12 |
|
#include "mpiSimulation.hpp" |
13 |
|
#endif |
14 |
|
|
15 |
+ |
// some defines for ensemble and Forcefield cases |
16 |
+ |
|
17 |
+ |
#define NVE_ENS 0 |
18 |
+ |
#define NVT_ENS 1 |
19 |
+ |
#define NPT_ENS 2 |
20 |
+ |
|
21 |
+ |
#define FF_DUFF 0 |
22 |
+ |
#define FF_LJ 1 |
23 |
+ |
|
24 |
+ |
|
25 |
|
SimSetup::SimSetup(){ |
26 |
|
stamps = new MakeStamps(); |
27 |
|
globals = new Globals(); |
76 |
|
|
77 |
|
MakeStamps *the_stamps; |
78 |
|
Globals* the_globals; |
79 |
< |
int i, j; |
79 |
> |
int i, j, k, globalAtomIndex; |
80 |
> |
|
81 |
> |
int ensembleCase; |
82 |
> |
int ffCase; |
83 |
> |
|
84 |
> |
ensembleCase = -1; |
85 |
> |
ffCase = -1; |
86 |
|
|
87 |
|
// get the stamps and globals; |
88 |
|
the_stamps = stamps; |
96 |
|
// get the ones we know are there, yet still may need some work. |
97 |
|
n_components = the_globals->getNComponents(); |
98 |
|
strcpy( force_field, the_globals->getForceField() ); |
99 |
+ |
|
100 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
101 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
102 |
+ |
else{ |
103 |
+ |
sprintf( painCave.errMsg, |
104 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
105 |
+ |
force_field ); |
106 |
+ |
painCave.isFatal = 1; |
107 |
+ |
simError(); |
108 |
+ |
} |
109 |
+ |
|
110 |
+ |
// get the ensemble: |
111 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
112 |
+ |
|
113 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ffCase = NVE_ENS; |
114 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; |
115 |
+ |
else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS; |
116 |
+ |
else{ |
117 |
+ |
sprintf( painCave.errMsg, |
118 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
119 |
+ |
"reverting to NVE for this simulation.\n", |
120 |
+ |
ensemble ); |
121 |
+ |
painCave.isFatal = 0; |
122 |
+ |
simError(); |
123 |
+ |
strcpy( ensemble, "NVE" ); |
124 |
+ |
ensembleCase = NVE_ENS; |
125 |
+ |
} |
126 |
|
strcpy( simnfo->ensemble, ensemble ); |
127 |
|
|
128 |
+ |
|
129 |
+ |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
130 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
131 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
132 |
+ |
// if (the_globals->haveTargetPressure()) |
133 |
+ |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
134 |
+ |
// else { |
135 |
+ |
// sprintf( painCave.errMsg, |
136 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
137 |
+ |
// " ensemble, you must set targetPressure.\n" |
138 |
+ |
// " This was found in the BASS file.\n"); |
139 |
+ |
// painCave.isFatal = 1; |
140 |
+ |
// simError(); |
141 |
+ |
// } |
142 |
+ |
|
143 |
+ |
// if (the_globals->haveTauThermostat()) |
144 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
145 |
+ |
// else if (the_globals->haveQmass()) |
146 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
147 |
+ |
// else { |
148 |
+ |
// sprintf( painCave.errMsg, |
149 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
150 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
151 |
+ |
// " Neither of these was found in the BASS file.\n"); |
152 |
+ |
// painCave.isFatal = 1; |
153 |
+ |
// simError(); |
154 |
+ |
// } |
155 |
+ |
|
156 |
+ |
// if (the_globals->haveTauBarostat()) |
157 |
+ |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
158 |
+ |
// else { |
159 |
+ |
// sprintf( painCave.errMsg, |
160 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
161 |
+ |
// " ensemble, you must set tauBarostat.\n" |
162 |
+ |
// " This was found in the BASS file.\n"); |
163 |
+ |
// painCave.isFatal = 1; |
164 |
+ |
