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root/group/trunk/mdtools/interface_implementation/SimSetup.cpp
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Comparing trunk/mdtools/interface_implementation/SimSetup.cpp (file contents):
Revision 194 by chuckv, Wed Dec 4 21:19:38 2002 UTC vs.
Revision 215 by chuckv, Thu Dec 19 21:59:51 2002 UTC

# Line 10 | Line 10
10  
11   #ifdef IS_MPI
12   #include "mpiBASS.h"
13 + #include "mpiSimulation.hpp"
14   #include "bassDiag.hpp"
15   #endif
16  
# Line 73 | Line 74 | void SimSetup::createSim( void ){
74  
75    MakeStamps *the_stamps;
76    Globals* the_globals;
77 <  int i;
77 >  int i, j;
78  
79    // get the stamps and globals;
80    the_stamps = stamps;
# Line 92 | Line 93 | void SimSetup::createSim( void ){
93    if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
94    else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
95    else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
96 +  else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
97    else{
98      sprintf( painCave.errMsg,
99               "SimSetup Error. Unrecognized force field -> %s\n",
# Line 161 | Line 163 | void SimSetup::createSim( void ){
163   #endif // is_mpi
164  
165    // make an array of molecule stamps that match the components used.
166 +  // also extract the used stamps out into a separate linked list
167  
168 +  simnfo->nComponents = n_components;
169 +  simnfo->componentsNmol = components_nmol;
170 +  simnfo->compStamps = comp_stamps;
171 +  simnfo->headStamp = new LinkedMolStamp();
172 +  
173 +  char* id;
174 +  LinkedMolStamp* headStamp = simnfo->headStamp;
175 +  LinkedMolStamp* currentStamp = NULL;
176    for( i=0; i<n_components; i++ ){
177  
178 <    comp_stamps[i] =
179 <      the_stamps->getMolecule( the_components[i]->getType() );
178 >    id = the_components[i]->getType();
179 >    comp_stamps[i] = NULL;
180 >    
181 >    // check to make sure the component isn't already in the list
182 >
183 >    comp_stamps[i] = headStamp->match( id );
184 >    if( comp_stamps[i] == NULL ){
185 >      
186 >      // extract the component from the list;
187 >      
188 >      currentStamp = the_stamps->extractMolStamp( id );
189 >      if( currentStamp == NULL ){
190 >        sprintf( painCave.errMsg,
191 >                 "SimSetup error: Component \"%s\" was not found in the "
192 >                 "list of declared molecules\n"
193 >                 id );
194 >        painCave.isFatal = 1;
195 >        simError();
196 >      }
197 >      
198 >      headStamp->add( currentStamp );
199 >      comp_stamps[i] = headStamp->match( id );
200 >    }
201    }
202  
203 + #ifdef IS_MPI
204 +  strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205 +  MPIcheckPoint();
206 + #endif // is_mpi
207 +  
208  
209  
210 +
211    // caclulate the number of atoms, bonds, bends and torsions
212  
213    tot_atoms = 0;
# Line 177 | Line 215 | void SimSetup::createSim( void ){
215    tot_bends = 0;
216    tot_torsions = 0;
217    for( i=0; i<n_components; i++ ){
218 <
219 <    tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
220 <    tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
221 <    tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
218 >    
219 >    tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220 >    tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221 >    tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223    }
224  
# Line 191 | Line 229 | void SimSetup::createSim( void ){
229    simnfo->n_bends = tot_bends;
230    simnfo->n_torsions = tot_torsions;
231    simnfo->n_SRI = tot_SRI;
232 +  simnfo->n_mol = tot_nmol;
233  
234 +  
235 + #ifdef IS_MPI
236 +
237    // divide the molecules among processors here.
