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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 489 by mmeineke, Thu Apr 10 20:08:56 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 +    if (the_globals->haveTargetPressure())
91 +      the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92 +    else {
93 +      sprintf( painCave.errMsg,
94 +               "SimSetup error: If you use the constant pressure\n"
95 +               "    ensemble, you must set targetPressure.\n"
96 +               "    This was found in the BASS file.\n");
97 +      painCave.isFatal = 1;
98 +      simError();
99 +    }
100 +
101 +    if (the_globals->haveTauThermostat())
102 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103 +    else if (the_globals->haveQmass())
104 +      the_extendedsystem->setQmass(the_globals->getQmass());
105 +    else {
106 +      sprintf( painCave.errMsg,
107 +               "SimSetup error: If you use one of the constant temperature\n"
108 +               "    ensembles, you must set either tauThermostat or qMass.\n"
109 +               "    Neither of these was found in the BASS file.\n");
110 +      painCave.isFatal = 1;
111 +      simError();
112 +    }
113 +
114 +    if (the_globals->haveTauBarostat())
115 +      the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116 +    else {
117 +      sprintf( painCave.errMsg,
118 +               "SimSetup error: If you use the constant pressure\n"
119 +               "    ensemble, you must set tauBarostat.\n"
120 +               "    This was found in the BASS file.\n");
121 +      painCave.isFatal = 1;
122 +      simError();
123 +    }
124 +
125 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
126 +    the_extendedsystem = new ExtendedSystem( simnfo );
127 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
128 +
129 +    if (the_globals->haveTauThermostat())
130 +      the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131 +    else if (the_globals->haveQmass())
132 +      the_extendedsystem->setQmass(the_globals->getQmass());
133 +    else {
134 +      sprintf( painCave.errMsg,
135 +               "SimSetup error: If you use one of the constant temperature\n"
136 +               "    ensembles, you must set either tauThermostat or qMass.\n"
137 +               "    Neither of these was found in the BASS file.\n");
138 +      painCave.isFatal = 1;
139 +      simError();
140 +    }
141 +
142 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
143 +  } else {
144 +    sprintf( painCave.errMsg,
145 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
146 +             "reverting to NVE for this simulation.\n",
147 +             ensemble );
148 +    painCave.isFatal = 0;
149 +    simError();
150 +    strcpy( ensemble, "NVE" );
151 +  }  
152    strcpy( simnfo->ensemble, ensemble );
153  
154    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155    simnfo->usePBC = the_globals->getPBC();
156            
157 <
158 <
159 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
160 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
157 >  int usesDipoles = 0;
158 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
159 >    the_ff = new TraPPE_ExFF();
160 >    usesDipoles = 1;
161 >  }
162 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163    else{
164      sprintf( painCave.errMsg,
165               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 240 | Line 310 | void SimSetup::createSim( void ){
310  
311    globalIndex = mpiSim->divideLabor();
312  
243 –
244 –
313    // set up the local variables
314    
315    int localMol, allMol;
# Line 260 | Line 328 | void SimSetup::createSim( void ){
328  
329      for( j=0; j<components_nmol[i]; j++ ){
330        
331 <      if( mol2proc[j] == worldRank ){
331 >      if( mol2proc[allMol] == worldRank ){
332          
333          local_atoms +=    comp_stamps[i]->getNAtoms();
334          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 316 | Line 384 | void SimSetup::createSim( void ){
384      
385      if(mol2proc[i] == worldRank ){
386        the_molecules[molIndex].setStampID( molCompType[i] );
387 +      the_molecules[molIndex].setMyIndex( molIndex );
388 +      the_molecules[molIndex].setGlobalIndex( i );
389        molIndex++;
390      }
391    }
# Line 326 | Line 396 | void SimSetup::createSim( void ){
396    for(i=0; i<n_components; i++){
397      for(j=0; j<components_nmol[i]; j++ ){
398        the_molecules[molIndex].setStampID( i );
399 +      the_molecules[molIndex].setMyIndex( molIndex );
400 +      the_molecules[molIndex].setGlobalIndex( molIndex );
401        molIndex++;
402      }
403    }
# Line 335 | Line 407 | void SimSetup::createSim( void ){
407  
408  
409    if( simnfo->n_SRI ){
410 +    
411      Exclude::createArray(simnfo->n_SRI);
412      the_excludes = new Exclude*[simnfo->n_SRI];
413 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
414      simnfo->globalExcludes = new int;
415 <    simnfo->n_exclude = tot_SRI;
415 >    simnfo->n_exclude = simnfo->n_SRI;
416    }
417    else{
418      
# Line 354 | Line 428 | void SimSetup::createSim( void ){
428    // set the arrays into the SimInfo object
429  
430    simnfo->atoms = the_atoms;
431 +  simnfo->molecules = the_molecules;
432    simnfo->nGlobalExcludes = 0;
433    simnfo->excludes = the_excludes;
434  
# Line 412 | Line 487 | void SimSetup::createSim( void ){
487  
488    makeMolecules();
489    simnfo->identArray = new int[simnfo->n_atoms];
490 +  simnfo->molMembershipArray = new int[simnfo->n_atoms];
491    for(i=0; i<simnfo->n_atoms; i++){
