# | Line 66 | Line 66 | void SimSetup::createSim( void ){ | |
---|---|---|
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; | |
# | 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 | + | 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", | |
# | Line 230 | Line 298 | void SimSetup::createSim( void ){ | |
298 | simnfo->n_torsions = tot_torsions; | |
299 | simnfo->n_SRI = tot_SRI; | |
300 | simnfo->n_mol = tot_nmol; | |
233 | – | |
301 | ||
302 | + | simnfo->molMembershipArray = new int[tot_atoms]; |
303 | + | |
304 | #ifdef IS_MPI | |
305 | ||
306 | // divide the molecules among processors here. | |
307 | ||
308 | mpiSim = new mpiSimulation( simnfo ); | |
309 | ||
241 | – | |
242 | – | |
310 | globalIndex = mpiSim->divideLabor(); | |
311 | ||
245 | – | |
246 | – | |
312 | // set up the local variables | |
313 | ||
314 | int localMol, allMol; | |
315 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
316 | + | |
317 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
318 | + | int* molCompType = mpiSim->getMolComponentType(); |
319 | ||
320 | allMol = 0; | |
321 | localMol = 0; | |
# | Line 255 | Line 323 | void SimSetup::createSim( void ){ | |
323 | local_bonds = 0; | |
324 | local_bends = 0; | |
325 | local_torsions = 0; | |
326 | + | globalAtomIndex = 0; |
327 | + | |
328 | + | |
329 | for( i=0; i<n_components; i++ ){ | |
330 | ||
331 | for( j=0; j<components_nmol[i]; j++ ){ | |
332 | ||
333 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
333 | > | if( mol2proc[allMol] == worldRank ){ |
334 | ||
335 | local_atoms += comp_stamps[i]->getNAtoms(); | |
336 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 268 | Line 338 | void SimSetup::createSim( void ){ | |
338 | local_torsions += comp_stamps[i]->getNTorsions(); | |
339 | localMol++; | |
340 | } | |
341 | < | allMol++; |
341 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
342 | > | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
343 | > | globalAtomIndex++; |
344 | > | } |
345 | > | |
346 | > | allMol++; |
347 | } | |
348 | } | |
349 | local_SRI = local_bonds + local_bends + local_torsions; | |
350 | ||
276 | – | |
351 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
352 | ||
353 | if( local_atoms != simnfo->n_atoms ){ | |
354 | sprintf( painCave.errMsg, | |
355 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
356 | < | " localAtom (%d) are note equal.\n", |
356 | > | " localAtom (%d) are not equal.\n", |
357 | simnfo->n_atoms, | |
358 | local_atoms ); | |
359 | painCave.isFatal = 1; | |
# | Line 304 | Line 378 | void SimSetup::createSim( void ){ | |
378 | Atom::createArrays(simnfo->n_atoms); | |
379 | the_atoms = new Atom*[simnfo->n_atoms]; | |
380 | the_molecules = new Molecule[simnfo->n_mol]; | |
381 | + | int molIndex; |
382 | ||
383 | + | // initialize the molecule's stampID's |
384 | ||
385 | < | if( simnfo->n_SRI ){ |
386 | < | the_sris = new SRI*[simnfo->n_SRI]; |
387 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
385 | > | #ifdef IS_MPI |
386 | > | |
387 | > | |
388 | > | molIndex = 0; |
389 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
390 | > | |
391 | > | if(mol2proc[i] == worldRank ){ |
392 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
393 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
394 | > | the_molecules[molIndex].setGlobalIndex( i ); |
395 | > | molIndex++; |
396 | > | } |
397 | > | } |
398 | > | |
399 | > | #else // is_mpi |
400 | > | |
401 | > | molIndex = 0; |
402 | > | globalAtomIndex = 0; |
403 | > | for(i=0; i<n_components; i++){ |
404 | > | for(j=0; j<components_nmol[i]; j++ ){ |
405 | > | the_molecules[molIndex].setStampID( i ); |
406 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
407 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
408 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
409 | > | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
410 | > | globalAtomIndex++; |
411 | > | } |
412 | > | molIndex++; |
413 | > | } |
414 | > | } |
415 | > | |
416 | > | |
417 | > | #endif // is_mpi |
418 | > | |
419 | > | |
420 | > | if( simnfo->n_SRI ){ |
421 | > | |
