# | 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 233 | Line 331 | void SimSetup::createSim( void ){ | |
331 | makeTorsions(); | |
332 | } | |
333 | ||
236 | – | // makeMolecules(); |
334 | ||
335 | // get some of the tricky things that may still be in the globals | |
336 | ||
# | Line 317 | Line 414 | void SimSetup::createSim( void ){ | |
414 | // delete fileInit; | |
415 | // } | |
416 | // else{ | |
417 | + | |
418 | + | #ifdef IS_MPI |
419 | + | |
420 | + | // no init from bass |
421 | + | |
422 | + | sprintf( painCave.errMsg, |
423 | + | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
424 | + | painCave.isFatal; |
425 | + | simError(); |
426 | + | |
427 | + | #else |
428 | ||
429 | initFromBass(); | |
430 | + | |
431 | + | #endif // is_mpi |
432 | ||
433 | #ifdef IS_MPI | |
434 | < | strcpy( checkPointMsg, "initFromBass successfully created the lattice" ); |
434 | > | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
435 | MPIcheckPoint(); | |
436 | #endif // is_mpi | |
437 | ||
# | Line 455 | Line 565 | void SimSetup::makeAtoms( void ){ | |
565 | double ux, uy, uz, uSqr, u; | |
566 | AtomStamp* current_atom; | |
567 | DirectionalAtom* dAtom; | |
568 | < | int molIndex, molStart, molEnd, nMemb; |
568 | > | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
569 | ||
570 | < | |
570 | > | lMolIndex = 0; |
571 | molIndex = 0; | |
572 | index = 0; | |
573 | for( i=0; i<n_components; i++ ){ | |
574 | ||
575 | for( j=0; j<components_nmol[i]; j++ ){ | |
576 | ||
577 | < | molStart = index; |
578 | < | nMemb = comp_stamps[i]->getNAtoms(); |
579 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
577 | > | #ifdef IS_MPI |
578 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
579 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
580 | > | #endif // is_mpi |
581 | ||
582 | < | current_atom = comp_stamps[i]->getAtom( k ); |
583 | < | if( current_atom->haveOrientation() ){ |
584 | < | |
585 | < | dAtom = new DirectionalAtom(index); |
586 | < | simnfo->n_oriented++; |
587 | < | the_atoms[index] = dAtom; |
588 | < | |
589 | < | ux = current_atom->getOrntX(); |
590 | < | uy = current_atom->getOrntY(); |
591 | < | uz = current_atom->getOrntZ(); |
592 | < | |
593 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
594 | < | |
595 | < | u = sqrt( uSqr ); |
596 | < | ux = ux / u; |
597 | < | uy = uy / u; |
598 | < | uz = uz / u; |
599 | < | |
600 | < | dAtom->setSUx( ux ); |
601 | < | dAtom->setSUy( uy ); |
602 | < | dAtom->setSUz( uz ); |
582 | > | molStart = index; |
583 | > | nMemb = comp_stamps[i]->getNAtoms(); |
584 | > | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
585 | > | |
586 | > | current_atom = comp_stamps[i]->getAtom( k ); |
587 | > | if( current_atom->haveOrientation() ){ |
588 | > | |
589 | > | dAtom = new DirectionalAtom(index); |
590 | > | simnfo->n_oriented++; |
591 | > | the_atoms[index] = dAtom; |
592 | > | |
593 | > | ux = current_atom->getOrntX(); |
594 | > | uy = current_atom->getOrntY(); |
595 | > | uz = current_atom->getOrntZ(); |
596 | > | |
597 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
598 | > | |
599 | > | u = sqrt( uSqr ); |
600 | > | ux = ux / u; |
601 | > | uy = uy / u; |
602 | > | uz = uz / u; |
603 | > | |
604 | > | dAtom->setSUx( ux ); |
605 | > | dAtom->setSUy( uy ); |
606 | > | dAtom->setSUz( uz ); |
607 | > | } |
608 | > | else{ |
609 | > | the_atoms[index] = new GeneralAtom(index); |
610 | > | } |
611 | > | the_atoms[index]->setType( current_atom->getType() ); |
612 | > | the_atoms[index]->setIndex( index ); |
613 | > | |
614 | > | // increment the index and repeat; |
615 | > | index++; |
616 | } | |
617 | < | else{ |
618 | < | the_atoms[index] = new GeneralAtom(index); |
619 | < | } |
620 | < | the_atoms[index]->setType( current_atom->getType() ); |
621 | < | the_atoms[index]->setIndex( index ); |
617 | > | |
618 | > | molEnd = index -1; |
619 | > | the_molecules[lMolIndex].setNMembers( nMemb ); |
620 | > | the_molecules[lMolIndex].setStartAtom( molStart ); |
621 | > | the_molecules[lMolIndex].setEndAtom( molEnd ); |
622 | > | the_molecules[lMolIndex].setStampID( i ); |
623 | > | lMolIndex++; |
624 | ||
625 | < | // increment the index and repeat; |
500 | < | index++; |
625 | > | #ifdef IS_MPI |
626 | } | |
627 | < | |
628 | < | molEnd = index -1; |
504 | < | the_molecules[molIndex].setNMembers( nMemb ); |
505 | < | the_molecules[molIndex].setStartAtom( molStart ); |
506 | < | the_molecules[molIndex].setEndAtom( molEnd ); |
627 | > | #endif //is_mpi |
628 | > | |
629 | molIndex++; | |
508 | – | |
630 | } | |
631 | } | |
632 | ||
# | Line 514 | Line 635 | void SimSetup::makeBonds( void ){ | |
635 | ||
636 | void SimSetup::makeBonds( void ){ | |
637 | ||
638 | < | int i, j, k, index, offset; |
638 | > | int i, j, k, index, offset, molIndex; |
639 | bond_pair* the_bonds; | |
640 | BondStamp* current_bond; | |
641 | ||
642 | the_bonds = new bond_pair[tot_bonds]; | |
