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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 490 by gezelter, Fri Apr 11 15:16:59 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;
301 +  simnfo->molMembershipArray = new int[tot_atoms];
302  
234 –  
303   #ifdef IS_MPI
304  
305    // divide the molecules among processors here.
306    
307    mpiSim = new mpiSimulation( simnfo );
308    
241 –  
242 –
309    globalIndex = mpiSim->divideLabor();
310  
245 –
246 –
311    // set up the local variables
312    
313    int localMol, allMol;
314    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
315 +
316 +  int* mol2proc = mpiSim->getMolToProcMap();
317 +  int* molCompType = mpiSim->getMolComponentType();
318    
319    allMol = 0;
320    localMol = 0;
# Line 255 | 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( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
332 >      if( mol2proc[allMol] == worldRank ){
333          
334          local_atoms +=    comp_stamps[i]->getNAtoms();
335          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | 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    
358    if( local_atoms != simnfo->n_atoms ){
359      sprintf( painCave.errMsg,
360               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
361 <             " localAtom (%d) are note equal.\n",
361 >             " localAtom (%d) are not equal.\n",
362               simnfo->n_atoms,
363               local_atoms );
364      painCave.isFatal = 1;
# Line 304 | Line 383 | void SimSetup::createSim( void ){
383    Atom::createArrays(simnfo->n_atoms);
384    the_atoms = new Atom*[simnfo->n_atoms];
385    the_molecules = new Molecule[simnfo->n_mol];
386 +  int molIndex;
387  
388 +  // initialize the molecule's stampID's
389  
390 + #ifdef IS_MPI
391 +  
392 +
393 +  molIndex = 0;
394 +  for(i=0; i<mpiSim->getTotNmol(); i++){
395 +    
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 +  }
403 +
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 +  }
420 +    
421 +
422 + #endif // is_mpi
423 +
424 +
425    if( simnfo->n_SRI ){
426 +    
427      Exclude::createArray(simnfo->n_SRI);
428      the_excludes = new Exclude*[simnfo->n_SRI];
429 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
430      simnfo->globalExcludes = new int;
431 <    simnfo->n_exclude = tot_SRI;
431 >    simnfo->n_exclude = simnfo->n_SRI;
432    }
433    else{
434      
# Line 326 | Line 444 | void SimSetup::createSim( void ){
444    // set the arrays into the SimInfo object
445  
446    simnfo->atoms = the_atoms;
447 <  simnfo->sr_interactions = the_sris;
447 >  simnfo->molecules = the_molecules;
448    simnfo->nGlobalExcludes = 0;
449    simnfo->excludes = the_excludes;
450  
# Line 383 | Line 501 | void SimSetup::createSim( void ){
501  
502    the_ff->setSimInfo( simnfo );
503  
504 <  makeAtoms();
504 >  makeMolecules();
505    simnfo->identArray = new int[simnfo->n_atoms];
506    for(i=0; i<simnfo->n_atoms; i++){
507      simnfo->identArray[i] = the_atoms[i]->getIdent();
508    }
509    
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 –
510    if (the_globals->getUseRF() ) {
511      simnfo->useReactionField = 1;
512    
# Line 443 | Line 548 | void SimSetup::createSim( void ){
548      }
549      simnfo->dielectric = the_globals->getDielectric();  
550    } else {
551 <    if (simnfo->n_dipoles) {
551 >    if (usesDipoles) {
552        
553        if( !the_globals->haveECR() ){
554          sprintf( painCave.errMsg,
555 <                 "SimSetup Warning: using default value of 1/2 the smallest"
555 >                 "SimSetup Warning: using default value of 1/2 the smallest "
556                   "box length for the electrostaticCutoffRadius.\n"
557                   "I hope you have a very fast processor!\n");
558          painCave.isFatal = 0;
# Line 463 | Line 568 | void SimSetup::createSim( void ){
568        
569        if( !the_globals->haveEST() ){
570          sprintf( painCave.errMsg,
571 <                 "SimSetup Warning: using default value of 5% of the"
571 >                 "SimSetup Warning: using default value of 5%% of the "
572                   "electrostaticCutoffRadius for the "
573                   "electrostaticSkinThickness\n"