// simError(); |
165 |
+ |
// } |
166 |
+ |
|
167 |
+ |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
168 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
169 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
170 |
+ |
|
171 |
+ |
// if (the_globals->haveTauThermostat()) |
172 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
173 |
+ |
// else if (the_globals->haveQmass()) |
174 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
175 |
+ |
// else { |
176 |
+ |
// sprintf( painCave.errMsg, |
177 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
178 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
179 |
+ |
// " Neither of these was found in the BASS file.\n"); |
180 |
+ |
// painCave.isFatal = 1; |
181 |
+ |
// simError(); |
182 |
+ |
// } |
183 |
+ |
|
184 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
185 |
|
simnfo->usePBC = the_globals->getPBC(); |
186 |
|
|
187 |
+ |
int usesDipoles = 0; |
188 |
+ |
switch( ffCase ){ |
189 |
|
|
190 |
+ |
case FF_DUFF: |
191 |
+ |
the_ff = new DUFF(); |
192 |
+ |
usesDipoles = 1; |
193 |
+ |
break; |
194 |
|
|
195 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
196 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
197 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
198 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
199 |
< |
else{ |
195 |
> |
case FF_LJ: |
196 |
> |
the_ff = LJFF(); |
197 |
> |
break; |
198 |
> |
|
199 |
> |
default: |
200 |
|
sprintf( painCave.errMsg, |
201 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
98 |
< |
force_field ); |
201 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
202 |
|
painCave.isFatal = 1; |
203 |
|
simError(); |
204 |
|
} |
208 |
|
MPIcheckPoint(); |
209 |
|
#endif // is_mpi |
210 |
|
|
108 |
– |
|
109 |
– |
|
211 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
212 |
|
the_components = the_globals->getComponents(); |
213 |
|
components_nmol = new int[n_components]; |
331 |
|
simnfo->n_torsions = tot_torsions; |
332 |
|
simnfo->n_SRI = tot_SRI; |
333 |
|
simnfo->n_mol = tot_nmol; |
233 |
– |
|
334 |
|
|
335 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
336 |
+ |
|
337 |
|
#ifdef IS_MPI |
338 |
|
|
339 |
|
// divide the molecules among processors here. |
340 |
|
|
341 |
|
mpiSim = new mpiSimulation( simnfo ); |
342 |
|
|
241 |
– |
|
242 |
– |
|
343 |
|
globalIndex = mpiSim->divideLabor(); |
344 |
|
|
245 |
– |
|
246 |
– |
|
345 |
|
// set up the local variables |
346 |
|
|
347 |
|
int localMol, allMol; |
348 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
349 |
+ |
|
350 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
351 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
352 |
|
|
353 |
|
allMol = 0; |
354 |
|
localMol = 0; |
356 |
|
local_bonds = 0; |
357 |
|
local_bends = 0; |
358 |
|
local_torsions = 0; |
359 |
+ |
globalAtomIndex = 0; |
360 |
+ |
|
361 |
+ |
|
362 |
|
for( i=0; i<n_components; i++ ){ |
363 |
|
|
364 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
365 |
|
|
366 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
366 |
> |
if( mol2proc[allMol] == worldRank ){ |
367 |
|
|
368 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
369 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
371 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
372 |
|
localMol++; |
373 |
|
} |
374 |
< |
allMol++; |
374 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
375 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
376 |
> |
globalAtomIndex++; |
377 |
> |
} |
378 |
> |
|
379 |
> |
allMol++; |
380 |
|
} |
381 |
|
} |
382 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