643 | index = 0; | |
644 | offset = 0; | |
645 | + | molIndex = 0; |
646 | for( i=0; i<n_components; i++ ){ | |
647 | ||
648 | for( j=0; j<components_nmol[i]; j++ ){ | |
649 | ||
650 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
651 | < | |
652 | < | current_bond = comp_stamps[i]->getBond( k ); |
653 | < | the_bonds[index].a = current_bond->getA() + offset; |
654 | < | the_bonds[index].b = current_bond->getB() + offset; |
655 | < | |
656 | < | the_excludes[index].i = the_bonds[index].a; |
657 | < | the_excludes[index].j = the_bonds[index].b; |
658 | < | |
659 | < | // increment the index and repeat; |
660 | < | index++; |
650 | > | #ifdef IS_MPI |
651 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
652 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
653 | > | #endif // is_mpi |
654 | > | |
655 | > | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
656 | > | |
657 | > | current_bond = comp_stamps[i]->getBond( k ); |
658 | > | the_bonds[index].a = current_bond->getA() + offset; |
659 | > | the_bonds[index].b = current_bond->getB() + offset; |
660 | > | |
661 | > | the_excludes[index].i = the_bonds[index].a; |
662 | > | the_excludes[index].j = the_bonds[index].b; |
663 | > | |
664 | > | // increment the index and repeat; |
665 | > | index++; |
666 | > | } |
667 | > | offset += comp_stamps[i]->getNAtoms(); |
668 | > | |
669 | > | #ifdef IS_MPI |
670 | } | |
671 | < | offset += comp_stamps[i]->getNAtoms(); |
672 | < | } |
671 | > | #endif is_mpi |
672 | > | |
673 | > | molIndex++; |
674 | > | } |
675 | } | |
676 | ||
677 | the_ff->initializeBonds( the_bonds ); | |
# | Line 546 | Line 679 | void SimSetup::makeBends( void ){ | |
679 | ||
680 | void SimSetup::makeBends( void ){ | |
681 | ||
682 | < | int i, j, k, index, offset; |
682 | > | int i, j, k, index, offset, molIndex; |
683 | bend_set* the_bends; | |
684 | BendStamp* current_bend; | |
685 | ||
686 | the_bends = new bend_set[tot_bends]; | |
687 | index = 0; | |
688 | offset = 0; | |
689 | + | molIndex = 0; |
690 | for( i=0; i<n_components; i++ ){ | |
691 | ||
692 | for( j=0; j<components_nmol[i]; j++ ){ | |
693 | ||
694 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
694 | > | #ifdef IS_MPI |
695 | > | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
696 | > | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
697 | > | #endif // is_mpi |
698 | ||
699 | < | current_bend = comp_stamps[i]->getBend( k ); |
700 | < | the_bends[index].a = current_bend->getA() + offset; |
701 | < | the_bends[index].b = current_bend->getB() + offset; |
702 | < | the_bends[index].c = current_bend->getC() + offset; |
703 | < | |
704 | < | the_excludes[index + tot_bonds].i = the_bends[index].a; |
705 | < | the_excludes[index + tot_bonds].j = the_bends[index].c; |
706 | < | |
707 | < | // increment the index and repeat; |
708 | < | index++; |
699 | > | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
700 | > | |
701 | > | current_bend = comp_stamps[i]->getBend( k ); |
702 | > | the_bends[index].a = current_bend->getA() + offset; |
703 | > | the_bends[index].b = current_bend->getB() + offset; |
704 | > | the_bends[index].c = current_bend->getC() + offset; |
705 | > | |
706 | > | the_excludes[index + tot_bonds].i = the_bends[index].a; |
707 | > | the_excludes[index + tot_bonds].j = the_bends[index].c; |
708 | > | |
709 | > | // increment the index and repeat; |
710 | > | index++; |
711 | > | } |
712 | > | offset += comp_stamps[i]->getNAtoms(); |
713 | > | |
714 | > | #ifdef IS_MPI |
715 | } | |
716 | < | offset += comp_stamps[i]->getNAtoms(); |
716 | > | #endif //is_mpi |
717 | > | |
718 | > | molIndex++; |
719 | } | |
720 | } | |
721 | ||
# | Line 579 | Line 724 | void SimSetup::makeTorsions( void ){ | |
724 | ||
725 | void SimSetup::makeTorsions( void ){ | |
726 | ||
727 | < | int i, j, k, index, offset; |
727 | > | int i, j, k, index, offset, molIndex; |
728 | torsion_set* the_torsions; | |
729 | TorsionStamp* current_torsion; | |
730 | ||
731 | the_torsions = new torsion_set[tot_torsions]; | |
732 | index = 0; | |
733 | offset = 0; | |
734 | + | molIndex = 0; |
735 | for( i=0; i<n_components; i++ ){ | |
736 | ||
737 | for( j=0; j<components_nmol[i]; j++ ){ | |
738 | ||
739 | + | #ifdef IS_MPI |
740 | + | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
741 | + | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
742 | + | #endif // is_mpi |
743 | + | |
744 | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ | |
745 | ||
746 | current_torsion = comp_stamps[i]->getTorsion( k ); | |
# | Line 605 | Line 756 | void SimSetup::makeTorsions( void ){ | |
756 | index++; | |
757 | } | |
758 | offset += comp_stamps[i]->getNAtoms(); | |
759 | + | |
760 | + | #ifdef IS_MPI |
761 | + | } |
762 | + | #endif //is_mpi |
763 | + | |
764 | + | molIndex++; |
765 | } | |
766 | } | |
767 |
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