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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 422 by mmeineke, Thu Mar 27 19:21:42 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            
109 <
110 <
91 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
109 >  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
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 242 | Line 258 | void SimSetup::createSim( void ){
258  
259    globalIndex = mpiSim->divideLabor();
260  
245 –
246 –
261    // set up the local variables
262    
263    int localMol, allMol;
# Line 318 | 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 328 | 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 337 | Line 353 | void SimSetup::createSim( void ){
353  
354  
355    if( simnfo->n_SRI ){
356 +    
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 356 | Line 374 | void SimSetup::createSim( void ){
374    // set the arrays into the SimInfo object
375  
376    simnfo->atoms = the_atoms;
377 +  simnfo->molecules = the_molecules;
378    simnfo->nGlobalExcludes = 0;
379    simnfo->excludes = the_excludes;
380  
# Line 654 | Line 673 | void SimSetup::createSim( void ){
673  
674   //   new AllLong( simnfo );
675  
676 <  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
677 <  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
678 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
679 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
680 <
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();
685 + #endif
686  
687    // initialize the Fortran
688 <  
688 >
689 >
690    simnfo->refreshSim();
691    
692    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 699 | Line 723 | void SimSetup::makeMolecules( void ){
723    BondStamp* currentBond;
724    BendStamp* currentBend;
725    TorsionStamp* currentTorsion;
726 +
727 +  bond_pair* theBonds;
728 +  bend_set* theBends;
729 +  torsion_set* theTorsions;
730 +
731    
732    //init the forceField paramters
733  
734    the_ff->readParams();
735  
736    
737 <  // init the molecules
737 >  // init the atoms
738  
739 +  double ux, uy, uz, u, uSqr;
740 +  
741    atomOffset = 0;
742    excludeOffset = 0;
743    for(i=0; i<simnfo->n_mol; i++){
# Line 723 | Line 754 | void SimSetup::makeMolecules( void ){
754      info.myExcludes = &the_excludes[excludeOffset];
755      info.myBonds = new Bond*[info.nBonds];
756      info.myBends = new Bend*[info.nBends];
757 <    info.myTorsions = new Torsions*[info.nTorsions];
757 >    info.myTorsions = new Torsion*[info.nTorsions];
758  
759      theBonds = new bond_pair[info.nBonds];
760      theBends = new bend_set[info.nBends];
# Line 733 | Line 764 | void SimSetup::makeMolecules( void ){
764      
765      for(j=0; j<info.nAtoms; j++){
766        
767 <      currentAtom = theComponents[stampID]->getAtom( j );
767 >      currentAtom = comp_stamps[stampID]->getAtom( j );
768        if( currentAtom->haveOrientation() ){
769          
770          dAtom = new DirectionalAtom(j + atomOffset);
# Line 774 | 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 791 | 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 806 | Line 838 | void SimSetup::makeMolecules( void ){
838            
839        if( currentBend->haveExtras() ){
840              
841 <        extras = current_bend->getExtras();
841 >        extras = currentBend->getExtras();
842          current_extra = extras;
843              
844          while( current_extra != NULL ){
# Line 828 | 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 922 | 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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