| 88 |
|
|
| 89 |
|
|
| 90 |
|
|
| 91 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
| 92 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
| 93 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
| 91 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
| 92 |
|
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
| 93 |
|
else{ |
| 94 |
|
sprintf( painCave.errMsg, |
| 246 |
|
|
| 247 |
|
int localMol, allMol; |
| 248 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 249 |
+ |
|
| 250 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
| 251 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
| 252 |
|
|
| 253 |
|
allMol = 0; |
| 254 |
|
localMol = 0; |
| 260 |
|
|
| 261 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 262 |
|
|
| 263 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
| 263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
| 263 |
> |
if( mol2proc[j] == worldRank ){ |
| 264 |
|
|
| 265 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 266 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 279 |
|
if( local_atoms != simnfo->n_atoms ){ |
| 280 |
|
sprintf( painCave.errMsg, |
| 281 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
| 282 |
< |
" localAtom (%d) are note equal.\n", |
| 282 |
> |
" localAtom (%d) are not equal.\n", |
| 283 |
|
simnfo->n_atoms, |
| 284 |
|
local_atoms ); |
| 285 |
|
painCave.isFatal = 1; |
| 304 |
|
Atom::createArrays(simnfo->n_atoms); |
| 305 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
| 306 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
| 307 |
+ |
int molIndex; |
| 308 |
+ |
|
| 309 |
+ |
// initialize the molecule's stampID's |
| 310 |
+ |
|
| 311 |
+ |
#ifdef IS_MPI |
| 312 |
+ |
|
| 313 |
+ |
|
| 314 |
+ |
molIndex = 0; |
| 315 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
| 316 |
+ |
|
| 317 |
+ |
if(mol2proc[i] == worldRank ){ |
| 318 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 319 |
+ |
molIndex++; |
| 320 |
+ |
} |
| 321 |
+ |
} |
| 322 |
|
|
| 323 |
+ |
#else // is_mpi |
| 324 |
+ |
|
| 325 |
+ |
molIndex = 0; |
| 326 |
+ |
for(i=0; i<n_components; i++){ |
| 327 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
| 328 |
+ |
the_molecules[molIndex].setStampID( i ); |
| 329 |
+ |
molIndex++; |
| 330 |
+ |
} |
| 331 |
+ |
} |
| 332 |
+ |
|
| 333 |
|
|
| 334 |
+ |
#endif // is_mpi |
| 335 |
+ |
|
| 336 |
+ |
|
| 337 |
|
if( simnfo->n_SRI ){ |
| 338 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
| 339 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
| 338 |
> |
Exclude::createArray(simnfo->n_SRI); |
| 339 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 340 |
|
simnfo->globalExcludes = new int; |
| 341 |
|
simnfo->n_exclude = tot_SRI; |
| 342 |
|
} |
| 343 |
|
else{ |
| 344 |
|
|
| 345 |
< |
the_excludes = new int[2]; |
| 346 |
< |
the_excludes[0] = 0; |
| 347 |
< |
the_excludes[1] = 0; |
| 345 |
> |
Exclude::createArray( 1 ); |
| 346 |
> |
the_excludes = new Exclude*; |
| 347 |
> |
the_excludes[0] = new Exclude(0); |
| 348 |
> |
the_excludes[0]->setPair( 0,0 ); |
| 349 |
|
simnfo->globalExcludes = new int; |
| 350 |
|
simnfo->globalExcludes[0] = 0; |
| 351 |
< |
|
| 323 |
< |
simnfo->n_exclude = 1; |
| 351 |
> |
simnfo->n_exclude = 0; |
| 352 |
|
} |
| 353 |
|
|
| 354 |
|
// set the arrays into the SimInfo object |
| 355 |
|
|
| 356 |
|
simnfo->atoms = the_atoms; |
| 329 |
– |
simnfo->sr_interactions = the_sris; |
| 357 |
|
simnfo->nGlobalExcludes = 0; |
| 358 |
|
simnfo->excludes = the_excludes; |
| 359 |
|
|
| 360 |
|
|
| 361 |
|
// get some of the tricky things that may still be in the globals |
| 362 |
|
|
| 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 |
– |
} |
| 351 |
– |
|
| 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 |
| 363 |
|
|
| 364 |
|
if( the_globals->haveBox() ){ |
