# | 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 | + | 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 242 | Line 310 | void SimSetup::createSim( void ){ | |
310 | ||
311 | globalIndex = mpiSim->divideLabor(); | |
312 | ||
245 | – | |
246 | – | |
313 | // set up the local variables | |
314 | ||
315 | int localMol, allMol; | |
316 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
317 | + | |
318 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
319 | + | int* molCompType = mpiSim->getMolComponentType(); |
320 | ||
321 | allMol = 0; | |
322 | localMol = 0; | |
# | Line 259 | Line 328 | void SimSetup::createSim( void ){ | |
328 | ||
329 | for( j=0; j<components_nmol[i]; j++ ){ | |
330 | ||
331 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
331 | > | if( mol2proc[j] == worldRank ){ |
332 | ||
333 | local_atoms += comp_stamps[i]->getNAtoms(); | |
334 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 279 | Line 347 | void SimSetup::createSim( void ){ | |
347 | if( local_atoms != simnfo->n_atoms ){ | |
348 | sprintf( painCave.errMsg, | |
349 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
350 | < | " localAtom (%d) are note equal.\n", |
350 | > | " localAtom (%d) are not equal.\n", |
351 | simnfo->n_atoms, | |
352 | local_atoms ); | |
353 | painCave.isFatal = 1; | |
# | Line 304 | Line 372 | void SimSetup::createSim( void ){ | |
372 | Atom::createArrays(simnfo->n_atoms); | |
373 | the_atoms = new Atom*[simnfo->n_atoms]; | |
374 | the_molecules = new Molecule[simnfo->n_mol]; | |
375 | + | int molIndex; |
376 | ||
377 | + | // initialize the molecule's stampID's |
378 | ||
379 | < | if( simnfo->n_SRI ){ |
380 | < | the_sris = new SRI*[simnfo->n_SRI]; |
381 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
379 | > | #ifdef IS_MPI |
380 | > | |
381 | > | |
382 | > | molIndex = 0; |
383 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
384 | > | |
385 | > | if(mol2proc[i] == worldRank ){ |
386 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
387 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
388 | > | molIndex++; |
389 | > | } |
390 | > | } |
391 | > | |
392 | > | #else // is_mpi |
393 | > | |
394 | > | molIndex = 0; |
395 | > | for(i=0; i<n_components; i++){ |
396 | > | for(j=0; j<components_nmol[i]; j++ ){ |
397 | > | the_molecules[molIndex].setStampID( i ); |
398 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
399 | > | molIndex++; |
400 | > | } |
401 | > | } |
402 | > | |
403 | > | |
404 | > | #endif // is_mpi |
405 | > | |
406 | > | |
407 | > | if( simnfo->n_SRI ){ |
408 | > | |
409 | > | Exclude::createArray(simnfo->n_SRI); |
410 | > | the_excludes = new Exclude*[simnfo->n_SRI]; |
411 | > | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
412 | simnfo->globalExcludes = new int; | |
413 | < | simnfo->n_exclude = tot_SRI; |
413 | > | simnfo->n_exclude = simnfo->n_SRI; |
414 | } | |
415 | else{ | |
416 | ||
417 | < | the_excludes = new int[2]; |
418 | < | the_excludes[0] = 0; |
419 | < | the_excludes[1] = 0; |
417 | > | Exclude::createArray( 1 ); |
418 | > | the_excludes = new Exclude*; |
419 | > | the_excludes[0] = new Exclude(0); |
420 | > | the_excludes[0]->setPair( 0,0 ); |
421 | simnfo->globalExcludes = new int; | |
422 | simnfo->globalExcludes[0] = 0; | |
423 | < | |
323 | < | simnfo->n_exclude = 1; |
423 | > | simnfo->n_exclude = 0; |
424 | } | |
425 | ||
426 | // set the arrays into the SimInfo object | |
427 | ||
428 | simnfo->atoms = the_atoms; | |
429 | < | simnfo->sr_interactions = the_sris; |
429 | > | simnfo->molecules = the_molecules; |
430 | simnfo->nGlobalExcludes = 0; | |
431 | simnfo->excludes = the_excludes; | |
432 | ||
433 | ||
434 | // get some of the tricky things that may still be in the globals | |
435 | ||
