ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 431 by mmeineke, Thu Mar 27 22:16:27 2003 UTC vs.
Revision 572 by mmeineke, Wed Jul 2 21:26:55 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_Ex" ) ) the_ff = new TraPPE_ExFF();
196 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
197 <  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",
96 <             force_field );
201 >             "SimSetup Error. Unrecognized force field in case statement.\n");
202      painCave.isFatal = 1;
203      simError();
204    }
# Line 103 | Line 208 | void SimSetup::createSim( void ){
208    MPIcheckPoint();
209   #endif // is_mpi
210  
106 –  
107 –
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 228 | Line 331 | void SimSetup::createSim( void ){
331    simnfo->n_torsions = tot_torsions;
332    simnfo->n_SRI = tot_SRI;
333    simnfo->n_mol = tot_nmol;
231 –
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    
239 –  
240 –
343    globalIndex = mpiSim->divideLabor();
344  
243 –
244 –
345    // set up the local variables
346    
347    int localMol, allMol;
# Line 256 | 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( mol2proc[j] == worldRank ){
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 ){
# Line 316 | Line 423 | void SimSetup::createSim( void ){
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    }
# Line 323 | Line 432 | void SimSetup::createSim( void ){
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    }
# Line 336 | Line 452 | void SimSetup::createSim( void ){
452  
453    if( simnfo->n_SRI ){
454      
339 –    std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
340 –    
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 365 | Line 479 | void SimSetup::createSim( void ){
479  
480    // get some of the tricky things that may still be in the globals
481  
482 <  
482 >  double boxVector[3];
483    if( the_globals->haveBox() ){
484 <    simnfo->box_x = the_globals->getBox();
485 <    simnfo->box_y = the_globals->getBox();
486 <    simnfo->box_z = the_globals->getBox();
484 >    boxVector[0] = the_globals->getBox();
485 >    boxVector[1] = the_globals->getBox();
486 >    boxVector[2] = the_globals->getBox();
487 >    
488 >    simnfo->setBox( boxVector );
489    }
490    else if( the_globals->haveDensity() ){
491  
492      double vol;
493      vol = (double)tot_nmol / the_globals->getDensity();
494 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
495 <    simnfo->box_y = simnfo->box_x;
496 <    simnfo->box_z = simnfo->box_x;
494 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
495 >     boxVector[1] = boxVector[0];
496 >     boxVector[2] = boxVector[0];
497 >
498 >    simnfo->setBox( boxVector );
499    }
500    else{
501      if( !the_globals->haveBoxX() ){
# Line 386 | Line 504 | void SimSetup::createSim( void ){
504        painCave.isFatal = 1;
505        simError();
506      }
507 <    simnfo->box_x = the_globals->getBoxX();
507 >    boxVector[0] = the_globals->getBoxX();
508  
509      if( !the_globals->haveBoxY() ){
510        sprintf( painCave.errMsg,
# Line 394 | Line 512 | void SimSetup::createSim( void ){
512        painCave.isFatal = 1;
513        simError();
514      }
515 <    simnfo->box_y = the_globals->getBoxY();
515 >    boxVector[1] = the_globals->getBoxY();
516  
517      if( !the_globals->haveBoxZ() ){
518        sprintf( painCave.errMsg,
# Line 402 | Line 520 | void SimSetup::createSim( void ){
520        painCave.isFatal = 1;
521        simError();
522      }
523 <    simnfo->box_z = the_globals->getBoxZ();
523 >    boxVector[2] = the_globals->getBoxZ();
524 >
525 >    simnfo->setBox( boxVector );
526    }
527  
528   #ifdef IS_MPI
# Line 432 | Line 552 | void SimSetup::createSim( void ){
552        painCave.isFatal = 0;
553        simError();
554        double smallest;
555 <      smallest = simnfo->box_x;
556 <      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
557 <      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
555 >      smallest = simnfo->boxLx;
556 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
557 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
558        simnfo->ecr = 0.5 * smallest;
559      } else {
560        simnfo->ecr        = the_globals->getECR();
# Line 462 | Line 582 | void SimSetup::createSim( void ){
582      }
583      simnfo->dielectric = the_globals->getDielectric();  
584    } else {
585 <    if (simnfo->n_dipoles) {
585 >    if (usesDipoles) {
586        
587        if( !the_globals->haveECR() ){
588          sprintf( painCave.errMsg,
589 <                 "SimSetup Warning: using default value of 1/2 the smallest"
589 >                 "SimSetup Warning: using default value of 1/2 the smallest "
590                   "box length for the electrostaticCutoffRadius.\n"
591                   "I hope you have a very fast processor!\n");
592          painCave.isFatal = 0;
593          simError();
594          double smallest;
595 <        smallest = simnfo->box_x;
596 <        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
597 <        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