| 365 |
|
simnfo->box_x = the_globals->getBox(); |
| 410 |
|
|
| 411 |
|
the_ff->setSimInfo( simnfo ); |
| 412 |
|
|
| 413 |
< |
makeAtoms(); |
| 413 |
> |
makeMolecules(); |
| 414 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 415 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 416 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 417 |
|
} |
| 418 |
|
|
| 419 |
< |
if( tot_bonds ){ |
| 420 |
< |
makeBonds(); |
| 421 |
< |
} |
| 422 |
< |
|
| 423 |
< |
if( tot_bends ){ |
| 424 |
< |
makeBends(); |
| 425 |
< |
} |
| 426 |
< |
|
| 427 |
< |
if( tot_torsions ){ |
| 428 |
< |
makeTorsions(); |
| 429 |
< |
} |
| 419 |
> |
if (the_globals->getUseRF() ) { |
| 420 |
> |
simnfo->useReactionField = 1; |
| 421 |
> |
|
| 422 |
> |
if( !the_globals->haveECR() ){ |
| 423 |
> |
sprintf( painCave.errMsg, |
| 424 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 425 |
> |
"box length for the electrostaticCutoffRadius.\n" |
| 426 |
> |
"I hope you have a very fast processor!\n"); |
| 427 |
> |
painCave.isFatal = 0; |
| 428 |
> |
simError(); |
| 429 |
> |
double smallest; |
| 430 |
> |
smallest = simnfo->box_x; |
| 431 |
> |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
| 432 |
> |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
| 433 |
> |
simnfo->ecr = 0.5 * smallest; |
| 434 |
> |
} else { |
| 435 |
> |
simnfo->ecr = the_globals->getECR(); |
| 436 |
> |
} |
| 437 |
|
|
| 438 |
+ |
if( !the_globals->haveEST() ){ |
| 439 |
+ |
sprintf( painCave.errMsg, |
| 440 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
| 441 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
| 442 |
+ |
); |
| 443 |
+ |
painCave.isFatal = 0; |
| 444 |
+ |
simError(); |
| 445 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
| 446 |
+ |
} else { |
| 447 |
+ |
simnfo->est = the_globals->getEST(); |
| 448 |
+ |
} |
| 449 |
+ |
|
| 450 |
+ |
if(!the_globals->haveDielectric() ){ |
| 451 |
+ |
sprintf( painCave.errMsg, |
| 452 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
| 453 |
+ |
"setting a dielectric constant!\n" |
| 454 |
+ |
); |
| 455 |
+ |
painCave.isFatal = 1; |
| 456 |
+ |
simError(); |
| 457 |
+ |
} |
| 458 |
+ |
simnfo->dielectric = the_globals->getDielectric(); |
| 459 |
+ |
} else { |
| 460 |
+ |
if (simnfo->n_dipoles) { |
| 461 |
+ |
|
| 462 |
+ |
if( !the_globals->haveECR() ){ |
| 463 |
+ |
sprintf( painCave.errMsg, |
| 464 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest" |
| 465 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
| 466 |
+ |
"I hope you have a very fast processor!\n"); |
| 467 |
+ |
painCave.isFatal = 0; |
| 468 |
+ |
simError(); |
| 469 |
+ |
double smallest; |
| 470 |
+ |
smallest = simnfo->box_x; |
| 471 |
+ |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
| 472 |
+ |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
| 473 |
+ |
simnfo->ecr = 0.5 * smallest; |
| 474 |
+ |
} else { |
| 475 |
+ |
simnfo->ecr = the_globals->getECR(); |
| 476 |
+ |
} |
| 477 |
+ |
|
| 478 |
+ |
if( !the_globals->haveEST() ){ |
| 479 |
+ |
sprintf( painCave.errMsg, |
| 480 |
+ |
"SimSetup Warning: using default value of 5% of the" |
| 481 |
+ |
"electrostaticCutoffRadius for the " |
| 482 |
+ |
"electrostaticSkinThickness\n" |
| 483 |
+ |
); |
| 484 |
+ |
painCave.isFatal = 0; |
| 485 |
+ |
simError(); |
| 486 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
| 487 |
+ |
} else { |
| 488 |
+ |
simnfo->est = the_globals->getEST(); |
| 489 |
+ |
} |
| 490 |
+ |
} |
| 491 |
+ |
} |
| 492 |
|
|
| 493 |
+ |
#ifdef IS_MPI |
| 494 |
+ |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
| 495 |
+ |
MPIcheckPoint(); |
| 496 |
+ |
#endif // is_mpi |
| 497 |
|
|
| 430 |
– |
|
| 431 |
– |
|
| 432 |
– |
|
| 498 |
|
if( the_globals->haveInitialConfig() ){ |
| 499 |
|
|
| 500 |
|
InitializeFromFile* fileInit; |
