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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 420 by mmeineke, Thu Mar 27 17:32:03 2003 UTC vs.
Revision 504 by mmeineke, Thu Apr 17 21:54:18 2003 UTC

# Line 66 | Line 66 | void SimSetup::createSim( void ){
66  
67    MakeStamps *the_stamps;
68    Globals* the_globals;
69 <  int i, j;
69 >  ExtendedSystem* the_extendedsystem;
70 >  int i, j, k, globalAtomIndex;
71  
72    // get the stamps and globals;
73    the_stamps = stamps;
# 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 230 | Line 298 | void SimSetup::createSim( void ){
298    simnfo->n_torsions = tot_torsions;
299    simnfo->n_SRI = tot_SRI;
300    simnfo->n_mol = tot_nmol;
233 –
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    
241 –  
242 –
310    globalIndex = mpiSim->divideLabor();
311  
245 –
246 –
312    // set up the local variables
313    
314    int localMol, allMol;
315    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
316 +
317 +  int* mol2proc = mpiSim->getMolToProcMap();
318 +  int* molCompType = mpiSim->getMolComponentType();
319    
320    allMol = 0;
321    localMol = 0;
# Line 255 | 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( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
333 >      if( mol2proc[allMol] == worldRank ){
334          
335          local_atoms +=    comp_stamps[i]->getNAtoms();
336          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | 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    
276 –
351    simnfo->n_atoms = mpiSim->getMyNlocal();  
352    
353    if( local_atoms != simnfo->n_atoms ){
354      sprintf( painCave.errMsg,
355               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356 <             " localAtom (%d) are note equal.\n",
356 >             " localAtom (%d) are not equal.\n",
357               simnfo->n_atoms,
358               local_atoms );
359      painCave.isFatal = 1;
# Line 304 | Line 378 | void SimSetup::createSim( void ){
378    Atom::createArrays(simnfo->n_atoms);
379    the_atoms = new Atom*[simnfo->n_atoms];
380    the_molecules = new Molecule[simnfo->n_mol];
381 +  int molIndex;
382  
383 +  // initialize the molecule's stampID's
384  
385 + #ifdef IS_MPI
386 +  
387 +
388 +  molIndex = 0;
389 +  for(i=0; i<mpiSim->getTotNmol(); i++){
390 +    
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 +  }
398 +
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 +  }
415 +    
416 +
417 + #endif // is_mpi
418 +
419 +
420    if( simnfo->n_SRI ){
421 +    
422      Exclude::createArray(simnfo->n_SRI);
423      the_excludes = new Exclude*[simnfo->n_SRI];
424 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
425      simnfo->globalExcludes = new int;
426 <    simnfo->n_exclude = tot_SRI;
426 >    simnfo->n_exclude = simnfo->n_SRI;
427    }
428    else{
429      
# Line 326 | Line 439 | void SimSetup::createSim( void ){
439    // set the arrays into the SimInfo object
440  
441    simnfo->atoms = the_atoms;
442 <  simnfo->sr_interactions = the_sris;
442 >  simnfo->molecules = the_molecules;
443    simnfo->nGlobalExcludes = 0;
444    simnfo->excludes = the_excludes;
445  
# Line 383 | Line 496 | void SimSetup::createSim( void ){
496  
497    the_ff->setSimInfo( simnfo );
498  
499 <  makeAtoms();
499 >  makeMolecules();
500    simnfo->identArray = new int[simnfo->n_atoms];
501    for(i=0; i<simnfo->n_atoms; i++){
502      simnfo->identArray[i] = the_atoms[i]->getIdent();
503    }
504    
392 –  if( tot_bonds ){
393 –    makeBonds();
394 –  }
395 –
396 –  if( tot_bends ){
397 –    makeBends();
398 –  }
399 –
400 –  if( tot_torsions ){
401 –    makeTorsions();
402 –  }
403 –
404 –
505    if (the_globals->getUseRF() ) {
506      simnfo->useReactionField = 1;
507    
# Line 443 | 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 463 | 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 638 | Line 738 | void SimSetup::createSim( void ){
738  