383 |
|
|
276 |
– |
|
384 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 |
|
|
386 |
|
if( local_atoms != simnfo->n_atoms ){ |
387 |
|
sprintf( painCave.errMsg, |
388 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
389 |
< |
" localAtom (%d) are note equal.\n", |
389 |
> |
" localAtom (%d) are not equal.\n", |
390 |
|
simnfo->n_atoms, |
391 |
|
local_atoms ); |
392 |
|
painCave.isFatal = 1; |
411 |
|
Atom::createArrays(simnfo->n_atoms); |
412 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
413 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
414 |
+ |
int molIndex; |
415 |
|
|
416 |
+ |
// initialize the molecule's stampID's |
417 |
|
|
418 |
+ |
#ifdef IS_MPI |
419 |
+ |
|
420 |
+ |
|
421 |
+ |
molIndex = 0; |
422 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
423 |
+ |
|
424 |
+ |
if(mol2proc[i] == worldRank ){ |
425 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
426 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
427 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
428 |
+ |
molIndex++; |
429 |
+ |
} |
430 |
+ |
} |
431 |
+ |
|
432 |
+ |
#else // is_mpi |
433 |
+ |
|
434 |
+ |
molIndex = 0; |
435 |
+ |
globalAtomIndex = 0; |
436 |
+ |
for(i=0; i<n_components; i++){ |
437 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
438 |
+ |
the_molecules[molIndex].setStampID( i ); |
439 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
440 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
441 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
442 |
+ |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
443 |
+ |
globalAtomIndex++; |
444 |
+ |
} |
445 |
+ |
molIndex++; |
446 |
+ |
} |
447 |
+ |
} |
448 |
+ |
|
449 |
+ |
|
450 |
+ |
#endif // is_mpi |
451 |
+ |
|
452 |
+ |
|
453 |
|
if( simnfo->n_SRI ){ |
454 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
455 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
454 |
> |
|
455 |
> |
Exclude::createArray(simnfo->n_SRI); |
456 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
457 |
> |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
458 |
|
simnfo->globalExcludes = new int; |
459 |
< |
simnfo->n_exclude = tot_SRI; |
459 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
460 |
|
} |
461 |
|
else{ |
462 |
|
|
463 |
< |
the_excludes = new int[2]; |
464 |
< |
the_excludes[0] = 0; |
465 |
< |
the_excludes[1] = 0; |
463 |
> |
Exclude::createArray( 1 ); |
464 |
> |
the_excludes = new Exclude*; |
465 |
> |
the_excludes[0] = new Exclude(0); |
466 |
> |
the_excludes[0]->setPair( 0,0 ); |
467 |
|
simnfo->globalExcludes = new int; |
468 |
|
simnfo->globalExcludes[0] = 0; |
469 |
< |
|
323 |
< |
simnfo->n_exclude = 1; |
469 |
> |
simnfo->n_exclude = 0; |
470 |
|
} |
471 |
|
|
472 |
|
// set the arrays into the SimInfo object |
473 |
|
|
474 |
|
simnfo->atoms = the_atoms; |
475 |
< |
simnfo->sr_interactions = the_sris; |
475 |
> |
simnfo->molecules = the_molecules; |
476 |
|
simnfo->nGlobalExcludes = 0; |
477 |
|
simnfo->excludes = the_excludes; |
478 |
|
|
479 |
|
|
480 |
|
// get some of the tricky things that may still be in the globals |
481 |
|
|
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 |
482 |
|
|
483 |
|
if( the_globals->haveBox() ){ |
484 |
|
simnfo->box_x = the_globals->getBox(); |
529 |
|
|
530 |
|
the_ff->setSimInfo( simnfo ); |
531 |
|
|
532 |
< |
makeAtoms(); |
532 |
> |
makeMolecules(); |
533 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
534 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
535 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
414 |
– |
} |
