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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 504 by mmeineke, Thu Apr 17 21:54:18 2003 UTC

# Line 67 | Line 67 | void SimSetup::createSim( void ){
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69    ExtendedSystem* the_extendedsystem;
70 <  int i, j;
70 >  int i, j, k, globalAtomIndex;
71  
72    // get the stamps and globals;
73    the_stamps = stamps;
# Line 87 | Line 87 | void SimSetup::createSim( void ){
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());
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,
# Line 106 | Line 154 | void SimSetup::createSim( void ){
154    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155    simnfo->usePBC = the_globals->getPBC();
156            
157 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
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,
# Line 246 | Line 298 | void SimSetup::createSim( void ){
298    simnfo->n_torsions = tot_torsions;
299    simnfo->n_SRI = tot_SRI;
300    simnfo->n_mol = tot_nmol;
249 –
301    
302 +  simnfo->molMembershipArray = new int[tot_atoms];
303 +
304   #ifdef IS_MPI
305  
306    // divide the molecules among processors here.
307    
308    mpiSim = new mpiSimulation( simnfo );
309    
257 –  
258 –
310    globalIndex = mpiSim->divideLabor();
311  
312    // set up the local variables
# Line 272 | Line 323 | void SimSetup::createSim( void ){
323    local_bonds = 0;
324    local_bends = 0;
325    local_torsions = 0;
326 +  globalAtomIndex = 0;
327 +
328 +
329    for( i=0; i<n_components; i++ ){
330  
331      for( j=0; j<components_nmol[i]; j++ ){
332        
333 <      if( mol2proc[j] == worldRank ){
333 >      if( mol2proc[allMol] == worldRank ){
334          
335          local_atoms +=    comp_stamps[i]->getNAtoms();
336          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 284 | Line 338 | void SimSetup::createSim( void ){
338          local_torsions += comp_stamps[i]->getNTorsions();
339          localMol++;
340        }      
341 <      allMol++;
341 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
343 >        globalAtomIndex++;
344 >      }
345 >
346 >      allMol++;      
347      }
348    }
349    local_SRI = local_bonds + local_bends + local_torsions;
350    
292 –
351    simnfo->n_atoms = mpiSim->getMyNlocal();  
352    
353    if( local_atoms != simnfo->n_atoms ){
# Line 333 | Line 391 | void SimSetup::createSim( void ){
391      if(mol2proc[i] == worldRank ){
392        the_molecules[molIndex].setStampID( molCompType[i] );
393        the_molecules[molIndex].setMyIndex( molIndex );
394 +      the_molecules[molIndex].setGlobalIndex( i );
395        molIndex++;
396      }
397    }
# Line 340 | Line 399 | void SimSetup::createSim( void ){
399   #else // is_mpi
400    
401    molIndex = 0;
402 +  globalAtomIndex = 0;
403    for(i=0; i<n_components; i++){
404      for(j=0; j<components_nmol[i]; j++ ){
405        the_molecules[molIndex].setStampID( i );
406        the_molecules[molIndex].setMyIndex( molIndex );
407 +      the_molecules[molIndex].setGlobalIndex( molIndex );
408 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410 +        globalAtomIndex++;
411 +      }
412        molIndex++;
413      }
414    }
# Line 478 | Line 543 | void SimSetup::createSim( void ){
543      }
544      simnfo->dielectric = the_globals->getDielectric();  
545    } else {
546 <    if (simnfo->n_dipoles) {
546 >    if (usesDipoles) {
547        
548        if( !the_globals->haveECR() ){
549          sprintf( painCave.errMsg,
550 <                 "SimSetup Warning: using default value of 1/2 the smallest"
550 >                 "SimSetup Warning: using default value of 1/2 the smallest "
551                   "box length for the electrostaticCutoffRadius.\n"
552                   "I hope you have a very fast processor!\n");
553          painCave.isFatal = 0;
# Line 498 | Line 563 | void SimSetup::createSim( void ){
563        
564        if( !the_globals->haveEST() ){
565          sprintf( painCave.errMsg,
566 <                 "SimSetup Warning: using default value of 5% of the"
566 >                 "SimSetup Warning: using default value of 5%% of the "
567                   "electrostaticCutoffRadius for the "
568                   "electrostaticSkinThickness\n"
569                   );
# Line 673 | Line 738 | void SimSetup::createSim( void ){
738  
739   //   new AllLong( simnfo );
740  
741 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
742 <                                                           the_ff,
743 <                                                           the_extendedsystem);
744 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
745 <                                                 the_ff,
746 <                                                 the_extendedsystem );
741 >
742 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
743 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
744 >  }
745 >  else if( !strcmp( force_field, "LJ" ) ){
746 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
747 >  }
748  
749   #ifdef IS_MPI
750    mpiSim->mpiRefresh();

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