422 | > | Exclude::createArray(simnfo->n_SRI); |
423 | > | the_excludes = new Exclude*[simnfo->n_SRI]; |
424 | > | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
425 | simnfo->globalExcludes = new int; | |
426 | < | simnfo->n_exclude = tot_SRI; |
426 | > | simnfo->n_exclude = simnfo->n_SRI; |
427 | } | |
428 | else{ | |
429 | ||
430 | < | the_excludes = new int[2]; |
431 | < | the_excludes[0] = 0; |
432 | < | the_excludes[1] = 0; |
430 | > | Exclude::createArray( 1 ); |
431 | > | the_excludes = new Exclude*; |
432 | > | the_excludes[0] = new Exclude(0); |
433 | > | the_excludes[0]->setPair( 0,0 ); |
434 | simnfo->globalExcludes = new int; | |
435 | simnfo->globalExcludes[0] = 0; | |
436 | < | |
323 | < | simnfo->n_exclude = 1; |
436 | > | simnfo->n_exclude = 0; |
437 | } | |
438 | ||
439 | // set the arrays into the SimInfo object | |
440 | ||
441 | simnfo->atoms = the_atoms; | |
442 | < | simnfo->sr_interactions = the_sris; |
442 | > | simnfo->molecules = the_molecules; |
443 | simnfo->nGlobalExcludes = 0; | |
444 | simnfo->excludes = the_excludes; | |
445 | ||
446 | ||
447 | // get some of the tricky things that may still be in the globals | |
448 | ||
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 |
449 | ||
450 | if( the_globals->haveBox() ){ | |
451 | simnfo->box_x = the_globals->getBox(); | |
# | Line 407 | Line 496 | void SimSetup::createSim( void ){ | |
496 | ||
497 | the_ff->setSimInfo( simnfo ); | |
498 | ||
499 | < | makeAtoms(); |
499 | > | makeMolecules(); |
500 | simnfo->identArray = new int[simnfo->n_atoms]; | |
501 | for(i=0; i<simnfo->n_atoms; i++){ | |
502 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
503 | } | |
504 | ||
505 | < | if( tot_bonds ){ |
506 | < | makeBonds(); |
507 | < | } |
505 | > | if (the_globals->getUseRF() ) { |
506 | > | simnfo->useReactionField = 1; |
507 | > | |
508 | > | if( !the_globals->haveECR() ){ |
509 | > | sprintf( painCave.errMsg, |
510 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
511 | > | "box length for the electrostaticCutoffRadius.\n" |
512 | > | "I hope you have a very fast processor!\n"); |
513 | > | painCave.isFatal = 0; |
514 | > | simError(); |
515 | > | double smallest; |
516 | > | smallest = simnfo->box_x; |
517 | > | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
518 | > | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
519 | > | simnfo->ecr = 0.5 * smallest; |
520 | > | } else { |
521 | > | simnfo->ecr = the_globals->getECR(); |
522 | > | } |
523 | ||
524 | < | if( tot_bends ){ |
525 | < | makeBends(); |
526 | < | } |
527 | < | |
528 | < | if( tot_torsions ){ |
529 | < | makeTorsions(); |
530 | < | } |
531 | < | |
532 | < | |
533 | < | |
534 | < | |
524 | > | if( !the_globals->haveEST() ){ |
525 | > | sprintf( painCave.errMsg, |
526 | > | "SimSetup Warning: using default value of 0.05 * the " |
527 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
528 | > | ); |
529 | > | painCave.isFatal = 0; |
530 | > | simError(); |
531 | > | simnfo->est = 0.05 * simnfo->ecr; |
532 | > | } else { |
533 | > | simnfo->est = the_globals->getEST(); |
534 | > | } |
535 | > | |
536 | > | if(!the_globals->haveDielectric() ){ |
537 | > | sprintf( painCave.errMsg, |
538 | > | "SimSetup Error: You are trying to use Reaction Field without" |
539 | > | "setting a dielectric constant!\n" |
540 | > | ); |
541 | > | painCave.isFatal = 1; |
542 | > | simError(); |
543 | > | } |
544 | > | simnfo->dielectric = the_globals->getDielectric(); |
545 | > | } else { |
546 | > | if (usesDipoles) { |
547 | > | |
548 | > | if( !the_globals->haveECR() ){ |
549 | > | sprintf( painCave.errMsg, |
550 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
551 | > | "box length for the electrostaticCutoffRadius.\n" |
552 | > | "I hope you have a very fast processor!\n"); |
553 | > | painCave.isFatal = 0; |
554 | > | simError(); |
555 | > | double smallest; |
556 | > | smallest = simnfo->box_x; |
557 | > | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
558 | > | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
559 | > | simnfo->ecr = 0.5 * smallest; |
560 | > | } else { |
