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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 474 by gezelter, Mon Apr 7 21:42:19 2003 UTC vs.
Revision 490 by gezelter, Fri Apr 11 15:16:59 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());
91 <    the_extendedsystem->setQmass(the_globals->getQmass());
92 <    the_extendedsystem->setTauRelax(the_globals->getTauRelax());
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 <    the_extendedsystem->setQmass(the_globals->getQmass());    
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 253 | Line 298 | void SimSetup::createSim( void ){
298    simnfo->n_torsions = tot_torsions;
299    simnfo->n_SRI = tot_SRI;
300    simnfo->n_mol = tot_nmol;
301 +  simnfo->molMembershipArray = new int[tot_atoms];
302  
257 –  
303   #ifdef IS_MPI
304  
305    // divide the molecules among processors here.
306    
307    mpiSim = new mpiSimulation( simnfo );
308    
264 –  
265 –
309    globalIndex = mpiSim->divideLabor();
310  
311    // set up the local variables
# Line 279 | Line 322 | void SimSetup::createSim( void ){
322    local_bonds = 0;
323    local_bends = 0;
324    local_torsions = 0;
325 +  globalAtomIndex = 0;
326 +
327 +
328    for( i=0; i<n_components; i++ ){
329  
330      for( j=0; j<components_nmol[i]; j++ ){
331        
332 <      if( mol2proc[j] == worldRank ){
332 >      if( mol2proc[allMol] == worldRank ){
333          
334          local_atoms +=    comp_stamps[i]->getNAtoms();
335          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 291 | Line 337 | void SimSetup::createSim( void ){
337          local_torsions += comp_stamps[i]->getNTorsions();
338          localMol++;
339        }      
340 <      allMol++;
340 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
341 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
342 >        globalAtomIndex++;
343 >      }
344 >
345 >      allMol++;      
346      }
347    }
348    local_SRI = local_bonds + local_bends + local_torsions;
349    
350 +  if (worldRank != 0) {
351 +    for (i =0; i < tot_atoms; i++){
352 +      std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n";
353 +    }
354 +  }
355  
356    simnfo->n_atoms = mpiSim->getMyNlocal();  
357    
# Line 340 | Line 396 | void SimSetup::createSim( void ){
396      if(mol2proc[i] == worldRank ){
397        the_molecules[molIndex].setStampID( molCompType[i] );
398        the_molecules[molIndex].setMyIndex( molIndex );
399 +      the_molecules[molIndex].setGlobalIndex( i );
400        molIndex++;
401      }
402    }
# Line 347 | Line 404 | void SimSetup::createSim( void ){
404   #else // is_mpi
405    
406    molIndex = 0;
407 +  globalAtomIndex = 0;
408    for(i=0; i<n_components; i++){
409      for(j=0; j<components_nmol[i]; j++ ){
410        the_molecules[molIndex].setStampID( i );
411        the_molecules[molIndex].setMyIndex( molIndex );
412 +      the_molecules[molIndex].setGlobalIndex( molIndex );
413 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
414 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
415 +        globalAtomIndex++;
416 +      }
417        molIndex++;
418      }
419    }
# Line 683 | Line 746 | void SimSetup::createSim( void ){
746  
747    if( !strcmp( force_field, "TraPPE_Ex" ) ){
748      new Symplectic(simnfo, the_ff, the_extendedsystem);
686 –    std::cerr << "called new Symplecic\n";
687 –    fprintf( stderr, "called new Symplectic. stderr\n" );
749    }
750    else if( !strcmp( force_field, "LJ" ) ){
751      new Verlet( *simnfo, the_ff, the_extendedsystem );
691 –    std::cerr << "called new Verlet\n";
692 –    fprintf( stderr, "called new Verlet. stderr\n" );
752    }
753    else {
754      std::cerr << "I'm a bug.\n";

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