415 |
– |
|
416 |
– |
if( tot_bonds ){ |
417 |
– |
makeBonds(); |
418 |
– |
} |
419 |
– |
|
420 |
– |
if( tot_bends ){ |
421 |
– |
makeBends(); |
422 |
– |
} |
423 |
– |
|
424 |
– |
if( tot_torsions ){ |
425 |
– |
makeTorsions(); |
536 |
|
} |
537 |
+ |
|
538 |
+ |
if (the_globals->getUseRF() ) { |
539 |
+ |
simnfo->useReactionField = 1; |
540 |
+ |
|
541 |
+ |
if( !the_globals->haveECR() ){ |
542 |
+ |
sprintf( painCave.errMsg, |
543 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
544 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
545 |
+ |
"I hope you have a very fast processor!\n"); |
546 |
+ |
painCave.isFatal = 0; |
547 |
+ |
simError(); |
548 |
+ |
double smallest; |
549 |
+ |
smallest = simnfo->box_x; |
550 |
+ |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
551 |
+ |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
552 |
+ |
simnfo->ecr = 0.5 * smallest; |
553 |
+ |
} else { |
554 |
+ |
simnfo->ecr = the_globals->getECR(); |
555 |
+ |
} |
556 |
|
|
557 |
+ |
if( !the_globals->haveEST() ){ |
558 |
+ |
sprintf( painCave.errMsg, |
559 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
560 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
561 |
+ |
); |
562 |
+ |
painCave.isFatal = 0; |
563 |
+ |
simError(); |
564 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
565 |
+ |
} else { |
566 |
+ |
simnfo->est = the_globals->getEST(); |
567 |
+ |
} |
568 |
+ |
|
569 |
+ |
if(!the_globals->haveDielectric() ){ |
570 |
+ |
sprintf( painCave.errMsg, |
571 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
572 |
+ |
"setting a dielectric constant!\n" |
573 |
+ |
); |
574 |
+ |
painCave.isFatal = 1; |
575 |
+ |
simError(); |
576 |
+ |
} |
577 |
+ |
simnfo->dielectric = the_globals->getDielectric(); |
578 |
+ |
} else { |
579 |
+ |
if (usesDipoles) { |
580 |
+ |
|
581 |
+ |
if( !the_globals->haveECR() ){ |
582 |
+ |
sprintf( painCave.errMsg, |
583 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
584 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
585 |
+ |
"I hope you have a very fast processor!\n"); |
586 |
+ |
painCave.isFatal = 0; |
587 |
+ |
simError(); |
588 |
+ |
double smallest; |
589 |
+ |
smallest = simnfo->box_x; |
590 |
+ |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
591 |
+ |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
592 |
+ |
simnfo->ecr = 0.5 * smallest; |
593 |
+ |
} else { |
594 |
+ |
simnfo->ecr = the_globals->getECR(); |
595 |
+ |
} |
596 |
+ |
|
597 |
+ |
if( !the_globals->haveEST() ){ |
598 |
+ |
sprintf( painCave.errMsg, |
599 |
+ |
"SimSetup Warning: using default value of 5%% of the " |
600 |
+ |
"electrostaticCutoffRadius for the " |
601 |
+ |
"electrostaticSkinThickness\n" |
602 |
+ |
); |
603 |
+ |
painCave.isFatal = 0; |
604 |
+ |
simError(); |
605 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
606 |
+ |
} else { |
607 |
+ |
simnfo->est = the_globals->getEST(); |
608 |
+ |
} |
609 |
+ |
} |
610 |
+ |
} |
611 |
|
|
612 |
+ |
#ifdef IS_MPI |
613 |
+ |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
614 |
+ |
MPIcheckPoint(); |
615 |
+ |
#endif // is_mpi |
616 |
|
|
430 |
– |
|
431 |
– |
|
432 |
– |
|
617 |
|
if( the_globals->haveInitialConfig() ){ |
618 |
|
|
619 |
|
InitializeFromFile* fileInit; |
767 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
768 |
|
|
769 |
|
|
770 |
< |
// // make the longe range forces and the integrator |
770 |
> |
// make the integrator |
771 |
|
|
588 |
– |
// new AllLong( simnfo ); |
772 |
|
|
773 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
774 |
< |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