561 | > | simnfo->ecr = the_globals->getECR(); |
562 | > | } |
563 | > | |
564 | > | if( !the_globals->haveEST() ){ |
565 | > | sprintf( painCave.errMsg, |
566 | > | "SimSetup Warning: using default value of 5%% of the " |
567 | > | "electrostaticCutoffRadius for the " |
568 | > | "electrostaticSkinThickness\n" |
569 | > | ); |
570 | > | painCave.isFatal = 0; |
571 | > | simError(); |
572 | > | simnfo->est = 0.05 * simnfo->ecr; |
573 | > | } else { |
574 | > | simnfo->est = the_globals->getEST(); |
575 | > | } |
576 | > | } |
577 | > | } |
578 | ||
579 | + | #ifdef IS_MPI |
580 | + | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
581 | + | MPIcheckPoint(); |
582 | + | #endif // is_mpi |
583 | ||
584 | if( the_globals->haveInitialConfig() ){ | |
585 | ||
# | Line 583 | Line 734 | void SimSetup::createSim( void ){ | |
734 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
735 | ||
736 | ||
737 | < | // // make the longe range forces and the integrator |
737 | > | // make the integrator |
738 | ||
588 | – | // new AllLong( simnfo ); |
739 | ||
740 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
741 | < | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
742 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
743 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
740 | > | if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
741 | > | new Symplectic(simnfo, the_ff, the_extendedsystem); |
742 | > | } |
743 | > | else if( !strcmp( force_field, "LJ" ) ){ |
744 | > | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
745 | > | } |
746 | ||
747 | + | #ifdef IS_MPI |
748 | + | mpiSim->mpiRefresh(); |
749 | + | #endif |
750 | ||
596 | – | |
751 | // initialize the Fortran | |
752 | < | |
752 | > | |
753 | > | |
754 | simnfo->refreshSim(); | |
755 | ||
756 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 620 | Line 775 | void SimSetup::createSim( void ){ | |
775 | #endif // is_mpi | |
776 | } | |
777 | ||
623 | – | void SimSetup::makeAtoms( void ){ |
778 | ||
779 | < | int i, j, k, index; |
626 | < | double ux, uy, uz, uSqr, u; |
627 | < | AtomStamp* current_atom; |
779 | > | void SimSetup::makeMolecules( void ){ |
780 | ||
781 | + | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
782 | + | molInit info; |
783 | DirectionalAtom* dAtom; | |
784 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
784 | > | LinkedAssign* extras; |
785 | > | LinkedAssign* current_extra; |
786 | > | AtomStamp* currentAtom; |
787 | > | BondStamp* currentBond; |
788 | > | BendStamp* currentBend; |
789 | > | TorsionStamp* currentTorsion; |
790 | ||
791 | < | lMolIndex = 0; |
792 | < | molIndex = 0; |
793 | < | index = 0; |
635 | < | for( i=0; i<n_components; i++ ){ |
791 | > | bond_pair* theBonds; |
792 | > | bend_set* theBends; |
793 | > | torsion_set* theTorsions; |
794 | ||
795 | < | for( j=0; j<components_nmol[i]; j++ ){ |
795 | > | |
796 | > | //init the forceField paramters |
797 | ||
798 | < | #ifdef IS_MPI |
640 | < | if( mpiSim->getMyMolStart() <= molIndex && |
641 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
642 | < | #endif // is_mpi |
798 | > | the_ff->readParams(); |
799 | ||
800 | < | molStart = index; |
801 | < | 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++; |
800 | > | |
801 | > | // init the atoms |
802 | ||
803 | < | #ifdef IS_MPI |
804 | < | } |
805 | < | #endif //is_mpi |
806 | < | |
807 | < | molIndex++; |
692 | < | } |
693 | < | } |
694 | < | |
695 | < | #ifdef IS_MPI |
696 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
803 | > | double ux, uy, uz, u, uSqr; |
804 | > | |
805 | > | atomOffset = 0; |
806 | > | excludeOffset = 0; |
807 | > | for(i=0; i<simnfo->n_mol; i++){ |
808 | ||
809 | < | delete[] globalIndex; |
809 | > | stampID = the_molecules[i].getStampID(); |
810 | ||
811 | < | mpiSim->mpiRefresh(); |
812 | < | #endif //IS_MPI |
813 | < | |
814 | < | the_ff->initializeAtoms(); |
815 | < | } |
811 | > | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
812 | > | info.nBonds = comp_stamps[stampID]->getNBonds(); |
813 | > | info.nBends = comp_stamps[stampID]->getNBends(); |