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 |
436 | ||
437 | if( the_globals->haveBox() ){ | |
438 | simnfo->box_x = the_globals->getBox(); | |
# | Line 407 | Line 483 | void SimSetup::createSim( void ){ | |
483 | ||
484 | the_ff->setSimInfo( simnfo ); | |
485 | ||
486 | < | makeAtoms(); |
486 | > | makeMolecules(); |
487 | simnfo->identArray = new int[simnfo->n_atoms]; | |
488 | + | simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
489 | for(i=0; i<simnfo->n_atoms; i++){ | |
490 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
491 | } | |
492 | < | |
493 | < | if( tot_bonds ){ |
417 | < | makeBonds(); |
492 | > | for(i=0; i< simnfo->n_mol; i++) { |
493 | > | the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
494 | } | |
495 | + | |
496 | + | if (the_globals->getUseRF() ) { |
497 | + | simnfo->useReactionField = 1; |
498 | + | |
499 | + | if( !the_globals->haveECR() ){ |
500 | + | sprintf( painCave.errMsg, |
501 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
502 | + | "box length for the electrostaticCutoffRadius.\n" |
503 | + | "I hope you have a very fast processor!\n"); |
504 | + | painCave.isFatal = 0; |
505 | + | simError(); |
506 | + | double smallest; |
507 | + | smallest = simnfo->box_x; |
508 | + | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
509 | + | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
510 | + | simnfo->ecr = 0.5 * smallest; |
511 | + | } else { |
512 | + | simnfo->ecr = the_globals->getECR(); |
513 | + | } |
514 | ||
515 | < | if( tot_bends ){ |
516 | < | makeBends(); |
517 | < | } |
518 | < | |
519 | < | if( tot_torsions ){ |
520 | < | makeTorsions(); |
521 | < | } |
522 | < | |
523 | < | |
524 | < | |
525 | < | |
515 | > | if( !the_globals->haveEST() ){ |
516 | > | sprintf( painCave.errMsg, |
517 | > | "SimSetup Warning: using default value of 0.05 * the " |
518 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
519 | > | ); |
520 | > | painCave.isFatal = 0; |
521 | > | simError(); |
522 | > | simnfo->est = 0.05 * simnfo->ecr; |
523 | > | } else { |
524 | > | simnfo->est = the_globals->getEST(); |
525 | > | } |
526 | > | |
527 | > | if(!the_globals->haveDielectric() ){ |
528 | > | sprintf( painCave.errMsg, |
529 | > | "SimSetup Error: You are trying to use Reaction Field without" |
530 | > | "setting a dielectric constant!\n" |
531 | > | ); |
532 | > | painCave.isFatal = 1; |
533 | > | simError(); |
534 | > | } |
535 | > | simnfo->dielectric = the_globals->getDielectric(); |
536 | > | } else { |
537 | > | if (usesDipoles) { |
538 | > | |
539 | > | if( !the_globals->haveECR() ){ |
540 | > | sprintf( painCave.errMsg, |
541 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
542 | > | "box length for the electrostaticCutoffRadius.\n" |
543 | > | "I hope you have a very fast processor!\n"); |
544 | > | painCave.isFatal = 0; |
545 | > | simError(); |
546 | > | double smallest; |
547 | > | smallest = simnfo->box_x; |
548 | > | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
549 | > | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
550 | > | simnfo->ecr = 0.5 * smallest; |
551 | > | } else { |
552 | > | simnfo->ecr = the_globals->getECR(); |
553 | > | } |
554 | > | |
555 | > | if( !the_globals->haveEST() ){ |
556 | > | sprintf( painCave.errMsg, |
557 | > | "SimSetup Warning: using default value of 5%% of the " |
558 | > | "electrostaticCutoffRadius for the " |
559 | > | "electrostaticSkinThickness\n" |
560 | > | ); |
561 | > | painCave.isFatal = 0; |
562 | > | simError(); |
563 | > | simnfo->est = 0.05 * simnfo->ecr; |
564 | > | } else { |
565 | > | simnfo->est = the_globals->getEST(); |
566 | > | } |
567 | > | } |
568 | > | } |
569 | ||
570 | + | #ifdef IS_MPI |
571 | + | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
572 | + | MPIcheckPoint(); |
