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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 429 by mmeineke, Thu Mar 27 21:52:21 2003 UTC vs.
Revision 580 by gezelter, Wed Jul 9 13:56:36 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 NPTi_ENS 2
20 + #define NPTf_ENS 3
21 +
22 + #define FF_DUFF 0
23 + #define FF_LJ   1
24 +
25 +
26   SimSetup::SimSetup(){
27    stamps = new MakeStamps();
28    globals = new Globals();
# Line 66 | Line 77 | void SimSetup::createSim( void ){
77  
78    MakeStamps *the_stamps;
79    Globals* the_globals;
80 <  int i, j;
80 >  int i, j, k, globalAtomIndex;
81 >  
82 >  int ensembleCase;
83 >  int ffCase;
84 >  
85 >  ensembleCase = -1;
86 >  ffCase = -1;
87  
88    // get the stamps and globals;
89    the_stamps = stamps;
# Line 80 | Line 97 | void SimSetup::createSim( void ){
97    // get the ones we know are there, yet still may need some work.
98    n_components = the_globals->getNComponents();
99    strcpy( force_field, the_globals->getForceField() );
100 +
101 +  if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
102 +  else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
103 +  else{
104 +    sprintf( painCave.errMsg,
105 +             "SimSetup Error. Unrecognized force field -> %s\n",
106 +             force_field );
107 +    painCave.isFatal = 1;
108 +    simError();
109 +  }
110 +
111 +  // get the ensemble:
112    strcpy( ensemble, the_globals->getEnsemble() );
113 +
114 +  if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
115 +  else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
116 +  else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
117 +    ensembleCase = NPTi_ENS;
118 +  else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
119 +  else{
120 +    sprintf( painCave.errMsg,
121 +             "SimSetup Warning. Unrecognized Ensemble -> %s, "
122 +             "reverting to NVE for this simulation.\n",
123 +             ensemble );
124 +    painCave.isFatal = 0;
125 +    simError();
126 +    strcpy( ensemble, "NVE" );
127 +    ensembleCase = NVE_ENS;
128 +  }  
129    strcpy( simnfo->ensemble, ensemble );
130  
131 +
132 + //   if( !strcasecmp( ensemble, "NPT" ) ) {
133 + //     the_extendedsystem = new ExtendedSystem( simnfo );
134 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
135 + //     if (the_globals->haveTargetPressure())
136 + //       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
137 + //     else {
138 + //       sprintf( painCave.errMsg,
139 + //                "SimSetup error: If you use the constant pressure\n"
140 + //                "    ensemble, you must set targetPressure.\n"
141 + //                "    This was found in the BASS file.\n");
142 + //       painCave.isFatal = 1;
143 + //       simError();
144 + //     }
145 +
146 + //     if (the_globals->haveTauThermostat())
147 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
148 + //     else if (the_globals->haveQmass())
149 + //       the_extendedsystem->setQmass(the_globals->getQmass());
150 + //     else {
151 + //       sprintf( painCave.errMsg,
152 + //                "SimSetup error: If you use one of the constant temperature\n"
153 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
154 + //                "    Neither of these was found in the BASS file.\n");
155 + //       painCave.isFatal = 1;
156 + //       simError();
157 + //     }
158 +
159 + //     if (the_globals->haveTauBarostat())
160 + //       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
161 + //     else {
162 + //       sprintf( painCave.errMsg,
163 + //                "SimSetup error: If you use the constant pressure\n"
164 + //                "    ensemble, you must set tauBarostat.\n"
165 + //                "    This was found in the BASS file.\n");
166 + //       painCave.isFatal = 1;
167 + //       simError();
168 + //     }
169 +
170 + //   } else if ( !strcasecmp( ensemble, "NVT") ) {
171 + //     the_extendedsystem = new ExtendedSystem( simnfo );
172 + //     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
173 +
174 + //     if (the_globals->haveTauThermostat())
175 + //       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
176 + //     else if (the_globals->haveQmass())
177 + //       the_extendedsystem->setQmass(the_globals->getQmass());
178 + //     else {
179 + //       sprintf( painCave.errMsg,