814 | > | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
815 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
816 | ||
817 | < | void SimSetup::makeBonds( void ){ |
818 | < | |
819 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
820 | < | bond_pair* the_bonds; |
821 | < | BondStamp* current_bond; |
711 | < | |
712 | < | the_bonds = new bond_pair[tot_bonds]; |
713 | < | index = 0; |
714 | < | offset = 0; |
715 | < | molIndex = 0; |
716 | < | |
717 | < | 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 |
725 | < | |
726 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
727 | < | |
728 | < | current_bond = comp_stamps[i]->getBond( k ); |
729 | < | the_bonds[index].a = current_bond->getA() + offset; |
730 | < | the_bonds[index].b = current_bond->getB() + offset; |
817 | > | info.myAtoms = &the_atoms[atomOffset]; |
818 | > | info.myExcludes = &the_excludes[excludeOffset]; |
819 | > | info.myBonds = new Bond*[info.nBonds]; |
820 | > | info.myBends = new Bend*[info.nBends]; |
821 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
822 | ||
823 | < | exI = the_bonds[index].a; |
824 | < | exJ = the_bonds[index].b; |
825 | < | |
826 | < | // exclude_I must always be the smaller of the pair |
827 | < | if( exI > exJ ){ |
828 | < | tempEx = exI; |
829 | < | exI = exJ; |
830 | < | exJ = tempEx; |
831 | < | } |
832 | < | |
742 | < | |
743 | < | #ifdef IS_MPI |
744 | < | |
745 | < | the_excludes[index*2] = |
746 | < | the_atoms[exI]->getGlobalIndex() + 1; |
747 | < | the_excludes[index*2 + 1] = |
748 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
749 | < | |
750 | < | #else // isn't MPI |
751 | < | |
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(); |
823 | > | theBonds = new bond_pair[info.nBonds]; |
824 | > | theBends = new bend_set[info.nBends]; |
825 | > | theTorsions = new torsion_set[info.nTorsions]; |
826 | > | |
827 | > | // make the Atoms |
828 | > | |
829 | > | for(j=0; j<info.nAtoms; j++){ |
830 | > | |
831 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
832 | > | if( currentAtom->haveOrientation() ){ |
833 | ||
834 | < | #ifdef IS_MPI |
834 | > | dAtom = new DirectionalAtom(j + atomOffset); |
835 | > | simnfo->n_oriented++; |
836 | > | info.myAtoms[j] = dAtom; |
837 | > | |
838 | > | ux = currentAtom->getOrntX(); |
839 | > | uy = currentAtom->getOrntY(); |
840 | > | uz = currentAtom->getOrntZ(); |
841 | > | |
842 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
843 | > | |
844 | > | u = sqrt( uSqr ); |
845 | > | ux = ux / u; |
846 | > | uy = uy / u; |
847 | > | uz = uz / u; |
848 | > | |
849 | > | dAtom->setSUx( ux ); |
850 | > | dAtom->setSUy( uy ); |
851 | > | dAtom->setSUz( uz ); |
852 | } | |
853 | < | #endif //is_mpi |
853 | > | else{ |
854 | > | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
855 | > | } |
856 | > | info.myAtoms[j]->setType( currentAtom->getType() ); |
857 | > | |
858 | > | #ifdef IS_MPI |
859 | ||
860 | < | molIndex++; |
861 | < | } |
862 | < | } |
860 | > | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
861 | > | |
862 | > | #endif // is_mpi |
863 | > | } |
864 | > | |
865 | > | // make the bonds |
866 | > | for(j=0; j<info.nBonds; j++){ |
867 | > | |
868 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
869 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
870 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
871 | ||
872 | < | the_ff->initializeBonds( the_bonds ); |
873 | < | } |
872 | > | exI = theBonds[j].a; |
873 | > | exJ = theBonds[j].b; |
874 | ||
875 | < | void SimSetup::makeBends( void ){ |
876 | < | |
877 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
878 | < | bend_set* the_bends; |
879 | < | BendStamp* current_bend; |
880 | < | 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 | < | |
875 | > | // exclude_I must always be the smaller of the pair |
876 | > | if( exI > exJ ){ |
877 | > | tempEx = exI; |
878 | > | exI = exJ; |
879 | > | exJ = tempEx; |
880 | > | } |
881 | #ifdef IS_MPI | |
882 | < | if( mpiSim->getMyMolStart() <= molIndex && |
883 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