775 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
776 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
773 |
> |
if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
774 |
> |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
775 |
> |
} |
776 |
> |
else if( !strcmp( force_field, "LJ" ) ){ |
777 |
> |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
778 |
> |
} |
779 |
|
|
780 |
+ |
#ifdef IS_MPI |
781 |
+ |
mpiSim->mpiRefresh(); |
782 |
+ |
#endif |
783 |
|
|
596 |
– |
|
784 |
|
// initialize the Fortran |
785 |
< |
|
785 |
> |
|
786 |
> |
|
787 |
|
simnfo->refreshSim(); |
788 |
|
|
789 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
808 |
|
#endif // is_mpi |
809 |
|
} |
810 |
|
|
623 |
– |
void SimSetup::makeAtoms( void ){ |
811 |
|
|
812 |
< |
int i, j, k, index; |
626 |
< |
double ux, uy, uz, uSqr, u; |
627 |
< |
AtomStamp* current_atom; |
812 |
> |
void SimSetup::makeMolecules( void ){ |
813 |
|
|
814 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
815 |
+ |
molInit info; |
816 |
|
DirectionalAtom* dAtom; |
817 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
817 |
> |
LinkedAssign* extras; |
818 |
> |
LinkedAssign* current_extra; |
819 |
> |
AtomStamp* currentAtom; |
820 |
> |
BondStamp* currentBond; |
821 |
> |
BendStamp* currentBend; |
822 |
> |
TorsionStamp* currentTorsion; |
823 |
|
|
824 |
< |
lMolIndex = 0; |
825 |
< |
molIndex = 0; |
826 |
< |
index = 0; |
635 |
< |
for( i=0; i<n_components; i++ ){ |
824 |
> |
bond_pair* theBonds; |
825 |
> |
bend_set* theBends; |
826 |
> |
torsion_set* theTorsions; |
827 |
|
|
828 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
828 |
> |
|
829 |
> |
//init the forceField paramters |
830 |
|
|
831 |
< |
#ifdef IS_MPI |
640 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
641 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
642 |
< |
#endif // is_mpi |
831 |
> |
the_ff->readParams(); |
832 |
|
|
833 |
< |
molStart = index; |
834 |
< |
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++; |
833 |
> |
|
834 |
> |
// init the atoms |
835 |
|
|
836 |
< |
#ifdef IS_MPI |
837 |
< |
} |
838 |
< |
#endif //is_mpi |
839 |
< |
|
840 |
< |
molIndex++; |
692 |
< |
} |
693 |
< |
} |
694 |
< |
|
695 |
< |
#ifdef IS_MPI |
696 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
836 |
> |
double ux, uy, uz, u, uSqr; |
837 |
> |
|
838 |
> |
atomOffset = 0; |
839 |
> |
excludeOffset = 0; |
840 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
841 |
|
|
842 |
< |
delete[] globalIndex; |
842 |
> |
stampID = the_molecules[i].getStampID(); |
843 |
|
|
844 |
< |
mpiSim->mpiRefresh(); |
845 |
< |
#endif //IS_MPI |
846 |
< |
|
847 |
< |
the_ff->initializeAtoms(); |
848 |
< |
} |
844 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
845 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
846 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
847 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
848 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
849 |
|
|
850 |
< |
void SimSetup::makeBonds( void ){ |
851 |
< |
|
852 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
853 |
< |
bond_pair* the_bonds; |
854 |
< |
BondStamp* current_bond; |
850 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
851 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
852 |
> |
info.myBonds = new Bond*[info.nBonds]; |
853 |
> |
info.myBends = new Bend*[info.nBends]; |
854 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
855 |
|
|
856 |
< |
the_bonds = new bond_pair[tot_bonds]; |
857 |
< |
index = 0; |
858 |
< |
offset = 0; |
859 |
< |