180 + //                "SimSetup error: If you use one of the constant temperature\n"
181 + //                "    ensembles, you must set either tauThermostat or qMass.\n"
182 + //                "    Neither of these was found in the BASS file.\n");
183 + //       painCave.isFatal = 1;
184 + //       simError();
185 + //     }
186 +
187    strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
188    simnfo->usePBC = the_globals->getPBC();
189            
190 +  int usesDipoles = 0;
191 +  switch( ffCase ){
192  
193 +  case FF_DUFF:
194 +    the_ff = new DUFF();
195 +    usesDipoles = 1;
196 +    break;
197  
198 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
199 <  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
200 <  else{
198 >  case FF_LJ:
199 >    the_ff = new LJFF();
200 >    break;
201 >
202 >  default:
203      sprintf( painCave.errMsg,
204 <             "SimSetup Error. Unrecognized force field -> %s\n",
96 <             force_field );
204 >             "SimSetup Error. Unrecognized force field in case statement.\n");
205      painCave.isFatal = 1;
206      simError();
207    }
# Line 103 | Line 211 | void SimSetup::createSim( void ){
211    MPIcheckPoint();
212   #endif // is_mpi
213  
106 –  
107 –
214    // get the components and calculate the tot_nMol and indvidual n_mol
215    the_components = the_globals->getComponents();
216    components_nmol = new int[n_components];
# Line 228 | Line 334 | void SimSetup::createSim( void ){
334    simnfo->n_torsions = tot_torsions;
335    simnfo->n_SRI = tot_SRI;
336    simnfo->n_mol = tot_nmol;
231 –
337    
338 +  simnfo->molMembershipArray = new int[tot_atoms];
339 +
340   #ifdef IS_MPI
341  
342    // divide the molecules among processors here.
343    
344    mpiSim = new mpiSimulation( simnfo );
345    
239 –  
240 –
346    globalIndex = mpiSim->divideLabor();
347  
243 –
244 –
348    // set up the local variables
349    
350    int localMol, allMol;
# Line 256 | Line 359 | void SimSetup::createSim( void ){
359    local_bonds = 0;
360    local_bends = 0;
361    local_torsions = 0;
362 +  globalAtomIndex = 0;
363 +
364 +
365    for( i=0; i<n_components; i++ ){
366  
367      for( j=0; j<components_nmol[i]; j++ ){
368        
369 <      if( mol2proc[j] == worldRank ){
369 >      if( mol2proc[allMol] == worldRank ){
370          
371          local_atoms +=    comp_stamps[i]->getNAtoms();
372          local_bonds +=    comp_stamps[i]->getNBonds();
# Line 268 | Line 374 | void SimSetup::createSim( void ){
374          local_torsions += comp_stamps[i]->getNTorsions();
375          localMol++;
376        }      
377 <      allMol++;
377 >      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
378 >        simnfo->molMembershipArray[globalAtomIndex] = allMol;
379 >        globalAtomIndex++;
380 >      }
381 >
382 >      allMol++;      
383      }
384    }
385    local_SRI = local_bonds + local_bends + local_torsions;
386    
276 –
387    simnfo->n_atoms = mpiSim->getMyNlocal();  
388    
389    if( local_atoms != simnfo->n_atoms ){
# Line 316 | Line 426 | void SimSetup::createSim( void ){
426      
427      if(mol2proc[i] == worldRank ){
428        the_molecules[molIndex].setStampID( molCompType[i] );
429 +      the_molecules[molIndex].setMyIndex( molIndex );
430 +      the_molecules[molIndex].setGlobalIndex( i );
431        molIndex++;
432      }
433    }
# Line 323 | Line 435 | void SimSetup::createSim( void ){
435   #else // is_mpi
436    
437    molIndex = 0;
438 +  globalAtomIndex = 0;
439    for(i=0; i<n_components; i++){
440      for(j=0; j<components_nmol[i]; j++ ){
441        the_molecules[molIndex].setStampID( i );
442 +      the_molecules[molIndex].setMyIndex( molIndex );
443 +      the_molecules[molIndex].setGlobalIndex( molIndex );
444 +      for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
445 +        simnfo->molMembershipArray[globalAtomIndex] = molIndex;
446 +        globalAtomIndex++;
447 +      }
448        molIndex++;
449      }
450    }
# Line 335 | Line 454 | void SimSetup::createSim( void ){
454  
455  
456    if( simnfo->n_SRI ){
457 +    
458      Exclude::createArray(simnfo->n_SRI);
459      the_excludes = new Exclude*[simnfo->n_SRI];
460 +    for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
461      simnfo->globalExcludes = new int;
462 <    simnfo->n_exclude = tot_SRI;
