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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 189 by mmeineke, Tue Nov 26 21:04:43 2002 UTC vs.
Revision 206 by chuckv, Thu Dec 12 21:21:59 2002 UTC

# Line 73 | Line 73 | void SimSetup::createSim( void ){
73  
74    MakeStamps *the_stamps;
75    Globals* the_globals;
76 <  int i;
76 >  int i, j;
77  
78    // get the stamps and globals;
79    the_stamps = stamps;
# Line 161 | Line 161 | void SimSetup::createSim( void ){
161   #endif // is_mpi
162  
163    // make an array of molecule stamps that match the components used.
164 +  // also extract the used stamps out into a separate linked list
165  
166 +  simnfo->nComponents = n_components;
167 +  simnfo->componentsNmol = components_nmol;
168 +  simnfo->compStamps = comp_stamps;
169 +  simnfo->headStamp = new LinkedMolStamp();
170 +  
171 +  char* id;
172 +  LinkedMolStamp* headStamp = simnfo->headStamp;
173 +  LinkedMolStamp* currentStamp = NULL;
174    for( i=0; i<n_components; i++ ){
175  
176 <    comp_stamps[i] =
177 <      the_stamps->getMolecule( the_components[i]->getType() );
176 >    id = the_components[i]->getType();
177 >    comp_stamps[i] = NULL;
178 >    
179 >    // check to make sure the component isn't already in the list
180 >
181 >    comp_stamps[i] = headStamp->match( id );
182 >    if( comp_stamps[i] == NULL ){
183 >      
184 >      // extract the component from the list;
185 >      
186 >      currentStamp = the_stamps->extractMolStamp( id );
187 >      if( currentStamp == NULL ){
188 >        sprintf( painCave.errMsg,
189 >                 "SimSetup error: Component \"%s\" was not found in the "
190 >                 "list of declared molecules\n"
191 >                 id );
192 >        painCave.isFatal = 1;
193 >        simError();
194 >      }
195 >      
196 >      headStamp->add( currentStamp );
197 >      comp_stamps[i] = headStamp->match( id );
198 >    }
199    }
200  
201 + #ifdef IS_MPI
202 +  strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203 +  MPIcheckPoint();
204 + #endif // is_mpi
205 +  
206  
207  
208 +
209    // caclulate the number of atoms, bonds, bends and torsions
210  
211    tot_atoms = 0;
# Line 177 | Line 213 | void SimSetup::createSim( void ){
213    tot_bends = 0;
214    tot_torsions = 0;
215    for( i=0; i<n_components; i++ ){
216 <
217 <    tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
218 <    tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
219 <    tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
216 >    
217 >    tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218 >    tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219 >    tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220      tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221    }
222  
# Line 191 | Line 227 | void SimSetup::createSim( void ){
227    simnfo->n_bends = tot_bends;
228    simnfo->n_torsions = tot_torsions;
229    simnfo->n_SRI = tot_SRI;
230 +  simnfo->n_mol = tot_nmol;
231  
232 +  
233 + #ifdef IS_MPI
234 +
235 +  // divide the molecules among processors here.
