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; |
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", |
298 |
|
simnfo->n_torsions = tot_torsions; |
299 |
|
simnfo->n_SRI = tot_SRI; |
300 |
|
simnfo->n_mol = tot_nmol; |
301 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
302 |
|
|
234 |
– |
|
303 |
|
#ifdef IS_MPI |
304 |
|
|
305 |
|
// divide the molecules among processors here. |
306 |
|
|
307 |
|
mpiSim = new mpiSimulation( simnfo ); |
308 |
|
|
241 |
– |
|
242 |
– |
|
309 |
|
globalIndex = mpiSim->divideLabor(); |
310 |
|
|
245 |
– |
|
246 |
– |
|
311 |
|
// set up the local variables |
312 |
|
|
313 |
|
int localMol, allMol; |
314 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
315 |
+ |
|
316 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
317 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
318 |
|
|
319 |
|
allMol = 0; |
320 |
|
localMol = 0; |
322 |
|
local_bonds = 0; |
323 |
|
local_bends = 0; |
324 |
|
local_torsions = 0; |
325 |
+ |
globalAtomIndex = 0; |
326 |
+ |
|
327 |
+ |
|
328 |
|
for( i=0; i<n_components; i++ ){ |
329 |
|
|
330 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
331 |
|
|
332 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
332 |
> |
if( mol2proc[allMol] == worldRank ){ |
333 |
|
|
334 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
335 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
337 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
338 |
|
localMol++; |
339 |
|
} |
340 |
< |
allMol++; |
340 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
341 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
342 |
> |
globalAtomIndex++; |
343 |
> |
} |
344 |
> |
|
345 |
> |
allMol++; |
346 |
|
} |
347 |
|
} |
348 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
349 |
|
|
350 |
+ |
if (worldRank != 0) { |
351 |
+ |
for (i =0; i < tot_atoms; i++){ |
352 |
+ |
std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n"; |
353 |
+ |
} |
354 |
+ |
} |
355 |
|
|
356 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
357 |
|
|
358 |
|
if( local_atoms != simnfo->n_atoms ){ |
359 |
|
sprintf( painCave.errMsg, |
360 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
361 |
< |
" localAtom (%d) are note equal.\n", |
361 |
> |
" localAtom (%d) are not equal.\n", |
362 |
|
simnfo->n_atoms, |
363 |
|
local_atoms ); |
364 |
|
painCave.isFatal = 1; |
383 |
|
Atom::createArrays(simnfo->n_atoms); |
384 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
385 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
386 |
+ |
int molIndex; |
387 |
|
|
388 |
+ |
// initialize the molecule's stampID's |
389 |
|
|
390 |
< |
if( simnfo->n_SRI ){ |
391 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
392 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
390 |
> |
#ifdef IS_MPI |
391 |
> |
|
392 |
> |
|
393 |
> |
molIndex = 0; |
394 |
> |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
395 |
> |
|
396 |
> |
if(mol2proc[i] == worldRank ){ |
397 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
398 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
399 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
400 |
> |
molIndex++; |
401 |
> |
} |
402 |
> |
} |
403 |
> |
|
404 |
> |
#else // is_mpi |
405 |
> |
|
406 |
> |
molIndex = 0; |
407 |
> |
globalAtomIndex = 0; |
408 |
> |
for(i=0; i<n_components; i++){ |
409 |
> |
for(j=0; j<components_nmol[i]; j++ ){ |
410 |
> |
the_molecules[molIndex].setStampID( i ); |
411 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
412 |
> |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
413 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
414 |
> |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
415 |
> |
globalAtomIndex++; |
416 |
> |
} |
417 |
> |
molIndex++; |
418 |
> |
} |
419 |
> |
} |
420 |
> |
