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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 128 by chuckv, Thu Oct 3 21:52:46 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 – #include "mpiInterface.h"
9  
10 + #ifdef IS_MPI
11 + #include "mpiBASS.h"
12 + #include "bassDiag.hpp"
13 + #endif
14 +
15   SimSetup::SimSetup(){
16    stamps = new MakeStamps();
17    globals = new Globals();
# Line 22 | Line 26 | void SimSetup::parseFile( char* fileName ){
26  
27    inFileName = fileName;
28    set_interface_stamps( stamps, globals );
29 < #ifdef MPI
29 > #ifdef IS_MPI
30    mpiEventInit();
31   #endif
32    yacc_BASS( fileName );
33 < #ifdef MPI
33 > #ifdef IS_MPI
34    throwMPIEvent(NULL);
35   #endif
36  
37   }
38  
39 < #ifdef MPI
39 > #ifdef IS_MPI
40   void SimSetup::receiveParse(void){
41  
42      set_interface_stamps( stamps, globals );
# Line 40 | Line 44 | void SimSetup::receiveParse(void){
44      mpiEventLoop();
45  
46   }
43 – #endif
47  
48 +
49   void SimSetup::testMe(void){
50    bassDiag* dumpMe = new bassDiag(globals,stamps);
51    dumpMe->dumpStamps();
52    delete dumpMe;
53   }
54 <
54 > #endif
55   void SimSetup::createSim( void ){
56  
57    MakeStamps *the_stamps;
# Line 152 | 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 388 | 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 408 | 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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