*[nAtoms];
867 +  for (i=0; i < nAtoms; i++) {
868 +          mainInfo->atoms[i] = new Atom(i, theConfig);
869 +          mainInfo->atoms[i]->setCoords();
870 +  }
871    atoms = mainInfo->atoms;
872 <  mainInfo->n_atoms = nAtoms;
872 >  std::cerr << "Flag0\n";
873    
874    // set up the SimInfo object
875    
# Line 889 | Line 903 | int buildRandomBilayer( double waterCell,
903    
904    // initialize lipid positions
905    
906 +  std::cerr << "Flag1\n";
907 +  
908    molIndex = 0;
909    for(i=0; i<nLipids; i++ ){
910      lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms,
# Line 897 | Line 913 | int buildRandomBilayer( double waterCell,
913    }
914  
915    // initialize the water positions
916 +  std::cerr << "Flag2\n";
917  
918    for(i=0; i<newWaters; i++){
919          
# Line 909 | Line 926 | int buildRandomBilayer( double waterCell,
926      }
927    }  
928  
929 +  std::cerr << "Flag3\n";
930  
931  
932    // set up the writer and write out
933    
934    writer = new DumpWriter( mainInfo );
935 +  std::cerr << "Flag4\n";
936    writer->writeFinal( 0.0 );
937 +  std::cerr << "Flag5\n";
938          
939    return 1;
940   }

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