492      simnfo->identArray[i] = the_atoms[i]->getIdent();
493    }
494 +  for(i=0; i< simnfo->n_mol; i++) {
495 +    the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
496 +  }
497    
498    if (the_globals->getUseRF() ) {
499      simnfo->useReactionField = 1;
# Line 457 | Line 536 | void SimSetup::createSim( void ){
536      }
537      simnfo->dielectric = the_globals->getDielectric();  
538    } else {
539 <    if (simnfo->n_dipoles) {
539 >    if (usesDipoles) {
540        
541        if( !the_globals->haveECR() ){
542          sprintf( painCave.errMsg,
543 <                 "SimSetup Warning: using default value of 1/2 the smallest"
543 >                 "SimSetup Warning: using default value of 1/2 the smallest "
544                   "box length for the electrostaticCutoffRadius.\n"
545                   "I hope you have a very fast processor!\n");
546          painCave.isFatal = 0;
# Line 477 | Line 556 | void SimSetup::createSim( void ){
556        
557        if( !the_globals->haveEST() ){
558          sprintf( painCave.errMsg,
559 <                 "SimSetup Warning: using default value of 5% of the"
559 >                 "SimSetup Warning: using default value of 5%% of the "
560                   "electrostaticCutoffRadius for the "
561                   "electrostaticSkinThickness\n"
562                   );
# Line 652 | Line 731 | void SimSetup::createSim( void ){
731  
732   //   new AllLong( simnfo );
733  
655 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
656 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
734  
735 <
735 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
736 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
737 >  }
738 >  else if( !strcmp( force_field, "LJ" ) ){
739 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
740 >  }
741 >  else {
742 >    std::cerr << "I'm a bug.\n";
743 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
744 >  }
745 > #ifdef IS_MPI
746 >  mpiSim->mpiRefresh();
747 > #endif
748  
749    // initialize the Fortran
750 <  
750 >
751 >
752    simnfo->refreshSim();
753    
754    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 695 | Line 785 | void SimSetup::makeMolecules( void ){
785    BondStamp* currentBond;
786    BendStamp* currentBend;
787    TorsionStamp* currentTorsion;
788 +
789 +  bond_pair* theBonds;
790 +  bend_set* theBends;
791 +  torsion_set* theTorsions;
792 +
793    
794    //init the forceField paramters
795  
796    the_ff->readParams();
797  
798    
799 <  // init the molecules
799 >  // init the atoms
800  
801 +  double ux, uy, uz, u, uSqr;
802 +  
803    atomOffset = 0;
804    excludeOffset = 0;
805    for(i=0; i<simnfo->n_mol; i++){
# Line 719 | Line 816 | void SimSetup::makeMolecules( void ){
816      info.myExcludes = &the_excludes[excludeOffset];
817      info.myBonds = new Bond*[info.nBonds];
818      info.myBends = new Bend*[info.nBends];
819 <    info.myTorsions = new Torsions*[info.nTorsions];
819 >    info.myTorsions = new Torsion*[info.nTorsions];
820  
821      theBonds = new bond_pair[info.nBonds];
822      theBends = new bend_set[info.nBends];
# Line 729 | Line 826 | void SimSetup::makeMolecules( void ){
826      
827      for(j=0; j<info.nAtoms; j++){
828        
829 <      currentAtom = theComponents[stampID]->getAtom( j );
829 >      currentAtom = comp_stamps[stampID]->getAtom( j );
830        if( currentAtom->haveOrientation() ){
831          
832          dAtom = new DirectionalAtom(j + atomOffset);
# Line 770 | Line 867 | void SimSetup::makeMolecules( void ){
867        theBonds[j].a = currentBond->getA() + atomOffset;
868        theBonds[j].b = currentBond->getB() + atomOffset;
869  
870 <      exI = theBonds[i].a;
871 <      exJ = theBonds[i].b;
870 >      exI = theBonds[j].a;
871 >      exJ = theBonds[j].b;
872  
873        // exclude_I must always be the smaller of the pair
874        if( exI > exJ ){
# Line 787 | Line 884 | void SimSetup::makeMolecules( void ){
884        
885        the_excludes[j+excludeOffset]->setPair( exI, exJ );
886   #else  // isn't MPI
887 +
888        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
889   #endif  //is_mpi
890      }
# Line 802 | Line 900 | void SimSetup::makeMolecules( void ){
900            
901        if( currentBend->haveExtras() ){
902              
903 <        extras = current_bend->getExtras();
903 >        extras = currentBend->getExtras();
904          current_extra = extras;
905              
906          while( current_extra != NULL ){
# Line 824 | Line 922 | void SimSetup::makeMolecules( void ){
922                
923              default:
924                sprintf( painCave.errMsg,
925 <                       "SimSetup Error: ghostVectorSource was neiter a "
925 >                       "SimSetup Error: ghostVectorSource was neither a "
926                         "double nor an int.\n"
927                         "-->Bend[%d] in %s\n",
928                         j, comp_stamps[stampID]->getID() );
# Line 918 | Line 1016 | void SimSetup::makeMolecules( void ){
1016  
1017  
1018      the_molecules[i].initialize( info );
1019 +
1020 +
1021      atomOffset += info.nAtoms;
1022 +    delete[] theBonds;
1023 +    delete[] theBends;
1024 +    delete[] theTorsions;
1025    }
1026  
1027 + #ifdef IS_MPI
1028 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1029 +  MPIcheckPoint();
1030 + #endif // is_mpi
1031 +
1032    // clean up the forcefield
1033    the_ff->calcRcut();
1034    the_ff->cleanMe();
1035 +
1036   }
1037  
1038   void SimSetup::initFromBass( void ){

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