| 652 |
|
|
| 653 |
|
// new AllLong( simnfo ); |
| 654 |
|
|
| 590 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
| 591 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
| 655 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
| 656 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 657 |
|
|
| 683 |
|
#endif // is_mpi |
| 684 |
|
} |
| 685 |
|
|
| 623 |
– |
void SimSetup::makeAtoms( void ){ |
| 686 |
|
|
| 687 |
< |
int i, j, k, index; |
| 626 |
< |
double ux, uy, uz, uSqr, u; |
| 627 |
< |
AtomStamp* current_atom; |
| 687 |
> |
void SimSetup::makeMolecules( void ){ |
| 688 |
|
|
| 689 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
| 690 |
+ |
molInit info; |
| 691 |
|
DirectionalAtom* dAtom; |
| 692 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
| 692 |
> |
LinkedAssign* extras; |
| 693 |
> |
LinkedAssign* current_extra; |
| 694 |
> |
AtomStamp* currentAtom; |
| 695 |
> |
BondStamp* currentBond; |
| 696 |
> |
BendStamp* currentBend; |
| 697 |
> |
TorsionStamp* currentTorsion; |
| 698 |
> |
|
| 699 |
> |
//init the forceField paramters |
| 700 |
|
|
| 701 |
< |
lMolIndex = 0; |
| 633 |
< |
molIndex = 0; |
| 634 |
< |
index = 0; |
| 635 |
< |
for( i=0; i<n_components; i++ ){ |
| 701 |
> |
the_ff->readParams(); |
| 702 |
|
|
| 703 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 703 |
> |
|
| 704 |
> |
// init the molecules |
| 705 |
|
|
| 706 |
< |
#ifdef IS_MPI |
| 707 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 708 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 642 |
< |
#endif // is_mpi |
| 643 |
< |
|
| 644 |
< |
molStart = index; |
| 645 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
| 646 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
| 647 |
< |
|
| 648 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
| 649 |
< |
if( current_atom->haveOrientation() ){ |
| 650 |
< |
|
| 651 |
< |
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] ); |
| 706 |
> |
atomOffset = 0; |
| 707 |
> |
excludeOffset = 0; |
| 708 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
| 709 |
|
|
| 710 |
< |
delete[] globalIndex; |
| 710 |
> |
stampID = the_molecules[i].getStampID(); |
| 711 |
|
|
| 712 |
< |
mpiSim->mpiRefresh(); |
| 713 |
< |
#endif //IS_MPI |
| 714 |
< |
|
| 715 |
< |
the_ff->initializeAtoms(); |
| 716 |
< |
} |
| 712 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
| 713 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
| 714 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
| 715 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 716 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
| 717 |
|
|
| 718 |
< |
void SimSetup::makeBonds( void ){ |
| 718 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
| 719 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
| 720 |
> |
info.myBonds = new Bond*[info.nBonds]; |
| 721 |
> |
info.myBends = new Bend*[info.nBends]; |
| 722 |
> |
info.myTorsions = new Torsions*[info.nTorsions]; |
| 723 |
|
|
| 724 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 725 |
< |
bond_pair* the_bonds; |
| 726 |
< |
BondStamp* current_bond; |
| 727 |
< |
|
| 728 |
< |
the_bonds = new bond_pair[tot_bonds]; |
| 729 |
< |
index = 0; |
| 730 |
< |
offset = 0; |
| 731 |
< |
molIndex = 0; |
| 732 |
< |
|
| 733 |
< |
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 |
| 724 |
> |
theBonds = new bond_pair[info.nBonds]; |
| 725 |
> |
theBends = new bend_set[info.nBends]; |
| 726 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
| 727 |
> |
|
| 728 |
> |
// make the Atoms |
| 729 |
> |
|
| 730 |
> |
for(j=0; j<info.nAtoms; j++){ |
| 731 |
> |
|
| 732 |
> |
currentAtom = theComponents[stampID]->getAtom( j ); |
| 733 |
> |
if( currentAtom->haveOrientation() ){ |
| 734 |
|
|
| 735 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