molIndex = 0; |
860 |
< |
|
861 |
< |
for( i=0; i<n_components; i++ ){ |
862 |
< |
|
863 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
864 |
< |
|
865 |
< |
#ifdef IS_MPI |
722 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
723 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
724 |
< |
#endif // is_mpi |
856 |
> |
theBonds = new bond_pair[info.nBonds]; |
857 |
> |
theBends = new bend_set[info.nBends]; |
858 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
859 |
> |
|
860 |
> |
// make the Atoms |
861 |
> |
|
862 |
> |
for(j=0; j<info.nAtoms; j++){ |
863 |
> |
|
864 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
865 |
> |
if( currentAtom->haveOrientation() ){ |
866 |
|
|
867 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
868 |
< |
|
869 |
< |
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(); |
867 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
868 |
> |
simnfo->n_oriented++; |
869 |
> |
info.myAtoms[j] = dAtom; |
870 |
|
|
871 |
< |
#ifdef IS_MPI |
871 |
> |
ux = currentAtom->getOrntX(); |
872 |
> |
uy = currentAtom->getOrntY(); |
873 |
> |
uz = currentAtom->getOrntZ(); |
874 |
> |
|
875 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
876 |
> |
|
877 |
> |
u = sqrt( uSqr ); |
878 |
> |
ux = ux / u; |
879 |
> |
uy = uy / u; |
880 |
> |
uz = uz / u; |
881 |
> |
|
882 |
> |
dAtom->setSUx( ux ); |
883 |
> |
dAtom->setSUy( uy ); |
884 |
> |
dAtom->setSUz( uz ); |
885 |
|
} |
886 |
< |
#endif //is_mpi |
886 |
> |
else{ |
887 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
888 |
> |
} |
889 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
890 |
> |
|
891 |
> |
#ifdef IS_MPI |
892 |
|
|
893 |
< |
molIndex++; |
894 |
< |
} |
895 |
< |
} |
893 |
> |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
894 |
> |
|
895 |
> |
#endif // is_mpi |
896 |
> |
} |
897 |
> |
|
898 |
> |
// make the bonds |
899 |
> |
for(j=0; j<info.nBonds; j++){ |
900 |
> |
|
901 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
902 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
903 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
904 |
|
|
905 |
< |
the_ff->initializeBonds( the_bonds ); |
906 |
< |
} |
905 |
> |
exI = theBonds[j].a; |
906 |
> |
exJ = theBonds[j].b; |
907 |
|
|
908 |
< |
void SimSetup::makeBends( void ){ |
909 |
< |
|
910 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
911 |
< |
bend_set* the_bends; |
912 |
< |
BendStamp* current_bend; |
913 |
< |
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 |
< |
|
908 |
> |
// exclude_I must always be the smaller of the pair |
909 |
> |
if( exI > exJ ){ |
910 |
> |
tempEx = exI; |
911 |
> |
exI = exJ; |
912 |
> |
exJ = tempEx; |
913 |
> |
} |
914 |
|
#ifdef IS_MPI |
915 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
916 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
917 |
< |
#endif // is_mpi |
915 |
> |
tempEx = exI; |
916 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
917 |
> |
tempEx = exJ; |
918 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
919 |
> |
|
920 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
921 |
> |
#else // isn't MPI |
922 |
|
|
923 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
923 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
924 |
> |
#endif //is_mpi |
925 |
> |
} |
926 |
> |
excludeOffset += info.nBonds; |
927 |
> |
|
928 |
> |
//make the bends |
929 |
> |
for(j=0; j<info.nBends; j++){ |
930 |
> |
|
931 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
932 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
933 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
