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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 427 by mmeineke, Thu Mar 27 20:48:37 2003 UTC vs.
Revision 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 +  ExtendedSystem* the_extendedsystem;
70    int i, j;
71  
72    // get the stamps and globals;
# Line 80 | Line 81 | void SimSetup::createSim( void ){
81    // get the ones we know are there, yet still may need some work.
82    n_components = the_globals->getNComponents();
83    strcpy( force_field, the_globals->getForceField() );
84 +
85 +  // get the ensemble and set up an extended system if we need it:
86    strcpy( ensemble, the_globals->getEnsemble() );
87 +  if( !strcasecmp( ensemble, "NPT" ) ) {
88 +    the_extendedsystem = new ExtendedSystem( simnfo );
89 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90 +    the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91 +    the_extendedsystem->setQmass(the_globals->getQmass());
92 +    the_extendedsystem->setTauRelax(the_globals->getTauRelax());
93 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
94 +    the_extendedsystem = new ExtendedSystem( simnfo );
95 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
96 +    the_extendedsystem->setQmass(the_globals->getQmass());    
97 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
98 +  } else {
99 +    sprintf( painCave.errMsg,
100 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
101 +             "reverting to NVE for this simulation.\n",
102 +             ensemble );
103 +    painCave.isFatal = 0;
104 +    simError();
105 +    strcpy( ensemble, "NVE" );
106 +  }  
107    strcpy( simnfo->ensemble, ensemble );
108  
109    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
110    simnfo->usePBC = the_globals->getPBC();
111            
112 <
113 <
114 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
115 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
112 >  int usesDipoles = 0;
113 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
114 >    the_ff = new TraPPE_ExFF();
115 >    usesDipoles = 1;
116 >  }
117 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
118    else{
119      sprintf( painCave.errMsg,
120               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 240 | Line 265 | void SimSetup::createSim( void ){
265  
266    globalIndex = mpiSim->divideLabor();
267  
243 –
244 –
268    // set up the local variables
269    
270    int localMol, allMol;
# Line 316 | Line 339 | void SimSetup::createSim( void ){
339      
340      if(mol2proc[i] == worldRank ){
341        the_molecules[molIndex].setStampID( molCompType[i] );
342 +      the_molecules[molIndex].setMyIndex( molIndex );
343        molIndex++;
344      }
345    }
# Line 326 | Line 350 | void SimSetup::createSim( void ){
350    for(i=0; i<n_components; i++){
351      for(j=0; j<components_nmol[i]; j++ ){
352        the_molecules[molIndex].setStampID( i );
353 +      the_molecules[molIndex].setMyIndex( molIndex );
354        molIndex++;
355      }
356    }
# Line 335 | Line 360 | void SimSetup::createSim( void ){
360  
361  
362    if( simnfo->n_SRI ){
363 +    
364      Exclude::createArray(simnfo->n_SRI);
365      the_excludes = new Exclude*[simnfo->n_SRI];
366 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
367      simnfo->globalExcludes = new int;
368 <    simnfo->n_exclude = tot_SRI;
368 >    simnfo->n_exclude = simnfo->n_SRI;
369    }
370    else{
371      
# Line 354 | Line 381 | void SimSetup::createSim( void ){
381    // set the arrays into the SimInfo object
382  
383    simnfo->atoms = the_atoms;
384 +  simnfo->molecules = the_molecules;
385    simnfo->nGlobalExcludes = 0;
386    simnfo->excludes = the_excludes;
387  
# Line 457 | Line 485 | void SimSetup::createSim( void ){
485      }
486      simnfo->dielectric = the_globals->getDielectric();  
487    } else {
488 <    if (simnfo->n_dipoles) {
488 >    if (usesDipoles) {
489        
490        if( !the_globals->haveECR() ){
491          sprintf( painCave.errMsg,
492 <                 "SimSetup Warning: using default value of 1/2 the smallest"
492 >                 "SimSetup Warning: using default value of 1/2 the smallest "
493                   "box length for the electrostaticCutoffRadius.\n"
494                   "I hope you have a very fast processor!\n");
495          painCave.isFatal = 0;
# Line 477 | Line 505 | void SimSetup::createSim( void ){
505        
506        if( !the_globals->haveEST() ){
507          sprintf( painCave.errMsg,
508 <                 "SimSetup Warning: using default value of 5% of the"
508 >                 "SimSetup Warning: using default value of 5%% of the "
509                   "electrostaticCutoffRadius for the "
510                   "electrostaticSkinThickness\n"
511                   );
# Line 652 | Line 680 | void SimSetup::createSim( void ){
680  
681   //   new AllLong( simnfo );
682  
655 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
656 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
683  
684 <
684 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
685 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
686 >    std::cerr << "called new Symplecic\n";
687 >    fprintf( stderr, "called new Symplectic. stderr\n" );
688 >  }
689 >  else if( !strcmp( force_field, "LJ" ) ){
690 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
691 >    std::cerr << "called new Verlet\n";
692 >    fprintf( stderr, "called new Verlet. stderr\n" );
693 >  }
694 >  else {
695 >    std::cerr << "I'm a bug.\n";
696 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
697 >  }
698 > #ifdef IS_MPI
699 >  mpiSim->mpiRefresh();
700 > #endif
701  
702    // initialize the Fortran
703 <  
703 >
704 >
705    simnfo->refreshSim();
706    
707    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 777 | Line 820 | void SimSetup::makeMolecules( void ){
820        theBonds[j].a = currentBond->getA() + atomOffset;
821        theBonds[j].b = currentBond->getB() + atomOffset;
822  
823 <      exI = theBonds[i].a;
824 <      exJ = theBonds[i].b;
823 >      exI = theBonds[j].a;
824 >      exJ = theBonds[j].b;
825  
826        // exclude_I must always be the smaller of the pair
827        if( exI > exJ ){
# Line 794 | Line 837 | void SimSetup::makeMolecules( void ){
837        
838        the_excludes[j+excludeOffset]->setPair( exI, exJ );
839   #else  // isn't MPI
840 +
841        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
842   #endif  //is_mpi
843      }
# Line 831 | Line 875 | void SimSetup::makeMolecules( void ){
875                
876              default:
877                sprintf( painCave.errMsg,
878 <                       "SimSetup Error: ghostVectorSource was neiter a "
878 >                       "SimSetup Error: ghostVectorSource was neither a "
879                         "double nor an int.\n"
880                         "-->Bend[%d] in %s\n",
881                         j, comp_stamps[stampID]->getID() );
# Line 925 | Line 969 | void SimSetup::makeMolecules( void ){
969  
970  
971      the_molecules[i].initialize( info );
972 +
973 +
974      atomOffset += info.nAtoms;
975      delete[] theBonds;
976      delete[] theBends;
977      delete[] theTorsions;
978    }
979 +
980 + #ifdef IS_MPI
981 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
982 +  MPIcheckPoint();
983 + #endif // is_mpi
984  
985    // clean up the forcefield
986    the_ff->calcRcut();
987    the_ff->cleanMe();
988 +
989   }
990  
991   void SimSetup::initFromBass( void ){

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