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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 561 by mmeineke, Fri Jun 20 20:29:36 2003 UTC

# Line 12 | Line 12 | SimSetup::SimSetup(){
12   #include "mpiSimulation.hpp"
13   #endif
14  
15 + // some defines for ensemble and Forcefield  cases
16 +
17 + #define NVE_ENS 0
18 + #define NVT_ENS 1
19 + #define NPT_ENS 2
20 +
21 + #define FF_DUFF 0
22 + #define FF_LJ   1
23 +
24 +
25   SimSetup::SimSetup(){
26    stamps = new MakeStamps();
27    globals = new Globals();
# Line 66 | Line 76 | void SimSetup::createSim( void ){
76  
77    MakeStamps *the_stamps;
78    Globals* the_globals;
79 <  int i, j;
79 >  int i, j, k, globalAtomIndex;
80 >  
81 >  int ensembleCase;
82 >  int ffCase;
83 >  
84 >  ensembleCase = -1;
85 >  ffCase = -1;
86  
87    // get the stamps and globals;
88    the_stamps = stamps;
# Line 80 | Line 96 | void SimSetup::createSim( void ){
96    // get the ones we know are there, yet still may need some work.
97    n_components = the_globals->getNComponents();
98    strcpy( force_field, the_globals->getForceField() );
99 +
100 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
101 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102 +  else{
103 +    sprintf( painCave.errMsg,
104 +             "SimSetup Error. Unrecognized force field -> %s\n",
105 +             force_field );
106 +    painCave.isFatal = 1;
107 +    simError();
108 +  }
109 +
110 +  // get the ensemble:
111    strcpy( ensemble, the_globals->getEnsemble() );
112 +
113 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
114 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
115 +  else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
116 +  else{
117 +    sprintf( painCave.errMsg,
118 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
119 +             "reverting to NVE for this simulation.\n",
120 +             ensemble );
121 +    painCave.isFatal = 0;
122 +    simError();
123 +    strcpy( ensemble, "NVE" );
124 +    ensembleCase = NVE_ENS;
125 +  }  
126    strcpy( simnfo->ensemble, ensemble );
127  
128 +
129 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
130 + //     the_extendedsystem = new ExtendedSystem( simnfo );
131 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132 + //     if (the_globals->haveTargetPressure())
133 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134 + //     else {
135 + //       sprintf( painCave.errMsg,
136 + //                "SimSetup error: If you use the constant pressure\n"
137 + //                "    ensemble, you must set targetPressure.\n"
138 + //                "    This was found in the BASS file.\n");
139 + //       painCave.isFatal = 1;
140 + //       simError();
141 + //     }
142 +
143 + //     if (the_globals->haveTauThermostat())
144 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145 + //     else if (the_globals->haveQmass())
146 + //       the_extendedsystem->setQmass(the_globals->getQmass());
147 + //     else {
148 + //       sprintf( painCave.errMsg,
149 + //                "SimSetup error: If you use one of the constant temperature\n"
150 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
151 + //                "    Neither of these was found in the BASS file.\n");
152 + //       painCave.isFatal = 1;
153 + //       simError();
154 + //     }
155 +
156 + //     if (the_globals->haveTauBarostat())
157 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158 + //     else {
159 + //       sprintf( painCave.errMsg,
160 + //                "SimSetup error: If you use the constant pressure\n"
161 + //                "    ensemble, you must set tauBarostat.\n"
162 + //                "    This was found in the BASS file.\n");
163 + //       painCave.isFatal = 1;
164 + //       simError();
165 + //     }
166 +
167 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
168 + //     the_extendedsystem = new ExtendedSystem( simnfo );
169 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
170 +
171 + //     if (the_globals->haveTauThermostat())
