| 66 |
|
|
| 67 |
|
MakeStamps *the_stamps; |
| 68 |
|
Globals* the_globals; |
| 69 |
< |
int i, j; |
| 69 |
> |
ExtendedSystem* the_extendedsystem; |
| 70 |
> |
int i, j, k, globalAtomIndex; |
| 71 |
|
|
| 72 |
|
// get the stamps and globals; |
| 73 |
|
the_stamps = stamps; |
| 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 |
+ |
if (the_globals->haveTargetPressure()) |
| 91 |
+ |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
| 92 |
+ |
else { |
| 93 |
+ |
sprintf( painCave.errMsg, |
| 94 |
+ |
"SimSetup error: If you use the constant pressure\n" |
| 95 |
+ |
" ensemble, you must set targetPressure.\n" |
| 96 |
+ |
" This was found in the BASS file.\n"); |
| 97 |
+ |
painCave.isFatal = 1; |
| 98 |
+ |
simError(); |
| 99 |
+ |
} |
| 100 |
+ |
|
| 101 |
+ |
if (the_globals->haveTauThermostat()) |
| 102 |
+ |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
| 103 |
+ |
else if (the_globals->haveQmass()) |
| 104 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
| 105 |
+ |
else { |
| 106 |
+ |
sprintf( painCave.errMsg, |
| 107 |
+ |
"SimSetup error: If you use one of the constant temperature\n" |
| 108 |
+ |
" ensembles, you must set either tauThermostat or qMass.\n" |
| 109 |
+ |
" Neither of these was found in the BASS file.\n"); |
| 110 |
+ |
painCave.isFatal = 1; |
| 111 |
+ |
simError(); |
| 112 |
+ |
} |
| 113 |
+ |
|
| 114 |
+ |
if (the_globals->haveTauBarostat()) |
| 115 |
+ |
the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
| 116 |
+ |
else { |
| 117 |
+ |
sprintf( painCave.errMsg, |
| 118 |
+ |
"SimSetup error: If you use the constant pressure\n" |
| 119 |
+ |
" ensemble, you must set tauBarostat.\n" |
| 120 |
+ |
" This was found in the BASS file.\n"); |
| 121 |
+ |
painCave.isFatal = 1; |
| 122 |
+ |
simError(); |
| 123 |
+ |
} |
| 124 |
+ |
|
| 125 |
+ |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
| 126 |
+ |
the_extendedsystem = new ExtendedSystem( simnfo ); |
| 127 |
+ |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
| 128 |
+ |
|
| 129 |
+ |
if (the_globals->haveTauThermostat()) |
| 130 |
+ |
the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
| 131 |
+ |
else if (the_globals->haveQmass()) |
| 132 |
+ |
the_extendedsystem->setQmass(the_globals->getQmass()); |
| 133 |
+ |
else { |
| 134 |
+ |
sprintf( painCave.errMsg, |
| 135 |
+ |
"SimSetup error: If you use one of the constant temperature\n" |
| 136 |
+ |
" ensembles, you must set either tauThermostat or qMass.\n" |
| 137 |
+ |
" Neither of these was found in the BASS file.\n"); |
| 138 |
+ |
painCave.isFatal = 1; |
| 139 |
+ |
simError(); |
| 140 |
+ |
} |
| 141 |
+ |
|
| 142 |
+ |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
| 143 |
+ |
} else { |
| 144 |
+ |
sprintf( painCave.errMsg, |
| 145 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
| 146 |
+ |
"reverting to NVE for this simulation.\n", |
| 147 |
+ |
ensemble ); |
| 148 |
+ |
painCave.isFatal = 0; |
| 149 |
+ |
simError(); |
| 150 |
+ |
strcpy( ensemble, "NVE" ); |
| 151 |
+ |
} |
| 152 |
|
strcpy( simnfo->ensemble, ensemble ); |
| 153 |
|
|
| 154 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
| 155 |
|
simnfo->usePBC = the_globals->getPBC(); |
| 156 |
|
|
| 157 |
< |
|
| 158 |
< |
|
| 159 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
| 160 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
| 161 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
| 162 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
| 157 |
> |
int usesDipoles = 0; |
| 158 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
| 159 |
> |
the_ff = new TraPPE_ExFF(); |
| 160 |
> |
usesDipoles = 1; |
| 161 |
> |
} |
| 162 |
> |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
| 163 |
|
else{ |
| 164 |
|
sprintf( painCave.errMsg, |
| 165 |
|
"SimSetup Error. Unrecognized force field -> %s\n", |
| 298 |
|
simnfo->n_torsions = tot_torsions; |
| 299 |
|
simnfo->n_SRI = tot_SRI; |
| 300 |
|