573 | + | #endif // is_mpi |
574 | ||
575 | if( the_globals->haveInitialConfig() ){ | |
576 | ||
# | Line 587 | Line 729 | void SimSetup::createSim( void ){ | |
729 | ||
730 | // new AllLong( simnfo ); | |
731 | ||
590 | – | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
591 | – | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
592 | – | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
593 | – | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
732 | ||
733 | + | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
734 | + | new Symplectic(simnfo, the_ff, the_extendedsystem); |
735 | + | } |
736 | + | else if( !strcmp( force_field, "LJ" ) ){ |
737 | + | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
738 | + | } |
739 | + | else { |
740 | + | std::cerr << "I'm a bug.\n"; |
741 | + | fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
742 | + | } |
743 | + | #ifdef IS_MPI |
744 | + | mpiSim->mpiRefresh(); |
745 | + | #endif |
746 | ||
596 | – | |
747 | // initialize the Fortran | |
748 | < | |
748 | > | |
749 | > | |
750 | simnfo->refreshSim(); | |
751 | ||
752 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 620 | Line 771 | void SimSetup::createSim( void ){ | |
771 | #endif // is_mpi | |
772 | } | |
773 | ||
623 | – | void SimSetup::makeAtoms( void ){ |
774 | ||
775 | < | int i, j, k, index; |
626 | < | double ux, uy, uz, uSqr, u; |
627 | < | AtomStamp* current_atom; |
775 | > | void SimSetup::makeMolecules( void ){ |
776 | ||
777 | + | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
778 | + | molInit info; |
779 | DirectionalAtom* dAtom; | |
780 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
780 | > | LinkedAssign* extras; |
781 | > | LinkedAssign* current_extra; |
782 | > | AtomStamp* currentAtom; |
783 | > | BondStamp* currentBond; |
784 | > | BendStamp* currentBend; |
785 | > | TorsionStamp* currentTorsion; |
786 | ||
787 | < | lMolIndex = 0; |
788 | < | molIndex = 0; |
789 | < | index = 0; |
635 | < | for( i=0; i<n_components; i++ ){ |
787 | > | bond_pair* theBonds; |
788 | > | bend_set* theBends; |
789 | > | torsion_set* theTorsions; |
790 | ||
791 | < | for( j=0; j<components_nmol[i]; j++ ){ |
791 | > | |
792 | > | //init the forceField paramters |
793 | ||
794 | < | #ifdef IS_MPI |
640 | < | if( mpiSim->getMyMolStart() <= molIndex && |
641 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
642 | < | #endif // is_mpi |
794 | > | the_ff->readParams(); |
795 | ||
796 | < | molStart = index; |
797 | < | 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++; |
796 | > | |
797 | > | // init the atoms |
798 | ||
799 | < | #ifdef IS_MPI |
800 | < | } |
801 | < | #endif //is_mpi |
802 | < | |
803 | < | molIndex++; |
692 | < | } |
693 | < | } |
694 | < | |
695 | < | #ifdef IS_MPI |
696 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
799 | > | double ux, uy, uz, u, uSqr; |
800 | > | |
801 | > | atomOffset = 0; |
802 | > | excludeOffset = 0; |
803 | > | for(i=0; i<simnfo->n_mol; i++){ |
804 | ||
805 | < | delete[] globalIndex; |
805 | > | stampID = the_molecules[i].getStampID(); |
806 | ||
807 | < | mpiSim->mpiRefresh(); |
808 | < | #endif //IS_MPI |
809 | < | |
810 | < | the_ff->initializeAtoms(); |
811 | < | } |
705 | < | |
706 | < | void SimSetup::makeBonds( void ){ |
707 | < | |
708 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
709 | < | bond_pair* the_bonds; |
710 | < | 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; |
731 | < | |
732 | < | exI = the_bonds[index].a; |
733 | < | exJ = the_bonds[index].b; |
734 | < | |
735 | < | // exclude_I must always be the smaller of the pair |
736 | < | if( exI > exJ ){ |
737 | < | tempEx = exI; |
738 | < | exI = exJ; |
739 | < | exJ = tempEx; |
740 | < | } |
741 | < | |
742 | < | |
743 | < | #ifdef IS_MPI |