172 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173 + //     else if (the_globals->haveQmass())
174 + //       the_extendedsystem->setQmass(the_globals->getQmass());
175 + //     else {
176 + //       sprintf( painCave.errMsg,
177 + //                "SimSetup error: If you use one of the constant temperature\n"
178 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
179 + //                "    Neither of these was found in the BASS file.\n");
180 + //       painCave.isFatal = 1;
181 + //       simError();
182 + //     }
183 +
184    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185    simnfo->usePBC = the_globals->getPBC();
186            
187 +  int usesDipoles = 0;
188 +  switch( ffCase ){
189  
190 +  case FF_DUFF:
191 +    the_ff = new DUFF();
192 +    usesDipoles = 1;
193 +    break;
194  
195 <  if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
196 <  else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
197 <  else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
198 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
199 <  else{
195 >  case FF_LJ:
196 >    the_ff = new LJFF();
197 >    break;
198 >
199 >  default:
200      sprintf( painCave.errMsg,
201 <             "SimSetup Error. Unrecognized force field -> %s\n",
98 <             force_field );
201 >             "SimSetup Error. Unrecognized force field in case statement.\n");
202      painCave.isFatal = 1;
203      simError();
204    }
# Line 105 | Line 208 | void SimSetup::createSim( void ){
208    MPIcheckPoint();
209   #endif // is_mpi
210  
108 –  
109 –
211    // get the components and calculate the tot_nMol and indvidual n_mol
212    the_components = the_globals->getComponents();
213    components_nmol = new int[n_components];
# Line 230 | Line 331 | void SimSetup::createSim( void ){
331    simnfo->n_torsions = tot_torsions;
332    simnfo->n_SRI = tot_SRI;
333    simnfo->n_mol = tot_nmol;
233 –
334    
335 +  simnfo->molMembershipArray = new int[tot_atoms];
336 +
337   #ifdef IS_MPI
338  
339    // divide the molecules among processors here.
340    
341    mpiSim = new mpiSimulation( simnfo );
342    
241 –  
242 –
343    globalIndex = mpiSim->divideLabor();
344  
245 –
246 –
345    // set up the local variables
346    
347    int localMol, allMol;
348    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
349 +
350 +  int* mol2proc = mpiSim->getMolToProcMap();
351 +  int* molCompType = mpiSim->getMolComponentType();
352    
353    allMol = 0;
354    localMol = 0;
# Line 255 | Line 356 | void SimSetup::createSim( void ){
356    local_bonds = 0;
357    local_bends = 0;
358    local_torsions = 0;
359 +  globalAtomIndex = 0;
360 +
361 +
362    for( i=0; i<n_components; i++ ){
363  
364      for( j=0; j<components_nmol[i]; j++ ){
365        
366 <      if( mpiSim->getMyMolStart() <= allMol &&
263 <          allMol <= mpiSim->getMyMolEnd() ){
366 >      if( mol2proc[allMol] == worldRank ){
367          
368          local_atoms +=    comp_stamps[i]->getNAtoms();
369          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 371 | void SimSetup::createSim( void ){
371          local_torsions += comp_stamps[i]->getNTorsions();
372          localMol++;
373        }      
374 <      allMol++;
374 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
376 >        globalAtomIndex++;
377 >      }
378 >
379 >      allMol++;      
380      }
381    }
382    local_SRI = local_bonds + local_bends + local_torsions;
383    
276 –
384    simnfo->n_atoms = mpiSim->getMyNlocal();  
385    
386    if( local_atoms != simnfo->n_atoms ){
387      sprintf( painCave.errMsg,
388               "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389 <             " localAtom (%d) are note equal.\n",
389 >             " localAtom (%d) are not equal.\n",
390               simnfo->n_atoms,
391               local_atoms );
392      painCave.isFatal = 1;
# Line 304 | Line 411 | void SimSetup::createSim( void ){
411    Atom::createArrays(simnfo->n_atoms);
412    the_atoms = new Atom*[simnfo->n_atoms];
413    the_molecules = new Molecule[simnfo->n_mol];
414 +  int molIndex;
415 +