simnfo->n_mol = tot_nmol; |
| 301 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
| 302 |
|
|
| 234 |
– |
|
| 303 |
|
#ifdef IS_MPI |
| 304 |
|
|
| 305 |
|
// divide the molecules among processors here. |
| 306 |
|
|
| 307 |
|
mpiSim = new mpiSimulation( simnfo ); |
| 308 |
|
|
| 241 |
– |
|
| 242 |
– |
|
| 309 |
|
globalIndex = mpiSim->divideLabor(); |
| 310 |
|
|
| 245 |
– |
|
| 246 |
– |
|
| 311 |
|
// set up the local variables |
| 312 |
|
|
| 313 |
|
int localMol, allMol; |
| 314 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 315 |
+ |
|
| 316 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
| 317 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
| 318 |
|
|
| 319 |
|
allMol = 0; |
| 320 |
|
localMol = 0; |
| 322 |
|
local_bonds = 0; |
| 323 |
|
local_bends = 0; |
| 324 |
|
local_torsions = 0; |
| 325 |
+ |
globalAtomIndex = 0; |
| 326 |
+ |
|
| 327 |
+ |
|
| 328 |
|
for( i=0; i<n_components; i++ ){ |
| 329 |
|
|
| 330 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 331 |
|
|
| 332 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
| 263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
| 332 |
> |
if( mol2proc[allMol] == worldRank ){ |
| 333 |
|
|
| 334 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 335 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 337 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
| 338 |
|
localMol++; |
| 339 |
|
} |
| 340 |
< |
allMol++; |
| 340 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 341 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
| 342 |
> |
globalAtomIndex++; |
| 343 |
> |
} |
| 344 |
> |
|
| 345 |
> |
allMol++; |
| 346 |
|
} |
| 347 |
|
} |
| 348 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
| 349 |
|
|
| 350 |
+ |
if (worldRank != 0) { |
| 351 |
+ |
for (i =0; i < tot_atoms; i++){ |
| 352 |
+ |
std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n"; |
| 353 |
+ |
} |
| 354 |
+ |
} |
| 355 |
|
|
| 356 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
| 357 |
|
|
| 358 |
|
if( local_atoms != simnfo->n_atoms ){ |
| 359 |
|
sprintf( painCave.errMsg, |
| 360 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
| 361 |
< |
" localAtom (%d) are note equal.\n", |
| 361 |
> |
" localAtom (%d) are not equal.\n", |
| 362 |
|
simnfo->n_atoms, |
| 363 |
|
local_atoms ); |
| 364 |
|
painCave.isFatal = 1; |
| 383 |
|
Atom::createArrays(simnfo->n_atoms); |
| 384 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
| 385 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
| 386 |
+ |
int molIndex; |
| 387 |
|
|
| 388 |
+ |
// initialize the molecule's stampID's |
| 389 |
|
|
| 390 |
+ |
#ifdef IS_MPI |
| 391 |
+ |
|
| 392 |
+ |
|
| 393 |
+ |
molIndex = 0; |
| 394 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
| 395 |
+ |
|
| 396 |
+ |
if(mol2proc[i] == worldRank ){ |
| 397 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 398 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 399 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
| 400 |
+ |
molIndex++; |
| 401 |
+ |
} |
| 402 |
+ |
} |
| 403 |
+ |
|
| 404 |
+ |
#else // is_mpi |
| 405 |
+ |
|
| 406 |
+ |
molIndex = 0; |
| 407 |
+ |
globalAtomIndex = 0; |
| 408 |
+ |
for(i=0; i<n_components; i++){ |
| 409 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
| 410 |
+ |
the_molecules[molIndex].setStampID( i ); |
| 411 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 412 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
| 413 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 414 |
+ |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
| 415 |
+ |
globalAtomIndex++; |
| 416 |
+ |
} |
| 417 |
+ |
molIndex++; |
| 418 |
+ |
} |
| 419 |
+ |
} |
| 420 |
+ |
|
| 421 |
+ |
|
| 422 |
+ |
#endif // is_mpi |
| 423 |
+ |
|
| 424 |
+ |
|
| 425 |
|
if( simnfo->n_SRI ){ |
| 426 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
| 427 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
| 426 |
> |
|
| 427 |