807 | > | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
808 | > | info.nBonds = comp_stamps[stampID]->getNBonds(); |
809 | > | info.nBends = comp_stamps[stampID]->getNBends(); |
810 | > | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
811 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
812 | ||
813 | < | the_excludes[index*2] = |
814 | < | the_atoms[exI]->getGlobalIndex() + 1; |
815 | < | the_excludes[index*2 + 1] = |
816 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
813 | > | info.myAtoms = &the_atoms[atomOffset]; |
814 | > | info.myExcludes = &the_excludes[excludeOffset]; |
815 | > | info.myBonds = new Bond*[info.nBonds]; |
816 | > | info.myBends = new Bend*[info.nBends]; |
817 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
818 | ||
819 | < | #else // isn't MPI |
820 | < | |
821 | < | the_excludes[index*2] = exI + 1; |
822 | < | the_excludes[index*2 + 1] = exJ + 1; |
823 | < | // fortran index from 1 (hence the +1 in the indexing) |
824 | < | #endif //is_mpi |
825 | < | |
826 | < | // increment the index and repeat; |
827 | < | index++; |
828 | < | } |
760 | < | offset += comp_stamps[i]->getNAtoms(); |
819 | > | theBonds = new bond_pair[info.nBonds]; |
820 | > | theBends = new bend_set[info.nBends]; |
821 | > | theTorsions = new torsion_set[info.nTorsions]; |
822 | > | |
823 | > | // make the Atoms |
824 | > | |
825 | > | for(j=0; j<info.nAtoms; j++){ |
826 | > | |
827 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
828 | > | if( currentAtom->haveOrientation() ){ |
829 | ||
830 | < | #ifdef IS_MPI |
830 | > | dAtom = new DirectionalAtom(j + atomOffset); |
831 | > | simnfo->n_oriented++; |
832 | > | info.myAtoms[j] = dAtom; |
833 | > | |
834 | > | ux = currentAtom->getOrntX(); |
835 | > | uy = currentAtom->getOrntY(); |
836 | > | uz = currentAtom->getOrntZ(); |
837 | > | |
838 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
839 | > | |
840 | > | u = sqrt( uSqr ); |
841 | > | ux = ux / u; |
842 | > | uy = uy / u; |
843 | > | uz = uz / u; |
844 | > | |
845 | > | dAtom->setSUx( ux ); |
846 | > | dAtom->setSUy( uy ); |
847 | > | dAtom->setSUz( uz ); |
848 | } | |
849 | < | #endif //is_mpi |
849 | > | else{ |
850 | > | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
851 | > | } |
852 | > | info.myAtoms[j]->setType( currentAtom->getType() ); |
853 | > | |
854 | > | #ifdef IS_MPI |
855 | ||
856 | < | molIndex++; |
857 | < | } |
858 | < | } |
856 | > | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
857 | > | |
858 | > | #endif // is_mpi |
859 | > | } |
860 | > | |
861 | > | // make the bonds |
862 | > | for(j=0; j<info.nBonds; j++){ |
863 | > | |
864 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
865 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
866 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
867 | ||
868 | < | the_ff->initializeBonds( the_bonds ); |
869 | < | } |
868 | > | exI = theBonds[j].a; |
869 | > | exJ = theBonds[j].b; |
870 | ||
871 | < | void SimSetup::makeBends( void ){ |
872 | < | |
873 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
874 | < | bend_set* the_bends; |
875 | < | BendStamp* current_bend; |
876 | < | 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 | < | |
871 | > | // exclude_I must always be the smaller of the pair |
872 | > | if( exI > exJ ){ |
873 | > | tempEx = exI; |
874 | > | exI = exJ; |
875 | > | exJ = tempEx; |
876 | > | } |
877 | #ifdef IS_MPI | |
878 | < | if( mpiSim->getMyMolStart() <= molIndex && |
879 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
880 | < | #endif // is_mpi |
878 | > | tempEx = exI; |
879 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
880 | > | tempEx = exJ; |
881 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
882 | > | |
883 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