416 +  // initialize the molecule's stampID's
417  
418 + #ifdef IS_MPI
419 +  
420  
421 +  molIndex = 0;
422 +  for(i=0; i<mpiSim->getTotNmol(); i++){
423 +    
424 +    if(mol2proc[i] == worldRank ){
425 +      the_molecules[molIndex].setStampID( molCompType[i] );
426 +      the_molecules[molIndex].setMyIndex( molIndex );
427 +      the_molecules[molIndex].setGlobalIndex( i );
428 +      molIndex++;
429 +    }
430 +  }
431 +
432 + #else // is_mpi
433 +  
434 +  molIndex = 0;
435 +  globalAtomIndex = 0;
436 +  for(i=0; i<n_components; i++){
437 +    for(j=0; j<components_nmol[i]; j++ ){
438 +      the_molecules[molIndex].setStampID( i );
439 +      the_molecules[molIndex].setMyIndex( molIndex );
440 +      the_molecules[molIndex].setGlobalIndex( molIndex );
441 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443 +        globalAtomIndex++;
444 +      }
445 +      molIndex++;
446 +    }
447 +  }
448 +    
449 +
450 + #endif // is_mpi
451 +
452 +
453    if( simnfo->n_SRI ){
454 +    
455      Exclude::createArray(simnfo->n_SRI);
456      the_excludes = new Exclude*[simnfo->n_SRI];
457 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
458      simnfo->globalExcludes = new int;
459 <    simnfo->n_exclude = tot_SRI;
459 >    simnfo->n_exclude = simnfo->n_SRI;
460    }
461    else{
462      
# Line 326 | Line 472 | void SimSetup::createSim( void ){
472    // set the arrays into the SimInfo object
473  
474    simnfo->atoms = the_atoms;
475 <  simnfo->sr_interactions = the_sris;
475 >  simnfo->molecules = the_molecules;
476    simnfo->nGlobalExcludes = 0;
477    simnfo->excludes = the_excludes;
478  
# Line 383 | Line 529 | void SimSetup::createSim( void ){
529  
530    the_ff->setSimInfo( simnfo );
531  
532 <  makeAtoms();
532 >  makeMolecules();
533    simnfo->identArray = new int[simnfo->n_atoms];
534    for(i=0; i<simnfo->n_atoms; i++){
535      simnfo->identArray[i] = the_atoms[i]->getIdent();
536    }
537    
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 –
538    if (the_globals->getUseRF() ) {
539      simnfo->useReactionField = 1;
540    
# Line 443 | Line 576 | void SimSetup::createSim( void ){
576      }
577      simnfo->dielectric = the_globals->getDielectric();  
578    } else {
579 <    if (simnfo->n_dipoles) {
579 >    if (usesDipoles) {
580        
581        if( !the_globals->haveECR() ){
582          sprintf( painCave.errMsg,
583 <                 "SimSetup Warning: using default value of 1/2 the smallest"
583 >                 "SimSetup Warning: using default value of 1/2 the smallest "
584                   "box length for the electrostaticCutoffRadius.\n"
585                   "I hope you have a very fast processor!\n");
586          painCave.isFatal = 0;
# Line 463 | Line 596 | void SimSetup::createSim( void ){
596        
597        if( !the_globals->haveEST() ){
598          sprintf( painCave.errMsg,
599 <                 "SimSetup Warning: using default value of 5% of the"
599 >                 "SimSetup Warning: using default value of 5%% of the "
600                   "electrostaticCutoffRadius for the "
601                   "electrostaticSkinThickness\n"
602                   );
# Line 634 | Line 767 | void SimSetup::createSim( void ){
767    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
768  
769  
770 < //   // make the longe range forces and the integrator
771 <
772 < //   new AllLong( simnfo );
773 <
774 <  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 );
770 >  // make the integrator
771 >  
772 >  
773 >  NVT* myNVT = NULL;
774 >  switch( ensembleCase ){
775  
776 +  case NVE_ENS:
777 +    new NVE( simnfo, the_ff );
778 +    break;
779  
780 +  case NVT_ENS:
781 +    myNVT = new NVT( simnfo, the_ff );
782 +    myNVT->setTargetTemp(the_globals->getTargetTemp());
783  
784 +    if (the_globals->haveTauThermostat())
785 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
786 +    else if (the_globals->haveQmass())
787 +      myNVT->setQmass(the_globals->getQmass());
788 +    else {
789 +      sprintf( painCave.errMsg,
790 +               "SimSetup error: If you use the NVT\n"