236 +  
237 +  mpiSimulation* mpiSim = new mpiSimulation( simnfo );
238 +  
239 +  mpiSim->divideLabor();
240 +
241 +  // set up the local variables
242 +  
243 +  int localMol, allMol;
244 +  int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
245 +  
246 +  allMol = 0;
247 +  localMol = 0;
248 +  local_atoms = 0;
249 +  local_bonds = 0;
250 +  local_bends = 0;
251 +  local_torsions = 0;
252 +  for( i=0; i<n_components; i++ ){
253 +
254 +    for( j=0; j<components_nmol[i]; j++ ){
255 +      
256 +      if( mpiSim->getMyMolStart() <= allMol &&
257 +          allMol <= mpiSim->getMyMolEnd() ){
258 +        
259 +        local_atoms +=    comp_stamps[i]->getNAtoms();
260 +        local_bonds +=    comp_stamps[i]->getNBonds();
261 +        local_bends +=    comp_stamps[i]->getNBends();
262 +        local_torsions += comp_stamps[i]->getNTorsions();
263 +        localMol++;
264 +      }      
265 +      allMol++;
266 +    }
267 +  }
268 +  local_SRI = local_bonds + local_bends + local_torsions;
269 +  
270 +
271 +  simnfo->n_atoms = mpiSim->getMyNlocal();  
272 +  
273 +  if( local_atoms != simnfo->n_atoms ){
274 +    sprintf( painCave.errMsg,
275 +             "SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
276 +             " localAtom (%d) are note equal.\n",
277 +             simnfo->n_atoms,
278 +             local_atoms );
279 +    painCave.isFatal = 1;
280 +    simError();
281 +  }
282 +
283 +  simnfo->n_bonds = local_bonds;
284 +  simnfo->n_bends = local_bends;
285 +  simnfo->n_torsions = local_torsions;
286 +  simnfo->n_SRI = local_SRI;
287 +  simnfo->n_mol = localMol;
288 +
289 +  strcpy( checkPointMsg, "Passed nlocal consistency check." );
290 +  MPIcheckPoint();
291 +  
292 +  
293 + #endif // is_mpi
294 +  
295 +
296    // create the atom and short range interaction arrays
297  
298 <  Atom::createArrays(tot_atoms);
299 <  the_atoms = new Atom*[tot_atoms];
300 <  the_molecules = new Molecule[tot_nmol];
298 >  Atom::createArrays(simnfo->n_atoms);
299 >  the_atoms = new Atom*[simnfo->n_atoms];
300 >  the_molecules = new Molecule[simnfo->n_mol];
301  
302  
303 <  if( tot_SRI ){
304 <    the_sris = new SRI*[tot_SRI];
305 <    the_excludes = new ex_pair[tot_SRI];
303 >  if( simnfo->n_SRI ){
304 >    the_sris = new SRI*[simnfo->n_SRI];
305 >    the_excludes = new ex_pair[simnfo->n_SRI];
306    }
307  
308    // set the arrays into the SimInfo object
# Line 230 | Line 331 | void SimSetup::createSim( void ){
331      makeTorsions();
332    }
333  
233 –  //  makeMolecules();
334  
335    // get some of the tricky things that may still be in the globals
336  
# Line 305 | Line 405 | void SimSetup::createSim( void ){
405  
406  
407  
408 < //   if( the_globals->haveInitialConfig() ){
309 < //        InitializeFromFile* fileInit;
310 < //     fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
311 <
312 < //     fileInit->read_xyz( simnfo ); // default velocities on
313 <
314 < //     delete fileInit;
315 < //   }
316 < //   else{
317 <
318 <  initFromBass();
408 > if( the_globals->haveInitialConfig() ){
409  
410 +     InitializeFromFile* fileInit;
411 + #ifdef IS_MPI // is_mpi
412 +     if( worldRank == 0 ){
413 + #endif //is_mpi
414 +   fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
415   #ifdef IS_MPI
416 <  strcpy( checkPointMsg, "initFromBass successfully created the lattice" );
416 >     }else fileInit = new InitializeFromFile( NULL );
417 > #endif
418 >   fileInit->read_xyz( simnfo ); // default velocities on
419 >
420 >   delete fileInit;
421 > }
422 > else{
423 >
424 > #ifdef IS_MPI
425 >
426 >  // no init from bass
427 >  
428 >  sprintf( painCave.errMsg,
429 >           "Cannot intialize a parallel simulation without an initial configuration file.\n" );
430 >  painCave.isFatal;
431 >  simError();
432 >  
433 > #else
434 >
435 >  initFromBass();
436 >
437 >
438 > #endif
439 > }
440 >
441 > #ifdef IS_MPI
442 >  strcpy( checkPointMsg, "Successfully read in the initial configuration" );
443    MPIcheckPoint();
444   #endif // is_mpi
445  
# Line 326 | Line 447 | void SimSetup::createSim( void ){
447    
448  
449    
450 <  //   }
450 >
451    
452   #ifdef IS_MPI
453    if( worldRank == 0 ){
# Line 452 | Line 573 | void SimSetup::makeAtoms( void ){
573    double ux, uy, uz, uSqr, u;