462 >    simnfo->n_exclude = simnfo->n_SRI;
463    }
464    else{
465      
# Line 361 | Line 482 | void SimSetup::createSim( void ){
482  
483    // get some of the tricky things that may still be in the globals
484  
485 <  
485 >  double boxVector[3];
486    if( the_globals->haveBox() ){
487 <    simnfo->box_x = the_globals->getBox();
488 <    simnfo->box_y = the_globals->getBox();
489 <    simnfo->box_z = the_globals->getBox();
487 >    boxVector[0] = the_globals->getBox();
488 >    boxVector[1] = the_globals->getBox();
489 >    boxVector[2] = the_globals->getBox();
490 >    
491 >    simnfo->setBox( boxVector );
492    }
493    else if( the_globals->haveDensity() ){
494  
495      double vol;
496      vol = (double)tot_nmol / the_globals->getDensity();
497 <    simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
498 <    simnfo->box_y = simnfo->box_x;
499 <    simnfo->box_z = simnfo->box_x;
497 >     boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
498 >     boxVector[1] = boxVector[0];
499 >     boxVector[2] = boxVector[0];
500 >
501 >    simnfo->setBox( boxVector );
502    }
503    else{
504      if( !the_globals->haveBoxX() ){
# Line 382 | Line 507 | void SimSetup::createSim( void ){
507        painCave.isFatal = 1;
508        simError();
509      }
510 <    simnfo->box_x = the_globals->getBoxX();
510 >    boxVector[0] = the_globals->getBoxX();
511  
512      if( !the_globals->haveBoxY() ){
513        sprintf( painCave.errMsg,
# Line 390 | Line 515 | void SimSetup::createSim( void ){
515        painCave.isFatal = 1;
516        simError();
517      }
518 <    simnfo->box_y = the_globals->getBoxY();
518 >    boxVector[1] = the_globals->getBoxY();
519  
520      if( !the_globals->haveBoxZ() ){
521        sprintf( painCave.errMsg,
# Line 398 | Line 523 | void SimSetup::createSim( void ){
523        painCave.isFatal = 1;
524        simError();
525      }
526 <    simnfo->box_z = the_globals->getBoxZ();
526 >    boxVector[2] = the_globals->getBoxZ();
527 >
528 >    simnfo->setBox( boxVector );
529    }
530  
531   #ifdef IS_MPI
# Line 428 | Line 555 | void SimSetup::createSim( void ){
555        painCave.isFatal = 0;
556        simError();
557        double smallest;
558 <      smallest = simnfo->box_x;
559 <      if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
560 <      if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
558 >      smallest = simnfo->boxLx;
559 >      if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
560 >      if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
561        simnfo->ecr = 0.5 * smallest;
562      } else {
563        simnfo->ecr        = the_globals->getECR();
# Line 458 | Line 585 | void SimSetup::createSim( void ){
585      }
586      simnfo->dielectric = the_globals->getDielectric();  
587    } else {
588 <    if (simnfo->n_dipoles) {
588 >    if (usesDipoles) {
589        
590        if( !the_globals->haveECR() ){
591          sprintf( painCave.errMsg,
592 <                 "SimSetup Warning: using default value of 1/2 the smallest"
592 >                 "SimSetup Warning: using default value of 1/2 the smallest "
593                   "box length for the electrostaticCutoffRadius.\n"
594                   "I hope you have a very fast processor!\n");
595          painCave.isFatal = 0;
596          simError();
597          double smallest;
598 <        smallest = simnfo->box_x;
599 <        if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
600 <        if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
598 >        smallest = simnfo->boxLx;
599 >        if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
600 >        if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
601          simnfo->ecr = 0.5 * smallest;
602        } else {
603          simnfo->ecr        = the_globals->getECR();
# Line 478 | Line 605 | void SimSetup::createSim( void ){
605        
606        if( !the_globals->haveEST() ){
607          sprintf( painCave.errMsg,
608 <                 "SimSetup Warning: using default value of 5% of the"
608 >                 "SimSetup Warning: using default value of 5%% of the "
609                   "electrostaticCutoffRadius for the "
610                   "electrostaticSkinThickness\n"
611                   );
# Line 649 | Line 776 | void SimSetup::createSim( void ){
776    if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