> |
Exclude::createArray(simnfo->n_SRI); |
| 428 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 429 |
> |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
| 430 |
|
simnfo->globalExcludes = new int; |
| 431 |
< |
simnfo->n_exclude = tot_SRI; |
| 431 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
| 432 |
|
} |
| 433 |
|
else{ |
| 434 |
|
|
| 435 |
< |
the_excludes = new int[2]; |
| 436 |
< |
the_excludes[0] = 0; |
| 437 |
< |
the_excludes[1] = 0; |
| 435 |
> |
Exclude::createArray( 1 ); |
| 436 |
> |
the_excludes = new Exclude*; |
| 437 |
> |
the_excludes[0] = new Exclude(0); |
| 438 |
> |
the_excludes[0]->setPair( 0,0 ); |
| 439 |
|
simnfo->globalExcludes = new int; |
| 440 |
|
simnfo->globalExcludes[0] = 0; |
| 441 |
< |
|
| 323 |
< |
simnfo->n_exclude = 1; |
| 441 |
> |
simnfo->n_exclude = 0; |
| 442 |
|
} |
| 443 |
|
|
| 444 |
|
// set the arrays into the SimInfo object |
| 445 |
|
|
| 446 |
|
simnfo->atoms = the_atoms; |
| 447 |
< |
simnfo->sr_interactions = the_sris; |
| 447 |
> |
simnfo->molecules = the_molecules; |
| 448 |
|
simnfo->nGlobalExcludes = 0; |
| 449 |
|
simnfo->excludes = the_excludes; |
| 450 |
|
|
| 501 |
|
|
| 502 |
|
the_ff->setSimInfo( simnfo ); |
| 503 |
|
|
| 504 |
< |
makeAtoms(); |
| 504 |
> |
makeMolecules(); |
| 505 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 506 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 507 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 508 |
|
} |
| 509 |
|
|
| 392 |
– |
if( tot_bonds ){ |
| 393 |
– |
makeBonds(); |
| 394 |
– |
} |
| 395 |
– |
|
| 396 |
– |
if( tot_bends ){ |
| 397 |
– |
makeBends(); |
| 398 |
– |
} |
| 399 |
– |
|
| 400 |
– |
if( tot_torsions ){ |
| 401 |
– |
makeTorsions(); |
| 402 |
– |
} |
| 403 |
– |
|
| 404 |
– |
|
| 510 |
|
if (the_globals->getUseRF() ) { |
| 511 |
|
simnfo->useReactionField = 1; |
| 512 |
|
|
| 548 |
|
} |
| 549 |
|
simnfo->dielectric = the_globals->getDielectric(); |
| 550 |
|
} else { |
| 551 |
< |
if (simnfo->n_dipoles) { |
| 551 |
> |
if (usesDipoles) { |
| 552 |
|
|
| 553 |
|
if( !the_globals->haveECR() ){ |
| 554 |
|
sprintf( painCave.errMsg, |
| 555 |
< |
"SimSetup Warning: using default value of 1/2 the smallest" |
| 555 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 556 |
|
"box length for the electrostaticCutoffRadius.\n" |
| 557 |
|
"I hope you have a very fast processor!\n"); |
| 558 |
|
painCave.isFatal = 0; |
| 568 |
|
|
| 569 |
|
if( !the_globals->haveEST() ){ |
| 570 |
|
sprintf( painCave.errMsg, |
| 571 |
< |
"SimSetup Warning: using default value of 5% of the" |
| 571 |
> |
"SimSetup Warning: using default value of 5%% of the " |
| 572 |
|
"electrostaticCutoffRadius for the " |
| 573 |
|
"electrostaticSkinThickness\n" |
| 574 |
|
); |
| 743 |
|
|
| 744 |
|
// new AllLong( simnfo ); |
| 745 |
|
|
| 641 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
| 642 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
| 643 |
– |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
| 644 |
– |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 746 |
|
|
| 747 |
< |
|
| 747 |
> |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
| 748 |
> |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
| 749 |
> |
} |
| 750 |
> |
else if( !strcmp( force_field, "LJ" ) ){ |
| 751 |
> |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
| 752 |
> |
} |
| 753 |
> |
else { |
| 754 |
> |
std::cerr << "I'm a bug.\n"; |
| 755 |
> |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
| 756 |
> |
} |
| 757 |
> |
#ifdef IS_MPI |
| 758 |
> |
mpiSim->mpiRefresh(); |
| 759 |
> |
#endif |
| 760 |
|
|
| 761 |
|
// initialize the Fortran |
| 762 |
< |
|
| 762 |
> |
|
| 763 |
> |
|
| 764 |
|
simnfo->refreshSim(); |
| 765 |
|
|
| 766 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
| 785 |
|
#endif // is_mpi |
| 786 |
|
} |
| 787 |
|
|
| 674 |
– |
void SimSetup::makeAtoms( void ){ |
| 788 |
|
|
| 789 |
< |
int i, j, k, index; |
| 677 |
