66 |
|
|
67 |
|
MakeStamps *the_stamps; |
68 |
|
Globals* the_globals; |
69 |
+ |
ExtendedSystem* the_extendedsystem; |
70 |
|
int i, j; |
71 |
|
|
72 |
|
// get the stamps and globals; |
81 |
|
// get the ones we know are there, yet still may need some work. |
82 |
|
n_components = the_globals->getNComponents(); |
83 |
|
strcpy( force_field, the_globals->getForceField() ); |
84 |
+ |
|
85 |
+ |
// get the ensemble and set up an extended system if we need it: |
86 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
87 |
+ |
if( !strcasecmp( ensemble, "NPT" ) ) { |
88 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
89 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 |
+ |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
91 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
92 |
+ |
the_extendedsystem->setTauRelax(the_globals->getTauRelax()); |
93 |
+ |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
94 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
95 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
96 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
97 |
+ |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
98 |
+ |
} else { |
99 |
+ |
sprintf( painCave.errMsg, |
100 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
101 |
+ |
"reverting to NVE for this simulation.\n", |
102 |
+ |
ensemble ); |
103 |
+ |
painCave.isFatal = 0; |
104 |
+ |
simError(); |
105 |
+ |
strcpy( ensemble, "NVE" ); |
106 |
+ |
} |
107 |
|
strcpy( simnfo->ensemble, ensemble ); |
108 |
|
|
109 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
110 |
|
simnfo->usePBC = the_globals->getPBC(); |
111 |
|
|
112 |
< |
|
113 |
< |
|
114 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
115 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
116 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
117 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
112 |
> |
int usesDipoles = 0; |
113 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
114 |
> |
the_ff = new TraPPE_ExFF(); |
115 |
> |
usesDipoles = 1; |
116 |
> |
} |
117 |
> |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
118 |
|
else{ |
119 |
|
sprintf( painCave.errMsg, |
120 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
265 |
|
|
266 |
|
globalIndex = mpiSim->divideLabor(); |
267 |
|
|
245 |
– |
|
246 |
– |
|
268 |
|
// set up the local variables |
269 |
|
|
270 |
|
int localMol, allMol; |
271 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
272 |
+ |
|
273 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
274 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
275 |
|
|
276 |
|
allMol = 0; |
277 |
|
localMol = 0; |
283 |
|
|
284 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
285 |
|
|
286 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
286 |
> |
if( mol2proc[j] == worldRank ){ |
287 |
|
|
288 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
289 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
302 |
|
if( local_atoms != simnfo->n_atoms ){ |
303 |
|
sprintf( painCave.errMsg, |
304 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
305 |
< |
" localAtom (%d) are note equal.\n", |
305 |
> |
" localAtom (%d) are not equal.\n", |
306 |
|
simnfo->n_atoms, |
307 |
|
local_atoms ); |
308 |
|
painCave.isFatal = 1; |
327 |
|
Atom::createArrays(simnfo->n_atoms); |
328 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
329 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
330 |
+ |
int molIndex; |
331 |
|
|
332 |
+ |
// initialize the molecule's stampID's |
333 |
|
|
334 |
< |
if( simnfo->n_SRI ){ |
335 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
336 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
334 |
> |
#ifdef IS_MPI |
335 |
> |
|
336 |
> |
|
337 |
> |
