# | 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 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 187 | Line 189 | void SimSetup::createSim( void ){ | |
189 | if( currentStamp == NULL ){ | |
190 | sprintf( painCave.errMsg, | |
191 | "SimSetup error: Component \"%s\" was not found in the " | |
192 | < | "list of declared molecules\n" |
192 | > | "list of declared molecules\n", |
193 | id ); | |
194 | painCave.isFatal = 1; | |
195 | simError(); | |
# | Line 234 | Line 236 | void SimSetup::createSim( void ){ | |
236 | ||
237 | // divide the molecules among processors here. | |
238 | ||
239 | < | mpiSimulation* mpiSim = new mpiSimulation( simnfo ); |
239 | > | mpiSim = new mpiSimulation( simnfo ); |
240 | ||
241 | < | mpiSim->divideLabor(); |
241 | > | |
242 | ||
243 | + | globalIndex = mpiSim->divideLabor(); |
244 | + | |
245 | + | |
246 | + | |
247 | // set up the local variables | |
248 | ||
249 | int localMol, allMol; | |
# | Line 313 | Line 319 | void SimSetup::createSim( void ){ | |
319 | simnfo->excludes = the_excludes; | |
320 | ||
321 | ||
316 | – | // initialize the arrays |
317 | – | |
318 | – | the_ff->setSimInfo( simnfo ); |
319 | – | |
320 | – | makeAtoms(); |
321 | – | |
322 | – | if( tot_bonds ){ |
323 | – | makeBonds(); |
324 | – | } |
325 | – | |
326 | – | if( tot_bends ){ |
327 | – | makeBends(); |
328 | – | } |
329 | – | |
330 | – | if( tot_torsions ){ |
331 | – | makeTorsions(); |
332 | – | } |
333 | – | |
334 | – | |
322 | // get some of the tricky things that may still be in the globals | |
323 | ||
324 | if( simnfo->n_dipoles ){ | |
# | Line 402 | Line 389 | void SimSetup::createSim( void ){ | |
389 | strcpy( checkPointMsg, "Box size set up" ); | |
390 | MPIcheckPoint(); | |
391 | #endif // is_mpi | |
392 | + | |
393 | + | |
394 | + | // initialize the arrays |
395 | + | |
396 | + | the_ff->setSimInfo( simnfo ); |
397 | + | |
398 | + | makeAtoms(); |
399 | + | // |
400 | + | if( tot_bonds ){ |
401 | + | makeBonds(); |
402 | + | } |
403 | + | |
404 | + | if( tot_bends ){ |
405 | + | makeBends(); |
406 | + | } |
407 | + | |
408 | + | if( tot_torsions ){ |
409 | + | makeTorsions(); |
410 | + | } |
411 | ||
412 | ||
413 | ||
414 | + | |
415 | + | |
416 | + | |
417 | if( the_globals->haveInitialConfig() ){ | |
418 | ||
419 | InitializeFromFile* fileInit; | |
# | Line 558 | Line 567 | void SimSetup::createSim( void ){ | |
567 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
568 | ||
569 | ||
570 | < | // make the longe range forces and the integrator |
570 | > | // // make the longe range forces and the integrator |
571 | ||
572 | < | new AllLong( simnfo ); |
572 | > | // new AllLong( simnfo ); |
573 | ||
574 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo ); |
574 | > | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
575 | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo ); | |
576 | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo ); | |
577 | + | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
578 | + | |
579 | } | |
580 | ||
581 | void SimSetup::makeAtoms( void ){ | |
# | Line 583 | Line 594 | void SimSetup::makeAtoms( void ){ | |
594 | for( j=0; j<components_nmol[i]; j++ ){ | |
595 | ||
596 | #ifdef IS_MPI | |
597 | < | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
598 | < | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
597 | > | if( mpiSim->getMyMolStart() <= molIndex && |
598 | > | molIndex <= mpiSim->getMyMolEnd() ){ |
599 | #endif // is_mpi | |
600 | ||
601 | molStart = index; | |
# | Line 637 | Line 648 | void SimSetup::makeAtoms( void ){ | |
648 | molIndex++; | |
649 | } | |
650 | } | |
651 | + | |
652 | + | #ifdef IS_MPI |
653 | + | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
654 | + | |
655 | + | delete[] globalIndex; |
656 | ||
657 | + | mpiSim->mpiRefresh(); |
658 | + | #endif //IS_MPI |
659 | + | |
660 | the_ff->initializeAtoms(); | |
661 | } | |
662 | ||
# | Line 651 | Line 670 | void SimSetup::makeBonds( void ){ | |
670 | index = 0; | |
671 | offset = 0; | |
672 | molIndex = 0; | |
673 | + | |
674 | for( i=0; i<n_components; i++ ){ | |
675 | ||
676 | for( j=0; j<components_nmol[i]; j++ ){ | |
677 | ||
678 | #ifdef IS_MPI | |
679 | < | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
680 | < | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
679 | > | if( mpiSim->getMyMolStart() <= molIndex && |
680 | > | molIndex <= mpiSim->getMyMolEnd() ){ |
681 | #endif // is_mpi | |
682 | ||
683 | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ | |
# | Line 676 | Line 696 | void SimSetup::makeBonds( void ){ | |
696 | ||
697 | #ifdef IS_MPI | |
698 | } | |
699 | < | #endif is_mpi |
699 | > | #endif //is_mpi |
700 | ||
701 | molIndex++; | |
702 | } | |
# | Line 700 | Line 720 | void SimSetup::makeBends( void ){ | |
720 | for( j=0; j<components_nmol[i]; j++ ){ | |
721 | ||
722 | #ifdef IS_MPI | |
723 | < | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
724 | < | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
723 | > | if( mpiSim->getMyMolStart() <= molIndex && |
724 | > | molIndex <= mpiSim->getMyMolEnd() ){ |
725 | #endif // is_mpi | |
726 | ||
727 | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ | |
# | Line 745 | Line 765 | void SimSetup::makeTorsions( void ){ | |
765 | for( j=0; j<components_nmol[i]; j++ ){ | |
766 | ||
767 | #ifdef IS_MPI | |
768 | < | if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
769 | < | molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
768 | > | if( mpiSim->getMyMolStart() <= molIndex && |
769 | > | molIndex <= mpiSim->getMyMolEnd() ){ |
770 | #endif // is_mpi | |
771 | ||
772 | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
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