| 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, |
| 239 |
|
|
| 240 |
|
|
| 241 |
|
globalIndex = mpiSim->divideLabor(); |
| 244 |
– |
|
| 245 |
– |
|
| 242 |
|
|
| 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 |
< |
if( simnfo->n_SRI ){ |
| 310 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
| 311 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
| 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 |
|
|
| 349 |
< |
the_excludes = new int[2]; |
| 350 |
< |
the_excludes[0] = 0; |
| 351 |
< |
the_excludes[1] = 0; |
| 349 |
> |
Exclude::createArray( 1 ); |
| 350 |
> |
the_excludes = new Exclude*; |
| 351 |
> |
the_excludes[0] = new Exclude(0); |
| 352 |
> |
the_excludes[0]->setPair( 0,0 ); |
| 353 |
|
simnfo->globalExcludes = new int; |
| 354 |
|
simnfo->globalExcludes[0] = 0; |
| 355 |
< |
|
| 323 |
< |
simnfo->n_exclude = 1; |
| 355 |
> |
simnfo->n_exclude = 0; |
| 356 |
|
} |
| 357 |
|
|
| 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 |
+ |
#ifdef IS_MPI |
| 664 |
+ |
mpiSim->mpiRefresh(); |
| 665 |
+ |
#endif |
| 666 |
|
|
| 647 |
– |
|
| 667 |
|
// initialize the Fortran |
| 668 |
< |
|
| 668 |
> |
|
| 669 |
> |
|
| 670 |
|
simnfo->refreshSim(); |
| 671 |
|
|
| 672 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
| 694 |
|
|
| 695 |
|
void SimSetup::makeMolecules( void ){ |
| 696 |
|
|
| 697 |
< |
int i, j, exI, exJ, tempEx, stampID, atomOffset; |
| 697 |
> |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
| 698 |
|
molInit info; |
| 699 |
|
DirectionalAtom* dAtom; |
| 700 |
+ |
LinkedAssign* extras; |
| 701 |
+ |
LinkedAssign* current_extra; |
| 702 |
|
AtomStamp* currentAtom; |
| 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++){ |
| 724 |
|
|
| 725 |
|
stampID = the_molecules[i].getStampID(); |
| 728 |
|
info.nBonds = comp_stamps[stampID]->getNBonds(); |
| 729 |
|
info.nBends = comp_stamps[stampID]->getNBends(); |
| 730 |
|
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 731 |
< |
|
| 731 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
| 732 |
> |
|
| 733 |
|
info.myAtoms = &the_atoms[atomOffset]; |
| 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); |
| 779 |
|
} |
| 780 |
|
|
| 781 |
|
// make the bonds |
| 782 |
< |
for(j=0; j<nBonds; j++){ |
| 782 |
> |
for(j=0; j<info.nBonds; j++){ |
| 783 |
|
|
| 784 |
|
currentBond = comp_stamps[stampID]->getBond( j ); |
| 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 ){ |
| 795 |
|
exJ = tempEx; |
| 796 |
|
} |
| 797 |
|
#ifdef IS_MPI |
| 798 |
+ |
tempEx = exI; |
| 799 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 800 |
+ |
tempEx = exJ; |
| 801 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 802 |
|
|
| 803 |
< |
the_excludes[index*2] = |
| 768 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 769 |
< |
the_excludes[index*2 + 1] = |
| 770 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 771 |
< |
|
| 803 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 804 |
|
#else // isn't MPI |
| 773 |
– |
|
| 774 |
– |
the_excludes[index*2] = exI + 1; |
| 775 |
– |
the_excludes[index*2 + 1] = exJ + 1; |
| 776 |
– |
// fortran index from 1 (hence the +1 in the indexing) |
| 805 |
|
|
| 806 |
+ |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 807 |
|