238 +  
239 +  mpiSim = new mpiSimulation( simnfo );
240 +  
241 +  mpiSim->divideLabor();
242  
243 +  // set up the local variables
244 +  
245 +  int localMol, allMol;
246 +  int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
247 +  
248 +  allMol = 0;
249 +  localMol = 0;
250 +  local_atoms = 0;
251 +  local_bonds = 0;
252 +  local_bends = 0;
253 +  local_torsions = 0;
254 +  for( i=0; i<n_components; i++ ){
255  
256 +    for( j=0; j<components_nmol[i]; j++ ){
257 +      
258 +      if( mpiSim->getMyMolStart() <= allMol &&
259 +          allMol <= mpiSim->getMyMolEnd() ){
260 +        
261 +        local_atoms +=    comp_stamps[i]->getNAtoms();
262 +        local_bonds +=    comp_stamps[i]->getNBonds();
263 +        local_bends +=    comp_stamps[i]->getNBends();
264 +        local_torsions += comp_stamps[i]->getNTorsions();
265 +        localMol++;
266 +      }      
267 +      allMol++;
268 +    }
269 +  }
270 +  local_SRI = local_bonds + local_bends + local_torsions;
271 +  
272 +
273 +  simnfo->n_atoms = mpiSim->getMyNlocal();  
274 +  
275 +  if( local_atoms != simnfo->n_atoms ){
276 +    sprintf( painCave.errMsg,
277 +             "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
278 +             " localAtom (%d) are note equal.\n",
279 +             simnfo->n_atoms,
280 +             local_atoms );
281 +    painCave.isFatal = 1;
282 +    simError();
283 +  }
284 +
285 +  simnfo->n_bonds = local_bonds;
286 +  simnfo->n_bends = local_bends;
287 +  simnfo->n_torsions = local_torsions;
288 +  simnfo->n_SRI = local_SRI;
289 +  simnfo->n_mol = localMol;
290 +
291 +  strcpy( checkPointMsg, "Passed nlocal consistency check." );
292 +  MPIcheckPoint();
293 +  
294 +  
295 + #endif // is_mpi
296 +  
297 +
298    // create the atom and short range interaction arrays
299  
300 <  Atom::createArrays(tot_atoms);
301 <  the_atoms = new Atom*[tot_atoms];
302 <  the_molecules = new Molecule[tot_nmol];
300 >  Atom::createArrays(simnfo->n_atoms);
301 >  the_atoms = new Atom*[simnfo->n_atoms];
302 >  the_molecules = new Molecule[simnfo->n_mol];
303  
304  
305 <  if( tot_SRI ){
306 <    the_sris = new SRI*[tot_SRI];
307 <    the_excludes = new ex_pair[tot_SRI];
305 >  if( simnfo->n_SRI ){
306 >    the_sris = new SRI*[simnfo->n_SRI];
307 >    the_excludes = new ex_pair[simnfo->n_SRI];
308    }
309  
310    // set the arrays into the SimInfo object
# Line 233 | Line 333 | void SimSetup::createSim( void ){
333      makeTorsions();
334    }
335  
236 –  //  makeMolecules();
336  
337    // get some of the tricky things that may still be in the globals
338  
# Line 308 | Line 407 | void SimSetup::createSim( void ){
407  
408  
409  
410 < //   if( the_globals->haveInitialConfig() ){
312 < //        InitializeFromFile* fileInit;
313 < //     fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
314 <
315 < //     fileInit->read_xyz( simnfo ); // default velocities on
316 <
317 < //     delete fileInit;
318 < //   }
319 < //   else{
320 <
321 <  initFromBass();
410 > if( the_globals->haveInitialConfig() ){
411  
412 +     InitializeFromFile* fileInit;
413 + #ifdef IS_MPI // is_mpi
414 +     if( worldRank == 0 ){
415 + #endif //is_mpi
416 +   fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
417   #ifdef IS_MPI
418 <  strcpy( checkPointMsg, "initFromBass successfully created the lattice" );
418 >     }else fileInit = new InitializeFromFile( NULL );
419 > #endif
420 >   fileInit->read_xyz( simnfo ); // default velocities on
421 >
422 >   delete fileInit;
423 > }
424 > else{
425 >
426 > #ifdef IS_MPI
427 >
428 >  // no init from bass
429 >  
430 >  sprintf( painCave.errMsg,
431 >           "Cannot intialize a parallel simulation without an initial configuration file.\n" );
432 >  painCave.isFatal;
433 >  simError();
434 >  
435 > #else
436 >
437 >  initFromBass();
438 >
439 >
440 > #endif
441 > }
442 >
443 > #ifdef IS_MPI
444 >  strcpy( checkPointMsg, "Successfully read in the initial configuration" );
445    MPIcheckPoint();
446   #endif // is_mpi
447  
# Line 329 | Line 449 | void SimSetup::createSim( void ){
449    
450  
451    
452 <  //   }
452 >
453    
454   #ifdef IS_MPI
455    if( worldRank == 0 ){
# Line 455 | Line 575 | void SimSetup::makeAtoms( void ){
575    double ux, uy, uz, uSqr, u;