| 736 |
< |
|
| 737 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
| 738 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
| 739 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
| 740 |
< |
|
| 741 |
< |
exI = the_bonds[index].a; |
| 742 |
< |
exJ = the_bonds[index].b; |
| 743 |
< |
|
| 744 |
< |
// exclude_I must always be the smaller of the pair |
| 745 |
< |
if( exI > exJ ){ |
| 746 |
< |
tempEx = exI; |
| 747 |
< |
exI = exJ; |
| 748 |
< |
exJ = tempEx; |
| 749 |
< |
} |
| 750 |
< |
|
| 751 |
< |
|
| 735 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
| 736 |
> |
simnfo->n_oriented++; |
| 737 |
> |
info.myAtoms[j] = dAtom; |
| 738 |
> |
|
| 739 |
> |
ux = currentAtom->getOrntX(); |
| 740 |
> |
uy = currentAtom->getOrntY(); |
| 741 |
> |
uz = currentAtom->getOrntZ(); |
| 742 |
> |
|
| 743 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 744 |
> |
|
| 745 |
> |
u = sqrt( uSqr ); |
| 746 |
> |
ux = ux / u; |
| 747 |
> |
uy = uy / u; |
| 748 |
> |
uz = uz / u; |
| 749 |
> |
|
| 750 |
> |
dAtom->setSUx( ux ); |
| 751 |
> |
dAtom->setSUy( uy ); |
| 752 |
> |
dAtom->setSUz( uz ); |
| 753 |
> |
} |
| 754 |
> |
else{ |
| 755 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
| 756 |
> |
} |
| 757 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
| 758 |
> |
|
| 759 |
|
#ifdef IS_MPI |
| 760 |
< |
|
| 761 |
< |
the_excludes[index*2] = |
| 762 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 763 |
< |
the_excludes[index*2 + 1] = |
| 764 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 765 |
< |
|
| 766 |
< |
#else // isn't MPI |
| 767 |
< |
|
| 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(); |
| 761 |
< |
|
| 762 |
< |
#ifdef IS_MPI |
| 763 |
< |
} |
| 764 |
< |
#endif //is_mpi |
| 760 |
> |
|
| 761 |
> |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
| 762 |
> |
|
| 763 |
> |
#endif // is_mpi |
| 764 |
> |
} |
| 765 |
> |
|
| 766 |
> |
// make the bonds |
| 767 |
> |
for(j=0; j<info.nBonds; j++){ |
| 768 |
|
|
| 769 |
< |
molIndex++; |
| 770 |
< |
} |
| 771 |
< |
} |
| 769 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
| 770 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
| 771 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
| 772 |
|
|
| 773 |
< |
the_ff->initializeBonds( the_bonds ); |
| 774 |
< |
} |
| 773 |
> |
exI = theBonds[i].a; |
| 774 |
> |
exJ = theBonds[i].b; |
| 775 |
|
|
| 776 |
< |
void SimSetup::makeBends( void ){ |
| 777 |
< |
|
| 778 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 779 |
< |
bend_set* the_bends; |
| 780 |
< |
BendStamp* current_bend; |
| 781 |
< |
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 |
< |
|
| 776 |
> |
// exclude_I must always be the smaller of the pair |
| 777 |
> |
if( exI > exJ ){ |
| 778 |
> |
tempEx = exI; |
| 779 |
> |
exI = exJ; |
| 780 |
> |
exJ = tempEx; |
| 781 |
> |
} |
| 782 |
|
#ifdef IS_MPI |
| 783 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 784 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 785 |
< |
#endif // is_mpi |
| 783 |
> |
tempEx = exI; |
| 784 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 785 |
> |
tempEx = exJ; |
| 786 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 787 |
> |
|
| 788 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 789 |
> |
#else // isn't MPI |
| 790 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 791 |
> |
#endif //is_mpi |
| 792 |
> |
} |
| 793 |
> |
excludeOffset += info.nBonds; |
| 794 |
|
|
| 795 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
| 795 |
> |
//make the bends |
| 796 |
> |
for(j=0; j<info.nBends; j++){ |
| 797 |
> |
|
| 798 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
| 799 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
| 800 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