791 +               "    ensemble, you must set either tauThermostat or qMass.\n"
792 +               "    Neither of these was found in the BASS file.\n");
793 +      painCave.isFatal = 1;
794 +      simError();
795 +    }
796 +    break;
797 +
798 +  default:
799 +    sprintf( painCave.errMsg,
800 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
801 +    painCave.isFatal = 1;
802 +    simError();
803 +  }
804 +
805 +
806 + #ifdef IS_MPI
807 +  mpiSim->mpiRefresh();
808 + #endif
809 +
810    // initialize the Fortran
811 <  
811 >
812 >
813    simnfo->refreshSim();
814    
815    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 683 | Line 846 | void SimSetup::makeMolecules( void ){
846    BondStamp* currentBond;
847    BendStamp* currentBend;
848    TorsionStamp* currentTorsion;
849 +
850 +  bond_pair* theBonds;
851 +  bend_set* theBends;
852 +  torsion_set* theTorsions;
853 +
854    
855    //init the forceField paramters
856  
857    the_ff->readParams();
858  
859    
860 <  // init the molecules
860 >  // init the atoms
861  
862 +  double ux, uy, uz, u, uSqr;
863 +  
864    atomOffset = 0;
865    excludeOffset = 0;
866    for(i=0; i<simnfo->n_mol; i++){
# Line 707 | Line 877 | void SimSetup::makeMolecules( void ){
877      info.myExcludes = &the_excludes[excludeOffset];
878      info.myBonds = new Bond*[info.nBonds];
879      info.myBends = new Bend*[info.nBends];
880 <    info.myTorsions = new Torsions*[info.nTorsions];
880 >    info.myTorsions = new Torsion*[info.nTorsions];
881  
882      theBonds = new bond_pair[info.nBonds];
883      theBends = new bend_set[info.nBends];
# Line 717 | Line 887 | void SimSetup::makeMolecules( void ){
887      
888      for(j=0; j<info.nAtoms; j++){
889        
890 <      currentAtom = theComponents[stampID]->getAtom( j );
890 >      currentAtom = comp_stamps[stampID]->getAtom( j );
891        if( currentAtom->haveOrientation() ){
892          
893          dAtom = new DirectionalAtom(j + atomOffset);
# Line 758 | Line 928 | void SimSetup::makeMolecules( void ){
928        theBonds[j].a = currentBond->getA() + atomOffset;
929        theBonds[j].b = currentBond->getB() + atomOffset;
930  
931 <      exI = theBonds[i].a;
932 <      exJ = theBonds[i].b;
931 >      exI = theBonds[j].a;
932 >      exJ = theBonds[j].b;
933  
934        // exclude_I must always be the smaller of the pair
935        if( exI > exJ ){
# Line 775 | Line 945 | void SimSetup::makeMolecules( void ){
945        
946        the_excludes[j+excludeOffset]->setPair( exI, exJ );
947   #else  // isn't MPI
948 +
949        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
950   #endif  //is_mpi
951      }
# Line 790 | Line 961 | void SimSetup::makeMolecules( void ){
961            
962        if( currentBend->haveExtras() ){
963              
964 <        extras = current_bend->getExtras();
964 >        extras = currentBend->getExtras();
965          current_extra = extras;
966              
967          while( current_extra != NULL ){
# Line 812 | Line 983 | void SimSetup::makeMolecules( void ){
983                
984              default:
985                sprintf( painCave.errMsg,
986 <                       "SimSetup Error: ghostVectorSource was neiter a "
986 >                       "SimSetup Error: ghostVectorSource was neither a "
987                         "double nor an int.\n"
988                         "-->Bend[%d] in %s\n",
989                         j, comp_stamps[stampID]->getID() );
# Line 906 | Line 1077 | void SimSetup::makeMolecules( void ){
1077  
1078  
1079      the_molecules[i].initialize( info );
1080 +
1081 +
1082      atomOffset += info.nAtoms;
1083 +    delete[] theBonds;
1084 +    delete[] theBends;
1085 +    delete[] theTorsions;
1086    }
1087  
1088 + #ifdef IS_MPI
1089 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1090 +  MPIcheckPoint();
1091 + #endif // is_mpi
1092 +
1093    // clean up the forcefield
1094    the_ff->calcRcut();
1095    the_ff->cleanMe();
1096 +
1097   }
1098  
1099   void SimSetup::initFromBass( void ){

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