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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 362 by mmeineke, Tue Mar 18 21:25:45 2003 UTC vs.
Revision 368 by chuckv, Thu Mar 20 00:02:39 2003 UTC

# Line 310 | Line 310 | void SimSetup::createSim( void ){
310      the_sris = new SRI*[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 <    the_excludes = new int;
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;
323 –  simnfo->n_exclude = tot_SRI;
330    simnfo->nGlobalExcludes = 0;
331    simnfo->excludes = the_excludes;
332  
# Line 592 | Line 598 | void SimSetup::createSim( void ){
598    
599    simnfo->refreshSim();
600    
601 <  if( !stcmp( simnfo->mixingRule, "standard") ){
601 >  if( !strcmp( simnfo->mixingRule, "standard") ){
602      the_ff->initForceField( LB_MIXING_RULE );
603    }
604 <  else if( !stcmp( simnfo->mixingRule, "explicit") ){
604 >  else if( !strcmp( simnfo->mixingRule, "explicit") ){
605      the_ff->initForceField( EXPLICIT_MIXING_RULE );
606    }
607    else{
# Line 619 | 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 698 | 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 765 | Line 772 | void SimSetup::makeBends( void ){
772  
773   void SimSetup::makeBends( void ){
774  
775 <  int i, j, k, index, offset, molIndex, exI, exJ;
775 >  int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
776    bend_set* the_bends;
777    BendStamp* current_bend;
778    LinkedAssign* extras;

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