| 801 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
| 802 |
|
|
| 803 |
< |
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() ){ |
| 803 |
> |
if( currentBend->haveExtras() ){ |
| 804 |
|
|
| 805 |
< |
extras = current_bend->getExtras(); |
| 806 |
< |
current_extra = extras; |
| 805 |
> |
extras = current_bend->getExtras(); |
| 806 |
> |
current_extra = extras; |
| 807 |
|
|
| 808 |
< |
while( current_extra != NULL ){ |
| 809 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 808 |
> |
while( current_extra != NULL ){ |
| 809 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 810 |
|
|
| 811 |
< |
switch( current_extra->getType() ){ |
| 811 |
> |
switch( current_extra->getType() ){ |
| 812 |
> |
|
| 813 |
> |
case 0: |
| 814 |
> |
theBends[j].ghost = |
| 815 |
> |
current_extra->getInt() + atomOffset; |
| 816 |
> |
theBends[j].isGhost = 1; |
| 817 |
> |
break; |
| 818 |
|
|
| 819 |
< |
case 0: |
| 820 |
< |
the_bends[index].ghost = |
| 821 |
< |
current_extra->getInt() + offset; |
| 822 |
< |
the_bends[index].isGhost = 1; |
| 823 |
< |
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 |
< |
} |
| 819 |
> |
case 1: |
| 820 |
> |
theBends[j].ghost = |
| 821 |
> |
(int)current_extra->getDouble() + atomOffset; |
| 822 |
> |
theBends[j].isGhost = 1; |
| 823 |
> |
break; |
| 824 |
|
|
| 825 |
< |
else{ |
| 826 |
< |
|
| 827 |
< |
sprintf( painCave.errMsg, |
| 828 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
| 829 |
< |
" -->%s in Bend[%d] in %s\n", |
| 830 |
< |
current_extra->getlhs(), |
| 831 |
< |
k, comp_stamps[i]->getID() ); |
| 832 |
< |
painCave.isFatal = 1; |
| 843 |
< |
simError(); |
| 844 |
< |
} |
| 845 |
< |
|
| 846 |
< |
current_extra = current_extra->getNext(); |
| 825 |
> |
default: |
| 826 |
> |
sprintf( painCave.errMsg, |
| 827 |
> |
"SimSetup Error: ghostVectorSource was neiter a " |
| 828 |
> |
"double nor an int.\n" |
| 829 |
> |
"-->Bend[%d] in %s\n", |
| 830 |
> |
j, comp_stamps[stampID]->getID() ); |
| 831 |
> |
painCave.isFatal = 1; |
| 832 |
> |
simError(); |
| 833 |
|
} |
| 834 |
|
} |
| 835 |
|
|
| 850 |
– |
if( !the_bends[index].isGhost ){ |
| 851 |
– |
|
| 852 |
– |
exI = the_bends[index].a; |
| 853 |
– |
exJ = the_bends[index].c; |
| 854 |
– |
} |
| 836 |
|
else{ |
| 837 |
|
|
| 838 |
< |
exI = the_bends[index].a; |
| 839 |
< |
exJ = the_bends[index].b; |
| 838 |
> |
sprintf( painCave.errMsg, |
| 839 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
| 840 |
> |
" -->%s in Bend[%d] in %s\n", |
| 841 |
> |
current_extra->getlhs(), |
| 842 |
> |
j, comp_stamps[stampID]->getID() ); |
| 843 |
> |
painCave.isFatal = 1; |
| 844 |
> |
simError(); |
| 845 |
|
} |
| 846 |
|
|
| 847 |
< |
// exclude_I must always be the smaller of the pair |
| 848 |
< |
if( exI > exJ ){ |
| 849 |
< |
tempEx = exI; |
| 850 |
< |
exI = exJ; |
| 851 |
< |
exJ = tempEx; |
| 852 |
< |
} |
| 853 |
< |
|
| 854 |
< |
|
| 847 |
> |
current_extra = current_extra->getNext(); |
| 848 |
> |
} |
| 849 |
> |
} |
| 850 |
> |
|
| 851 |
> |
if( !theBends[j].isGhost ){ |
| 852 |
> |
|
| 853 |
> |
exI = theBends[j].a; |
| 854 |
> |
exJ = theBends[j].c; |
| 855 |
> |
} |
| 856 |
> |
else{ |
| 857 |
> |
|
| 858 |
> |
exI = theBends[j].a; |
| 859 |
> |
exJ = theBends[j].b; |
| 860 |
> |
} |
| 861 |
> |
|
| 862 |
> |
// exclude_I must always be the smaller of the pair |
| 863 |
> |
if( exI > exJ ){ |
| 864 |
> |
tempEx = exI; |
| 865 |
> |
exI = exJ; |
| 866 |
> |
exJ = tempEx; |
| 867 |
> |
} |
| 868 |
|
#ifdef IS_MPI |
| 869 |
< |
|
| 870 |
< |
the_excludes[(index + tot_bonds)*2] = |
| 871 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 872 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
| 873 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 874 |
< |
|
| 869 |
> |
tempEx = exI; |
| 870 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 871 |