934 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
935 |
|
|
936 |
< |
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() ){ |
936 |
> |
if( currentBend->haveExtras() ){ |
937 |
|
|
938 |
< |
extras = current_bend->getExtras(); |
939 |
< |
current_extra = extras; |
938 |
> |
extras = currentBend->getExtras(); |
939 |
> |
current_extra = extras; |
940 |
|
|
941 |
< |
while( current_extra != NULL ){ |
942 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
941 |
> |
while( current_extra != NULL ){ |
942 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
943 |
|
|
944 |
< |
switch( current_extra->getType() ){ |
944 |
> |
switch( current_extra->getType() ){ |
945 |
> |
|
946 |
> |
case 0: |
947 |
> |
theBends[j].ghost = |
948 |
> |
current_extra->getInt() + atomOffset; |
949 |
> |
theBends[j].isGhost = 1; |
950 |
> |
break; |
951 |
|
|
952 |
< |
case 0: |
953 |
< |
the_bends[index].ghost = |
954 |
< |
current_extra->getInt() + offset; |
955 |
< |
the_bends[index].isGhost = 1; |
956 |
< |
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 |
< |
} |
952 |
> |
case 1: |
953 |
> |
theBends[j].ghost = |
954 |
> |
(int)current_extra->getDouble() + atomOffset; |
955 |
> |
theBends[j].isGhost = 1; |
956 |
> |
break; |
957 |
|
|
958 |
< |
else{ |
959 |
< |
|
960 |
< |
sprintf( painCave.errMsg, |
961 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
962 |
< |
" -->%s in Bend[%d] in %s\n", |
963 |
< |
current_extra->getlhs(), |
964 |
< |
k, comp_stamps[i]->getID() ); |
965 |
< |
painCave.isFatal = 1; |
843 |
< |
simError(); |
844 |
< |
} |
845 |
< |
|
846 |
< |
current_extra = current_extra->getNext(); |
958 |
> |
default: |
959 |
> |
sprintf( painCave.errMsg, |
960 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
961 |
> |
"double nor an int.\n" |
962 |
> |
"-->Bend[%d] in %s\n", |
963 |
> |
j, comp_stamps[stampID]->getID() ); |
964 |
> |
painCave.isFatal = 1; |
965 |
> |
simError(); |
966 |
|
} |
967 |
|
} |
968 |
|
|
850 |
– |
if( !the_bends[index].isGhost ){ |
851 |
– |
|
852 |
– |
exI = the_bends[index].a; |
853 |
– |
exJ = the_bends[index].c; |
854 |
– |
} |
969 |
|
else{ |
970 |
|
|
971 |
< |
exI = the_bends[index].a; |
972 |
< |
exJ = the_bends[index].b; |
971 |
> |
sprintf( painCave.errMsg, |
972 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
973 |
> |
" -->%s in Bend[%d] in %s\n", |
974 |
> |
current_extra->getlhs(), |
975 |
> |
j, comp_stamps[stampID]->getID() ); |
976 |
> |
painCave.isFatal = 1; |
977 |
> |
simError(); |
978 |
|
} |
979 |
|
|
980 |
< |
// exclude_I must always be the smaller of the pair |
862 |
< |
if( exI > exJ ){ |
863 |
< |
tempEx = exI; |
864 |
< |
exI = exJ; |
865 |
< |
exJ = tempEx; |
866 |
< |
} |
867 |
< |
|
868 |
< |
|
869 |
< |
#ifdef IS_MPI |
870 |
< |
|
871 |
< |
the_excludes[(index + tot_bonds)*2] = |
872 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
873 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
874 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
875 |
< |
|
876 |
< |
#else // isn't MPI |
877 |
< |
|
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) |
881 |
< |
#endif //is_mpi |
882 |
< |
|
883 |
< |
|
884 |
< |
// increment the index and repeat; |
885 |
< |
index++; |
980 |
> |
current_extra = current_extra->getNext(); |
981 |
|
} |
982 |
< |
offset += comp_stamps[i]->getNAtoms(); |
982 |
> |
} |
983 |
> |
|
984 |
> |
if( !theBends[j].isGhost ){ |
985 |
> |
|
986 |
> |
exI = theBends[j].a; |
987 |
> |
exJ = theBends[j].c; |
988 |
> |
} |
989 |
> |
else{ |
990 |
|
|
991 |
< |
#ifdef IS_MPI |
991 |
> |
exI = theBends[j].a; |
992 |