molIndex = 0; |
338 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
339 |
> |
|
340 |
> |
if(mol2proc[i] == worldRank ){ |
341 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
342 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
343 |
> |
molIndex++; |
344 |
> |
} |
345 |
> |
} |
346 |
> |
|
347 |
> |
#else // is_mpi |
348 |
> |
|
349 |
> |
molIndex = 0; |
350 |
> |
for(i=0; i<n_components; i++){ |
351 |
> |
for(j=0; j<components_nmol[i]; j++ ){ |
352 |
> |
the_molecules[molIndex].setStampID( i ); |
353 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
354 |
> |
molIndex++; |
355 |
> |
} |
356 |
> |
} |
357 |
> |
|
358 |
> |
|
359 |
> |
#endif // is_mpi |
360 |
> |
|
361 |
> |
|
362 |
> |
if( simnfo->n_SRI ){ |
363 |
> |
|
364 |
> |
Exclude::createArray(simnfo->n_SRI); |
365 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
366 |
> |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
367 |
|
simnfo->globalExcludes = new int; |
368 |
< |
simnfo->n_exclude = tot_SRI; |
368 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
369 |
|
} |
370 |
|
else{ |
371 |
|
|
372 |
< |
the_excludes = new int[2]; |
373 |
< |
the_excludes[0] = 0; |
374 |
< |
the_excludes[1] = 0; |
372 |
> |
Exclude::createArray( 1 ); |
373 |
> |
the_excludes = new Exclude*; |
374 |
> |
the_excludes[0] = new Exclude(0); |
375 |
> |
the_excludes[0]->setPair( 0,0 ); |
376 |
|
simnfo->globalExcludes = new int; |
377 |
|
simnfo->globalExcludes[0] = 0; |
378 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
378 |
> |
simnfo->n_exclude = 0; |
379 |
|
} |
380 |
|
|
381 |
|
// set the arrays into the SimInfo object |
382 |
|
|
383 |
|
simnfo->atoms = the_atoms; |
384 |
< |
simnfo->sr_interactions = the_sris; |
384 |
> |
simnfo->molecules = the_molecules; |
385 |
|
simnfo->nGlobalExcludes = 0; |
386 |
|
simnfo->excludes = the_excludes; |
387 |
|
|
388 |
|
|
389 |
|
// get some of the tricky things that may still be in the globals |
335 |
– |
|
336 |
– |
if( simnfo->n_dipoles ){ |
337 |
– |
|
338 |
– |
if( !the_globals->haveRRF() ){ |
339 |
– |
sprintf( painCave.errMsg, |
340 |
– |
"SimSetup Error, system has dipoles, but no rRF was set.\n"); |
341 |
– |
painCave.isFatal = 1; |
342 |
– |
simError(); |
343 |
– |
} |
344 |
– |
if( !the_globals->haveDielectric() ){ |
345 |
– |
sprintf( painCave.errMsg, |
346 |
– |
"SimSetup Error, system has dipoles, but no" |
347 |
– |
" dielectric was set.\n" ); |
348 |
– |
painCave.isFatal = 1; |
349 |
– |
simError(); |
350 |
– |
} |
390 |
|
|
352 |
– |
simnfo->rRF = the_globals->getRRF(); |
353 |
– |
simnfo->dielectric = the_globals->getDielectric(); |
354 |
– |
} |
355 |
– |
|
356 |
– |
#ifdef IS_MPI |
357 |
– |
strcpy( checkPointMsg, "rRf and dielectric check out" ); |
358 |
– |
MPIcheckPoint(); |
359 |
– |
#endif // is_mpi |
391 |
|
|
392 |
|
if( the_globals->haveBox() ){ |
393 |
|
simnfo->box_x = the_globals->getBox(); |
438 |
|
|
439 |
|
the_ff->setSimInfo( simnfo ); |
440 |
|
|
441 |
< |
makeAtoms(); |
441 |
> |
makeMolecules(); |
442 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
443 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
444 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
445 |
|
} |
446 |
|
|
447 |
< |
if( tot_bonds ){ |
448 |
< |
makeBonds(); |
449 |
< |
} |
447 |
> |
if (the_globals->getUseRF() ) { |
448 |
> |
simnfo->useReactionField = 1; |
449 |
> |
|
450 |
> |
if( !the_globals->haveECR() ){ |
451 |
> |
sprintf( painCave.errMsg, |
452 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
453 |
> |
"box length for the electrostaticCutoffRadius.\n" |
454 |
> |
"I hope you have a very fast processor!\n"); |
455 |
> |
painCave.isFatal = 0; |
456 |
> |
simError(); |
457 |
> |
double smallest; |
458 |
> |
smallest = simnfo->box_x; |
459 |