< |
double ux, uy, uz, uSqr, u; |
| 678 |
< |
AtomStamp* current_atom; |
| 789 |
> |
void SimSetup::makeMolecules( void ){ |
| 790 |
|
|
| 791 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
| 792 |
+ |
molInit info; |
| 793 |
|
DirectionalAtom* dAtom; |
| 794 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
| 794 |
> |
LinkedAssign* extras; |
| 795 |
> |
LinkedAssign* current_extra; |
| 796 |
> |
AtomStamp* currentAtom; |
| 797 |
> |
BondStamp* currentBond; |
| 798 |
> |
BendStamp* currentBend; |
| 799 |
> |
TorsionStamp* currentTorsion; |
| 800 |
|
|
| 801 |
< |
lMolIndex = 0; |
| 802 |
< |
molIndex = 0; |
| 803 |
< |
index = 0; |
| 686 |
< |
for( i=0; i<n_components; i++ ){ |
| 801 |
> |
bond_pair* theBonds; |
| 802 |
> |
bend_set* theBends; |
| 803 |
> |
torsion_set* theTorsions; |
| 804 |
|
|
| 805 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 805 |
> |
|
| 806 |
> |
//init the forceField paramters |
| 807 |
|
|
| 808 |
< |
#ifdef IS_MPI |
| 691 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 692 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 693 |
< |
#endif // is_mpi |
| 808 |
> |
the_ff->readParams(); |
| 809 |
|
|
| 810 |
< |
molStart = index; |
| 811 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
| 697 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
| 698 |
< |
|
| 699 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
| 700 |
< |
if( current_atom->haveOrientation() ){ |
| 701 |
< |
|
| 702 |
< |
dAtom = new DirectionalAtom(index); |
| 703 |
< |
simnfo->n_oriented++; |
| 704 |
< |
the_atoms[index] = dAtom; |
| 705 |
< |
|
| 706 |
< |
ux = current_atom->getOrntX(); |
| 707 |
< |
uy = current_atom->getOrntY(); |
| 708 |
< |
uz = current_atom->getOrntZ(); |
| 709 |
< |
|
| 710 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 711 |
< |
|
| 712 |
< |
u = sqrt( uSqr ); |
| 713 |
< |
ux = ux / u; |
| 714 |
< |
uy = uy / u; |
| 715 |
< |
uz = uz / u; |
| 716 |
< |
|
| 717 |
< |
dAtom->setSUx( ux ); |
| 718 |
< |
dAtom->setSUy( uy ); |
| 719 |
< |
dAtom->setSUz( uz ); |
| 720 |
< |
} |
| 721 |
< |
else{ |
| 722 |
< |
the_atoms[index] = new GeneralAtom(index); |
| 723 |
< |
} |
| 724 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
| 725 |
< |
the_atoms[index]->setIndex( index ); |
| 726 |
< |
|
| 727 |
< |
// increment the index and repeat; |
| 728 |
< |
index++; |
| 729 |
< |
} |
| 730 |
< |
|
| 731 |
< |
molEnd = index -1; |
| 732 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
| 733 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
| 734 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
| 735 |
< |
the_molecules[lMolIndex].setStampID( i ); |
| 736 |
< |
lMolIndex++; |
| 810 |
> |
|
| 811 |
> |
// init the atoms |
| 812 |
|
|
| 813 |
< |
#ifdef IS_MPI |
| 814 |
< |
} |
| 815 |
< |
#endif //is_mpi |
| 816 |
< |
|
| 817 |
< |
molIndex++; |
| 743 |
< |
} |
| 744 |
< |
} |
| 745 |
< |
|
| 746 |
< |
#ifdef IS_MPI |
| 747 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
| 813 |
> |
double ux, uy, uz, u, uSqr; |
| 814 |
> |
|
| 815 |
> |
atomOffset = 0; |
| 816 |
> |
excludeOffset = 0; |
| 817 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
| 818 |
|
|
| 819 |
< |
delete[] globalIndex; |
| 819 |
> |
stampID = the_molecules[i].getStampID(); |
| 820 |
|
|
| 821 |
< |
mpiSim->mpiRefresh(); |
| 822 |
< |
#endif //IS_MPI |
| 823 |
< |
|
| 824 |
< |
the_ff->initializeAtoms(); |
| 825 |
< |
} |
| 821 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
| 822 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
| 823 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
| 824 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 825 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
| 826 |
|
|
| 827 |
< |
void SimSetup::makeBonds( void ){ |
| 827 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
| 828 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
| 829 |
> |
info.myBonds = new Bond*[info.nBonds]; |