739   //   new AllLong( simnfo );
740  
641 –  if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642 –  if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643 –  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644 –  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
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();
751 + #endif
752  
753    // initialize the Fortran
754 <  
754 >
755 >
756    simnfo->refreshSim();
757    
758    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 789 | void SimSetup::makeMolecules( void ){
789    BondStamp* currentBond;
790    BendStamp* currentBend;
791    TorsionStamp* currentTorsion;
792 +
793 +  bond_pair* theBonds;
794 +  bend_set* theBends;
795 +  torsion_set* theTorsions;
796 +
797    
798    //init the forceField paramters
799  
800    the_ff->readParams();
801  
802    
803 <  // init the molecules
803 >  // init the atoms
804  
805 +  double ux, uy, uz, u, uSqr;
806 +  
807    atomOffset = 0;
808    excludeOffset = 0;
809    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 820 | void SimSetup::makeMolecules( void ){
820      info.myExcludes = &the_excludes[excludeOffset];
821      info.myBonds = new Bond*[info.nBonds];
822      info.myBends = new Bend*[info.nBends];
823 <    info.myTorsions = new Torsions*[info.nTorsions];
823 >    info.myTorsions = new Torsion*[info.nTorsions];
824  
825      theBonds = new bond_pair[info.nBonds];
826      theBends = new bend_set[info.nBends];
# Line 717 | Line 830 | void SimSetup::makeMolecules( void ){
830      
831      for(j=0; j<info.nAtoms; j++){
832        
833 <      currentAtom = theComponents[stampID]->getAtom( j );
833 >      currentAtom = comp_stamps[stampID]->getAtom( j );
834        if( currentAtom->haveOrientation() ){
835          
836          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 871 | void SimSetup::makeMolecules( void ){
871        theBonds[j].a = currentBond->getA() + atomOffset;
872        theBonds[j].b = currentBond->getB() + atomOffset;
873  
874 <      exI = theBonds[i].a;
875 <      exJ = theBonds[i].b;
874 >      exI = theBonds[j].a;
875 >      exJ = theBonds[j].b;
876  
877        // exclude_I must always be the smaller of the pair
878        if( exI > exJ ){
# Line 775 | Line 888 | void SimSetup::makeMolecules( void ){
888        
889        the_excludes[j+excludeOffset]->setPair( exI, exJ );
890   #else  // isn't MPI
891 +
892        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
893   #endif  //is_mpi
894      }
# Line 790 | Line 904 | void SimSetup::makeMolecules( void ){
904            
905        if( currentBend->haveExtras() ){
906              
907 <        extras = current_bend->getExtras();
907 >        extras = currentBend->getExtras();
908          current_extra = extras;
909              
910          while( current_extra != NULL ){
# Line 812 | Line 926 | void SimSetup::makeMolecules( void ){
926                
927              default:
928                sprintf( painCave.errMsg,
929 <                       "SimSetup Error: ghostVectorSource was neiter a "
929 >                       "SimSetup Error: ghostVectorSource was neither a "
930                         "double nor an int.\n"
931                         "-->Bend[%d] in %s\n",
932                         j, comp_stamps[stampID]->getID() );
# Line 906 | Line 1020 | void SimSetup::makeMolecules( void ){
1020  
1021  
1022      the_molecules[i].initialize( info );
1023 +
1024 +
1025      atomOffset += info.nAtoms;
1026 +    delete[] theBonds;
1027 +    delete[] theBends;
1028 +    delete[] theTorsions;
1029    }
1030  
1031 + #ifdef IS_MPI
1032 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1033 +  MPIcheckPoint();
1034 + #endif // is_mpi
1035 +
1036    // clean up the forcefield
1037    the_ff->calcRcut();
1038    the_ff->cleanMe();
1039 +
1040   }
1041  
1042   void SimSetup::initFromBass( void ){

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