> |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
460 |
> |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
461 |
> |
simnfo->ecr = 0.5 * smallest; |
462 |
> |
} else { |
463 |
> |
simnfo->ecr = the_globals->getECR(); |
464 |
> |
} |
465 |
|
|
466 |
< |
if( tot_bends ){ |
467 |
< |
makeBends(); |
468 |
< |
} |
466 |
> |
if( !the_globals->haveEST() ){ |
467 |
> |
sprintf( painCave.errMsg, |
468 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
469 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
470 |
> |
); |
471 |
> |
painCave.isFatal = 0; |
472 |
> |
simError(); |
473 |
> |
simnfo->est = 0.05 * simnfo->ecr; |
474 |
> |
} else { |
475 |
> |
simnfo->est = the_globals->getEST(); |
476 |
> |
} |
477 |
> |
|
478 |
> |
if(!the_globals->haveDielectric() ){ |
479 |
> |
sprintf( painCave.errMsg, |
480 |
> |
"SimSetup Error: You are trying to use Reaction Field without" |
481 |
> |
"setting a dielectric constant!\n" |
482 |
> |
); |
483 |
> |
painCave.isFatal = 1; |
484 |
> |
simError(); |
485 |
> |
} |
486 |
> |
simnfo->dielectric = the_globals->getDielectric(); |
487 |
> |
} else { |
488 |
> |
if (usesDipoles) { |
489 |
> |
|
490 |
> |
if( !the_globals->haveECR() ){ |
491 |
> |
sprintf( painCave.errMsg, |
492 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
493 |
> |
"box length for the electrostaticCutoffRadius.\n" |
494 |
> |
"I hope you have a very fast processor!\n"); |
495 |
> |
painCave.isFatal = 0; |
496 |
> |
simError(); |
497 |
> |
double smallest; |
498 |
> |
smallest = simnfo->box_x; |
499 |
> |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
500 |
> |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
501 |
> |
simnfo->ecr = 0.5 * smallest; |
502 |
> |
} else { |
503 |
> |
simnfo->ecr = the_globals->getECR(); |
504 |
> |
} |
505 |
> |
|
506 |
> |
if( !the_globals->haveEST() ){ |
507 |
> |
sprintf( painCave.errMsg, |
508 |
> |
"SimSetup Warning: using default value of 5%% of the " |
509 |
> |
"electrostaticCutoffRadius for the " |
510 |
> |
"electrostaticSkinThickness\n" |
511 |
> |
); |
512 |
> |
painCave.isFatal = 0; |
513 |
> |
simError(); |
514 |
> |
simnfo->est = 0.05 * simnfo->ecr; |
515 |
> |
} else { |
516 |
> |
simnfo->est = the_globals->getEST(); |
517 |
> |
} |
518 |
> |
} |
519 |
> |
} |
520 |
|
|
521 |
< |
if( tot_torsions ){ |
522 |
< |
makeTorsions(); |
523 |
< |
} |
524 |
< |
|
428 |
< |
|
429 |
< |
|
430 |
< |
|
431 |
< |
|
521 |
> |
#ifdef IS_MPI |
522 |
> |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
523 |
> |
MPIcheckPoint(); |
524 |
> |
#endif // is_mpi |
525 |
|
|
526 |
|
if( the_globals->haveInitialConfig() ){ |
527 |
|
|
680 |
|
|
681 |
|
// new AllLong( simnfo ); |
682 |
|
|
590 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
591 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
592 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
593 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
683 |
|
|
684 |
+ |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
685 |
+ |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
686 |
+ |
std::cerr << "called new Symplecic\n"; |
687 |
+ |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
688 |
+ |
} |
689 |
+ |
else if( !strcmp( force_field, "LJ" ) ){ |
690 |
+ |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
691 |
+ |
std::cerr << "called new Verlet\n"; |
692 |
+ |
fprintf( stderr, "called new Verlet. stderr\n" ); |
693 |
+ |
} |
694 |
+ |
else { |
695 |
+ |
std::cerr << "I'm a bug.\n"; |
696 |
+ |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
697 |
+ |
} |
698 |
+ |
#ifdef IS_MPI |
699 |
+ |
mpiSim->mpiRefresh(); |
700 |
+ |
#endif |
701 |
|
|
596 |
– |
|
702 |
|
// initialize the Fortran |
703 |
< |
|
703 |
> |
|
704 |
> |
|
705 |
|
simnfo->refreshSim(); |
706 |
|