|
421 |
> |
|
422 |
> |
#endif // is_mpi |
423 |
> |
|
424 |
> |
|
425 |
> |
if( simnfo->n_SRI ){ |
426 |
> |
|
427 |
> |
Exclude::createArray(simnfo->n_SRI); |
428 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
429 |
> |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
430 |
|
simnfo->globalExcludes = new int; |
431 |
< |
simnfo->n_exclude = tot_SRI; |
431 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
432 |
|
} |
433 |
|
else{ |
434 |
|
|
435 |
< |
the_excludes = new int[2]; |
436 |
< |
the_excludes[0] = 0; |
437 |
< |
the_excludes[1] = 0; |
435 |
> |
Exclude::createArray( 1 ); |
436 |
> |
the_excludes = new Exclude*; |
437 |
> |
the_excludes[0] = new Exclude(0); |
438 |
> |
the_excludes[0]->setPair( 0,0 ); |
439 |
|
simnfo->globalExcludes = new int; |
440 |
|
simnfo->globalExcludes[0] = 0; |
441 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
441 |
> |
simnfo->n_exclude = 0; |
442 |
|
} |
443 |
|
|
444 |
|
// set the arrays into the SimInfo object |
445 |
|
|
446 |
|
simnfo->atoms = the_atoms; |
447 |
< |
simnfo->sr_interactions = the_sris; |
447 |
> |
simnfo->molecules = the_molecules; |
448 |
|
simnfo->nGlobalExcludes = 0; |
449 |
|
simnfo->excludes = the_excludes; |
450 |
|
|
451 |
|
|
452 |
|
// get some of the tricky things that may still be in the globals |
453 |
|
|
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 |
454 |
|
|
455 |
|
if( the_globals->haveBox() ){ |
456 |
|
simnfo->box_x = the_globals->getBox(); |
501 |
|
|
502 |
|
the_ff->setSimInfo( simnfo ); |
503 |
|
|
504 |
< |
makeAtoms(); |
504 |
> |
makeMolecules(); |
505 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
506 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
507 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
508 |
|
} |
509 |
|
|
510 |
< |
if( tot_bonds ){ |
511 |
< |
makeBonds(); |
512 |
< |
} |
510 |
> |
if (the_globals->getUseRF() ) { |
511 |
> |
simnfo->useReactionField = 1; |
512 |
> |
|
513 |
> |
if( !the_globals->haveECR() ){ |
514 |
> |
sprintf( painCave.errMsg, |
515 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
516 |
> |
"box length for the electrostaticCutoffRadius.\n" |
517 |
> |
"I hope you have a very fast processor!\n"); |
518 |
> |
painCave.isFatal = 0; |
519 |
> |
simError(); |
520 |
> |
double smallest; |
521 |
> |
smallest = simnfo->box_x; |
522 |
> |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
523 |
> |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
524 |
> |
simnfo->ecr = 0.5 * smallest; |
525 |
> |
} else { |
526 |
> |
simnfo->ecr = the_globals->getECR(); |
527 |
> |
} |
528 |
|
|
529 |
< |
if( tot_bends ){ |
530 |
< |
makeBends(); |
531 |
< |
} |
532 |
< |
|
533 |
< |
if( tot_torsions ){ |
534 |
< |
makeTorsions(); |
535 |
< |
} |
536 |
< |
|
537 |
< |
|
538 |
< |
|
539 |
< |
|
529 |
> |
if( !the_globals->haveEST() ){ |
530 |
> |
sprintf( painCave.errMsg, |
531 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
532 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
533 |
> |
); |
534 |
> |
painCave.isFatal = 0; |
535 |
> |
simError(); |
536 |
> |
simnfo->est = 0.05 * simnfo->ecr; |
537 |
> |
} else { |
538 |
> |
simnfo->est = the_globals->getEST(); |
539 |
> |
} |
540 |
> |
|
541 |
> |
if(!the_globals->haveDielectric() ){ |
542 |
> |
sprintf( painCave.errMsg, |
543 |
> |
"SimSetup Error: You are trying to use Reaction Field without" |
544 |
> |
"setting a dielectric constant!\n" |
545 |
> |
); |
546 |
> |
painCave.isFatal = 1; |
547 |
> |
simError(); |
548 |
> |
} |
549 |
> |
simnfo->dielectric = the_globals->getDielectric(); |
550 |
> |
} else { |
551 |
> |
if (usesDipoles) { |
552 |
> |
|
553 |
> |
if( !the_globals->haveECR() ){ |
554 |
> |
sprintf( painCave.errMsg, |
555 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
556 |
> |
