| 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, |
| 240 |
|
|
| 241 |
|
globalIndex = mpiSim->divideLabor(); |
| 242 |
|
|
| 245 |
– |
|
| 246 |
– |
|
| 243 |
|
// set up the local variables |
| 244 |
|
|
| 245 |
|
int localMol, allMol; |
| 246 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 247 |
+ |
|
| 248 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
| 249 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
| 250 |
|
|
| 251 |
|
allMol = 0; |
| 252 |
|
localMol = 0; |
| 258 |
|
|
| 259 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 260 |
|
|
| 261 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
| 263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
| 261 |
> |
if( mol2proc[j] == worldRank ){ |
| 262 |
|
|
| 263 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 264 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 277 |
|
if( local_atoms != simnfo->n_atoms ){ |
| 278 |
|
sprintf( painCave.errMsg, |
| 279 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
| 280 |
< |
" localAtom (%d) are note equal.\n", |
| 280 |
> |
" localAtom (%d) are not equal.\n", |
| 281 |
|
simnfo->n_atoms, |
| 282 |
|
local_atoms ); |
| 283 |
|
painCave.isFatal = 1; |
| 302 |
|
Atom::createArrays(simnfo->n_atoms); |
| 303 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
| 304 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
| 305 |
+ |
int molIndex; |
| 306 |
|
|
| 307 |
+ |
// initialize the molecule's stampID's |
| 308 |
|
|
| 309 |
+ |
#ifdef IS_MPI |
| 310 |
+ |
|
| 311 |
+ |
|
| 312 |
+ |
molIndex = 0; |
| 313 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
| 314 |
+ |
|
| 315 |
+ |
if(mol2proc[i] == worldRank ){ |
| 316 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 317 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 318 |
+ |
molIndex++; |
| 319 |
+ |
} |
| 320 |
+ |
} |
| 321 |
+ |
|
| 322 |
+ |
#else // is_mpi |
| 323 |
+ |
|
| 324 |
+ |
molIndex = 0; |
| 325 |
+ |
for(i=0; i<n_components; i++){ |
| 326 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
| 327 |
+ |
the_molecules[molIndex].setStampID( i ); |
| 328 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 329 |
+ |
molIndex++; |
| 330 |
+ |
} |
| 331 |
+ |
} |
| 332 |
+ |
|
| 333 |
+ |
|
| 334 |
+ |
#endif // is_mpi |
| 335 |
+ |
|
| 336 |
+ |
|
| 337 |
|
if( simnfo->n_SRI ){ |
| 338 |
+ |
|
| 339 |
+ |
std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
| 340 |
+ |
|
| 341 |
|
Exclude::createArray(simnfo->n_SRI); |
| 342 |
|
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 343 |
+ |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
| 344 |
|
simnfo->globalExcludes = new int; |
| 345 |
< |
simnfo->n_exclude = tot_SRI; |
| 345 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
| 346 |
|
} |
| 347 |
|
else{ |
| 348 |
|
|
| 358 |
|
// set the arrays into the SimInfo object |
| 359 |
|
|
| 360 |
|
simnfo->atoms = the_atoms; |
| 361 |
< |
simnfo->sr_interactions = the_sris; |
| 361 |
> |
simnfo->molecules = the_molecules; |
| 362 |
|
simnfo->nGlobalExcludes = 0; |
| 363 |
|
simnfo->excludes = the_excludes; |
| 364 |
|
|
| 415 |
|
|
| 416 |
|
the_ff->setSimInfo( simnfo ); |
| 417 |
|
|
| 418 |
< |
makeAtoms(); |
| 418 |
> |
makeMolecules(); |
| 419 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 420 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 421 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 422 |
|
} |
| 423 |
|
|
| 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 |
– |
|
| 424 |
|
if (the_globals->getUseRF() ) { |
| 425 |
|
simnfo->useReactionField = 1; |
| 426 |
|
|
| 657 |
|
|
| 658 |
|
// new AllLong( simnfo ); |
| 659 |
|
|
| 641 |