|
707 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
726 |
|
#endif // is_mpi |
727 |
|
} |
728 |
|
|
623 |
– |
void SimSetup::makeAtoms( void ){ |
729 |
|
|
730 |
< |
int i, j, k, index; |
626 |
< |
double ux, uy, uz, uSqr, u; |
627 |
< |
AtomStamp* current_atom; |
730 |
> |
void SimSetup::makeMolecules( void ){ |
731 |
|
|
732 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
733 |
+ |
molInit info; |
734 |
|
DirectionalAtom* dAtom; |
735 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
735 |
> |
LinkedAssign* extras; |
736 |
> |
LinkedAssign* current_extra; |
737 |
> |
AtomStamp* currentAtom; |
738 |
> |
BondStamp* currentBond; |
739 |
> |
BendStamp* currentBend; |
740 |
> |
TorsionStamp* currentTorsion; |
741 |
|
|
742 |
< |
lMolIndex = 0; |
743 |
< |
molIndex = 0; |
744 |
< |
index = 0; |
635 |
< |
for( i=0; i<n_components; i++ ){ |
742 |
> |
bond_pair* theBonds; |
743 |
> |
bend_set* theBends; |
744 |
> |
torsion_set* theTorsions; |
745 |
|
|
746 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
746 |
> |
|
747 |
> |
//init the forceField paramters |
748 |
|
|
749 |
< |
#ifdef IS_MPI |
640 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
641 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
642 |
< |
#endif // is_mpi |
749 |
> |
the_ff->readParams(); |
750 |
|
|
751 |
< |
molStart = index; |
752 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
753 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
754 |
< |
|
755 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
756 |
< |
if( current_atom->haveOrientation() ){ |
757 |
< |
|
758 |
< |
dAtom = new DirectionalAtom(index); |
652 |
< |
simnfo->n_oriented++; |
653 |
< |
the_atoms[index] = dAtom; |
654 |
< |
|
655 |
< |
ux = current_atom->getOrntX(); |
656 |
< |
uy = current_atom->getOrntY(); |
657 |
< |
uz = current_atom->getOrntZ(); |
658 |
< |
|
659 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
660 |
< |
|
661 |
< |
u = sqrt( uSqr ); |
662 |
< |
ux = ux / u; |
663 |
< |
uy = uy / u; |
664 |
< |
uz = uz / u; |
665 |
< |
|
666 |
< |
dAtom->setSUx( ux ); |
667 |
< |
dAtom->setSUy( uy ); |
668 |
< |
dAtom->setSUz( uz ); |
669 |
< |
} |
670 |
< |
else{ |
671 |
< |
the_atoms[index] = new GeneralAtom(index); |
672 |
< |
} |
673 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
674 |
< |
the_atoms[index]->setIndex( index ); |
675 |
< |
|
676 |
< |
// increment the index and repeat; |
677 |
< |
index++; |
678 |
< |
} |
679 |
< |
|
680 |
< |
molEnd = index -1; |
681 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
682 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
683 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
684 |
< |
the_molecules[lMolIndex].setStampID( i ); |
685 |
< |
lMolIndex++; |
686 |
< |
|
687 |
< |
#ifdef IS_MPI |
688 |
< |
} |
689 |
< |
#endif //is_mpi |
690 |
< |
|
691 |
< |
molIndex++; |
692 |
< |
} |
693 |
< |
} |
694 |
< |
|
695 |
< |
#ifdef IS_MPI |
696 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
751 |
> |
|
752 |
> |
// init the atoms |
753 |
> |
|
754 |
> |
double ux, uy, uz, u, uSqr; |
755 |
> |
|
756 |
> |
atomOffset = 0; |
757 |
> |
excludeOffset = 0; |
758 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
759 |
|
|
760 |
< |
delete[] globalIndex; |
760 |
> |
stampID = the_molecules[i].getStampID(); |
761 |
|
|
762 |
< |
mpiSim->mpiRefresh(); |
763 |
< |
#endif //IS_MPI |
764 |
< |
|
765 |
< |
the_ff->initializeAtoms(); |
766 |
< |
} |
762 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
763 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
764 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
765 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
766 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
767 |
|
|
768 |
< |