884 | > | #else // isn't MPI |
885 | ||
886 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
886 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
887 | > | #endif //is_mpi |
888 | > | } |
889 | > | excludeOffset += info.nBonds; |
890 | > | |
891 | > | //make the bends |
892 | > | for(j=0; j<info.nBends; j++){ |
893 | > | |
894 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
895 | > | theBends[j].a = currentBend->getA() + atomOffset; |
896 | > | theBends[j].b = currentBend->getB() + atomOffset; |
897 | > | theBends[j].c = currentBend->getC() + atomOffset; |
898 | ||
899 | < | 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() ){ |
899 | > | if( currentBend->haveExtras() ){ |
900 | ||
901 | < | extras = current_bend->getExtras(); |
902 | < | current_extra = extras; |
901 | > | extras = currentBend->getExtras(); |
902 | > | current_extra = extras; |
903 | ||
904 | < | while( current_extra != NULL ){ |
905 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
904 | > | while( current_extra != NULL ){ |
905 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
906 | ||
907 | < | switch( current_extra->getType() ){ |
907 | > | switch( current_extra->getType() ){ |
908 | > | |
909 | > | case 0: |
910 | > | theBends[j].ghost = |
911 | > | current_extra->getInt() + atomOffset; |
912 | > | theBends[j].isGhost = 1; |
913 | > | break; |
914 | ||
915 | < | case 0: |
916 | < | the_bends[index].ghost = |
917 | < | current_extra->getInt() + offset; |
918 | < | the_bends[index].isGhost = 1; |
919 | < | 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 | < | } |
915 | > | case 1: |
916 | > | theBends[j].ghost = |
917 | > | (int)current_extra->getDouble() + atomOffset; |
918 | > | theBends[j].isGhost = 1; |
919 | > | break; |
920 | ||
921 | < | else{ |
922 | < | |
923 | < | sprintf( painCave.errMsg, |
924 | < | "SimSetup Error: unhandled bend assignment:\n" |
925 | < | " -->%s in Bend[%d] in %s\n", |
926 | < | current_extra->getlhs(), |
927 | < | k, comp_stamps[i]->getID() ); |
928 | < | painCave.isFatal = 1; |
843 | < | simError(); |
844 | < | } |
845 | < | |
846 | < | current_extra = current_extra->getNext(); |
921 | > | default: |
922 | > | sprintf( painCave.errMsg, |
923 | > | "SimSetup Error: ghostVectorSource was neither a " |
924 | > | "double nor an int.\n" |
925 | > | "-->Bend[%d] in %s\n", |
926 | > | j, comp_stamps[stampID]->getID() ); |
927 | > | painCave.isFatal = 1; |
928 | > | simError(); |
929 | } | |
930 | } | |
931 | ||
850 | – | if( !the_bends[index].isGhost ){ |
851 | – | |
852 | – | exI = the_bends[index].a; |
853 | – | exJ = the_bends[index].c; |
854 | – | } |
932 | else{ | |
933 | ||
934 | < | exI = the_bends[index].a; |
935 | < | exJ = the_bends[index].b; |
934 | > | sprintf( painCave.errMsg, |
935 | > | "SimSetup Error: unhandled bend assignment:\n" |
936 | > | " -->%s in Bend[%d] in %s\n", |
937 | > | current_extra->getlhs(), |
938 | > | j, comp_stamps[stampID]->getID() ); |
939 | > | painCave.isFatal = 1; |
940 | > | simError(); |
941 | } | |
942 | ||
943 | < | // exclude_I must always be the smaller of the pair |
944 | < | if( exI > exJ ){ |
945 | < | tempEx = exI; |
946 | < | exI = exJ; |
947 | < | exJ = tempEx; |
948 | < | } |
943 | > | current_extra = current_extra->getNext(); |
944 | > | } |
945 | > | } |
946 | > | |
947 | > | if( !theBends[j].isGhost ){ |
948 | > | |
949 | > | exI = theBends[j].a; |
950 | > | exJ = theBends[j].c; |
951 | > | } |
952 | > | else{ |
953 | > | |
954 | > | exI = theBends[j].a; |
955 | > | exJ = theBends[j].b; |
956 | > | } |
957 | > | |
958 | > | // exclude_I must always be the smaller of the pair |
959 | > | if( exI > exJ ){ |
960 | > | tempEx = exI; |
961 | > | exI = exJ; |
962 | > | exJ = tempEx; |
963 | > | } |
964 | > | #ifdef IS_MPI |