> |
tempEx = exJ; |
| 872 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 873 |
> |
|
| 874 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 875 |
|
#else // isn't MPI |
| 876 |
< |
|
| 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) |
| 876 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 877 |
|
#endif //is_mpi |
| 882 |
– |
|
| 883 |
– |
|
| 884 |
– |
// increment the index and repeat; |
| 885 |
– |
index++; |
| 886 |
– |
} |
| 887 |
– |
offset += comp_stamps[i]->getNAtoms(); |
| 888 |
– |
|
| 889 |
– |
#ifdef IS_MPI |
| 890 |
– |
} |
| 891 |
– |
#endif //is_mpi |
| 892 |
– |
|
| 893 |
– |
molIndex++; |
| 878 |
|
} |
| 879 |
< |
} |
| 879 |
> |
excludeOffset += info.nBends; |
| 880 |
|
|
| 881 |
< |
#ifdef IS_MPI |
| 882 |
< |
sprintf( checkPointMsg, |
| 883 |
< |
"Successfully created the bends list.\n" ); |
| 884 |
< |
MPIcheckPoint(); |
| 885 |
< |
#endif // is_mpi |
| 886 |
< |
|
| 887 |
< |
|
| 888 |
< |
the_ff->initializeBends( the_bends ); |
| 889 |
< |
} |
| 890 |
< |
|
| 907 |
< |
void SimSetup::makeTorsions( void ){ |
| 908 |
< |
|
| 909 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 910 |
< |
torsion_set* the_torsions; |
| 911 |
< |
TorsionStamp* current_torsion; |
| 912 |
< |
|
| 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++ ){ |
| 881 |
> |
for(j=0; j<info.nTorsions; j++){ |
| 882 |
> |
|
| 883 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
| 884 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
| 885 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
| 886 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
| 887 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
| 888 |
> |
|
| 889 |
> |
exI = theTorsions[j].a; |
| 890 |
> |
exJ = theTorsions[j].d; |
| 891 |
|
|
| 892 |
+ |
// exclude_I must always be the smaller of the pair |
| 893 |
+ |
if( exI > exJ ){ |
| 894 |
+ |
tempEx = exI; |
| 895 |
+ |
exI = exJ; |
| 896 |
+ |
exJ = tempEx; |
| 897 |
+ |
} |
| 898 |
|
#ifdef IS_MPI |
| 899 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 900 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 901 |
< |
#endif // is_mpi |
| 902 |
< |
|
| 903 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
| 904 |
< |
|
| 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 |
< |
|
| 899 |
> |
tempEx = exI; |
| 900 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 901 |
> |
tempEx = exJ; |
| 902 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 903 |
> |
|
| 904 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 905 |
|
#else // isn't MPI |
| 906 |
< |
|
| 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) |
| 906 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 907 |
|
#endif //is_mpi |
| 908 |
< |
|
| 908 |
> |
} |
| 909 |
> |
excludeOffset += info.nTorsions; |
| 910 |
|
|
| 911 |
< |
// increment the index and repeat; |
| 912 |
< |
index++; |
| 963 |
< |
} |
| 964 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 911 |
> |
|
| 912 |
> |
// send the arrays off to the forceField for init. |
| 913 |
|
|
| 914 |
< |
#ifdef IS_MPI |
| 915 |
< |
} |
| 916 |
< |
#endif //is_mpi |
| 914 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
| 915 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
| 916 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
| 917 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
| 918 |
|
|
| 919 |
< |
molIndex++; |
| 920 |
< |
} |
| 919 |
> |
|
| 920 |
> |
the_molecules[i].initialize( info ); |
| 921 |
> |
atomOffset += info.nAtoms; |
| 922 |
|
} |
| 923 |
|
|
| 924 |
< |
the_ff->initializeTorsions( the_torsions ); |
| 924 |
> |
// clean up the forcefield |
| 925 |
> |
the_ff->calcRcut(); |
| 926 |
> |
the_ff->cleanMe(); |
| 927 |
|
} |
| 928 |
|
|
| 929 |
|
void SimSetup::initFromBass( void ){ |