| 830 |
> |
info.myBends = new Bend*[info.nBends]; |
| 831 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
| 832 |
|
|
| 833 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 834 |
< |
bond_pair* the_bonds; |
| 835 |
< |
BondStamp* current_bond; |
| 836 |
< |
|
| 837 |
< |
the_bonds = new bond_pair[tot_bonds]; |
| 838 |
< |
index = 0; |
| 839 |
< |
offset = 0; |
| 840 |
< |
molIndex = 0; |
| 841 |
< |
|
| 842 |
< |
for( i=0; i<n_components; i++ ){ |
| 769 |
< |
|
| 770 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 771 |
< |
|
| 772 |
< |
#ifdef IS_MPI |
| 773 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 774 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 775 |
< |
#endif // is_mpi |
| 833 |
> |
theBonds = new bond_pair[info.nBonds]; |
| 834 |
> |
theBends = new bend_set[info.nBends]; |
| 835 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
| 836 |
> |
|
| 837 |
> |
// make the Atoms |
| 838 |
> |
|
| 839 |
> |
for(j=0; j<info.nAtoms; j++){ |
| 840 |
> |
|
| 841 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
| 842 |
> |
if( currentAtom->haveOrientation() ){ |
| 843 |
|
|
| 844 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
| 845 |
< |
|
| 846 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
| 847 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
| 848 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
| 849 |
< |
|
| 850 |
< |
exI = the_bonds[index].a; |
| 851 |
< |
exJ = the_bonds[index].b; |
| 852 |
< |
|
| 853 |
< |
// exclude_I must always be the smaller of the pair |
| 854 |
< |
if( exI > exJ ){ |
| 855 |
< |
tempEx = exI; |
| 856 |
< |
exI = exJ; |
| 857 |
< |
exJ = tempEx; |
| 858 |
< |
} |
| 859 |
< |
|
| 860 |
< |
|
| 844 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
| 845 |
> |
simnfo->n_oriented++; |
| 846 |
> |
info.myAtoms[j] = dAtom; |
| 847 |
> |
|
| 848 |
> |
ux = currentAtom->getOrntX(); |
| 849 |
> |
uy = currentAtom->getOrntY(); |
| 850 |
> |
uz = currentAtom->getOrntZ(); |
| 851 |
> |
|
| 852 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 853 |
> |
|
| 854 |
> |
u = sqrt( uSqr ); |
| 855 |
> |
ux = ux / u; |
| 856 |
> |
uy = uy / u; |
| 857 |
> |
uz = uz / u; |
| 858 |
> |
|
| 859 |
> |
dAtom->setSUx( ux ); |
| 860 |
> |
dAtom->setSUy( uy ); |
| 861 |
> |
dAtom->setSUz( uz ); |
| 862 |
> |
} |
| 863 |
> |
else{ |
| 864 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
| 865 |
> |
} |
| 866 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
| 867 |
> |
|
| 868 |
|
#ifdef IS_MPI |
| 869 |
+ |
|
| 870 |
+ |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
| 871 |
+ |
|
| 872 |
+ |
#endif // is_mpi |
| 873 |
+ |
} |
| 874 |
+ |
|
| 875 |
+ |
// make the bonds |
| 876 |
+ |
for(j=0; j<info.nBonds; j++){ |
| 877 |
+ |
|
| 878 |
+ |
currentBond = comp_stamps[stampID]->getBond( j ); |
| 879 |
+ |
theBonds[j].a = currentBond->getA() + atomOffset; |
| 880 |
+ |
theBonds[j].b = currentBond->getB() + atomOffset; |
| 881 |
|
|
| 882 |
< |
the_excludes[index*2] = |
| 883 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 798 |
< |
the_excludes[index*2 + 1] = |
| 799 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 882 |
> |
exI = theBonds[j].a; |
| 883 |
> |
exJ = theBonds[j].b; |
| 884 |
|
|
| 885 |
< |
#else // isn't MPI |
| 886 |
< |
|
| 887 |
< |
the_excludes[index*2] = exI + 1; |
| 888 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
| 889 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
| 806 |
< |
#endif //is_mpi |
| 807 |
< |
|
| 808 |
< |
// increment the index and repeat; |
| 809 |
< |
index++; |
| 810 |
< |
} |
| 811 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 812 |
< |
|
| 813 |
< |
#ifdef IS_MPI |
| 885 |
> |
// exclude_I must always be the smaller of the pair |
| 886 |
> |
if( exI > exJ ){ |
| 887 |
> |
tempEx = exI; |
| 888 |
> |
exI = exJ; |
| 889 |
> |
exJ = tempEx; |
| 890 |
|
} |
| 891 |
< |
#endif //is_mpi |
| 891 |
> |