void SimSetup::makeBonds( void ){ |
768 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
769 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
770 |
> |
info.myBonds = new Bond*[info.nBonds]; |
771 |
> |
info.myBends = new Bend*[info.nBends]; |
772 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
773 |
|
|
774 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
775 |
< |
bond_pair* the_bonds; |
776 |
< |
BondStamp* current_bond; |
777 |
< |
|
778 |
< |
the_bonds = new bond_pair[tot_bonds]; |
779 |
< |
index = 0; |
780 |
< |
offset = 0; |
781 |
< |
molIndex = 0; |
782 |
< |
|
783 |
< |
for( i=0; i<n_components; i++ ){ |
718 |
< |
|
719 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
720 |
< |
|
721 |
< |
#ifdef IS_MPI |
722 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
723 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
724 |
< |
#endif // is_mpi |
774 |
> |
theBonds = new bond_pair[info.nBonds]; |
775 |
> |
theBends = new bend_set[info.nBends]; |
776 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
777 |
> |
|
778 |
> |
// make the Atoms |
779 |
> |
|
780 |
> |
for(j=0; j<info.nAtoms; j++){ |
781 |
> |
|
782 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
783 |
> |
if( currentAtom->haveOrientation() ){ |
784 |
|
|
785 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
786 |
< |
|
787 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
788 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
789 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
790 |
< |
|
791 |
< |
exI = the_bonds[index].a; |
733 |
< |
exJ = the_bonds[index].b; |
734 |
< |
|
735 |
< |
// exclude_I must always be the smaller of the pair |
736 |
< |
if( exI > exJ ){ |
737 |
< |
tempEx = exI; |
738 |
< |
exI = exJ; |
739 |
< |
exJ = tempEx; |
740 |
< |
} |
741 |
< |
|
742 |
< |
|
743 |
< |
#ifdef IS_MPI |
744 |
< |
|
745 |
< |
the_excludes[index*2] = |
746 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
747 |
< |
the_excludes[index*2 + 1] = |
748 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
749 |
< |
|
750 |
< |
#else // isn't MPI |
751 |
< |
|
752 |
< |
the_excludes[index*2] = exI + 1; |
753 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
754 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
755 |
< |
#endif //is_mpi |
756 |
< |
|
757 |
< |
// increment the index and repeat; |
758 |
< |
index++; |
759 |
< |
} |
760 |
< |
offset += comp_stamps[i]->getNAtoms(); |
785 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
786 |
> |
simnfo->n_oriented++; |
787 |
> |
info.myAtoms[j] = dAtom; |
788 |
> |
|
789 |
> |
ux = currentAtom->getOrntX(); |
790 |
> |
uy = currentAtom->getOrntY(); |
791 |
> |
uz = currentAtom->getOrntZ(); |
792 |
|
|
793 |
< |
#ifdef IS_MPI |
793 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
794 |
> |
|
795 |
> |
u = sqrt( uSqr ); |
796 |
> |
ux = ux / u; |
797 |
> |
uy = uy / u; |
798 |
> |
uz = uz / u; |
799 |
> |
|
800 |
> |
dAtom->setSUx( ux ); |
801 |
> |
dAtom->setSUy( uy ); |
802 |
> |
dAtom->setSUz( uz ); |
803 |
|
} |
804 |
< |
#endif //is_mpi |
804 |
> |
else{ |
805 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
806 |
> |
} |
807 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
808 |
> |
|
809 |
> |
#ifdef IS_MPI |
810 |
|
|
811 |
< |
molIndex++; |
812 |
< |
} |
813 |
< |
} |
811 |
> |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
812 |
> |
|
813 |
> |
#endif // is_mpi |
814 |
> |
} |
815 |
> |
|
816 |
> |
// make the bonds |
817 |
> |
for(j=0; j<info.nBonds; j++){ |
818 |
> |
|
819 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
820 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
821 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
822 |
|
|
823 |
< |
the_ff->initializeBonds( the_bonds ); |