884 | < | #endif // is_mpi |
882 | > | tempEx = exI; |
883 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
884 | > | tempEx = exJ; |
885 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
886 | > | |
887 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
888 | > | #else // isn't MPI |
889 | ||
890 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
890 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
891 | > | #endif //is_mpi |
892 | > | } |
893 | > | excludeOffset += info.nBonds; |
894 | > | |
895 | > | //make the bends |
896 | > | for(j=0; j<info.nBends; j++){ |
897 | > | |
898 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
899 | > | theBends[j].a = currentBend->getA() + atomOffset; |
900 | > | theBends[j].b = currentBend->getB() + atomOffset; |
901 | > | theBends[j].c = currentBend->getC() + atomOffset; |
902 | ||
903 | < | 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() ){ |
903 | > | if( currentBend->haveExtras() ){ |
904 | ||
905 | < | extras = current_bend->getExtras(); |
906 | < | current_extra = extras; |
905 | > | extras = currentBend->getExtras(); |
906 | > | current_extra = extras; |
907 | ||
908 | < | while( current_extra != NULL ){ |
909 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
908 | > | while( current_extra != NULL ){ |
909 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
910 | ||
911 | < | switch( current_extra->getType() ){ |
911 | > | switch( current_extra->getType() ){ |
912 | > | |
913 | > | case 0: |
914 | > | theBends[j].ghost = |
915 | > | current_extra->getInt() + atomOffset; |
916 | > | theBends[j].isGhost = 1; |
917 | > | break; |
918 | ||
919 | < | case 0: |
920 | < | the_bends[index].ghost = |
921 | < | current_extra->getInt() + offset; |
922 | < | the_bends[index].isGhost = 1; |
923 | < | 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 | < | } |
919 | > | case 1: |
920 | > | theBends[j].ghost = |
921 | > | (int)current_extra->getDouble() + atomOffset; |
922 | > | theBends[j].isGhost = 1; |
923 | > | break; |
924 | ||
925 | < | else{ |
926 | < | |
927 | < | sprintf( painCave.errMsg, |
928 | < | "SimSetup Error: unhandled bend assignment:\n" |
929 | < | " -->%s in Bend[%d] in %s\n", |
930 | < | current_extra->getlhs(), |
931 | < | k, comp_stamps[i]->getID() ); |
932 | < | painCave.isFatal = 1; |
843 | < | simError(); |
844 | < | } |
845 | < | |
846 | < | current_extra = current_extra->getNext(); |
925 | > | default: |
926 | > | sprintf( painCave.errMsg, |
927 | > | "SimSetup Error: ghostVectorSource was neither a " |
928 | > | "double nor an int.\n" |
929 | > | "-->Bend[%d] in %s\n", |
930 | > | j, comp_stamps[stampID]->getID() ); |
931 | > | painCave.isFatal = 1; |
932 | > | simError(); |
933 | } | |
934 | } | |
935 | ||
850 | – | if( !the_bends[index].isGhost ){ |
851 | – | |
852 | – | exI = the_bends[index].a; |
853 | – | exJ = the_bends[index].c; |
854 | – | } |
936 | else{ | |
937 | ||
938 | < | exI = the_bends[index].a; |
939 | < | exJ = the_bends[index].b; |
938 | > | sprintf( painCave.errMsg, |
939 | > | "SimSetup Error: unhandled bend assignment:\n" |
940 | > | " -->%s in Bend[%d] in %s\n", |
941 | > | current_extra->getlhs(), |
942 | > | j, comp_stamps[stampID]->getID() ); |
943 | > | painCave.isFatal = 1; |
944 | > | simError(); |
945 | } | |
946 | ||
947 | < | // exclude_I must always be the smaller of the pair |
948 | < | if( exI > exJ ){ |
949 | < | tempEx = exI; |
950 | < | exI = exJ; |
951 | < | exJ = tempEx; |
952 | < | } |
947 | > | current_extra = current_extra->getNext(); |
948 | > | } |
949 | > | } |
950 | > | |
951 | > | if( !theBends[j].isGhost ){ |
952 | > | |
953 | > | exI = theBends[j].a; |
954 | > | exJ = theBends[j].c; |
955 | > | } |
956 | > | else{ |
957 | > | |
958 | > | exI = theBends[j].a; |
959 | > | exJ = theBends[j].b; |
960 | > | } |
961 | > | |
962 | > | // exclude_I must always be the smaller of the pair |
963 | > | if( exI > exJ ){ |
964 | > | tempEx = exI; |
965 | > | exI = exJ; |
966 | > | exJ = tempEx; |
967 | > | } |
968 | > | #ifdef IS_MPI |
969 | > | tempEx = exI; |
970 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