#endif //is_mpi |
| 808 |
< |
|
| 809 |
< |
} |
| 781 |
< |
|
| 782 |
< |
|
| 783 |
< |
|
| 784 |
< |
|
| 785 |
< |
|
| 786 |
< |
|
| 787 |
< |
|
| 788 |
< |
|
| 789 |
< |
|
| 790 |
< |
|
| 791 |
< |
|
| 792 |
< |
|
| 793 |
< |
|
| 794 |
< |
|
| 795 |
< |
|
| 796 |
< |
void SimSetup::makeAtoms( void ){ |
| 797 |
< |
|
| 798 |
< |
int i, j, k, index; |
| 799 |
< |
double ux, uy, uz, uSqr, u; |
| 800 |
< |
AtomStamp* current_atom; |
| 801 |
< |
|
| 802 |
< |
DirectionalAtom* dAtom; |
| 803 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
| 804 |
< |
|
| 805 |
< |
lMolIndex = 0; |
| 806 |
< |
molIndex = 0; |
| 807 |
< |
index = 0; |
| 808 |
< |
for( i=0; i<n_components; i++ ){ |
| 808 |
> |
} |
| 809 |
> |
excludeOffset += info.nBonds; |
| 810 |
|
|
| 811 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 812 |
< |
|
| 813 |
< |
#ifdef IS_MPI |
| 814 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 815 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 816 |
< |
#endif // is_mpi |
| 817 |
< |
|
| 817 |
< |
molStart = index; |
| 818 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
| 819 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
| 811 |
> |
//make the bends |
| 812 |
> |
for(j=0; j<info.nBends; j++){ |
| 813 |
> |
|
| 814 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
| 815 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
| 816 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
| 817 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
| 818 |
|
|
| 819 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
| 822 |
< |
if( current_atom->haveOrientation() ){ |
| 819 |
> |
if( currentBend->haveExtras() ){ |
| 820 |
|
|
| 821 |
< |
dAtom = new DirectionalAtom(index); |
| 822 |
< |
simnfo->n_oriented++; |
| 826 |
< |
the_atoms[index] = dAtom; |
| 821 |
> |
extras = currentBend->getExtras(); |
| 822 |
> |
current_extra = extras; |
| 823 |
|
|
| 824 |
< |
ux = current_atom->getOrntX(); |
| 825 |
< |
uy = current_atom->getOrntY(); |
| 826 |
< |
uz = current_atom->getOrntZ(); |
| 827 |
< |
|
| 828 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 829 |
< |
|
| 830 |
< |
u = sqrt( uSqr ); |
| 831 |
< |
ux = ux / u; |
| 832 |
< |
uy = uy / u; |
| 833 |
< |
uz = uz / u; |
| 834 |
< |
|
| 835 |
< |
dAtom->setSUx( ux ); |
| 836 |
< |
dAtom->setSUy( uy ); |
| 837 |
< |
dAtom->setSUz( uz ); |
| 824 |
> |
while( current_extra != NULL ){ |
| 825 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 826 |
> |
|
| 827 |
> |
switch( current_extra->getType() ){ |
| 828 |
> |
|
| 829 |
> |
case 0: |
| 830 |
> |
theBends[j].ghost = |
| 831 |
> |
current_extra->getInt() + atomOffset; |
| 832 |
> |
theBends[j].isGhost = 1; |
| 833 |
> |
break; |
| 834 |
> |
|
| 835 |
> |
case 1: |
| 836 |
> |
theBends[j].ghost = |
| 837 |
> |
(int)current_extra->getDouble() + atomOffset; |
| 838 |
> |
theBends[j].isGhost = 1; |
| 839 |
> |
break; |
| 840 |
> |
|
| 841 |
> |
default: |
| 842 |
> |
sprintf( painCave.errMsg, |
| 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() ); |
| 847 |
> |
painCave.isFatal = 1; |
| 848 |
> |
simError(); |
| 849 |
> |
} |
| 850 |
|
} |
| 851 |
+ |
|
| 852 |
|
else{ |
| 853 |
< |
the_atoms[index] = new GeneralAtom(index); |
| 853 |
> |
|
| 854 |
> |