824 |
< |
} |
823 |
> |
exI = theBonds[j].a; |
824 |
> |
exJ = theBonds[j].b; |
825 |
|
|
826 |
< |
void SimSetup::makeBends( void ){ |
827 |
< |
|
828 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
829 |
< |
bend_set* the_bends; |
830 |
< |
BendStamp* current_bend; |
831 |
< |
LinkedAssign* extras; |
779 |
< |
LinkedAssign* current_extra; |
780 |
< |
|
781 |
< |
|
782 |
< |
the_bends = new bend_set[tot_bends]; |
783 |
< |
index = 0; |
784 |
< |
offset = 0; |
785 |
< |
molIndex = 0; |
786 |
< |
for( i=0; i<n_components; i++ ){ |
787 |
< |
|
788 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
789 |
< |
|
826 |
> |
// exclude_I must always be the smaller of the pair |
827 |
> |
if( exI > exJ ){ |
828 |
> |
tempEx = exI; |
829 |
> |
exI = exJ; |
830 |
> |
exJ = tempEx; |
831 |
> |
} |
832 |
|
#ifdef IS_MPI |
833 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
834 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
835 |
< |
#endif // is_mpi |
833 |
> |
tempEx = exI; |
834 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
835 |
> |
tempEx = exJ; |
836 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
837 |
> |
|
838 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
839 |
> |
#else // isn't MPI |
840 |
|
|
841 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
841 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
842 |
> |
#endif //is_mpi |
843 |
> |
} |
844 |
> |
excludeOffset += info.nBonds; |
845 |
> |
|
846 |
> |
//make the bends |
847 |
> |
for(j=0; j<info.nBends; j++){ |
848 |
> |
|
849 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
850 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
851 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
852 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
853 |
|
|
854 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
798 |
< |
the_bends[index].a = current_bend->getA() + offset; |
799 |
< |
the_bends[index].b = current_bend->getB() + offset; |
800 |
< |
the_bends[index].c = current_bend->getC() + offset; |
801 |
< |
|
802 |
< |
if( current_bend->haveExtras() ){ |
854 |
> |
if( currentBend->haveExtras() ){ |
855 |
|
|
856 |
< |
extras = current_bend->getExtras(); |
857 |
< |
current_extra = extras; |
856 |
> |
extras = currentBend->getExtras(); |
857 |
> |
current_extra = extras; |
858 |
|
|
859 |
< |
while( current_extra != NULL ){ |
860 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
859 |
> |
while( current_extra != NULL ){ |
860 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
861 |
|
|
862 |
< |
switch( current_extra->getType() ){ |
862 |
> |
switch( current_extra->getType() ){ |
863 |
> |
|
864 |
> |
case 0: |
865 |
> |
theBends[j].ghost = |
866 |
> |
current_extra->getInt() + atomOffset; |
867 |
> |
theBends[j].isGhost = 1; |
868 |
> |
break; |
869 |
|
|
870 |
< |
case 0: |
871 |
< |
the_bends[index].ghost = |
872 |
< |
current_extra->getInt() + offset; |
873 |
< |
the_bends[index].isGhost = 1; |
874 |
< |
break; |
817 |
< |
|
818 |
< |
case 1: |
819 |
< |
the_bends[index].ghost = |
820 |
< |
(int)current_extra->getDouble() + offset; |
821 |
< |
the_bends[index].isGhost = 1; |
822 |
< |
break; |
823 |
< |
|
824 |
< |
default: |
825 |
< |
sprintf( painCave.errMsg, |
826 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
827 |
< |
"double nor an int.\n" |
828 |
< |
"-->Bend[%d] in %s\n", |
829 |
< |
k, comp_stamps[i]->getID() ); |
830 |
< |
painCave.isFatal = 1; |
831 |
< |
simError(); |
832 |
< |
} |
833 |
< |
} |
870 |
> |
case 1: |
871 |
> |
theBends[j].ghost = |
872 |
> |
(int)current_extra->getDouble() + atomOffset; |
873 |
> |
theBends[j].isGhost = 1; |
874 |
> |
break; |
875 |
|
|
876 |
< |
else{ |
877 |
< |
|
878 |
< |
sprintf( painCave.errMsg, |
879 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