"box length for the electrostaticCutoffRadius.\n" |
557 |
> |
"I hope you have a very fast processor!\n"); |
558 |
> |
painCave.isFatal = 0; |
559 |
> |
simError(); |
560 |
> |
double smallest; |
561 |
> |
smallest = simnfo->box_x; |
562 |
> |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
563 |
> |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
564 |
> |
simnfo->ecr = 0.5 * smallest; |
565 |
> |
} else { |
566 |
> |
simnfo->ecr = the_globals->getECR(); |
567 |
> |
} |
568 |
> |
|
569 |
> |
if( !the_globals->haveEST() ){ |
570 |
> |
sprintf( painCave.errMsg, |
571 |
> |
"SimSetup Warning: using default value of 5%% of the " |
572 |
> |
"electrostaticCutoffRadius for the " |
573 |
> |
"electrostaticSkinThickness\n" |
574 |
> |
); |
575 |
> |
painCave.isFatal = 0; |
576 |
> |
simError(); |
577 |
> |
simnfo->est = 0.05 * simnfo->ecr; |
578 |
> |
} else { |
579 |
> |
simnfo->est = the_globals->getEST(); |
580 |
> |
} |
581 |
> |
} |
582 |
> |
} |
583 |
|
|
584 |
+ |
#ifdef IS_MPI |
585 |
+ |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
586 |
+ |
MPIcheckPoint(); |
587 |
+ |
#endif // is_mpi |
588 |
|
|
589 |
|
if( the_globals->haveInitialConfig() ){ |
590 |
|
|
743 |
|
|
744 |
|
// new AllLong( simnfo ); |
745 |
|
|
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 ); |
746 |
|
|
747 |
+ |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
748 |
+ |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
749 |
+ |
} |
750 |
+ |
else if( !strcmp( force_field, "LJ" ) ){ |
751 |
+ |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
752 |
+ |
} |
753 |
+ |
else { |
754 |
+ |
std::cerr << "I'm a bug.\n"; |
755 |
+ |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
756 |
+ |
} |
757 |
+ |
#ifdef IS_MPI |
758 |
+ |
mpiSim->mpiRefresh(); |
759 |
+ |
#endif |
760 |
|
|
596 |
– |
|
761 |
|
// initialize the Fortran |
762 |
< |
|
762 |
> |
|
763 |
> |
|
764 |
|
simnfo->refreshSim(); |
765 |
|
|
766 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
785 |
|
#endif // is_mpi |
786 |
|
} |
787 |
|
|
623 |
– |
void SimSetup::makeAtoms( void ){ |
788 |
|
|
789 |
< |
int i, j, k, index; |
626 |
< |
double ux, uy, uz, uSqr, u; |
627 |
< |
AtomStamp* current_atom; |
789 |
> |
void SimSetup::makeMolecules( void ){ |
790 |
|
|
791 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
792 |
+ |
molInit info; |
793 |
|
DirectionalAtom* dAtom; |
794 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
794 |
> |
LinkedAssign* extras; |
795 |
> |
LinkedAssign* current_extra; |
796 |
> |
AtomStamp* currentAtom; |
797 |
> |
BondStamp* currentBond; |
798 |
> |
BendStamp* currentBend; |
799 |
> |
TorsionStamp* currentTorsion; |
800 |
|
|
801 |
< |
lMolIndex = 0; |
802 |
< |
molIndex = 0; |
803 |
< |
index = 0; |
635 |
< |
for( i=0; i<n_components; i++ ){ |
801 |
> |
bond_pair* theBonds; |
802 |
> |
bend_set* theBends; |
803 |
> |
torsion_set* theTorsions; |
804 |
|
|
805 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
805 |
> |
|
806 |
> |
//init the forceField paramters |
807 |
|
|
808 |
< |
#ifdef IS_MPI |
640 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
641 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
642 |
< |
#endif // is_mpi |
808 |
> |
the_ff->readParams(); |
809 |
|
|
810 |
< |
molStart = index; |
811 |
< |
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++; |
810 |
> |
|
811 |
> |
// init the atoms |
812 |
|
|
813 |
< |
#ifdef IS_MPI |
814 |
< |
} |
815 |
< |
#endif //is_mpi |
816 |
< |
|
817 |
< |
molIndex++; |
692 |
< |
} |
693 |
< |
} |
694 |
< |
|
695 |
< |
#ifdef IS_MPI |
696 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
813 |
> |
double ux, uy, uz, u, uSqr; |
814 |
> |
|
815 |
> |
atomOffset = 0; |
816 |
> |
excludeOffset = 0; |
817 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
818 |
|
|
819 |
< |
