10 |
|
|
11 |
|
#ifdef IS_MPI |
12 |
|
#include "mpiBASS.h" |
13 |
+ |
#include "mpiSimulation.hpp" |
14 |
|
#include "bassDiag.hpp" |
15 |
|
#endif |
16 |
|
|
93 |
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if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
94 |
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else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
95 |
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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", |
236 |
|
|
237 |
|
// divide the molecules among processors here. |
238 |
|
|
239 |
< |
mpiSimulation* mpiSim = new mpiSimulation( simnfo ); |
239 |
> |
mpiSim = new mpiSimulation( simnfo ); |
240 |
|
|
241 |
|
mpiSim->divideLabor(); |
242 |
|
|
407 |
|
|
408 |
|
|
409 |
|
|
410 |
< |
// if( the_globals->haveInitialConfig() ){ |
411 |
< |
// InitializeFromFile* fileInit; |
412 |
< |
// fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
413 |
< |
|
414 |
< |
// fileInit->read_xyz( simnfo ); // default velocities on |
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 |
> |
}else fileInit = new InitializeFromFile( NULL ); |
419 |
> |
#endif |
420 |
> |
fileInit->read_xyz( simnfo ); // default velocities on |
421 |
|
|
422 |
< |
// delete fileInit; |
423 |
< |
// } |
424 |
< |
// else{ |
422 |
> |
delete fileInit; |
423 |
> |
} |
424 |
> |
else{ |
425 |
|
|
426 |
|
#ifdef IS_MPI |
427 |
|
|
436 |
|
|
437 |
|
initFromBass(); |
438 |
|
|
439 |
< |
#endif // is_mpi |
440 |
< |
|
439 |
> |
|
440 |
> |
#endif |
441 |
> |
} |
442 |
> |
|
443 |
|
#ifdef IS_MPI |
444 |
|
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
445 |
|
MPIcheckPoint(); |
449 |
|
|
450 |
|
|
451 |
|
|
452 |
< |
// } |
452 |
> |
|
453 |
|
|
454 |
|
#ifdef IS_MPI |
455 |
|
if( worldRank == 0 ){ |
585 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
586 |
|
|
587 |
|
#ifdef IS_MPI |
588 |
< |
if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
589 |
< |
molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
588 |
> |
if( mpiSim->getMyMolStart() <= molIndex && |
589 |
> |
molIndex <= mpiSim->getMyMolEnd() ){ |
590 |
|
#endif // is_mpi |
591 |
|
|
592 |
|
molStart = index; |
652 |
|
the_bonds = new bond_pair[tot_bonds]; |
653 |
|
index = 0; |
654 |
|
offset = 0; |
655 |
< |
molIndex = 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 |
|
#ifdef IS_MPI |
662 |
< |
if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
663 |
< |
molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
662 |
> |
if( mpiSim->getMyMolStart() <= molIndex && |
663 |
> |
molIndex <= mpiSim->getMyMolEnd() ){ |
664 |
|
#endif // is_mpi |
665 |
|
|
666 |
|
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
703 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
704 |
|
|
705 |
|
#ifdef IS_MPI |
706 |
< |
if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
707 |
< |
molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
706 |
> |
if( mpiSim->getMyMolStart() <= molIndex && |
707 |
> |
molIndex <= mpiSim->getMyMolEnd() ){ |
708 |
|
#endif // is_mpi |
709 |
|
|
710 |
|
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
748 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
749 |
|
|
750 |
|
#ifdef IS_MPI |
751 |
< |
if( simnfo->mpiSim->getMyMolStart() <= molIndex && |
752 |
< |
molIndex <= simnfo->mpiSim->getMyMolEnd() ){ |
751 |
> |
if( mpiSim->getMyMolStart() <= molIndex && |
752 |
> |
molIndex <= mpiSim->getMyMolEnd() ){ |
753 |
|
#endif // is_mpi |
754 |
|
|
755 |
|
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |