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root/group/trunk/mdtools/interface_implementation/SimSetup.cpp
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Comparing trunk/mdtools/interface_implementation/SimSetup.cpp (file contents):
Revision 131 by chuckv, Wed Oct 9 22:29:40 2002 UTC vs.
Revision 145 by mmeineke, Fri Oct 18 15:34:21 2002 UTC

# Line 6 | Line 6
6   #include "parse_me.h"
7   #include "LRI.hpp"
8   #include "Integrator.hpp"
9 +
10   #ifdef IS_MPI
11 < #include "mpiInterface.h"
11 > #include "mpiBASS.h"
12   #include "bassDiag.hpp"
13   #endif
14  
# Line 155 | Line 156 | void SimSetup::createSim( void ){
156    // create the atom and short range interaction arrays
157  
158    the_atoms = new Atom*[tot_atoms];
159 +  Atom::createArrays(tot_atoms);
160    the_molecules = new Molecule[tot_nmol];
161  
162  
# Line 391 | Line 393 | void SimSetup::makeAtoms( void ){
393          current_atom = comp_stamps[i]->getAtom( k );
394          if( current_atom->haveOrientation() ){
395  
396 <          dAtom = new DirectionalAtom;
396 >          dAtom = new DirectionalAtom(index);
397            simnfo->n_oriented++;
398            the_atoms[index] = dAtom;
399  
# Line 411 | Line 413 | void SimSetup::makeAtoms( void ){
413            dAtom->setSUz( uz );
414          }
415          else{
416 <          the_atoms[index] = new GeneralAtom;
416 >          the_atoms[index] = new GeneralAtom(index);
417          }
418          the_atoms[index]->setType( current_atom->getType() );
419          the_atoms[index]->setIndex( index );

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