576    AtomStamp* current_atom;
577    DirectionalAtom* dAtom;
578 <  int molIndex, molStart, molEnd, nMemb;
578 >  int molIndex, molStart, molEnd, nMemb, lMolIndex;
579  
580 <
580 >  lMolIndex = 0;
581    molIndex = 0;
582    index = 0;
583    for( i=0; i<n_components; i++ ){
584  
585      for( j=0; j<components_nmol[i]; j++ ){
586  
587 <      molStart = index;
588 <      nMemb = comp_stamps[i]->getNAtoms();
589 <      for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
590 <
471 <        current_atom = comp_stamps[i]->getAtom( k );
472 <        if( current_atom->haveOrientation() ){
587 > #ifdef IS_MPI
588 >      if( mpiSim->getMyMolStart() <= molIndex &&
589 >          molIndex <= mpiSim->getMyMolEnd() ){
590 > #endif // is_mpi        
591  
592 <          dAtom = new DirectionalAtom(index);
593 <          simnfo->n_oriented++;
594 <          the_atoms[index] = dAtom;
595 <
596 <          ux = current_atom->getOrntX();
597 <          uy = current_atom->getOrntY();
598 <          uz = current_atom->getOrntZ();
599 <
600 <          uSqr = (ux * ux) + (uy * uy) + (uz * uz);
601 <
602 <          u = sqrt( uSqr );
603 <          ux = ux / u;
604 <          uy = uy / u;
605 <          uz = uz / u;
606 <
607 <          dAtom->setSUx( ux );
608 <          dAtom->setSUy( uy );
609 <          dAtom->setSUz( uz );
592 >        molStart = index;
593 >        nMemb = comp_stamps[i]->getNAtoms();
594 >        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
595 >          
596 >          current_atom = comp_stamps[i]->getAtom( k );
597 >          if( current_atom->haveOrientation() ){
598 >            
599 >            dAtom = new DirectionalAtom(index);
600 >            simnfo->n_oriented++;
601 >            the_atoms[index] = dAtom;
602 >            
603 >            ux = current_atom->getOrntX();
604 >            uy = current_atom->getOrntY();
605 >            uz = current_atom->getOrntZ();
606 >            
607 >            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
608 >            
609 >            u = sqrt( uSqr );
610 >            ux = ux / u;
611 >            uy = uy / u;
612 >            uz = uz / u;
613 >            
614 >            dAtom->setSUx( ux );
615 >            dAtom->setSUy( uy );
616 >            dAtom->setSUz( uz );
617 >          }
618 >          else{
619 >            the_atoms[index] = new GeneralAtom(index);
620 >          }
621 >          the_atoms[index]->setType( current_atom->getType() );
622 >          the_atoms[index]->setIndex( index );
623 >          
624 >          // increment the index and repeat;
625 >          index++;
626          }
627 <        else{
628 <          the_atoms[index] = new GeneralAtom(index);
629 <        }
630 <        the_atoms[index]->setType( current_atom->getType() );
631 <        the_atoms[index]->setIndex( index );
627 >        
628 >        molEnd = index -1;
629 >        the_molecules[lMolIndex].setNMembers( nMemb );
630 >        the_molecules[lMolIndex].setStartAtom( molStart );
631 >        the_molecules[lMolIndex].setEndAtom( molEnd );
632 >        the_molecules[lMolIndex].setStampID( i );
633 >        lMolIndex++;
634  
635 <        // increment the index and repeat;
500 <        index++;
635 > #ifdef IS_MPI
636        }
637 <
638 <      molEnd = index -1;
504 <      the_molecules[molIndex].setNMembers( nMemb );
505 <      the_molecules[molIndex].setStartAtom( molStart );
506 <      the_molecules[molIndex].setEndAtom( molEnd );
637 > #endif //is_mpi
638 >      
639        molIndex++;
508 –
640      }
641    }
642  
# Line 514 | Line 645 | void SimSetup::makeBonds( void ){
645  
646   void SimSetup::makeBonds( void ){
647  
648 <  int i, j, k, index, offset;
648 >  int i, j, k, index, offset, molIndex;
649    bond_pair* the_bonds;
650    BondStamp* current_bond;
651  
652    the_bonds = new bond_pair[tot_bonds];
653    index = 0;
654    offset = 0;
655 +  molIndex = 0;g1
656 +
657    for( i=0; i<n_components; i++ ){
658  
659      for( j=0; j<components_nmol[i]; j++ ){
660  
661 <      for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
662 <
663 <        current_bond = comp_stamps[i]->getBond( k );
664 <        the_bonds[index].a = current_bond->getA() + offset;
665 <        the_bonds[index].b = current_bond->getB() + offset;