delete[] globalIndex; |
819 |
> |
stampID = the_molecules[i].getStampID(); |
820 |
|
|
821 |
< |
mpiSim->mpiRefresh(); |
822 |
< |
#endif //IS_MPI |
823 |
< |
|
824 |
< |
the_ff->initializeAtoms(); |
825 |
< |
} |
821 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
822 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
823 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
824 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
825 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
826 |
|
|
827 |
< |
void SimSetup::makeBonds( void ){ |
827 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
828 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
829 |
> |
info.myBonds = new Bond*[info.nBonds]; |
830 |
> |
info.myBends = new Bend*[info.nBends]; |
831 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
832 |
|
|
833 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
834 |
< |
bond_pair* the_bonds; |
835 |
< |
BondStamp* current_bond; |
836 |
< |
|
837 |
< |
the_bonds = new bond_pair[tot_bonds]; |
838 |
< |
index = 0; |
839 |
< |
offset = 0; |
840 |
< |
molIndex = 0; |
841 |
< |
|
842 |
< |
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 |
833 |
> |
theBonds = new bond_pair[info.nBonds]; |
834 |
> |
theBends = new bend_set[info.nBends]; |
835 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
836 |
> |
|
837 |
> |
// make the Atoms |
838 |
> |
|
839 |
> |
for(j=0; j<info.nAtoms; j++){ |
840 |
> |
|
841 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
842 |
> |
if( currentAtom->haveOrientation() ){ |
843 |
|
|
844 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
845 |
< |
|
846 |
< |
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 |
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(); |
844 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
845 |
> |
simnfo->n_oriented++; |
846 |
> |
info.myAtoms[j] = dAtom; |
847 |
|
|
848 |
< |
#ifdef IS_MPI |
848 |
> |
ux = currentAtom->getOrntX(); |
849 |
> |
uy = currentAtom->getOrntY(); |
850 |
> |
uz = currentAtom->getOrntZ(); |
851 |
> |
|
852 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
853 |
> |
|
854 |
> |
u = sqrt( uSqr ); |
855 |
> |
ux = ux / u; |
856 |
> |
uy = uy / u; |
857 |
> |
uz = uz / u; |
858 |
> |
|
859 |
> |
dAtom->setSUx( ux ); |
860 |
> |
dAtom->setSUy( uy ); |
861 |
> |
dAtom->setSUz( uz ); |
862 |
|
} |
863 |
< |
#endif //is_mpi |
863 |
> |
else{ |
864 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
865 |
> |
} |
866 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
867 |
> |
|
868 |
> |
#ifdef IS_MPI |
869 |
|
|
870 |
< |
molIndex++; |
871 |
< |
} |
872 |
< |
} |
870 |
> |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
871 |
> |
|
872 |
> |
#endif // is_mpi |
873 |
> |
} |
874 |
> |
|
875 |
> |
// make the bonds |
876 |
> |
for(j=0; j<info.nBonds; j++){ |
877 |
> |
|
878 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
879 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
880 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
881 |
|
|
882 |
< |
the_ff->initializeBonds( the_bonds ); |
883 |
< |
} |
882 |
> |
exI = theBonds[j].a; |
883 |
> |
exJ = theBonds[j].b; |
884 |
|
|
885 |
< |
void SimSetup::makeBends( void ){ |
886 |
< |
|
887 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
888 |
< |
bend_set* the_bends; |
889 |
< |
BendStamp* current_bend; |
890 |
< |
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 |
< |
|
885 |
> |
// exclude_I must always be the smaller of the pair |
886 |
> |
if( exI > exJ ){ |
887 |
> |
tempEx = exI; |
888 |
> |
exI = exJ; |
889 |
> |
exJ = tempEx; |
890 |
> |
} |
891 |
|
#ifdef IS_MPI |
892 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
893 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
894 |
< |
#endif // is_mpi |
892 |
> |
tempEx = exI; |