sprintf( painCave.errMsg, |
| 855 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
| 856 |
> |
" -->%s in Bend[%d] in %s\n", |
| 857 |
> |
current_extra->getlhs(), |
| 858 |
> |
j, comp_stamps[stampID]->getID() ); |
| 859 |
> |
painCave.isFatal = 1; |
| 860 |
> |
simError(); |
| 861 |
|
} |
| 846 |
– |
the_atoms[index]->setType( current_atom->getType() ); |
| 847 |
– |
the_atoms[index]->setIndex( index ); |
| 862 |
|
|
| 863 |
< |
// increment the index and repeat; |
| 850 |
< |
index++; |
| 863 |
> |
current_extra = current_extra->getNext(); |
| 864 |
|
} |
| 865 |
+ |
} |
| 866 |
+ |
|
| 867 |
+ |
if( !theBends[j].isGhost ){ |
| 868 |
+ |
|
| 869 |
+ |
exI = theBends[j].a; |
| 870 |
+ |
exJ = theBends[j].c; |
| 871 |
+ |
} |
| 872 |
+ |
else{ |
| 873 |
|
|
| 874 |
< |
molEnd = index -1; |
| 875 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
| 855 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
| 856 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
| 857 |
< |
the_molecules[lMolIndex].setStampID( i ); |
| 858 |
< |
lMolIndex++; |
| 859 |
< |
|
| 860 |
< |
#ifdef IS_MPI |
| 874 |
> |
exI = theBends[j].a; |
| 875 |
> |
exJ = theBends[j].b; |
| 876 |
|
} |
| 862 |
– |
#endif //is_mpi |
| 877 |
|
|
| 878 |
< |
molIndex++; |
| 879 |
< |
} |
| 880 |
< |
} |
| 881 |
< |
|
| 878 |
> |
// exclude_I must always be the smaller of the pair |
| 879 |
> |
if( exI > exJ ){ |
| 880 |
> |
tempEx = exI; |
| 881 |
> |
exI = exJ; |
| 882 |
> |
exJ = tempEx; |
| 883 |
> |
} |
| 884 |
|
#ifdef IS_MPI |
| 885 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
| 886 |
< |
|
| 887 |
< |
delete[] globalIndex; |
| 888 |
< |
|
| 889 |
< |
mpiSim->mpiRefresh(); |
| 890 |
< |
#endif //IS_MPI |
| 891 |
< |
|
| 892 |
< |
the_ff->initializeAtoms(); |
| 893 |
< |
} |
| 894 |
< |
|
| 895 |
< |
void SimSetup::makeBonds( void ){ |
| 880 |
< |
|
| 881 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 882 |
< |
bond_pair* the_bonds; |
| 883 |
< |
BondStamp* current_bond; |
| 884 |
< |
|
| 885 |
< |
the_bonds = new bond_pair[tot_bonds]; |
| 886 |
< |
index = 0; |
| 887 |
< |
offset = 0; |
| 888 |
< |
molIndex = 0; |
| 889 |
< |
|
| 890 |
< |
for( i=0; i<n_components; i++ ){ |
| 891 |
< |
|
| 892 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 885 |
> |
tempEx = exI; |
| 886 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 887 |
> |
tempEx = exJ; |
| 888 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 889 |
> |
|
| 890 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 891 |
> |
#else // isn't MPI |
| 892 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 893 |
> |
#endif //is_mpi |
| 894 |
> |
} |
| 895 |
> |
excludeOffset += info.nBends; |
| 896 |
|
|
| 897 |
< |
#ifdef IS_MPI |
| 898 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 899 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 900 |
< |
#endif // is_mpi |
| 901 |
< |
|
| 902 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
| 903 |
< |
|
| 904 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
| 905 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
| 906 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
| 897 |
> |
for(j=0; j<info.nTorsions; j++){ |
| 898 |
> |
|
| 899 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