666 <
667 <        the_excludes[index].i = the_bonds[index].a;
668 <        the_excludes[index].j = the_bonds[index].b;
669 <
670 <        // increment the index and repeat;
671 <        index++;
661 > #ifdef IS_MPI
662 >      if( mpiSim->getMyMolStart() <= molIndex &&
663 >          molIndex <= mpiSim->getMyMolEnd() ){
664 > #endif // is_mpi        
665 >        
666 >        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
667 >          
668 >          current_bond = comp_stamps[i]->getBond( k );
669 >          the_bonds[index].a = current_bond->getA() + offset;
670 >          the_bonds[index].b = current_bond->getB() + offset;
671 >          
672 >          the_excludes[index].i = the_bonds[index].a;
673 >          the_excludes[index].j = the_bonds[index].b;
674 >          
675 >          // increment the index and repeat;
676 >          index++;
677 >        }
678 >        offset += comp_stamps[i]->getNAtoms();
679 >        
680 > #ifdef IS_MPI
681        }
682 <      offset += comp_stamps[i]->getNAtoms();
683 <    }
682 > #endif is_mpi
683 >      
684 >      molIndex++;
685 >    }      
686    }
687  
688    the_ff->initializeBonds( the_bonds );
# Line 546 | Line 690 | void SimSetup::makeBends( void ){
690  
691   void SimSetup::makeBends( void ){
692  
693 <  int i, j, k, index, offset;
693 >  int i, j, k, index, offset, molIndex;
694    bend_set* the_bends;
695    BendStamp* current_bend;
696  
697    the_bends = new bend_set[tot_bends];
698    index = 0;
699    offset = 0;
700 +  molIndex = 0;
701    for( i=0; i<n_components; i++ ){
702  
703      for( j=0; j<components_nmol[i]; j++ ){
704  
705 <      for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
705 > #ifdef IS_MPI
706 >      if( mpiSim->getMyMolStart() <= molIndex &&
707 >          molIndex <= mpiSim->getMyMolEnd() ){
708 > #endif // is_mpi        
709  
710 <        current_bend = comp_stamps[i]->getBend( k );
711 <        the_bends[index].a = current_bend->getA() + offset;
712 <        the_bends[index].b = current_bend->getB() + offset;
713 <        the_bends[index].c = current_bend->getC() + offset;
714 <
715 <        the_excludes[index + tot_bonds].i = the_bends[index].a;
716 <        the_excludes[index + tot_bonds].j = the_bends[index].c;
717 <
718 <        // increment the index and repeat;
719 <        index++;
710 >        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
711 >          
712 >          current_bend = comp_stamps[i]->getBend( k );
713 >          the_bends[index].a = current_bend->getA() + offset;
714 >          the_bends[index].b = current_bend->getB() + offset;
715 >          the_bends[index].c = current_bend->getC() + offset;
716 >          
717 >          the_excludes[index + tot_bonds].i = the_bends[index].a;
718 >          the_excludes[index + tot_bonds].j = the_bends[index].c;
719 >          
720 >          // increment the index and repeat;
721 >          index++;
722 >        }
723 >        offset += comp_stamps[i]->getNAtoms();
724 >        
725 > #ifdef IS_MPI
726        }
727 <      offset += comp_stamps[i]->getNAtoms();
727 > #endif //is_mpi
728 >
729 >      molIndex++;
730      }
731    }
732  
# Line 579 | Line 735 | void SimSetup::makeTorsions( void ){
735  
736   void SimSetup::makeTorsions( void ){
737  
738 <  int i, j, k, index, offset;
738 >  int i, j, k, index, offset, molIndex;
739    torsion_set* the_torsions;
740    TorsionStamp* current_torsion;
741  
742    the_torsions = new torsion_set[tot_torsions];
743    index = 0;
744    offset = 0;
745 +  molIndex = 0;
746    for( i=0; i<n_components; i++ ){
747  
748      for( j=0; j<components_nmol[i]; j++ ){
749  
750 + #ifdef IS_MPI
751 +      if( mpiSim->getMyMolStart() <= molIndex &&
752 +          molIndex <= mpiSim->getMyMolEnd() ){
753 + #endif // is_mpi        
754 +
755        for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
756  
757          current_torsion = comp_stamps[i]->getTorsion( k );
# Line 605 | Line 767 | void SimSetup::makeTorsions( void ){
767          index++;
768        }
769        offset += comp_stamps[i]->getNAtoms();
770 +
771 + #ifdef IS_MPI
772 +      }
773 + #endif //is_mpi      
774 +
775 +      molIndex++;
776      }
777    }
778  

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