893 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
894 |
> |
tempEx = exJ; |
895 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
896 |
> |
|
897 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
898 |
> |
#else // isn't MPI |
899 |
|
|
900 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
900 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
901 |
> |
#endif //is_mpi |
902 |
> |
} |
903 |
> |
excludeOffset += info.nBonds; |
904 |
> |
|
905 |
> |
//make the bends |
906 |
> |
for(j=0; j<info.nBends; j++){ |
907 |
> |
|
908 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
909 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
910 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
911 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
912 |
|
|
913 |
< |
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() ){ |
913 |
> |
if( currentBend->haveExtras() ){ |
914 |
|
|
915 |
< |
extras = current_bend->getExtras(); |
916 |
< |
current_extra = extras; |
915 |
> |
extras = currentBend->getExtras(); |
916 |
> |
current_extra = extras; |
917 |
|
|
918 |
< |
while( current_extra != NULL ){ |
919 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
918 |
> |
while( current_extra != NULL ){ |
919 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
920 |
|
|
921 |
< |
switch( current_extra->getType() ){ |
921 |
> |
switch( current_extra->getType() ){ |
922 |
> |
|
923 |
> |
case 0: |
924 |
> |
theBends[j].ghost = |
925 |
> |
current_extra->getInt() + atomOffset; |
926 |
> |
theBends[j].isGhost = 1; |
927 |
> |
break; |
928 |
|
|
929 |
< |
case 0: |
930 |
< |
the_bends[index].ghost = |
931 |
< |
current_extra->getInt() + offset; |
932 |
< |
the_bends[index].isGhost = 1; |
933 |
< |
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 |
< |
} |
929 |
> |
case 1: |
930 |
> |
theBends[j].ghost = |
931 |
> |
(int)current_extra->getDouble() + atomOffset; |
932 |
> |
theBends[j].isGhost = 1; |
933 |
> |
break; |
934 |
|
|
935 |
< |
else{ |
936 |
< |
|
937 |
< |
sprintf( painCave.errMsg, |
938 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
939 |
< |
" -->%s in Bend[%d] in %s\n", |
940 |
< |
current_extra->getlhs(), |
941 |
< |
k, comp_stamps[i]->getID() ); |
942 |
< |
painCave.isFatal = 1; |
843 |
< |
simError(); |
844 |
< |
} |
845 |
< |
|
846 |
< |
current_extra = current_extra->getNext(); |
935 |
> |
default: |
936 |
> |
sprintf( painCave.errMsg, |
937 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
938 |
> |
"double nor an int.\n" |
939 |
> |
"-->Bend[%d] in %s\n", |
940 |
> |
j, comp_stamps[stampID]->getID() ); |
941 |
> |
painCave.isFatal = 1; |
942 |
> |
simError(); |
943 |
|
} |
944 |
|
} |
945 |
|
|
850 |
– |
if( !the_bends[index].isGhost ){ |
851 |
– |
|
852 |
– |
exI = the_bends[index].a; |
853 |
– |
exJ = the_bends[index].c; |
854 |
– |
} |
946 |
|
else{ |
947 |
|
|
948 |
< |
exI = the_bends[index].a; |
949 |
< |
exJ = the_bends[index].b; |
948 |
> |
sprintf( painCave.errMsg, |
949 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
950 |
> |
" -->%s in Bend[%d] in %s\n", |
951 |
> |
current_extra->getlhs(), |
952 |
> |
j, comp_stamps[stampID]->getID() ); |
953 |
> |
painCave.isFatal = 1; |
954 |
> |
simError(); |
955 |
|
} |
956 |
|
|
957 |
< |
// exclude_I must always be the smaller of the pair |
958 |
< |
if( exI > exJ ){ |
959 |
< |
tempEx = exI; |
960 |
< |
exI = exJ; |
961 |
< |
exJ = tempEx; |
962 |
< |
} |
957 |
> |
current_extra = current_extra->getNext(); |
958 |
> |
} |
959 |
> |
} |
960 |
> |
|
961 |
> |
if( !theBends[j].isGhost ){ |
962 |
> |
|
963 |
> |
exI = theBends[j].a; |
964 |
> |
exJ = theBends[j].c; |
965 |
> |
} |
966 |
> |
else{ |
967 |
> |
|
968 |
> |
exI = theBends[j].a; |
969 |
> |
exJ = theBends[j].b; |
970 |
> |
} |
971 |
> |
|
972 |
> |