#ifdef IS_MPI |
| 892 |
> |
tempEx = exI; |
| 893 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 894 |
> |
tempEx = exJ; |
| 895 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 896 |
|
|
| 897 |
< |
molIndex++; |
| 898 |
< |
} |
| 819 |
< |
} |
| 897 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 898 |
> |
#else // isn't MPI |
| 899 |
|
|
| 900 |
< |
the_ff->initializeBonds( the_bonds ); |
| 901 |
< |
} |
| 900 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 901 |
> |
#endif //is_mpi |
| 902 |
> |
} |
| 903 |
> |
excludeOffset += info.nBonds; |
| 904 |
|
|
| 905 |
< |
void SimSetup::makeBends( void ){ |
| 906 |
< |
|
| 907 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 908 |
< |
bend_set* the_bends; |
| 909 |
< |
BendStamp* current_bend; |
| 910 |
< |
LinkedAssign* extras; |
| 911 |
< |
LinkedAssign* current_extra; |
| 831 |
< |
|
| 832 |
< |
|
| 833 |
< |
the_bends = new bend_set[tot_bends]; |
| 834 |
< |
index = 0; |
| 835 |
< |
offset = 0; |
| 836 |
< |
molIndex = 0; |
| 837 |
< |
for( i=0; i<n_components; i++ ){ |
| 838 |
< |
|
| 839 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 840 |
< |
|
| 841 |
< |
#ifdef IS_MPI |
| 842 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 843 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 844 |
< |
#endif // is_mpi |
| 845 |
< |
|
| 846 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
| 905 |
> |
//make the bends |
| 906 |
> |
for(j=0; j<info.nBends; j++){ |
| 907 |
> |
|
| 908 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
| 909 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
| 910 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
| 911 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
| 912 |
|
|
| 913 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
| 849 |
< |
the_bends[index].a = current_bend->getA() + offset; |
| 850 |
< |
the_bends[index].b = current_bend->getB() + offset; |
| 851 |
< |
the_bends[index].c = current_bend->getC() + offset; |
| 852 |
< |
|
| 853 |
< |
if( current_bend->haveExtras() ){ |
| 913 |
> |
if( currentBend->haveExtras() ){ |
| 914 |
|
|
| 915 |
< |
extras = current_bend->getExtras(); |
| 916 |
< |
current_extra = extras; |
| 915 |
> |
extras = currentBend->getExtras(); |
| 916 |
> |
current_extra = extras; |
| 917 |
|
|
| 918 |
< |
while( current_extra != NULL ){ |
| 919 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 918 |
> |
while( current_extra != NULL ){ |
| 919 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 920 |
|
|
| 921 |
< |
switch( current_extra->getType() ){ |
| 921 |
> |
switch( current_extra->getType() ){ |
| 922 |
> |
|
| 923 |
> |
case 0: |
| 924 |
> |
theBends[j].ghost = |
| 925 |
> |
current_extra->getInt() + atomOffset; |
| 926 |
> |
theBends[j].isGhost = 1; |
| 927 |
> |
break; |
| 928 |
|
|
| 929 |
< |
case 0: |
| 930 |
< |
the_bends[index].ghost = |
| 931 |
< |
current_extra->getInt() + offset; |
| 932 |
< |
the_bends[index].isGhost = 1; |
| 933 |
< |
break; |
| 868 |
< |
|
| 869 |
< |
case 1: |
| 870 |
< |
the_bends[index].ghost = |
| 871 |
< |
(int)current_extra->getDouble() + offset; |
| 872 |
< |
the_bends[index].isGhost = 1; |
| 873 |
< |
break; |
| 874 |
< |
|
| 875 |
< |
default: |
| 876 |
< |
sprintf( painCave.errMsg, |
| 877 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
| 878 |
< |
"double nor an int.\n" |
| 879 |
< |
"-->Bend[%d] in %s\n", |
| 880 |
< |
k, comp_stamps[i]->getID() ); |
| 881 |
< |
painCave.isFatal = 1; |
| 882 |
< |
simError(); |
| 883 |
< |
} |
| 884 |
< |
} |
| 929 |
> |
case 1: |
| 930 |
> |
theBends[j].ghost = |
| 931 |
> |
(int)current_extra->getDouble() + atomOffset; |
| 932 |
> |
theBends[j].isGhost = 1; |
| 933 |
> |
break; |
| 934 |
|
|
| 935 |
< |
else{ |
| 936 |
< |
|
| 937 |
< |
sprintf( painCave.errMsg, |
| 938 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
| 939 |
< |
" -->%s in Bend[%d] in %s\n", |
| 940 |
< |
current_extra->getlhs(), |
| 941 |