971 | > | tempEx = exJ; |
972 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
973 | > | |
974 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
975 | > | #else // isn't MPI |
976 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
977 | > | #endif //is_mpi |
978 | > | } |
979 | > | excludeOffset += info.nBends; |
980 | ||
981 | + | for(j=0; j<info.nTorsions; j++){ |
982 | + | |
983 | + | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
984 | + | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
985 | + | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
986 | + | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
987 | + | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
988 | + | |
989 | + | exI = theTorsions[j].a; |
990 | + | exJ = theTorsions[j].d; |
991 | ||
992 | + | // exclude_I must always be the smaller of the pair |
993 | + | if( exI > exJ ){ |
994 | + | tempEx = exI; |
995 | + | exI = exJ; |
996 | + | exJ = tempEx; |
997 | + | } |
998 | #ifdef IS_MPI | |
999 | < | |
1000 | < | the_excludes[(index + tot_bonds)*2] = |
1001 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1002 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
1003 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1004 | < | |
999 | > | tempEx = exI; |
1000 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1001 | > | tempEx = exJ; |
1002 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1003 | > | |
1004 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1005 | #else // isn't MPI | |
1006 | < | |
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) |
1006 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1007 | #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++; |
1008 | } | |
1009 | < | } |
1009 | > | excludeOffset += info.nTorsions; |
1010 | ||
1011 | < | #ifdef IS_MPI |
1012 | < | sprintf( checkPointMsg, |
899 | < | "Successfully created the bends list.\n" ); |
900 | < | MPIcheckPoint(); |
901 | < | #endif // is_mpi |
902 | < | |
1011 | > | |
1012 | > | // send the arrays off to the forceField for init. |
1013 | ||
1014 | < | the_ff->initializeBends( the_bends ); |
1015 | < | } |
1014 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1015 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1016 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1017 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1018 | ||
907 | – | void SimSetup::makeTorsions( void ){ |
1019 | ||
1020 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
910 | < | torsion_set* the_torsions; |
911 | < | TorsionStamp* current_torsion; |
1020 | > | the_molecules[i].initialize( info ); |
1021 | ||
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++ ){ |
1022 | ||
1023 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1023 | > | atomOffset += info.nAtoms; |
1024 | > | delete[] theBonds; |
1025 | > | delete[] theBends; |
1026 | > | delete[] theTorsions; |
1027 | > | } |
1028 | ||
1029 | #ifdef IS_MPI | |
1030 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1031 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1032 | < | #endif // is_mpi |
1030 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1031 | > | MPIcheckPoint(); |
1032 | > | #endif // is_mpi |
1033 | ||
1034 | < | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1034 | > | // clean up the forcefield |
1035 | > | the_ff->calcRcut(); |
1036 | > | the_ff->cleanMe(); |
1037 | ||
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 | – | |
953 | – | #else // isn't MPI |
954 | – | |
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) |
958 | – | #endif //is_mpi |
959 | – | |
960 | – | |
961 | – | // increment the index and repeat; |
962 | – | index++; |
963 | – | } |
964 | – | offset += comp_stamps[i]->getNAtoms(); |
965 | – | |
966 | – | #ifdef IS_MPI |
967 | – | } |
968 | – | #endif //is_mpi |
969 | – | |
970 | – | molIndex++; |
971 | – | } |
972 | – | } |
973 | – | |
974 | – | the_ff->initializeTorsions( the_torsions ); |
1038 | } | |
1039 | ||
1040 | void SimSetup::initFromBass( void ){ |
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