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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 424 by mmeineke, Thu Mar 27 20:36:16 2003 UTC vs.
Revision 469 by mmeineke, Mon Apr 7 20:06:31 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 <
111 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
112 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
109 >  int usesDipoles = 0;
110 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
111 >    the_ff = new TraPPE_ExFF();
112 >    usesDipoles = 1;
113 >  }
114 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
115    else{
116      sprintf( painCave.errMsg,
117               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 240 | Line 262 | void SimSetup::createSim( void ){
262  
263    globalIndex = mpiSim->divideLabor();
264  
243 –
244 –
265    // set up the local variables
266    
267    int localMol, allMol;
# Line 316 | Line 336 | void SimSetup::createSim( void ){
336      
337      if(mol2proc[i] == worldRank ){
338        the_molecules[molIndex].setStampID( molCompType[i] );
339 +      the_molecules[molIndex].setMyIndex( molIndex );
340        molIndex++;
341      }
342    }
# Line 326 | Line 347 | void SimSetup::createSim( void ){
347    for(i=0; i<n_components; i++){
348      for(j=0; j<components_nmol[i]; j++ ){
349        the_molecules[molIndex].setStampID( i );
350 +      the_molecules[molIndex].setMyIndex( molIndex );
351        molIndex++;
352      }
353    }
# Line 335 | Line 357 | void SimSetup::createSim( void ){
357  
358  
359    if( simnfo->n_SRI ){
360 +    
361      Exclude::createArray(simnfo->n_SRI);
362      the_excludes = new Exclude*[simnfo->n_SRI];
363 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
364      simnfo->globalExcludes = new int;
365 <    simnfo->n_exclude = tot_SRI;
365 >    simnfo->n_exclude = simnfo->n_SRI;
366    }
367    else{
368      
# Line 354 | Line 378 | void SimSetup::createSim( void ){
378    // set the arrays into the SimInfo object
379  
380    simnfo->atoms = the_atoms;
381 +  simnfo->molecules = the_molecules;
382    simnfo->nGlobalExcludes = 0;
383    simnfo->excludes = the_excludes;
384  
# Line 457 | Line 482 | void SimSetup::createSim( void ){
482      }
483      simnfo->dielectric = the_globals->getDielectric();  
484    } else {
485 <    if (simnfo->n_dipoles) {
485 >    if (usesDipoles) {
486        
487        if( !the_globals->haveECR() ){
488          sprintf( painCave.errMsg,
489 <                 "SimSetup Warning: using default value of 1/2 the smallest"
489 >                 "SimSetup Warning: using default value of 1/2 the smallest "
490                   "box length for the electrostaticCutoffRadius.\n"
491                   "I hope you have a very fast processor!\n");
492          painCave.isFatal = 0;
# Line 477 | Line 502 | void SimSetup::createSim( void ){
502        
503        if( !the_globals->haveEST() ){
504          sprintf( painCave.errMsg,
505 <                 "SimSetup Warning: using default value of 5% of the"
505 >                 "SimSetup Warning: using default value of 5%% of the "
506                   "electrostaticCutoffRadius for the "
507                   "electrostaticSkinThickness\n"
508                   );
# Line 652 | Line 677 | void SimSetup::createSim( void ){
677  
678   //   new AllLong( simnfo );
679  
655 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
656 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
680  
681 <
681 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
682 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
683 >    std::cerr << "called new Symplecic\n";
684 >    fprintf( stderr, "called new Symplectic. stderr\n" );
685 >  }
686 >  else if( !strcmp( force_field, "LJ" ) ){
687 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
688 >    std::cerr << "called new Verlet\n";
689 >    fprintf( stderr, "called new Verlet. stderr\n" );
690 >  }
691 >  else {
692 >    std::cerr << "I'm a bug.\n";
693 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
694 >  }
695 > #ifdef IS_MPI
696 >  mpiSim->mpiRefresh();
697 > #endif
698  
699    // initialize the Fortran
700 <  
700 >
701 >
702    simnfo->refreshSim();
703    
704    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 695 | Line 735 | void SimSetup::makeMolecules( void ){
735    BondStamp* currentBond;
736    BendStamp* currentBend;
737    TorsionStamp* currentTorsion;
738 +
739 +  bond_pair* theBonds;
740 +  bend_set* theBends;
741 +  torsion_set* theTorsions;
742 +
743    
744    //init the forceField paramters
745  
746    the_ff->readParams();
747  
748    
749 <  // init the molecules
749 >  // init the atoms
750  
751 +  double ux, uy, uz, u, uSqr;
752 +  
753    atomOffset = 0;
754    excludeOffset = 0;
755    for(i=0; i<simnfo->n_mol; i++){
# Line 719 | Line 766 | void SimSetup::makeMolecules( void ){
766      info.myExcludes = &the_excludes[excludeOffset];
767      info.myBonds = new Bond*[info.nBonds];
768      info.myBends = new Bend*[info.nBends];
769 <    info.myTorsions = new Torsions*[info.nTorsions];
769 >    info.myTorsions = new Torsion*[info.nTorsions];
770  
771      theBonds = new bond_pair[info.nBonds];
772      theBends = new bend_set[info.nBends];
# Line 729 | Line 776 | void SimSetup::makeMolecules( void ){
776      
777      for(j=0; j<info.nAtoms; j++){
778        
779 <      currentAtom = theComponents[stampID]->getAtom( j );
779 >      currentAtom = comp_stamps[stampID]->getAtom( j );
780        if( currentAtom->haveOrientation() ){
781          
782          dAtom = new DirectionalAtom(j + atomOffset);
# Line 770 | Line 817 | void SimSetup::makeMolecules( void ){
817        theBonds[j].a = currentBond->getA() + atomOffset;
818        theBonds[j].b = currentBond->getB() + atomOffset;
819  
820 <      exI = theBonds[i].a;
821 <      exJ = theBonds[i].b;
820 >      exI = theBonds[j].a;
821 >      exJ = theBonds[j].b;
822  
823        // exclude_I must always be the smaller of the pair
824        if( exI > exJ ){
# Line 787 | Line 834 | void SimSetup::makeMolecules( void ){
834        
835        the_excludes[j+excludeOffset]->setPair( exI, exJ );
836   #else  // isn't MPI
837 +
838        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
839   #endif  //is_mpi
840      }
# Line 802 | Line 850 | void SimSetup::makeMolecules( void ){
850            
851        if( currentBend->haveExtras() ){
852              
853 <        extras = current_bend->getExtras();
853 >        extras = currentBend->getExtras();
854          current_extra = extras;
855              
856          while( current_extra != NULL ){
# Line 824 | Line 872 | void SimSetup::makeMolecules( void ){
872                
873              default:
874                sprintf( painCave.errMsg,
875 <                       "SimSetup Error: ghostVectorSource was neiter a "
875 >                       "SimSetup Error: ghostVectorSource was neither a "
876                         "double nor an int.\n"
877                         "-->Bend[%d] in %s\n",
878                         j, comp_stamps[stampID]->getID() );
# Line 918 | Line 966 | void SimSetup::makeMolecules( void ){
966  
967  
968      the_molecules[i].initialize( info );
969 +
970 +
971      atomOffset += info.nAtoms;
972 +    delete[] theBonds;
973 +    delete[] theBends;
974 +    delete[] theTorsions;
975    }
976  
977 + #ifdef IS_MPI
978 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
979 +  MPIcheckPoint();
980 + #endif // is_mpi
981 +
982    // clean up the forcefield
983    the_ff->calcRcut();
984    the_ff->cleanMe();
985 +
986   }
987  
988   void SimSetup::initFromBass( void ){

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