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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 487 by mmeineke, Thu Apr 10 16:27:21 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" ) ) the_ff = new TraPPEFF();
160 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
161 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
162 <  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 242 | Line 310 | void SimSetup::createSim( void ){
310  
311    globalIndex = mpiSim->divideLabor();
312  
245 –
246 –
313    // set up the local variables
314    
315    int localMol, allMol;
# Line 262 | 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 318 | 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        molIndex++;
389      }
390    }
# Line 328 | Line 395 | void SimSetup::createSim( void ){
395    for(i=0; i<n_components; i++){
396      for(j=0; j<components_nmol[i]; j++ ){
397        the_molecules[molIndex].setStampID( i );
398 +      the_molecules[molIndex].setMyIndex( molIndex );
399        molIndex++;
400      }
401    }
# Line 337 | Line 405 | void SimSetup::createSim( void ){
405  
406  
407    if( simnfo->n_SRI ){
408 +    
409      Exclude::createArray(simnfo->n_SRI);
410      the_excludes = new Exclude*[simnfo->n_SRI];
411 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
412      simnfo->globalExcludes = new int;
413 <    simnfo->n_exclude = tot_SRI;
413 >    simnfo->n_exclude = simnfo->n_SRI;
414    }
415    else{
416      
# Line 356 | Line 426 | void SimSetup::createSim( void ){
426    // set the arrays into the SimInfo object
427  
428    simnfo->atoms = the_atoms;
429 +  simnfo->molecules = the_molecules;
430    simnfo->nGlobalExcludes = 0;
431    simnfo->excludes = the_excludes;
432  
# Line 414 | Line 485 | void SimSetup::createSim( void ){
485  
486    makeMolecules();
487    simnfo->identArray = new int[simnfo->n_atoms];
488 +  simnfo->molMembershipArray = new int[simnfo->n_atoms];
489    for(i=0; i<simnfo->n_atoms; i++){
490      simnfo->identArray[i] = the_atoms[i]->getIdent();
491    }
492 +  for(i=0; i< simnfo->n_mol; i++) {
493 +    the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
494 +  }
495    
496    if (the_globals->getUseRF() ) {
497      simnfo->useReactionField = 1;
# Line 459 | Line 534 | void SimSetup::createSim( void ){
534      }
535      simnfo->dielectric = the_globals->getDielectric();  
536    } else {
537 <    if (simnfo->n_dipoles) {
537 >    if (usesDipoles) {
538        
539        if( !the_globals->haveECR() ){
540          sprintf( painCave.errMsg,
541 <                 "SimSetup Warning: using default value of 1/2 the smallest"
541 >                 "SimSetup Warning: using default value of 1/2 the smallest "
542                   "box length for the electrostaticCutoffRadius.\n"
543                   "I hope you have a very fast processor!\n");
544          painCave.isFatal = 0;
# Line 479 | Line 554 | void SimSetup::createSim( void ){
554        
555        if( !the_globals->haveEST() ){
556          sprintf( painCave.errMsg,
557 <                 "SimSetup Warning: using default value of 5% of the"
557 >                 "SimSetup Warning: using default value of 5%% of the "
558                   "electrostaticCutoffRadius for the "
559                   "electrostaticSkinThickness\n"
560                   );
# Line 654 | Line 729 | void SimSetup::createSim( void ){
729  
730   //   new AllLong( simnfo );
731  
657 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
658 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
659 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
660 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
732  
733 +  if( !strcmp( force_field, "TraPPE_Ex" ) ){
734 +    new Symplectic(simnfo, the_ff, the_extendedsystem);
735 +  }
736 +  else if( !strcmp( force_field, "LJ" ) ){