965 | > | tempEx = exI; |
966 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
967 | > | tempEx = exJ; |
968 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
969 | > | |
970 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
971 | > | #else // isn't MPI |
972 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
973 | > | #endif //is_mpi |
974 | > | } |
975 | > | excludeOffset += info.nBends; |
976 | ||
977 | + | for(j=0; j<info.nTorsions; j++){ |
978 | + | |
979 | + | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
980 | + | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
981 | + | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
982 | + | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
983 | + | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
984 | + | |
985 | + | exI = theTorsions[j].a; |
986 | + | exJ = theTorsions[j].d; |
987 | ||
988 | + | // exclude_I must always be the smaller of the pair |
989 | + | if( exI > exJ ){ |
990 | + | tempEx = exI; |
991 | + | exI = exJ; |
992 | + | exJ = tempEx; |
993 | + | } |
994 | #ifdef IS_MPI | |
995 | < | |
996 | < | the_excludes[(index + tot_bonds)*2] = |
997 | < | the_atoms[exI]->getGlobalIndex() + 1; |
998 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
999 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1000 | < | |
995 | > | tempEx = exI; |
996 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
997 | > | tempEx = exJ; |
998 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
999 | > | |
1000 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1001 | #else // isn't MPI | |
1002 | < | |
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) |
1002 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1003 | #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++; |
1004 | } | |
1005 | < | } |
1005 | > | excludeOffset += info.nTorsions; |
1006 | > | |
1007 | > | |
1008 | > | // send the arrays off to the forceField for init. |
1009 | ||
1010 | < | #ifdef IS_MPI |
1011 | < | sprintf( checkPointMsg, |
1012 | < | "Successfully created the bends list.\n" ); |
1013 | < | MPIcheckPoint(); |
901 | < | #endif // is_mpi |
902 | < | |
1010 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1011 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1012 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1013 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1014 | ||
904 | – | the_ff->initializeBends( the_bends ); |
905 | – | } |
1015 | ||
1016 | < | void SimSetup::makeTorsions( void ){ |
1016 | > | the_molecules[i].initialize( info ); |
1017 | ||
909 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
910 | – | torsion_set* the_torsions; |
911 | – | TorsionStamp* current_torsion; |
1018 | ||
1019 | < | the_torsions = new torsion_set[tot_torsions]; |
1020 | < | index = 0; |
1021 | < | offset = 0; |
1022 | < | molIndex = 0; |
1023 | < | for( i=0; i<n_components; i++ ){ |
1019 | > | atomOffset += info.nAtoms; |
1020 | > | delete[] theBonds; |
1021 | > | delete[] theBends; |
1022 | > | delete[] theTorsions; |
1023 | > | } |
1024 | ||
919 | – | for( j=0; j<components_nmol[i]; j++ ){ |
920 | – | |
1025 | #ifdef IS_MPI | |
1026 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1027 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1028 | < | #endif // is_mpi |
1026 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1027 | > | MPIcheckPoint(); |
1028 | > | #endif // is_mpi |
1029 | ||
1030 | < | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1030 | > | // clean up the forcefield |
1031 | > | the_ff->calcRcut(); |
1032 | > | the_ff->cleanMe(); |
1033 | ||
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 ); |
1034 | } | |
1035 | ||
1036 | void SimSetup::initFromBass( void ){ |
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