880 |
< |
" -->%s in Bend[%d] in %s\n", |
881 |
< |
current_extra->getlhs(), |
882 |
< |
k, comp_stamps[i]->getID() ); |
883 |
< |
painCave.isFatal = 1; |
843 |
< |
simError(); |
844 |
< |
} |
845 |
< |
|
846 |
< |
current_extra = current_extra->getNext(); |
876 |
> |
default: |
877 |
> |
sprintf( painCave.errMsg, |
878 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
879 |
> |
"double nor an int.\n" |
880 |
> |
"-->Bend[%d] in %s\n", |
881 |
> |
j, comp_stamps[stampID]->getID() ); |
882 |
> |
painCave.isFatal = 1; |
883 |
> |
simError(); |
884 |
|
} |
885 |
|
} |
886 |
|
|
850 |
– |
if( !the_bends[index].isGhost ){ |
851 |
– |
|
852 |
– |
exI = the_bends[index].a; |
853 |
– |
exJ = the_bends[index].c; |
854 |
– |
} |
887 |
|
else{ |
888 |
|
|
889 |
< |
exI = the_bends[index].a; |
890 |
< |
exJ = the_bends[index].b; |
891 |
< |
} |
892 |
< |
|
893 |
< |
// exclude_I must always be the smaller of the pair |
894 |
< |
if( exI > exJ ){ |
895 |
< |
tempEx = exI; |
864 |
< |
exI = exJ; |
865 |
< |
exJ = tempEx; |
889 |
> |
sprintf( painCave.errMsg, |
890 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
891 |
> |
" -->%s in Bend[%d] in %s\n", |
892 |
> |
current_extra->getlhs(), |
893 |
> |
j, comp_stamps[stampID]->getID() ); |
894 |
> |
painCave.isFatal = 1; |
895 |
> |
simError(); |
896 |
|
} |
867 |
– |
|
868 |
– |
|
869 |
– |
#ifdef IS_MPI |
870 |
– |
|
871 |
– |
the_excludes[(index + tot_bonds)*2] = |
872 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
873 |
– |
the_excludes[(index + tot_bonds)*2 + 1] = |
874 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
897 |
|
|
898 |
< |
#else // isn't MPI |
877 |
< |
|
878 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
879 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
880 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
881 |
< |
#endif //is_mpi |
882 |
< |
|
883 |
< |
|
884 |
< |
// increment the index and repeat; |
885 |
< |
index++; |
898 |
> |
current_extra = current_extra->getNext(); |
899 |
|
} |
900 |
< |
offset += comp_stamps[i]->getNAtoms(); |
900 |
> |
} |
901 |
> |
|
902 |
> |
if( !theBends[j].isGhost ){ |
903 |
> |
|
904 |
> |
exI = theBends[j].a; |
905 |
> |
exJ = theBends[j].c; |
906 |
> |
} |
907 |
> |
else{ |
908 |
|
|
909 |
< |
#ifdef IS_MPI |
909 |
> |
exI = theBends[j].a; |
910 |
> |
exJ = theBends[j].b; |
911 |
|
} |
912 |
< |
#endif //is_mpi |
912 |
> |
|
913 |
> |
// exclude_I must always be the smaller of the pair |
914 |
> |
if( exI > exJ ){ |
915 |
> |
tempEx = exI; |
916 |
> |
exI = exJ; |
917 |
> |
exJ = tempEx; |
918 |
> |
} |
919 |
> |
#ifdef IS_MPI |
920 |
> |
tempEx = exI; |
921 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
922 |
> |
tempEx = exJ; |
923 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
924 |
> |
|
925 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
926 |
> |
#else // isn't MPI |
927 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
928 |
> |
#endif //is_mpi |
929 |
> |
} |
930 |
> |
excludeOffset += info.nBends; |
931 |
|
|
932 |
< |
molIndex++; |
932 |
> |
for(j=0; j<info.nTorsions; j++){ |
933 |
> |
|
934 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
935 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
936 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
937 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
938 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
939 |
> |
|
940 |
> |
exI = theTorsions[j].a; |
941 |
> |
exJ = theTorsions[j].d; |
942 |
> |
|
943 |
> |
// exclude_I must always be the smaller of the pair |
944 |
> |
if( exI > exJ ){ |
945 |
> |
tempEx = exI; |
946 |
> |
exI = exJ; |
947 |
> |
exJ = tempEx; |
948 |
> |
} |
949 |
> |
#ifdef IS_MPI |
950 |
> |
tempEx = exI; |