< |
k, comp_stamps[i]->getID() ); |
| 942 |
< |
painCave.isFatal = 1; |
| 894 |
< |
simError(); |
| 895 |
< |
} |
| 896 |
< |
|
| 897 |
< |
current_extra = current_extra->getNext(); |
| 935 |
> |
default: |
| 936 |
> |
sprintf( painCave.errMsg, |
| 937 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
| 938 |
> |
"double nor an int.\n" |
| 939 |
> |
"-->Bend[%d] in %s\n", |
| 940 |
> |
j, comp_stamps[stampID]->getID() ); |
| 941 |
> |
painCave.isFatal = 1; |
| 942 |
> |
simError(); |
| 943 |
|
} |
| 944 |
|
} |
| 945 |
|
|
| 901 |
– |
if( !the_bends[index].isGhost ){ |
| 902 |
– |
|
| 903 |
– |
exI = the_bends[index].a; |
| 904 |
– |
exJ = the_bends[index].c; |
| 905 |
– |
} |
| 946 |
|
else{ |
| 947 |
|
|
| 948 |
< |
exI = the_bends[index].a; |
| 949 |
< |
exJ = the_bends[index].b; |
| 948 |
> |
sprintf( painCave.errMsg, |
| 949 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
| 950 |
> |
" -->%s in Bend[%d] in %s\n", |
| 951 |
> |
current_extra->getlhs(), |
| 952 |
> |
j, comp_stamps[stampID]->getID() ); |
| 953 |
> |
painCave.isFatal = 1; |
| 954 |
> |
simError(); |
| 955 |
|
} |
| 956 |
|
|
| 957 |
< |
// exclude_I must always be the smaller of the pair |
| 958 |
< |
if( exI > exJ ){ |
| 959 |
< |
tempEx = exI; |
| 960 |
< |
exI = exJ; |
| 961 |
< |
exJ = tempEx; |
| 962 |
< |
} |
| 957 |
> |
current_extra = current_extra->getNext(); |
| 958 |
> |
} |
| 959 |
> |
} |
| 960 |
> |
|
| 961 |
> |
if( !theBends[j].isGhost ){ |
| 962 |
> |
|
| 963 |
> |
exI = theBends[j].a; |
| 964 |
> |
exJ = theBends[j].c; |
| 965 |
> |
} |
| 966 |
> |
else{ |
| 967 |
> |
|
| 968 |
> |
exI = theBends[j].a; |
| 969 |
> |
exJ = theBends[j].b; |
| 970 |
> |
} |
| 971 |
> |
|
| 972 |
> |
// exclude_I must always be the smaller of the pair |
| 973 |
> |
if( exI > exJ ){ |
| 974 |
> |
tempEx = exI; |
| 975 |
> |
exI = exJ; |
| 976 |
> |
exJ = tempEx; |
| 977 |
> |
} |
| 978 |
> |
#ifdef IS_MPI |
| 979 |
> |
tempEx = exI; |
| 980 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 981 |
> |
tempEx = exJ; |
| 982 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 983 |
> |
|
| 984 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 985 |
> |
#else // isn't MPI |
| 986 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 987 |
> |
#endif //is_mpi |
| 988 |
> |
} |
| 989 |
> |
excludeOffset += info.nBends; |
| 990 |
|
|
| 991 |
+ |
for(j=0; j<info.nTorsions; j++){ |
| 992 |
+ |
|
| 993 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
| 994 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
| 995 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
| 996 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
| 997 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
| 998 |
+ |
|
| 999 |
+ |
exI = theTorsions[j].a; |
| 1000 |
+ |
exJ = theTorsions[j].d; |
| 1001 |
|
|
| 1002 |
+ |
// exclude_I must always be the smaller of the pair |
| 1003 |
+ |
if( exI > exJ ){ |
| 1004 |
+ |
tempEx = exI; |
| 1005 |
+ |
exI = exJ; |
| 1006 |
+ |
exJ = tempEx; |
| 1007 |
+ |
} |
| 1008 |
|
#ifdef IS_MPI |
| 1009 |
< |
|
| 1010 |
< |
the_excludes[(index + tot_bonds)*2] = |
| 1011 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 1012 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
| 1013 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 1014 |
< |
|
| 1009 |
> |
tempEx = exI; |
| 1010 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1011 |
> |
tempEx = exJ; |
| 1012 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1013 |
> |
|
| 1014 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 1015 |
|
#else // isn't MPI |
| 1016 |
< |
|
| 929 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
| 930 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
| 931 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
| 1016 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 1017 |
|
#endif //is_mpi |
| 933 |
– |
|
| 934 |
– |
|
| 935 |
– |
// increment the index and repeat; |
| 936 |