– |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
| 642 |
– |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
| 660 |
|
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
| 661 |
|
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 662 |
|
|
| 663 |
< |
|
| 663 |
> |
#ifdef IS_MPI |
| 664 |
> |
mpiSim->mpiRefresh(); |
| 665 |
> |
#endif |
| 666 |
|
|
| 667 |
|
// initialize the Fortran |
| 668 |
< |
|
| 668 |
> |
|
| 669 |
> |
|
| 670 |
|
simnfo->refreshSim(); |
| 671 |
|
|
| 672 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
| 703 |
|
BondStamp* currentBond; |
| 704 |
|
BendStamp* currentBend; |
| 705 |
|
TorsionStamp* currentTorsion; |
| 706 |
+ |
|
| 707 |
+ |
bond_pair* theBonds; |
| 708 |
+ |
bend_set* theBends; |
| 709 |
+ |
torsion_set* theTorsions; |
| 710 |
+ |
|
| 711 |
|
|
| 712 |
|
//init the forceField paramters |
| 713 |
|
|
| 714 |
|
the_ff->readParams(); |
| 715 |
|
|
| 716 |
|
|
| 717 |
< |
// init the molecules |
| 717 |
> |
// init the atoms |
| 718 |
|
|
| 719 |
+ |
double ux, uy, uz, u, uSqr; |
| 720 |
+ |
|
| 721 |
|
atomOffset = 0; |
| 722 |
|
excludeOffset = 0; |
| 723 |
|
for(i=0; i<simnfo->n_mol; i++){ |
| 734 |
|
info.myExcludes = &the_excludes[excludeOffset]; |
| 735 |
|
info.myBonds = new Bond*[info.nBonds]; |
| 736 |
|
info.myBends = new Bend*[info.nBends]; |
| 737 |
< |
info.myTorsions = new Torsions*[info.nTorsions]; |
| 737 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
| 738 |
|
|
| 739 |
|
theBonds = new bond_pair[info.nBonds]; |
| 740 |
|
theBends = new bend_set[info.nBends]; |
| 744 |
|
|
| 745 |
|
for(j=0; j<info.nAtoms; j++){ |
| 746 |
|
|
| 747 |
< |
currentAtom = theComponents[stampID]->getAtom( j ); |
| 747 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
| 748 |
|
if( currentAtom->haveOrientation() ){ |
| 749 |
|
|
| 750 |
|
dAtom = new DirectionalAtom(j + atomOffset); |
| 785 |
|
theBonds[j].a = currentBond->getA() + atomOffset; |
| 786 |
|
theBonds[j].b = currentBond->getB() + atomOffset; |
| 787 |
|
|
| 788 |
< |
exI = theBonds[i].a; |
| 789 |
< |
exJ = theBonds[i].b; |
| 788 |
> |
exI = theBonds[j].a; |
| 789 |
> |
exJ = theBonds[j].b; |
| 790 |
|
|
| 791 |
|
// exclude_I must always be the smaller of the pair |
| 792 |
|
if( exI > exJ ){ |
| 802 |
|
|
| 803 |
|
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 804 |
|
#else // isn't MPI |
| 805 |
+ |
|
| 806 |
|
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 807 |
|
#endif //is_mpi |
| 808 |
|
} |
| 818 |
|
|
| 819 |
|
if( currentBend->haveExtras() ){ |
| 820 |
|
|
| 821 |
< |
extras = current_bend->getExtras(); |
| 821 |
> |
extras = currentBend->getExtras(); |
| 822 |
|
current_extra = extras; |
| 823 |
|
|
| 824 |
|
while( current_extra != NULL ){ |
| 840 |
|
|
| 841 |
|
default: |
| 842 |
|
sprintf( painCave.errMsg, |
| 843 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
| 843 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
| 844 |
|
"double nor an int.\n" |
| 845 |
|
"-->Bend[%d] in %s\n", |
| 846 |
|
j, comp_stamps[stampID]->getID() ); |
| 934 |
|
|
| 935 |
|
|
| 936 |
|
the_molecules[i].initialize( info ); |
| 937 |
+ |
|
| 938 |
+ |
|
| 939 |
|
atomOffset += info.nAtoms; |
| 940 |
+ |
delete[] theBonds; |
| 941 |
+ |
delete[] theBends; |
| 942 |
+ |
delete[] theTorsions; |
| 943 |
|
} |
| 944 |
|
|
| 945 |
+ |
#ifdef IS_MPI |
| 946 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
| 947 |
+ |
MPIcheckPoint(); |
| 948 |
+ |
#endif // is_mpi |
| 949 |
+ |
|
| 950 |
|
// clean up the forcefield |
| 951 |
|
the_ff->calcRcut(); |
| 952 |
|
the_ff->cleanMe(); |
| 953 |
+ |
|
| 954 |
|
} |
| 955 |
|
|
| 956 |
|
void SimSetup::initFromBass( void ){ |
