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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 474 by gezelter, Mon Apr 7 21:42:19 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 +    the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91 +    the_extendedsystem->setQmass(the_globals->getQmass());
92 +    the_extendedsystem->setTauRelax(the_globals->getTauRelax());
93 +  } else if ( !strcasecmp( ensemble, "NVT") ) {
94 +    the_extendedsystem = new ExtendedSystem( simnfo );
95 +    the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
96 +    the_extendedsystem->setQmass(the_globals->getQmass());    
97 +  } else if ( !strcasecmp( ensemble, "NVE") ) {
98 +  } else {
99 +    sprintf( painCave.errMsg,
100 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
101 +             "reverting to NVE for this simulation.\n",
102 +             ensemble );
103 +    painCave.isFatal = 0;
104 +    simError();
105 +    strcpy( ensemble, "NVE" );
106 +  }  
107    strcpy( simnfo->ensemble, ensemble );
108  
109    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
110    simnfo->usePBC = the_globals->getPBC();
111            
112 <
113 <
114 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
115 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
116 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
117 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
112 >  int usesDipoles = 0;
113 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
114 >    the_ff = new TraPPE_ExFF();
115 >    usesDipoles = 1;
116 >  }
117 >  else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
118    else{
119      sprintf( painCave.errMsg,
120               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 242 | Line 265 | void SimSetup::createSim( void ){
265  
266    globalIndex = mpiSim->divideLabor();
267  
245 –
246 –
268    // set up the local variables
269    
270    int localMol, allMol;
271    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
272 +
273 +  int* mol2proc = mpiSim->getMolToProcMap();
274 +  int* molCompType = mpiSim->getMolComponentType();
275    
276    allMol = 0;
277    localMol = 0;
# Line 259 | Line 283 | void SimSetup::createSim( void ){
283  
284      for( j=0; j<components_nmol[i]; j++ ){
285        
286 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
286 >      if( mol2proc[j] == worldRank ){
287          
288          local_atoms +=    comp_stamps[i]->getNAtoms();
289          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 279 | Line 302 | void SimSetup::createSim( void ){
302    if( local_atoms != simnfo->n_atoms ){
303      sprintf( painCave.errMsg,
304               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
305 <             " localAtom (%d) are note equal.\n",
305 >             " localAtom (%d) are not equal.\n",
306               simnfo->n_atoms,
307               local_atoms );
308      painCave.isFatal = 1;
# Line 304 | Line 327 | void SimSetup::createSim( void ){
327    Atom::createArrays(simnfo->n_atoms);
328    the_atoms = new Atom*[simnfo->n_atoms];
329    the_molecules = new Molecule[simnfo->n_mol];
330 +  int molIndex;
331  
332 +  // initialize the molecule's stampID's
333  
334 + #ifdef IS_MPI
335 +  
336 +
337 +  molIndex = 0;
338 +  for(i=0; i<mpiSim->getTotNmol(); i++){
339 +    
340 +    if(mol2proc[i] == worldRank ){
341 +      the_molecules[molIndex].setStampID( molCompType[i] );
342 +      the_molecules[molIndex].setMyIndex( molIndex );
343 +      molIndex++;
344 +    }
345 +  }
346 +
347 + #else // is_mpi
348 +  
349 +  molIndex = 0;
350 +  for(i=0; i<n_components; i++){
351 +    for(j=0; j<components_nmol[i]; j++ ){
352 +      the_molecules[molIndex].setStampID( i );
353 +      the_molecules[molIndex].setMyIndex( molIndex );
354 +      molIndex++;
355 +    }
356 +  }
357 +    
358 +
359 + #endif // is_mpi
360 +
361 +
362    if( simnfo->n_SRI ){
363 +    
364      Exclude::createArray(simnfo->n_SRI);
365      the_excludes = new Exclude*[simnfo->n_SRI];
366 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
367      simnfo->globalExcludes = new int;
368 <    simnfo->n_exclude = tot_SRI;
368 >    simnfo->n_exclude = simnfo->n_SRI;
369    }
370    else{
371      
# Line 326 | Line 381 | void SimSetup::createSim( void ){
381    // set the arrays into the SimInfo object
382  
383    simnfo->atoms = the_atoms;
384 <  simnfo->sr_interactions = the_sris;
384 >  simnfo->molecules = the_molecules;
385    simnfo->nGlobalExcludes = 0;
386    simnfo->excludes = the_excludes;
387  
# Line 383 | Line 438 | void SimSetup::createSim( void ){
438  
439    the_ff->setSimInfo( simnfo );
440  
441 <  makeAtoms();
441 >  makeMolecules();
442    simnfo->identArray = new int[simnfo->n_atoms];
443    for(i=0; i<simnfo->n_atoms; i++){
444      simnfo->identArray[i] = the_atoms[i]->getIdent();
445    }
446    
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 –
447    if (the_globals->getUseRF() ) {
448      simnfo->useReactionField = 1;
449    
# Line 443 | Line 485 | void SimSetup::createSim( void ){
485      }
486      simnfo->dielectric = the_globals->getDielectric();  
487    } else {
488 <    if (simnfo->n_dipoles) {
488 >    if (usesDipoles) {
489        