| 900 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
| 901 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
| 902 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
| 903 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
| 904 |
> |
|
| 905 |
> |
exI = theTorsions[j].a; |
| 906 |
> |
exJ = theTorsions[j].d; |
| 907 |
|
|
| 908 |
< |
exI = the_bonds[index].a; |
| 909 |
< |
exJ = the_bonds[index].b; |
| 910 |
< |
|
| 911 |
< |
// exclude_I must always be the smaller of the pair |
| 912 |
< |
if( exI > exJ ){ |
| 913 |
< |
tempEx = exI; |
| 911 |
< |
exI = exJ; |
| 912 |
< |
exJ = tempEx; |
| 913 |
< |
} |
| 914 |
< |
|
| 915 |
< |
|
| 908 |
> |
// exclude_I must always be the smaller of the pair |
| 909 |
> |
if( exI > exJ ){ |
| 910 |
> |
tempEx = exI; |
| 911 |
> |
exI = exJ; |
| 912 |
> |
exJ = tempEx; |
| 913 |
> |
} |
| 914 |
|
#ifdef IS_MPI |
| 915 |
< |
|
| 916 |
< |
the_excludes[index*2] = |
| 917 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 918 |
< |
the_excludes[index*2 + 1] = |
| 919 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 920 |
< |
|
| 915 |
> |
tempEx = exI; |
| 916 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 917 |
> |
tempEx = exJ; |
| 918 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 919 |
> |
|
| 920 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 921 |
|
#else // isn't MPI |
| 922 |
< |
|
| 925 |
< |
the_excludes[index*2] = exI + 1; |
| 926 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
| 927 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
| 922 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 923 |
|
#endif //is_mpi |
| 924 |
< |
|
| 925 |
< |
// increment the index and repeat; |
| 931 |
< |
index++; |
| 932 |
< |
} |
| 933 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 934 |
< |
|
| 935 |
< |
#ifdef IS_MPI |
| 936 |
< |
} |
| 937 |
< |
#endif //is_mpi |
| 938 |
< |
|
| 939 |
< |
molIndex++; |
| 940 |
< |
} |
| 941 |
< |
} |
| 924 |
> |
} |
| 925 |
> |
excludeOffset += info.nTorsions; |
| 926 |
|
|
| 927 |
< |
the_ff->initializeBonds( the_bonds ); |
| 928 |
< |
} |
| 927 |
> |
|
| 928 |
> |
// send the arrays off to the forceField for init. |
| 929 |
|
|
| 930 |
< |
void SimSetup::makeBends( void ){ |
| 930 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
| 931 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
| 932 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
| 933 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
| 934 |
|
|
| 948 |
– |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 949 |
– |
bend_set* the_bends; |
| 950 |
– |
BendStamp* current_bend; |
| 951 |
– |
LinkedAssign* extras; |
| 952 |
– |
LinkedAssign* current_extra; |
| 953 |
– |
|
| 935 |
|
|
| 936 |
< |
the_bends = new bend_set[tot_bends]; |
| 956 |
< |
index = 0; |
| 957 |
< |
offset = 0; |
| 958 |
< |
molIndex = 0; |
| 959 |
< |
for( i=0; i<n_components; i++ ){ |
| 960 |
< |
|
| 961 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 962 |
< |
|
| 963 |
< |
#ifdef IS_MPI |
| 964 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 965 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 966 |
< |
#endif // is_mpi |
| 967 |
< |
|
| 968 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
| 969 |
< |
|
| 970 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
| 971 |
< |
the_bends[index].a = current_bend->getA() + offset; |
| 972 |
< |
the_bends[index].b = current_bend->getB() + offset; |
| 973 |
< |
the_bends[index].c = current_bend->getC() + offset; |
| 974 |
< |
|
| 975 |
< |
if( current_bend->haveExtras() ){ |
| 976 |
< |
|
| 977 |
< |
extras = current_bend->getExtras(); |
| 978 |
< |
current_extra = extras; |
| 979 |
< |
|
| 980 |
< |
while( current_extra != NULL ){ |
| 981 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 982 |
< |
|
| 983 |
< |
switch( current_extra->getType() ){ |
| 984 |
< |
|
| 985 |
< |
case 0: |
| 986 |
< |
the_bends[index].ghost = |
| 987 |
< |
current_extra->getInt() + offset; |
| 988 |
< |
the_bends[index].isGhost = 1; |
| 989 |
< |
break; |
| 990 |
< |
|
| 991 |
< |
case 1: |
| 992 |
< |
the_bends[index].ghost = |
| 993 |
< |
(int)current_extra->getDouble() + offset; |
| 994 |
< |
the_bends[index].isGhost = 1; |
| 995 |
< |
break; |
| 996 |
< |
|
| 997 |
< |
default: |
| 998 |
< |
sprintf( painCave.errMsg, |
| 999 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
| 1000 |
< |
"double nor an int.\n" |
| 1001 |
< |
"-->Bend[%d] in %s\n", |
| 1002 |
< |
k, comp_stamps[i]->getID() ); |
| 1003 |
< |
painCave.isFatal = 1; |
| 1004 |
< |
simError(); |
| 1005 |
< |
} |
| 1006 |
< |
} |
| 1007 |
< |
|
| 1008 |
< |
else{ |
| 1009 |
< |
|
| 1010 |
< |
sprintf( painCave.errMsg, |
| 1011 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
| 1012 |
< |
" -->%s in Bend[%d] in %s\n", |
| 1013 |
< |
current_extra->getlhs(), |
| 1014 |
< |
k, comp_stamps[i]->getID() ); |
| 1015 |
< |
painCave.isFatal = 1; |
| 1016 |
< |
simError(); |
| 1017 |
< |
} |
| 1018 |
< |
|
| 1019 |
< |
current_extra = current_extra->getNext(); |
| 1020 |
< |
} |
| 1021 |
< |
} |
| 1022 |
< |
|
| 1023 |
< |
if( !the_bends[index].isGhost ){ |
| 1024 |
< |
|
| 1025 |
< |
exI = the_bends[index].a; |
| 1026 |
< |
exJ = the_bends[index].c; |
| 1027 |
< |
} |
| 1028 |
< |
else{ |
| 1029 |
< |
|
| 1030 |
< |
exI = the_bends[index].a; |
| 1031 |
< |
exJ = the_bends[index].b; |
| 1032 |
< |
} |
| 1033 |
< |
|
| 1034 |
< |
// exclude_I must always be the smaller of the pair |
| 1035 |
< |
if( exI > exJ ){ |
| 1036 |
< |
tempEx = exI; |
| 1037 |
< |
exI = exJ; |
| 1038 |
< |
exJ = tempEx; |
| 1039 |
< |
} |
| 936 |
> |
the_molecules[i].initialize( info ); |
| 937 |
|
|
| 938 |
|
|
| 939 |
< |
#ifdef IS_MPI |
| 940 |
< |
|
| 941 |
< |
the_excludes[(index + tot_bonds)*2] = |
| 942 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 1046 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
| 1047 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 1048 |
< |
|
| 1049 |
< |
#else // isn't MPI |
| 1050 |
< |
|
| 1051 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
| 1052 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
| 1053 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
| 1054 |
< |
#endif //is_mpi |
| 1055 |
< |
|
| 1056 |
< |
|
| 1057 |
< |
// increment the index and repeat; |
| 1058 |
< |
index++; |
| 1059 |
< |
} |
| 1060 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 1061 |
< |
|
| 1062 |
< |
#ifdef IS_MPI |
| 1063 |
< |
} |
| 1064 |
< |
#endif //is_mpi |
| 1065 |
< |
|
| 1066 |
< |
molIndex++; |
| 1067 |
< |
} |
| 939 |
> |
atomOffset += info.nAtoms; |
| 940 |
> |
delete[] theBonds; |
| 941 |
> |
delete[] theBends; |
| 942 |
> |
delete[] theTorsions; |
| 943 |
|
} |
| 944 |
|
|
| 945 |
|
#ifdef IS_MPI |
| 946 |
< |
sprintf( checkPointMsg, |
| 1072 |
< |
"Successfully created the bends list.\n" ); |
| 946 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
| 947 |
|
MPIcheckPoint(); |
| 948 |
|
#endif // is_mpi |
| 1075 |
– |
|
| 1076 |
– |
|
| 1077 |
– |
the_ff->initializeBends( the_bends ); |
| 1078 |
– |
} |
| 949 |
|
|
| 950 |
< |
void SimSetup::makeTorsions( void ){ |
| 950 |
> |
// clean up the forcefield |
| 951 |
> |
the_ff->calcRcut(); |
| 952 |
> |
the_ff->cleanMe(); |
| 953 |
|
|
| 1082 |
– |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 1083 |
– |
torsion_set* the_torsions; |
| 1084 |
– |
TorsionStamp* current_torsion; |
| 1085 |
– |
|
| 1086 |
– |
the_torsions = new torsion_set[tot_torsions]; |
| 1087 |
– |
index = 0; |
| 1088 |
– |
offset = 0; |
| 1089 |
– |
molIndex = 0; |
| 1090 |
– |
for( i=0; i<n_components; i++ ){ |
| 1091 |
– |
|
| 1092 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
| 1093 |
– |
|
| 1094 |
– |
#ifdef IS_MPI |
| 1095 |
– |
if( mpiSim->getMyMolStart() <= molIndex && |
| 1096 |
– |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 1097 |
– |
#endif // is_mpi |
| 1098 |
– |
|
| 1099 |
– |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
| 1100 |
– |
|
| 1101 |
– |
current_torsion = comp_stamps[i]->getTorsion( k ); |
| 1102 |
– |
the_torsions[index].a = current_torsion->getA() + offset; |
| 1103 |
– |
the_torsions[index].b = current_torsion->getB() + offset; |
| 1104 |
– |
the_torsions[index].c = current_torsion->getC() + offset; |
| 1105 |
– |
the_torsions[index].d = current_torsion->getD() + offset; |
| 1106 |
– |
|
| 1107 |
– |
exI = the_torsions[index].a; |
| 1108 |
– |
exJ = the_torsions[index].d; |
| 1109 |
– |
|
| 1110 |
– |
|
| 1111 |
– |
// exclude_I must always be the smaller of the pair |
| 1112 |
– |
if( exI > exJ ){ |
| 1113 |
– |
tempEx = exI; |
| 1114 |
– |
exI = exJ; |
| 1115 |
– |
exJ = tempEx; |
| 1116 |
– |
} |
| 1117 |
– |
|
| 1118 |
– |
|
| 1119 |
– |
#ifdef IS_MPI |
| 1120 |
– |
|
| 1121 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
| 1122 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
| 1123 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
| 1124 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 1125 |
– |
|
| 1126 |
– |
#else // isn't MPI |
| 1127 |
– |
|
| 1128 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
| 1129 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
| 1130 |
– |
// fortran indexes from 1 (hence the +1 in the indexing) |
| 1131 |
– |
#endif //is_mpi |
| 1132 |
– |
|
| 1133 |
– |
|
| 1134 |
– |
// increment the index and repeat; |
| 1135 |
– |
index++; |
| 1136 |
– |
} |
| 1137 |
– |
offset += comp_stamps[i]->getNAtoms(); |
| 1138 |
– |
|
| 1139 |
– |
#ifdef IS_MPI |
| 1140 |
– |
} |
| 1141 |
– |
#endif //is_mpi |
| 1142 |
– |
|
| 1143 |
– |
molIndex++; |
| 1144 |
– |
} |
| 1145 |
– |
} |
| 1146 |
– |
|
| 1147 |
– |
the_ff->initializeTorsions( the_torsions ); |
| 954 |
|
} |
| 955 |
|
|
| 956 |
|
void SimSetup::initFromBass( void ){ |