// exclude_I must always be the smaller of the pair |
973 |
> |
if( exI > exJ ){ |
974 |
> |
tempEx = exI; |
975 |
> |
exI = exJ; |
976 |
> |
exJ = tempEx; |
977 |
> |
} |
978 |
> |
#ifdef IS_MPI |
979 |
> |
tempEx = exI; |
980 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
981 |
> |
tempEx = exJ; |
982 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
983 |
> |
|
984 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
985 |
> |
#else // isn't MPI |
986 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
987 |
> |
#endif //is_mpi |
988 |
> |
} |
989 |
> |
excludeOffset += info.nBends; |
990 |
|
|
991 |
+ |
for(j=0; j<info.nTorsions; j++){ |
992 |
+ |
|
993 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
994 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
995 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
996 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
997 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
998 |
+ |
|
999 |
+ |
exI = theTorsions[j].a; |
1000 |
+ |
exJ = theTorsions[j].d; |
1001 |
|
|
1002 |
+ |
// exclude_I must always be the smaller of the pair |
1003 |
+ |
if( exI > exJ ){ |
1004 |
+ |
tempEx = exI; |
1005 |
+ |
exI = exJ; |
1006 |
+ |
exJ = tempEx; |
1007 |
+ |
} |
1008 |
|
#ifdef IS_MPI |
1009 |
< |
|
1010 |
< |
the_excludes[(index + tot_bonds)*2] = |
1011 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
1012 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
1013 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
1014 |
< |
|
1009 |
> |
tempEx = exI; |
1010 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1011 |
> |
tempEx = exJ; |
1012 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1013 |
> |
|
1014 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1015 |
|
#else // isn't MPI |
1016 |
< |
|
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) |
1016 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1017 |
|
#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++; |
1018 |
|
} |
1019 |
< |
} |
1019 |
> |
excludeOffset += info.nTorsions; |
1020 |
|
|
1021 |
< |
#ifdef IS_MPI |
1022 |
< |
sprintf( checkPointMsg, |
899 |
< |
"Successfully created the bends list.\n" ); |
900 |
< |
MPIcheckPoint(); |
901 |
< |
#endif // is_mpi |
902 |
< |
|
1021 |
> |
|
1022 |
> |
// send the arrays off to the forceField for init. |
1023 |
|
|
1024 |
< |
the_ff->initializeBends( the_bends ); |
1025 |
< |
} |
1024 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1025 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1026 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1027 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1028 |
|
|
907 |
– |
void SimSetup::makeTorsions( void ){ |
1029 |
|
|
1030 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
910 |
< |
torsion_set* the_torsions; |
911 |
< |
TorsionStamp* current_torsion; |
1030 |
> |
the_molecules[i].initialize( info ); |
1031 |
|
|
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++ ){ |
1032 |
|
|
1033 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1033 |
> |
atomOffset += info.nAtoms; |
1034 |
> |
delete[] theBonds; |
1035 |
> |
delete[] theBends; |
1036 |
> |
delete[] theTorsions; |
1037 |
> |
} |
1038 |
|
|
1039 |
|
#ifdef IS_MPI |
1040 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
1041 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
1042 |
< |
#endif // is_mpi |
1040 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1041 |
> |
MPIcheckPoint(); |
1042 |
> |
#endif // is_mpi |
1043 |
|
|
1044 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1044 |
> |
// clean up the forcefield |
1045 |
> |
the_ff->calcRcut(); |
1046 |
> |
the_ff->cleanMe(); |
1047 |
|
|
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 ); |
1048 |
|
} |
1049 |
|
|
1050 |
|
void SimSetup::initFromBass( void ){ |