– |
index++; |
| 937 |
– |
} |
| 938 |
– |
offset += comp_stamps[i]->getNAtoms(); |
| 939 |
– |
|
| 940 |
– |
#ifdef IS_MPI |
| 941 |
– |
} |
| 942 |
– |
#endif //is_mpi |
| 943 |
– |
|
| 944 |
– |
molIndex++; |
| 1018 |
|
} |
| 1019 |
+ |
excludeOffset += info.nTorsions; |
| 1020 |
+ |
|
| 1021 |
+ |
|
| 1022 |
+ |
// send the arrays off to the forceField for init. |
| 1023 |
+ |
|
| 1024 |
+ |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
| 1025 |
+ |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
| 1026 |
+ |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
| 1027 |
+ |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
| 1028 |
+ |
|
| 1029 |
+ |
|
| 1030 |
+ |
the_molecules[i].initialize( info ); |
| 1031 |
+ |
|
| 1032 |
+ |
|
| 1033 |
+ |
atomOffset += info.nAtoms; |
| 1034 |
+ |
delete[] theBonds; |
| 1035 |
+ |
delete[] theBends; |
| 1036 |
+ |
delete[] theTorsions; |
| 1037 |
|
} |
| 1038 |
|
|
| 1039 |
|
#ifdef IS_MPI |
| 1040 |
< |
sprintf( checkPointMsg, |
| 950 |
< |
"Successfully created the bends list.\n" ); |
| 1040 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
| 1041 |
|
MPIcheckPoint(); |
| 1042 |
|
#endif // is_mpi |
| 953 |
– |
|
| 1043 |
|
|
| 1044 |
< |
the_ff->initializeBends( the_bends ); |
| 1045 |
< |
} |
| 1044 |
> |
// clean up the forcefield |
| 1045 |
> |
the_ff->calcRcut(); |
| 1046 |
> |
the_ff->cleanMe(); |
| 1047 |
|
|
| 958 |
– |
void SimSetup::makeTorsions( void ){ |
| 959 |
– |
|
| 960 |
– |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 961 |
– |
torsion_set* the_torsions; |
| 962 |
– |
TorsionStamp* current_torsion; |
| 963 |
– |
|
| 964 |
– |
the_torsions = new torsion_set[tot_torsions]; |
| 965 |
– |
index = 0; |
| 966 |
– |
offset = 0; |
| 967 |
– |
molIndex = 0; |
| 968 |
– |
for( i=0; i<n_components; i++ ){ |
| 969 |
– |
|
| 970 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
| 971 |
– |
|
| 972 |
– |
#ifdef IS_MPI |
| 973 |
– |
if( mpiSim->getMyMolStart() <= molIndex && |
| 974 |
– |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 975 |
– |
#endif // is_mpi |
| 976 |
– |
|
| 977 |
– |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
| 978 |
– |
|
| 979 |
– |
current_torsion = comp_stamps[i]->getTorsion( k ); |
| 980 |
– |
the_torsions[index].a = current_torsion->getA() + offset; |
| 981 |
– |
the_torsions[index].b = current_torsion->getB() + offset; |
| 982 |
– |
the_torsions[index].c = current_torsion->getC() + offset; |
| 983 |
– |
the_torsions[index].d = current_torsion->getD() + offset; |
| 984 |
– |
|
| 985 |
– |
exI = the_torsions[index].a; |
| 986 |
– |
exJ = the_torsions[index].d; |
| 987 |
– |
|
| 988 |
– |
|
| 989 |
– |
// exclude_I must always be the smaller of the pair |
| 990 |
– |
if( exI > exJ ){ |
| 991 |
– |
tempEx = exI; |
| 992 |
– |
exI = exJ; |
| 993 |
– |
exJ = tempEx; |
| 994 |
– |
} |
| 995 |
– |
|
| 996 |
– |
|
| 997 |
– |
#ifdef IS_MPI |
| 998 |
– |
|
| 999 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
| 1000 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
| 1001 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
| 1002 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 1003 |
– |
|
| 1004 |
– |
#else // isn't MPI |
| 1005 |
– |
|
| 1006 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
| 1007 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
| 1008 |
– |
// fortran indexes from 1 (hence the +1 in the indexing) |
| 1009 |
– |
#endif //is_mpi |
| 1010 |
– |
|
| 1011 |
– |
|
| 1012 |
– |
// increment the index and repeat; |
| 1013 |
– |
index++; |
| 1014 |
– |
} |
| 1015 |
– |
offset += comp_stamps[i]->getNAtoms(); |
| 1016 |
– |
|
| 1017 |
– |
#ifdef IS_MPI |
| 1018 |
– |
} |
| 1019 |
– |
#endif //is_mpi |
| 1020 |
– |
|
| 1021 |
– |
molIndex++; |
| 1022 |
– |
} |
| 1023 |
– |
} |
| 1024 |
– |
|
| 1025 |
– |
the_ff->initializeTorsions( the_torsions ); |
| 1048 |
|
} |
| 1049 |
|
|
| 1050 |
|
void SimSetup::initFromBass( void ){ |