737 +    new Verlet( *simnfo, the_ff, the_extendedsystem );
738 +  }
739 +  else {
740 +    std::cerr << "I'm a bug.\n";
741 +    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
742 +  }
743 + #ifdef IS_MPI
744 +  mpiSim->mpiRefresh();
745 + #endif
746  
663 –
747    // initialize the Fortran
748 <  
748 >
749 >
750    simnfo->refreshSim();
751    
752    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 699 | Line 783 | void SimSetup::makeMolecules( void ){
783    BondStamp* currentBond;
784    BendStamp* currentBend;
785    TorsionStamp* currentTorsion;
786 +
787 +  bond_pair* theBonds;
788 +  bend_set* theBends;
789 +  torsion_set* theTorsions;
790 +
791    
792    //init the forceField paramters
793  
794    the_ff->readParams();
795  
796    
797 <  // init the molecules
797 >  // init the atoms
798  
799 +  double ux, uy, uz, u, uSqr;
800 +  
801    atomOffset = 0;
802    excludeOffset = 0;
803    for(i=0; i<simnfo->n_mol; i++){
# Line 723 | Line 814 | void SimSetup::makeMolecules( void ){
814      info.myExcludes = &the_excludes[excludeOffset];
815      info.myBonds = new Bond*[info.nBonds];
816      info.myBends = new Bend*[info.nBends];
817 <    info.myTorsions = new Torsions*[info.nTorsions];
817 >    info.myTorsions = new Torsion*[info.nTorsions];
818  
819      theBonds = new bond_pair[info.nBonds];
820      theBends = new bend_set[info.nBends];
# Line 733 | Line 824 | void SimSetup::makeMolecules( void ){
824      
825      for(j=0; j<info.nAtoms; j++){
826        
827 <      currentAtom = theComponents[stampID]->getAtom( j );
827 >      currentAtom = comp_stamps[stampID]->getAtom( j );
828        if( currentAtom->haveOrientation() ){
829          
830          dAtom = new DirectionalAtom(j + atomOffset);
# Line 774 | Line 865 | void SimSetup::makeMolecules( void ){
865        theBonds[j].a = currentBond->getA() + atomOffset;
866        theBonds[j].b = currentBond->getB() + atomOffset;
867  
868 <      exI = theBonds[i].a;
869 <      exJ = theBonds[i].b;
868 >      exI = theBonds[j].a;
869 >      exJ = theBonds[j].b;
870  
871        // exclude_I must always be the smaller of the pair
872        if( exI > exJ ){
# Line 791 | Line 882 | void SimSetup::makeMolecules( void ){
882        
883        the_excludes[j+excludeOffset]->setPair( exI, exJ );
884   #else  // isn't MPI
885 +
886        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
887   #endif  //is_mpi
888      }
# Line 806 | Line 898 | void SimSetup::makeMolecules( void ){
898            
899        if( currentBend->haveExtras() ){
900              
901 <        extras = current_bend->getExtras();
901 >        extras = currentBend->getExtras();
902          current_extra = extras;
903              
904          while( current_extra != NULL ){
# Line 828 | Line 920 | void SimSetup::makeMolecules( void ){
920                
921              default:
922                sprintf( painCave.errMsg,
923 <                       "SimSetup Error: ghostVectorSource was neiter a "
923 >                       "SimSetup Error: ghostVectorSource was neither a "
924                         "double nor an int.\n"
925                         "-->Bend[%d] in %s\n",
926                         j, comp_stamps[stampID]->getID() );
# Line 922 | Line 1014 | void SimSetup::makeMolecules( void ){
1014  
1015  
1016      the_molecules[i].initialize( info );
1017 +
1018 +
1019      atomOffset += info.nAtoms;
1020 +    delete[] theBonds;
1021 +    delete[] theBends;
1022 +    delete[] theTorsions;
1023    }
1024  
1025 + #ifdef IS_MPI
1026 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1027 +  MPIcheckPoint();
1028 + #endif // is_mpi
1029 +
1030    // clean up the forcefield
1031    the_ff->calcRcut();
1032    the_ff->cleanMe();
1033 +
1034   }
1035  
1036   void SimSetup::initFromBass( void ){

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