777  
778  
779 < //   // make the longe range forces and the integrator
780 <
781 < //   new AllLong( simnfo );
782 <
783 <  if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
657 <  if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
779 >  // make the integrator
780 >  
781 >  
782 >  NVT* myNVT = NULL;
783 >  switch( ensembleCase ){
784  
785 +  case NVE_ENS:
786 +    new NVE( simnfo, the_ff );
787 +    break;
788  
789 +  case NVT_ENS:
790 +    myNVT = new NVT( simnfo, the_ff );
791 +    myNVT->setTargetTemp(the_globals->getTargetTemp());
792  
793 +    if (the_globals->haveTauThermostat())
794 +      myNVT->setTauThermostat(the_globals->getTauThermostat());
795 + //     else if (the_globals->haveQmass())
796 + //       myNVT->setQmass(the_globals->getQmass());
797 +    else {
798 +      sprintf( painCave.errMsg,
799 +               "SimSetup error: If you use the NVT\n"
800 +               "    ensemble, you must set either tauThermostat or qMass.\n"
801 +               "    Neither of these was found in the BASS file.\n");
802 +      painCave.isFatal = 1;
803 +      simError();
804 +    }
805 +    break;
806 +
807 +  default:
808 +    sprintf( painCave.errMsg,
809 +             "SimSetup Error. Unrecognized ensemble in case statement.\n");
810 +    painCave.isFatal = 1;
811 +    simError();
812 +  }
813 +
814 +
815 + #ifdef IS_MPI
816 +  mpiSim->mpiRefresh();
817 + #endif
818 +
819    // initialize the Fortran
820 <  
820 >
821 >
822    simnfo->refreshSim();
823    
824    if( !strcmp( simnfo->mixingRule, "standard") ){
# Line 778 | Line 937 | void SimSetup::makeMolecules( void ){
937        theBonds[j].a = currentBond->getA() + atomOffset;
938        theBonds[j].b = currentBond->getB() + atomOffset;
939  
940 <      exI = theBonds[i].a;
941 <      exJ = theBonds[i].b;
940 >      exI = theBonds[j].a;
941 >      exJ = theBonds[j].b;
942  
943        // exclude_I must always be the smaller of the pair
944        if( exI > exJ ){
# Line 795 | Line 954 | void SimSetup::makeMolecules( void ){
954        
955        the_excludes[j+excludeOffset]->setPair( exI, exJ );
956   #else  // isn't MPI
957 +
958        the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
959   #endif  //is_mpi
960      }
# Line 832 | Line 992 | void SimSetup::makeMolecules( void ){
992                
993              default:
994                sprintf( painCave.errMsg,
995 <                       "SimSetup Error: ghostVectorSource was neiter a "
995 >                       "SimSetup Error: ghostVectorSource was neither a "
996                         "double nor an int.\n"
997                         "-->Bend[%d] in %s\n",
998                         j, comp_stamps[stampID]->getID() );
# Line 926 | Line 1086 | void SimSetup::makeMolecules( void ){
1086  
1087  
1088      the_molecules[i].initialize( info );
1089 +
1090 +
1091      atomOffset += info.nAtoms;
1092      delete[] theBonds;
1093      delete[] theBends;
1094      delete[] theTorsions;
1095    }
1096 +
1097 + #ifdef IS_MPI
1098 +  sprintf( checkPointMsg, "all molecules initialized succesfully" );
1099 +  MPIcheckPoint();
1100 + #endif // is_mpi
1101  
1102    // clean up the forcefield
1103    the_ff->calcRcut();
1104    the_ff->cleanMe();
1105 +
1106   }
1107  
1108   void SimSetup::initFromBass( void ){
# Line 956 | Line 1124 | void SimSetup::initFromBass( void ){
1124      have_extra =1;
1125  
1126      n_cells = (int)temp3 - 1;
1127 <    cellx = simnfo->box_x / temp3;
1128 <    celly = simnfo->box_y / temp3;
1129 <    cellz = simnfo->box_z / temp3;
1127 >    cellx = simnfo->boxLx / temp3;
1128 >    celly = simnfo->boxLy / temp3;
1129 >    cellz = simnfo->boxLz / temp3;
1130      n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1131      temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1132      n_per_extra = (int)ceil( temp1 );
# Line 973 | Line 1141 | void SimSetup::initFromBass( void ){
1141    }
1142    else{
1143      n_cells = (int)temp3;
1144 <    cellx = simnfo->box_x / temp3;
1145 <    celly = simnfo->box_y / temp3;
1146 <    cellz = simnfo->box_z / temp3;
1144 >    cellx = simnfo->boxLx / temp3;
1145 >    celly = simnfo->boxLy / temp3;
1146 >    cellz = simnfo->boxLz / temp3;
1147    }
1148  
1149    current_mol = 0;

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