951 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
952 |
> |
tempEx = exJ; |
953 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
954 |
> |
|
955 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
956 |
> |
#else // isn't MPI |
957 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
958 |
> |
#endif //is_mpi |
959 |
|
} |
960 |
< |
} |
960 |
> |
excludeOffset += info.nTorsions; |
961 |
> |
|
962 |
> |
|
963 |
> |
// send the arrays off to the forceField for init. |
964 |
> |
|
965 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
966 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
967 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
968 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
969 |
|
|
897 |
– |
#ifdef IS_MPI |
898 |
– |
sprintf( checkPointMsg, |
899 |
– |
"Successfully created the bends list.\n" ); |
900 |
– |
MPIcheckPoint(); |
901 |
– |
#endif // is_mpi |
902 |
– |
|
970 |
|
|
971 |
< |
the_ff->initializeBends( the_bends ); |
905 |
< |
} |
971 |
> |
the_molecules[i].initialize( info ); |
972 |
|
|
907 |
– |
void SimSetup::makeTorsions( void ){ |
973 |
|
|
974 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
975 |
< |
torsion_set* the_torsions; |
976 |
< |
TorsionStamp* current_torsion; |
974 |
> |
atomOffset += info.nAtoms; |
975 |
> |
delete[] theBonds; |
976 |
> |
delete[] theBends; |
977 |
> |
delete[] theTorsions; |
978 |
> |
} |
979 |
|
|
913 |
– |
the_torsions = new torsion_set[tot_torsions]; |
914 |
– |
index = 0; |
915 |
– |
offset = 0; |
916 |
– |
molIndex = 0; |
917 |
– |
for( i=0; i<n_components; i++ ){ |
918 |
– |
|
919 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
920 |
– |
|
980 |
|
#ifdef IS_MPI |
981 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
982 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
983 |
< |
#endif // is_mpi |
981 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
982 |
> |
MPIcheckPoint(); |
983 |
> |
#endif // is_mpi |
984 |
|
|
985 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
985 |
> |
// clean up the forcefield |
986 |
> |
the_ff->calcRcut(); |
987 |
> |
the_ff->cleanMe(); |
988 |
|
|
928 |
– |
current_torsion = comp_stamps[i]->getTorsion( k ); |
929 |
– |
the_torsions[index].a = current_torsion->getA() + offset; |
930 |
– |
the_torsions[index].b = current_torsion->getB() + offset; |
931 |
– |
the_torsions[index].c = current_torsion->getC() + offset; |
932 |
– |
the_torsions[index].d = current_torsion->getD() + offset; |
933 |
– |
|
934 |
– |
exI = the_torsions[index].a; |
935 |
– |
exJ = the_torsions[index].d; |
936 |
– |
|
937 |
– |
|
938 |
– |
// exclude_I must always be the smaller of the pair |
939 |
– |
if( exI > exJ ){ |
940 |
– |
tempEx = exI; |
941 |
– |
exI = exJ; |
942 |
– |
exJ = tempEx; |
943 |
– |
} |
944 |
– |
|
945 |
– |
|
946 |
– |
#ifdef IS_MPI |
947 |
– |
|
948 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
949 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
950 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
951 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
952 |
– |
|
953 |
– |
#else // isn't MPI |
954 |
– |
|
955 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
956 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
957 |
– |
// fortran indexes from 1 (hence the +1 in the indexing) |
958 |
– |
#endif //is_mpi |
959 |
– |
|
960 |
– |
|
961 |
– |
// increment the index and repeat; |
962 |
– |
index++; |
963 |
– |
} |
964 |
– |
offset += comp_stamps[i]->getNAtoms(); |
965 |
– |
|
966 |
– |
#ifdef IS_MPI |
967 |
– |
} |
968 |
– |
#endif //is_mpi |
969 |
– |
|
970 |
– |
molIndex++; |
971 |
– |
} |
972 |
– |
} |
973 |
– |
|
974 |
– |
the_ff->initializeTorsions( the_torsions ); |
989 |
|
} |
990 |
|
|
991 |
|
void SimSetup::initFromBass( void ){ |