574    AtomStamp* current_atom;
575    DirectionalAtom* dAtom;
576 <  int molIndex, molStart, molEnd, nMemb;
576 >  int molIndex, molStart, molEnd, nMemb, lMolIndex;
577  
578 <
578 >  lMolIndex = 0;
579    molIndex = 0;
580    index = 0;
581    for( i=0; i<n_components; i++ ){
582  
583      for( j=0; j<components_nmol[i]; j++ ){
584  
585 <      molStart = index;
586 <      nMemb = comp_stamps[i]->getNAtoms();
587 <      for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
588 <
468 <        current_atom = comp_stamps[i]->getAtom( k );
469 <        if( current_atom->haveOrientation() ){
585 > #ifdef IS_MPI
586 >      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
587 >          molIndex <= simnfo->mpiSim->getMyMolEnd() ){
588 > #endif // is_mpi        
589  
590 <          dAtom = new DirectionalAtom(index);
591 <          simnfo->n_oriented++;
592 <          the_atoms[index] = dAtom;
593 <
594 <          ux = current_atom->getOrntX();
595 <          uy = current_atom->getOrntY();
596 <          uz = current_atom->getOrntZ();
597 <
598 <          uSqr = (ux * ux) + (uy * uy) + (uz * uz);
599 <
600 <          u = sqrt( uSqr );
601 <          ux = ux / u;
602 <          uy = uy / u;
603 <          uz = uz / u;
604 <
605 <          dAtom->setSUx( ux );
606 <          dAtom->setSUy( uy );
607 <          dAtom->setSUz( uz );
590 >        molStart = index;
591 >        nMemb = comp_stamps[i]->getNAtoms();
592 >        for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
593 >          
594 >          current_atom = comp_stamps[i]->getAtom( k );
595 >          if( current_atom->haveOrientation() ){
596 >            
597 >            dAtom = new DirectionalAtom(index);
598 >            simnfo->n_oriented++;
599 >            the_atoms[index] = dAtom;
600 >            
601 >            ux = current_atom->getOrntX();
602 >            uy = current_atom->getOrntY();
603 >            uz = current_atom->getOrntZ();
604 >            
605 >            uSqr = (ux * ux) + (uy * uy) + (uz * uz);
606 >            
607 >            u = sqrt( uSqr );
608 >            ux = ux / u;
609 >            uy = uy / u;
610 >            uz = uz / u;
611 >            
612 >            dAtom->setSUx( ux );
613 >            dAtom->setSUy( uy );
614 >            dAtom->setSUz( uz );
615 >          }
616 >          else{
617 >            the_atoms[index] = new GeneralAtom(index);
618 >          }
619 >          the_atoms[index]->setType( current_atom->getType() );
620 >          the_atoms[index]->setIndex( index );
621 >          
622 >          // increment the index and repeat;
623 >          index++;
624          }
625 <        else{
626 <          the_atoms[index] = new GeneralAtom(index);
627 <        }
628 <        the_atoms[index]->setType( current_atom->getType() );
629 <        the_atoms[index]->setIndex( index );
625 >        
626 >        molEnd = index -1;
627 >        the_molecules[lMolIndex].setNMembers( nMemb );
628 >        the_molecules[lMolIndex].setStartAtom( molStart );
629 >        the_molecules[lMolIndex].setEndAtom( molEnd );
630 >        the_molecules[lMolIndex].setStampID( i );
631 >        lMolIndex++;
632  
633 <        // increment the index and repeat;
497 <        index++;
633 > #ifdef IS_MPI
634        }
635 <
636 <      molEnd = index -1;
501 <      the_molecules[molIndex].setNMembers( nMemb );
502 <      the_molecules[molIndex].setStartAtom( molStart );
503 <      the_molecules[molIndex].setEndAtom( molEnd );
635 > #endif //is_mpi
636 >      
637        molIndex++;
505 –
638      }
639    }
640  
# Line 511 | Line 643 | void SimSetup::makeBonds( void ){
643  
644   void SimSetup::makeBonds( void ){
645  
646 <  int i, j, k, index, offset;
646 >  int i, j, k, index, offset, molIndex;
647    bond_pair* the_bonds;
648    BondStamp* current_bond;
649  
650    the_bonds = new bond_pair[tot_bonds];
651    index = 0;
652    offset = 0;
653 +  molIndex = 0;
654    for( i=0; i<n_components; i++ ){
655  
656      for( j=0; j<components_nmol[i]; j++ ){
657  
658 <      for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
659 <
660 <        current_bond = comp_stamps[i]->getBond( k );
661 <        the_bonds[index].a = current_bond->getA() + offset;
662 <        the_bonds[index].b = current_bond->getB() + offset;
663 <
