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root/group/branches/no-template-branch/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 432 by chuckv, Thu Mar 27 23:33:40 2003 UTC vs.
Revision 466 by gezelter, Mon Apr 7 14:30:36 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 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
92 +    the_extendedsystem = new ExtendedSystem( simnfo );
93 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
95 +  } else {
96 +    sprintf( painCave.errMsg,
97 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
98 +             "reverting to NVE for this simulation.\n",
99 +             ensemble );
100 +    painCave.isFatal = 0;
101 +    simError();
102 +    strcpy( ensemble, "NVE" );
103 +  }  
104    strcpy( simnfo->ensemble, ensemble );
105  
106    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107    simnfo->usePBC = the_globals->getPBC();
108            
89 –
90 –
109    if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
110 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111    else{
112      sprintf( painCave.errMsg,
113               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 314 | Line 332 | void SimSetup::createSim( void ){
332      
333      if(mol2proc[i] == worldRank ){
334        the_molecules[molIndex].setStampID( molCompType[i] );
335 +      the_molecules[molIndex].setMyIndex( molIndex );
336        molIndex++;
337      }
338    }
# Line 324 | Line 343 | void SimSetup::createSim( void ){
343    for(i=0; i<n_components; i++){
344      for(j=0; j<components_nmol[i]; j++ ){
345        the_molecules[molIndex].setStampID( i );
346 +      the_molecules[molIndex].setMyIndex( molIndex );
347        molIndex++;
348      }
349    }
# Line 334 | Line 354 | void SimSetup::createSim( void ){
354  
355    if( simnfo->n_SRI ){
356      
337 –    std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
338 –    
357      Exclude::createArray(simnfo->n_SRI);
358      the_excludes = new Exclude*[simnfo->n_SRI];
359      for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360      simnfo->globalExcludes = new int;
361 <    simnfo->n_exclude = tot_SRI;
361 >    simnfo->n_exclude = simnfo->n_SRI;
362    }
363    else{
364      
# Line 655 | Line 673 | void SimSetup::createSim( void ){
673  
674   //   new AllLong( simnfo );
675  
676 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
677 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
676 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
677 >                                                           the_ff,
678 >                                                           the_extendedsystem);
679 >  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680 >                                                 the_ff,
681 >                                                 the_extendedsystem );
682  
683   #ifdef IS_MPI
684    mpiSim->mpiRefresh();
# Line 783 | Line 805 | void SimSetup::makeMolecules( void ){
805        theBonds[j].a = currentBond->getA() + atomOffset;
806        theBonds[j].b = currentBond->getB() + atomOffset;
807  
808 <      exI = theBonds[i].a;
809 <      exJ = theBonds[i].b;
808 >      exI = theBonds[j].a;
809 >      exJ = theBonds[j].b;
810  
811        // exclude_I must always be the smaller of the pair
812        if( exI > exJ ){
# Line 800 | Line 822 | void SimSetup::makeMolecules( void ){
822        
823        the_excludes[j+excludeOffset]->setPair( exI, exJ );
824   #else  // isn't MPI
825 +
826        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
827   #endif  //is_mpi
828      }
# Line 837 | Line 860 | void SimSetup::makeMolecules( void ){
860                
861              default:
862                sprintf( painCave.errMsg,
863 <                       "SimSetup Error: ghostVectorSource was neiter a "
863 >                       "SimSetup Error: ghostVectorSource was neither a "
864                         "double nor an int.\n"
865                         "-->Bend[%d] in %s\n",
866                         j, comp_stamps[stampID]->getID() );
# Line 931 | Line 954 | void SimSetup::makeMolecules( void ){
954  
955  
956      the_molecules[i].initialize( info );
957 +
958 +
959      atomOffset += info.nAtoms;
960      delete[] theBonds;
961      delete[] theBends;
962      delete[] theTorsions;
963    }
964  
965 + #ifdef IS_MPI
966 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
967 +  MPIcheckPoint();
968 + #endif // is_mpi
969 +
970    // clean up the forcefield
971    the_ff->calcRcut();
972    the_ff->cleanMe();
973 +
974   }
975  
976   void SimSetup::initFromBass( void ){

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