> |
exJ = theBends[j].b; |
993 |
|
} |
994 |
< |
#endif //is_mpi |
994 |
> |
|
995 |
> |
// exclude_I must always be the smaller of the pair |
996 |
> |
if( exI > exJ ){ |
997 |
> |
tempEx = exI; |
998 |
> |
exI = exJ; |
999 |
> |
exJ = tempEx; |
1000 |
> |
} |
1001 |
> |
#ifdef IS_MPI |
1002 |
> |
tempEx = exI; |
1003 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1004 |
> |
tempEx = exJ; |
1005 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1006 |
> |
|
1007 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1008 |
> |
#else // isn't MPI |
1009 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1010 |
> |
#endif //is_mpi |
1011 |
> |
} |
1012 |
> |
excludeOffset += info.nBends; |
1013 |
|
|
1014 |
< |
molIndex++; |
1014 |
> |
for(j=0; j<info.nTorsions; j++){ |
1015 |
> |
|
1016 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1017 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1018 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1019 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1020 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1021 |
> |
|
1022 |
> |
exI = theTorsions[j].a; |
1023 |
> |
exJ = theTorsions[j].d; |
1024 |
> |
|
1025 |
> |
// exclude_I must always be the smaller of the pair |
1026 |
> |
if( exI > exJ ){ |
1027 |
> |
tempEx = exI; |
1028 |
> |
exI = exJ; |
1029 |
> |
exJ = tempEx; |
1030 |
> |
} |
1031 |
> |
#ifdef IS_MPI |
1032 |
> |
tempEx = exI; |
1033 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1034 |
> |
tempEx = exJ; |
1035 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1036 |
> |
|
1037 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1038 |
> |
#else // isn't MPI |
1039 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1040 |
> |
#endif //is_mpi |
1041 |
|
} |
1042 |
< |
} |
1042 |
> |
excludeOffset += info.nTorsions; |
1043 |
|
|
1044 |
< |
#ifdef IS_MPI |
1045 |
< |
sprintf( checkPointMsg, |
899 |
< |
"Successfully created the bends list.\n" ); |
900 |
< |
MPIcheckPoint(); |
901 |
< |
#endif // is_mpi |
902 |
< |
|
1044 |
> |
|
1045 |
> |
// send the arrays off to the forceField for init. |
1046 |
|
|
1047 |
< |
the_ff->initializeBends( the_bends ); |
1048 |
< |
} |
1047 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1048 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1049 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1050 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1051 |
|
|
907 |
– |
void SimSetup::makeTorsions( void ){ |
1052 |
|
|
1053 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
910 |
< |
torsion_set* the_torsions; |
911 |
< |
TorsionStamp* current_torsion; |
1053 |
> |
the_molecules[i].initialize( info ); |
1054 |
|
|
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++ ){ |
1055 |
|
|
1056 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
1056 |
> |
atomOffset += info.nAtoms; |
1057 |
> |
delete[] theBonds; |
1058 |
> |
delete[] theBends; |
1059 |
> |
delete[] theTorsions; |
1060 |
> |
} |
1061 |
|
|
1062 |
|
#ifdef IS_MPI |
1063 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
1064 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
1065 |
< |
#endif // is_mpi |
1063 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1064 |
> |
MPIcheckPoint(); |
1065 |
> |
#endif // is_mpi |
1066 |
|
|
1067 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1067 |
> |
// clean up the forcefield |
1068 |
> |
the_ff->calcRcut(); |
1069 |
> |
the_ff->cleanMe(); |
1070 |
|
|
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 ); |
1071 |
|
} |
1072 |
|
|
1073 |
|
void SimSetup::initFromBass( void ){ |