664 <        the_excludes[index].i = the_bonds[index].a;
665 <        the_excludes[index].j = the_bonds[index].b;
666 <
667 <        // increment the index and repeat;
668 <        index++;
658 > #ifdef IS_MPI
659 >      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
660 >          molIndex <= simnfo->mpiSim->getMyMolEnd() ){
661 > #endif // is_mpi        
662 >        
663 >        for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
664 >          
665 >          current_bond = comp_stamps[i]->getBond( k );
666 >          the_bonds[index].a = current_bond->getA() + offset;
667 >          the_bonds[index].b = current_bond->getB() + offset;
668 >          
669 >          the_excludes[index].i = the_bonds[index].a;
670 >          the_excludes[index].j = the_bonds[index].b;
671 >          
672 >          // increment the index and repeat;
673 >          index++;
674 >        }
675 >        offset += comp_stamps[i]->getNAtoms();
676 >        
677 > #ifdef IS_MPI
678        }
679 <      offset += comp_stamps[i]->getNAtoms();
680 <    }
679 > #endif is_mpi
680 >      
681 >      molIndex++;
682 >    }      
683    }
684  
685    the_ff->initializeBonds( the_bonds );
# Line 543 | Line 687 | void SimSetup::makeBends( void ){
687  
688   void SimSetup::makeBends( void ){
689  
690 <  int i, j, k, index, offset;
690 >  int i, j, k, index, offset, molIndex;
691    bend_set* the_bends;
692    BendStamp* current_bend;
693  
694    the_bends = new bend_set[tot_bends];
695    index = 0;
696    offset = 0;
697 +  molIndex = 0;
698    for( i=0; i<n_components; i++ ){
699  
700      for( j=0; j<components_nmol[i]; j++ ){
701  
702 <      for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
702 > #ifdef IS_MPI
703 >      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
704 >          molIndex <= simnfo->mpiSim->getMyMolEnd() ){
705 > #endif // is_mpi        
706  
707 <        current_bend = comp_stamps[i]->getBend( k );
708 <        the_bends[index].a = current_bend->getA() + offset;
709 <        the_bends[index].b = current_bend->getB() + offset;
710 <        the_bends[index].c = current_bend->getC() + offset;
711 <
712 <        the_excludes[index + tot_bonds].i = the_bends[index].a;
713 <        the_excludes[index + tot_bonds].j = the_bends[index].c;
714 <
715 <        // increment the index and repeat;
716 <        index++;
707 >        for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
708 >          
709 >          current_bend = comp_stamps[i]->getBend( k );
710 >          the_bends[index].a = current_bend->getA() + offset;
711 >          the_bends[index].b = current_bend->getB() + offset;
712 >          the_bends[index].c = current_bend->getC() + offset;
713 >          
714 >          the_excludes[index + tot_bonds].i = the_bends[index].a;
715 >          the_excludes[index + tot_bonds].j = the_bends[index].c;
716 >          
717 >          // increment the index and repeat;
718 >          index++;
719 >        }
720 >        offset += comp_stamps[i]->getNAtoms();
721 >        
722 > #ifdef IS_MPI
723        }
724 <      offset += comp_stamps[i]->getNAtoms();
724 > #endif //is_mpi
725 >
726 >      molIndex++;
727      }
728    }
729  
# Line 576 | Line 732 | void SimSetup::makeTorsions( void ){
732  
733   void SimSetup::makeTorsions( void ){
734  
735 <  int i, j, k, index, offset;
735 >  int i, j, k, index, offset, molIndex;
736    torsion_set* the_torsions;
737    TorsionStamp* current_torsion;
738  
739    the_torsions = new torsion_set[tot_torsions];
740    index = 0;
741    offset = 0;
742 +  molIndex = 0;
743    for( i=0; i<n_components; i++ ){
744  
745      for( j=0; j<components_nmol[i]; j++ ){
746  
747 + #ifdef IS_MPI
748 +      if( simnfo->mpiSim->getMyMolStart() <= molIndex &&
749 +          molIndex <= simnfo->mpiSim->getMyMolEnd() ){
750 + #endif // is_mpi        
751 +
752        for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
753  
754          current_torsion = comp_stamps[i]->getTorsion( k );
# Line 602 | Line 764 | void SimSetup::makeTorsions( void ){
764          index++;
765        }
766        offset += comp_stamps[i]->getNAtoms();
767 +
768 + #ifdef IS_MPI
769 +      }
770 + #endif //is_mpi      
771 +
772 +      molIndex++;
773      }
774    }
775  

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