574                   );
# Line 638 | Line 743 | void SimSetup::createSim( void ){
743  
744   //   new AllLong( simnfo );
745  
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 );
746  
747 +  if( !strcmp( force_field, "TraPPE_Ex" ) ){
748 +    new Symplectic(simnfo, the_ff, the_extendedsystem);
749 +  }
750 +  else if( !strcmp( force_field, "LJ" ) ){
751 +    new Verlet( *simnfo, the_ff, the_extendedsystem );
752 +  }
753 +  else {
754 +    std::cerr << "I'm a bug.\n";
755 +    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
756 +  }
757 + #ifdef IS_MPI
758 +  mpiSim->mpiRefresh();
759 + #endif
760  
647 –
761    // initialize the Fortran
762 <  
762 >
763 >
764    simnfo->refreshSim();
765    
766    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 797 | void SimSetup::makeMolecules( void ){
797    BondStamp* currentBond;
798    BendStamp* currentBend;
799    TorsionStamp* currentTorsion;
800 +
801 +  bond_pair* theBonds;
802 +  bend_set* theBends;
803 +  torsion_set* theTorsions;
804 +
805    
806    //init the forceField paramters
807  
808    the_ff->readParams();
809  
810    
811 <  // init the molecules
811 >  // init the atoms
812  
813 +  double ux, uy, uz, u, uSqr;
814 +  
815    atomOffset = 0;
816    excludeOffset = 0;
817    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 828 | void SimSetup::makeMolecules( void ){
828      info.myExcludes = &the_excludes[excludeOffset];
829      info.myBonds = new Bond*[info.nBonds];
830      info.myBends = new Bend*[info.nBends];
831 <    info.myTorsions = new Torsions*[info.nTorsions];
831 >    info.myTorsions = new Torsion*[info.nTorsions];
832  
833      theBonds = new bond_pair[info.nBonds];
834      theBends = new bend_set[info.nBends];
# Line 717 | Line 838 | void SimSetup::makeMolecules( void ){
838      
839      for(j=0; j<info.nAtoms; j++){
840        
841 <      currentAtom = theComponents[stampID]->getAtom( j );
841 >      currentAtom = comp_stamps[stampID]->getAtom( j );
842        if( currentAtom->haveOrientation() ){
843          
844          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 879 | void SimSetup::makeMolecules( void ){
879        theBonds[j].a = currentBond->getA() + atomOffset;
880        theBonds[j].b = currentBond->getB() + atomOffset;
881  
882 <      exI = theBonds[i].a;
883 <      exJ = theBonds[i].b;
882 >      exI = theBonds[j].a;
883 >      exJ = theBonds[j].b;
884  
885        // exclude_I must always be the smaller of the pair
886        if( exI > exJ ){
# Line 775 | Line 896 | void SimSetup::makeMolecules( void ){
896        
897        the_excludes[j+excludeOffset]->setPair( exI, exJ );
898   #else  // isn't MPI
899 +
900        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
901   #endif  //is_mpi
902      }
# Line 790 | Line 912 | void SimSetup::makeMolecules( void ){
912            
913        if( currentBend->haveExtras() ){
914              
915 <        extras = current_bend->getExtras();
915 >        extras = currentBend->getExtras();
916          current_extra = extras;
917              
918          while( current_extra != NULL ){
# Line 812 | Line 934 | void SimSetup::makeMolecules( void ){
934                
935              default:
936                sprintf( painCave.errMsg,
937 <                       "SimSetup Error: ghostVectorSource was neiter a "
937 >                       "SimSetup Error: ghostVectorSource was neither a "
938                         "double nor an int.\n"
939                         "-->Bend[%d] in %s\n",
940                         j, comp_stamps[stampID]->getID() );
# Line 906 | Line 1028 | void SimSetup::makeMolecules( void ){
1028  
1029  
1030      the_molecules[i].initialize( info );
1031 +
1032 +
1033      atomOffset += info.nAtoms;
1034 +    delete[] theBonds;
1035 +    delete[] theBends;
1036 +    delete[] theTorsions;
1037    }
1038  
1039 + #ifdef IS_MPI
1040 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1041 +  MPIcheckPoint();
1042 + #endif // is_mpi
1043 +
1044    // clean up the forcefield
1045    the_ff->calcRcut();
1046    the_ff->cleanMe();
1047 +
1048   }
1049  
1050   void SimSetup::initFromBass( void ){

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