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root/group/trunk/mdtools/interface_implementation/SimSetup.cpp
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Comparing:
branches/mmeineke/mdtools/interface_implementation/SimSetup.cpp (file contents), Revision 10 by mmeineke, Tue Jul 9 18:40:59 2002 UTC vs.
trunk/mdtools/interface_implementation/SimSetup.cpp (file contents), Revision 117 by mmeineke, Tue Sep 24 22:10:55 2002 UTC

# Line 128 | Line 128 | void SimSetup::createSim( void ){
128    // create the atom and short range interaction arrays
129    
130    the_atoms = new Atom*[tot_atoms];
131 <  //  the_molecules = new Molecule[tot_nmol];
131 >  the_molecules = new Molecule[tot_nmol];
132    
133    
134    if( tot_SRI ){
# Line 142 | Line 142 | void SimSetup::createSim( void ){
142    simnfo->sr_interactions = the_sris;
143    simnfo->n_exclude = tot_SRI;
144    simnfo->excludes = the_excludes;
145 +  
146  
147    // initialize the arrays
148    
# Line 342 | Line 343 | void SimSetup::makeAtoms( void ){
343    double ux, uy, uz, uSqr, u;
344    AtomStamp* current_atom;
345    DirectionalAtom* dAtom;
346 +  int molIndex, molStart, molEnd, nMemb;
347 +  
348  
349 +  molIndex = 0;
350    index = 0;
351    for( i=0; i<n_components; i++ ){
352      
353      for( j=0; j<components_nmol[i]; j++ ){
354        
355 +      molStart = index;
356 +      nMemb = comp_stamps[i]->getNAtoms();
357        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
358          
359          current_atom = comp_stamps[i]->getAtom( k );
# Line 381 | Line 387 | void SimSetup::makeAtoms( void ){
387          // increment the index and repeat;
388          index++;
389        }
390 +      
391 +      molEnd = index -1;
392 +      the_molecules[molIndex].setNMembers( nMemb );
393 +      the_molecules[molIndex].setStartAtom( molStart );
394 +      the_molecules[molIndex].setEndAtom( molEnd );
395 +      molIndex++;
396 +
397      }
398    }
399    
# Line 486 | Line 499 | void SimSetup::makeTorsions( void ){
499    the_ff->initializeTorsions( the_torsions );
500   }
501  
489 – void SimSetup::makeMolecules( void ){
490 –
491 –  //empy for now
492 – }
493 –
502   void SimSetup::initFromBass( void ){
503  
504    int i, j, k;

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