490        if( !the_globals->haveECR() ){
491          sprintf( painCave.errMsg,
492 <                 "SimSetup Warning: using default value of 1/2 the smallest"
492 >                 "SimSetup Warning: using default value of 1/2 the smallest "
493                   "box length for the electrostaticCutoffRadius.\n"
494                   "I hope you have a very fast processor!\n");
495          painCave.isFatal = 0;
# Line 463 | Line 505 | void SimSetup::createSim( void ){
505        
506        if( !the_globals->haveEST() ){
507          sprintf( painCave.errMsg,
508 <                 "SimSetup Warning: using default value of 5% of the"
508 >                 "SimSetup Warning: using default value of 5%% of the "
509                   "electrostaticCutoffRadius for the "
510                   "electrostaticSkinThickness\n"
511                   );
# Line 638 | Line 680 | void SimSetup::createSim( void ){
680  
681   //   new AllLong( simnfo );
682  
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 );
683  
684 <
684 >  if( !strcmp( force_field, "TraPPE_Ex" ) ){
685 >    new Symplectic(simnfo, the_ff, the_extendedsystem);
686 >    std::cerr << "called new Symplecic\n";
687 >    fprintf( stderr, "called new Symplectic. stderr\n" );
688 >  }
689 >  else if( !strcmp( force_field, "LJ" ) ){
690 >    new Verlet( *simnfo, the_ff, the_extendedsystem );
691 >    std::cerr << "called new Verlet\n";
692 >    fprintf( stderr, "called new Verlet. stderr\n" );
693 >  }
694 >  else {
695 >    std::cerr << "I'm a bug.\n";
696 >    fprintf( stderr, "Ima bug. stderr %s\n", force_field);
697 >  }
698 > #ifdef IS_MPI
699 >  mpiSim->mpiRefresh();
700 > #endif
701  
702    // initialize the Fortran
703 <  
703 >
704 >
705    simnfo->refreshSim();
706    
707    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 738 | void SimSetup::makeMolecules( void ){
738    BondStamp* currentBond;
739    BendStamp* currentBend;
740    TorsionStamp* currentTorsion;
741 +
742 +  bond_pair* theBonds;
743 +  bend_set* theBends;
744 +  torsion_set* theTorsions;
745 +
746    
747    //init the forceField paramters
748  
749    the_ff->readParams();
750  
751    
752 <  // init the molecules
752 >  // init the atoms
753  
754 +  double ux, uy, uz, u, uSqr;
755 +  
756    atomOffset = 0;
757    excludeOffset = 0;
758    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 769 | void SimSetup::makeMolecules( void ){
769      info.myExcludes = &the_excludes[excludeOffset];
770      info.myBonds = new Bond*[info.nBonds];
771      info.myBends = new Bend*[info.nBends];
772 <    info.myTorsions = new Torsions*[info.nTorsions];
772 >    info.myTorsions = new Torsion*[info.nTorsions];
773  
774      theBonds = new bond_pair[info.nBonds];
775      theBends = new bend_set[info.nBends];
# Line 717 | Line 779 | void SimSetup::makeMolecules( void ){
779      
780      for(j=0; j<info.nAtoms; j++){
781        
782 <      currentAtom = theComponents[stampID]->getAtom( j );
782 >      currentAtom = comp_stamps[stampID]->getAtom( j );
783        if( currentAtom->haveOrientation() ){
784          
785          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 820 | void SimSetup::makeMolecules( void ){
820        theBonds[j].a = currentBond->getA() + atomOffset;
821        theBonds[j].b = currentBond->getB() + atomOffset;
822  
823 <      exI = theBonds[i].a;
824 <      exJ = theBonds[i].b;
823 >      exI = theBonds[j].a;
824 >      exJ = theBonds[j].b;
825  
826        // exclude_I must always be the smaller of the pair
827        if( exI > exJ ){
# Line 775 | Line 837 | void SimSetup::makeMolecules( void ){
837        
838        the_excludes[j+excludeOffset]->setPair( exI, exJ );
839   #else  // isn't MPI
840 +
841        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
842   #endif  //is_mpi
843      }
# Line 790 | Line 853 | void SimSetup::makeMolecules( void ){
853            
854        if( currentBend->haveExtras() ){
855              
856 <        extras = current_bend->getExtras();
856 >        extras = currentBend->getExtras();
857          current_extra = extras;
858              
859          while( current_extra != NULL ){
# Line 812 | Line 875 | void SimSetup::makeMolecules( void ){
875                
876              default:
877                sprintf( painCave.errMsg,
878 <                       "SimSetup Error: ghostVectorSource was neiter a "
878 >                       "SimSetup Error: ghostVectorSource was neither a "
879                         "double nor an int.\n"
880                         "-->Bend[%d] in %s\n",
881                         j, comp_stamps[stampID]->getID() );
# Line 906 | Line 969 | void SimSetup::makeMolecules( void ){
969  
970  
971      the_molecules[i].initialize( info );
972 +
973 +
974      atomOffset += info.nAtoms;
975 +    delete[] theBonds;
976 +    delete[] theBends;
977 +    delete[] theTorsions;
978    }
979  
980 + #ifdef IS_MPI
981 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
982 +  MPIcheckPoint();
983 + #endif // is_mpi
984 +
985    // clean up the forcefield
986    the_ff->calcRcut();
987    the_ff->cleanMe();
988 +
989   }
990  
991   void SimSetup::initFromBass( void ){

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