595 >        smallest = simnfo->boxLx;
596 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
597 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
598          simnfo->ecr = 0.5 * smallest;
599        } else {
600          simnfo->ecr        = the_globals->getECR();
# Line 482 | Line 602 | void SimSetup::createSim( void ){
602        
603        if( !the_globals->haveEST() ){
604          sprintf( painCave.errMsg,
605 <                 "SimSetup Warning: using default value of 5% of the"
605 >                 "SimSetup Warning: using default value of 5%% of the "
606                   "electrostaticCutoffRadius for the "
607                   "electrostaticSkinThickness\n"
608                   );
# Line 653 | Line 773 | void SimSetup::createSim( void ){
773    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
774  
775  
776 < //   // make the longe range forces and the integrator
777 <
778 < //   new AllLong( simnfo );
779 <
780 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
661 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
776 >  // make the integrator
777 >  
778 >  
779 >  NVT* myNVT = NULL;
780 >  switch( ensembleCase ){
781  
782 +  case NVE_ENS:
783 +    new NVE( simnfo, the_ff );
784 +    break;
785  
786 +  case NVT_ENS:
787 +    myNVT = new NVT( simnfo, the_ff );
788 +    myNVT->setTargetTemp(the_globals->getTargetTemp());
789  
790 +    if (the_globals->haveTauThermostat())
791 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
792 + //     else if (the_globals->haveQmass())
793 + //       myNVT->setQmass(the_globals->getQmass());
794 +    else {
795 +      sprintf( painCave.errMsg,
796 +               "SimSetup error: If you use the NVT\n"
797 +               "    ensemble, you must set either tauThermostat or qMass.\n"
798 +               "    Neither of these was found in the BASS file.\n");
799 +      painCave.isFatal = 1;
800 +      simError();
801 +    }
802 +    break;
803 +
804 +  default:
805 +    sprintf( painCave.errMsg,
806 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
807 +    painCave.isFatal = 1;
808 +    simError();
809 +  }
810 +
811 +
812 + #ifdef IS_MPI
813 +  mpiSim->mpiRefresh();
814 + #endif
815 +
816    // initialize the Fortran
817 <  
817 >
818 >
819    simnfo->refreshSim();
820    
821    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 782 | Line 934 | void SimSetup::makeMolecules( void ){
934        theBonds[j].a = currentBond->getA() + atomOffset;
935        theBonds[j].b = currentBond->getB() + atomOffset;
936  
937 <      exI = theBonds[i].a;
938 <      exJ = theBonds[i].b;
937 >      exI = theBonds[j].a;
938 >      exJ = theBonds[j].b;
939  
940        // exclude_I must always be the smaller of the pair
941        if( exI > exJ ){
# Line 799 | Line 951 | void SimSetup::makeMolecules( void ){
951        
952        the_excludes[j+excludeOffset]->setPair( exI, exJ );
953   #else  // isn't MPI
954 +
955        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
956   #endif  //is_mpi
957      }
# Line 836 | Line 989 | void SimSetup::makeMolecules( void ){
989                
990              default:
991                sprintf( painCave.errMsg,
992 <                       "SimSetup Error: ghostVectorSource was neiter a "
992 >                       "SimSetup Error: ghostVectorSource was neither a "
993                         "double nor an int.\n"
994                         "-->Bend[%d] in %s\n",
995                         j, comp_stamps[stampID]->getID() );
# Line 930 | Line 1083 | void SimSetup::makeMolecules( void ){
1083  
1084  
1085      the_molecules[i].initialize( info );
1086 +
1087 +
1088      atomOffset += info.nAtoms;
1089      delete[] theBonds;
1090      delete[] theBends;
1091      delete[] theTorsions;
1092    }
1093 +
1094 + #ifdef IS_MPI
1095 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1096 +  MPIcheckPoint();
1097 + #endif // is_mpi
1098  
1099    // clean up the forcefield
1100    the_ff->calcRcut();
1101    the_ff->cleanMe();
1102 +
1103   }
1104  
1105   void SimSetup::initFromBass( void ){
# Line 960 | Line 1121 | void SimSetup::initFromBass( void ){
1121      have_extra =1;
1122  
1123      n_cells = (int)temp3 - 1;
1124 <    cellx = simnfo->box_x / temp3;
1125 <    celly = simnfo->box_y / temp3;
1126 <    cellz = simnfo->box_z / temp3;
1124 >    cellx = simnfo->boxLx / temp3;
1125 >    celly = simnfo->boxLy / temp3;
1126 >    cellz = simnfo->boxLz / temp3;
1127      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1128      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1129      n_per_extra = (int)ceil( temp1 );
# Line 977 | Line 1138 | void SimSetup::initFromBass( void ){
1138    }
1139    else{
1140      n_cells = (int)temp3;
1141 <    cellx = simnfo->box_x / temp3;
1142 <    celly = simnfo->box_y / temp3;
1143 <    cellz = simnfo->box_z / temp3;
1141 >    cellx = simnfo->boxLx / temp3;
1142 >    celly = simnfo->boxLy / temp3;
1143 >    cellz = simnfo->boxLz / temp3;
1144    }
1145  
1146    current_mol = 0;

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines