# | Line 66 | Line 66 | void SimSetup::createSim( void ){ | |
---|---|---|
66 | ||
67 | MakeStamps *the_stamps; | |
68 | Globals* the_globals; | |
69 | + | ExtendedSystem* the_extendedsystem; |
70 | int i, j; | |
71 | ||
72 | // get the stamps and globals; | |
# | Line 80 | Line 81 | void SimSetup::createSim( void ){ | |
81 | // get the ones we know are there, yet still may need some work. | |
82 | n_components = the_globals->getNComponents(); | |
83 | strcpy( force_field, the_globals->getForceField() ); | |
84 | + | |
85 | + | // get the ensemble and set up an extended system if we need it: |
86 | strcpy( ensemble, the_globals->getEnsemble() ); | |
87 | + | if( !strcasecmp( ensemble, "NPT" ) ) { |
88 | + | the_extendedsystem = new ExtendedSystem( simnfo ); |
89 | + | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 | + | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
91 | + | } else if ( !strcasecmp( ensemble, "NVT") ) { |
92 | + | the_extendedsystem = new ExtendedSystem( simnfo ); |
93 | + | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
94 | + | } else if ( !strcasecmp( ensemble, "NVE") ) { |
95 | + | } else { |
96 | + | sprintf( painCave.errMsg, |
97 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
98 | + | "reverting to NVE for this simulation.\n", |
99 | + | ensemble ); |
100 | + | painCave.isFatal = 0; |
101 | + | simError(); |
102 | + | strcpy( ensemble, "NVE" ); |
103 | + | } |
104 | strcpy( simnfo->ensemble, ensemble ); | |
105 | ||
106 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
107 | simnfo->usePBC = the_globals->getPBC(); | |
108 | ||
109 | < | |
110 | < | |
111 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
112 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
113 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
114 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
109 | > | int usesDipoles = 0; |
110 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
111 | > | the_ff = new TraPPE_ExFF(); |
112 | > | usesDipoles = 1; |
113 | > | } |
114 | > | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
115 | else{ | |
116 | sprintf( painCave.errMsg, | |
117 | "SimSetup Error. Unrecognized force field -> %s\n", | |
# | Line 242 | Line 262 | void SimSetup::createSim( void ){ | |
262 | ||
263 | globalIndex = mpiSim->divideLabor(); | |
264 | ||
245 | – | |
246 | – | |
265 | // set up the local variables | |
266 | ||
267 | int localMol, allMol; | |
268 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
269 | + | |
270 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
271 | + | int* molCompType = mpiSim->getMolComponentType(); |
272 | ||
273 | allMol = 0; | |
274 | localMol = 0; | |
# | Line 259 | Line 280 | void SimSetup::createSim( void ){ | |
280 | ||
281 | for( j=0; j<components_nmol[i]; j++ ){ | |
282 | ||
283 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
283 | > | if( mol2proc[j] == worldRank ){ |
284 | ||
285 | local_atoms += comp_stamps[i]->getNAtoms(); | |
286 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 279 | Line 299 | void SimSetup::createSim( void ){ | |
299 | if( local_atoms != simnfo->n_atoms ){ | |
300 | sprintf( painCave.errMsg, | |
301 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
302 | < | " localAtom (%d) are note equal.\n", |
302 | > | " localAtom (%d) are not equal.\n", |
303 | simnfo->n_atoms, | |
304 | local_atoms ); | |
305 | painCave.isFatal = 1; | |
# | Line 304 | Line 324 | void SimSetup::createSim( void ){ | |
324 | Atom::createArrays(simnfo->n_atoms); | |
325 | the_atoms = new Atom*[simnfo->n_atoms]; | |
326 | the_molecules = new Molecule[simnfo->n_mol]; | |
327 | + | int molIndex; |
328 | ||
329 | + | // initialize the molecule's stampID's |
330 | ||
331 | + | #ifdef IS_MPI |
332 | + | |
333 | + | |
334 | + | molIndex = 0; |
335 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
336 | + | |
337 | + | if(mol2proc[i] == worldRank ){ |
338 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
339 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
340 | + | molIndex++; |
341 | + | } |
342 | + | } |
343 | + | |
344 | + | #else // is_mpi |
345 | + | |
346 | + | molIndex = 0; |
347 | + | for(i=0; i<n_components; i++){ |
348 | + | for(j=0; j<components_nmol[i]; j++ ){ |
349 | + | the_molecules[molIndex].setStampID( i ); |
350 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
351 | + | molIndex++; |
352 | + | } |
353 | + | } |
354 | + | |
355 | + | |
356 | + | #endif // is_mpi |
357 | + | |
358 | + | |
359 | if( simnfo->n_SRI ){ | |
360 | + | |
361 | Exclude::createArray(simnfo->n_SRI); | |
362 | the_excludes = new Exclude*[simnfo->n_SRI]; | |
363 | + | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
364 | simnfo->globalExcludes = new int; | |
365 | < | simnfo->n_exclude = tot_SRI; |
365 | > | simnfo->n_exclude = simnfo->n_SRI; |
366 | } | |
367 | else{ | |
368 | ||
# | Line 326 | Line 378 | void SimSetup::createSim( void ){ | |
378 | // set the arrays into the SimInfo object | |
379 | ||
380 | simnfo->atoms = the_atoms; | |
381 | < | simnfo->sr_interactions = the_sris; |
381 | > | simnfo->molecules = the_molecules; |
382 | simnfo->nGlobalExcludes = 0; | |
383 | simnfo->excludes = the_excludes; | |
384 | ||
# | Line 383 | Line 435 | void SimSetup::createSim( void ){ | |
435 | ||
436 | the_ff->setSimInfo( simnfo ); | |
437 | ||
438 | < | makeAtoms(); |
438 | > | makeMolecules(); |
439 | simnfo->identArray = new int[simnfo->n_atoms]; | |
440 | for(i=0; i<simnfo->n_atoms; i++){ | |
441 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
442 | } | |
443 | ||
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 | – | |
444 | if (the_globals->getUseRF() ) { | |
445 | simnfo->useReactionField = 1; | |
446 | ||
# | Line 443 | Line 482 | void SimSetup::createSim( void ){ | |
482 | } | |
483 | simnfo->dielectric = the_globals->getDielectric(); | |
484 | } else { | |
485 | < | if (simnfo->n_dipoles) { |
485 | > | if (usesDipoles) { |
486 | ||
487 | if( !the_globals->haveECR() ){ | |
488 | sprintf( painCave.errMsg, | |
489 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
489 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
490 | "box length for the electrostaticCutoffRadius.\n" | |
491 | "I hope you have a very fast processor!\n"); | |
492 | painCave.isFatal = 0; | |
# | Line 463 | Line 502 | void SimSetup::createSim( void ){ | |
502 | ||
503 | if( !the_globals->haveEST() ){ | |
504 | sprintf( painCave.errMsg, | |
505 | < | "SimSetup Warning: using default value of 5% of the" |
505 | > | "SimSetup Warning: using default value of 5%% of the " |
506 | "electrostaticCutoffRadius for the " | |
507 | "electrostaticSkinThickness\n" | |
508 | ); | |
# | Line 638 | Line 677 | void SimSetup::createSim( void ){ | |
677 | ||
678 | // new AllLong( simnfo ); | |
679 | ||
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 ); |
680 | ||
681 | < | |
681 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
682 | > | new Symplectic(simnfo, the_ff, the_extendedsystem); |
683 | > | std::cerr << "called new Symplecic\n"; |
684 | > | fprintf( stderr, "called new Symplectic. stderr\n" ); |
685 | > | } |
686 | > | else if( !strcmp( force_field, "LJ" ) ){ |
687 | > | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
688 | > | std::cerr << "called new Verlet\n"; |
689 | > | fprintf( stderr, "called new Verlet. stderr\n" ); |
690 | > | } |
691 | > | else { |
692 | > | std::cerr << "I'm a bug.\n"; |
693 | > | fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
694 | > | } |
695 | > | #ifdef IS_MPI |
696 | > | mpiSim->mpiRefresh(); |
697 | > | #endif |
698 | ||
699 | // initialize the Fortran | |
700 | < | |
700 | > | |
701 | > | |
702 | simnfo->refreshSim(); | |
703 | ||
704 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 683 | Line 735 | void SimSetup::makeMolecules( void ){ | |
735 | BondStamp* currentBond; | |
736 | BendStamp* currentBend; | |
737 | TorsionStamp* currentTorsion; | |
738 | + | |
739 | + | bond_pair* theBonds; |
740 | + | bend_set* theBends; |
741 | + | torsion_set* theTorsions; |
742 | + | |
743 | ||
744 | //init the forceField paramters | |
745 | ||
746 | the_ff->readParams(); | |
747 | ||
748 | ||
749 | < | // init the molecules |
749 | > | // init the atoms |
750 | ||
751 | + | double ux, uy, uz, u, uSqr; |
752 | + | |
753 | atomOffset = 0; | |
754 | excludeOffset = 0; | |
755 | for(i=0; i<simnfo->n_mol; i++){ | |
# | Line 707 | Line 766 | void SimSetup::makeMolecules( void ){ | |
766 | info.myExcludes = &the_excludes[excludeOffset]; | |
767 | info.myBonds = new Bond*[info.nBonds]; | |
768 | info.myBends = new Bend*[info.nBends]; | |
769 | < | info.myTorsions = new Torsions*[info.nTorsions]; |
769 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
770 | ||
771 | theBonds = new bond_pair[info.nBonds]; | |
772 | theBends = new bend_set[info.nBends]; | |
# | Line 717 | Line 776 | void SimSetup::makeMolecules( void ){ | |
776 | ||
777 | for(j=0; j<info.nAtoms; j++){ | |
778 | ||
779 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
779 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
780 | if( currentAtom->haveOrientation() ){ | |
781 | ||
782 | dAtom = new DirectionalAtom(j + atomOffset); | |
# | Line 758 | Line 817 | void SimSetup::makeMolecules( void ){ | |
817 | theBonds[j].a = currentBond->getA() + atomOffset; | |
818 | theBonds[j].b = currentBond->getB() + atomOffset; | |
819 | ||
820 | < | exI = theBonds[i].a; |
821 | < | exJ = theBonds[i].b; |
820 | > | exI = theBonds[j].a; |
821 | > | exJ = theBonds[j].b; |
822 | ||
823 | // exclude_I must always be the smaller of the pair | |
824 | if( exI > exJ ){ | |
# | Line 775 | Line 834 | void SimSetup::makeMolecules( void ){ | |
834 | ||
835 | the_excludes[j+excludeOffset]->setPair( exI, exJ ); | |
836 | #else // isn't MPI | |
837 | + | |
838 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
839 | #endif //is_mpi | |
840 | } | |
# | Line 790 | Line 850 | void SimSetup::makeMolecules( void ){ | |
850 | ||
851 | if( currentBend->haveExtras() ){ | |
852 | ||
853 | < | extras = current_bend->getExtras(); |
853 | > | extras = currentBend->getExtras(); |
854 | current_extra = extras; | |
855 | ||
856 | while( current_extra != NULL ){ | |
# | Line 812 | Line 872 | void SimSetup::makeMolecules( void ){ | |
872 | ||
873 | default: | |
874 | sprintf( painCave.errMsg, | |
875 | < | "SimSetup Error: ghostVectorSource was neiter a " |
875 | > | "SimSetup Error: ghostVectorSource was neither a " |
876 | "double nor an int.\n" | |
877 | "-->Bend[%d] in %s\n", | |
878 | j, comp_stamps[stampID]->getID() ); | |
# | Line 906 | Line 966 | void SimSetup::makeMolecules( void ){ | |
966 | ||
967 | ||
968 | the_molecules[i].initialize( info ); | |
969 | + | |
970 | + | |
971 | atomOffset += info.nAtoms; | |
972 | + | delete[] theBonds; |
973 | + | delete[] theBends; |
974 | + | delete[] theTorsions; |
975 | } | |
976 | ||
977 | + | #ifdef IS_MPI |
978 | + | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
979 | + | MPIcheckPoint(); |
980 | + | #endif // is_mpi |
981 | + | |
982 | // clean up the forcefield | |
983 | the_ff->calcRcut(); | |
984 | the_ff->cleanMe(); | |
985 | + | |
986 | } | |
987 | ||
988 | void SimSetup::initFromBass( void ){ |
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