189 |
|
// make the Atoms |
190 |
|
|
191 |
|
for(j=0; j<molInfo.nAtoms; j++){ |
192 |
< |
|
193 |
< |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
194 |
< |
if( currentAtom->haveOrientation() ){ |
195 |
< |
|
196 |
< |
dAtom = new DirectionalAtom( (j + atomOffset), |
197 |
< |
info[k].getConfiguration() ); |
198 |
< |
info[k].n_oriented++; |
199 |
< |
molInfo.myAtoms[j] = dAtom; |
200 |
< |
|
201 |
< |
ux = currentAtom->getOrntX(); |
202 |
< |
uy = currentAtom->getOrntY(); |
203 |
< |
uz = currentAtom->getOrntZ(); |
204 |
< |
|
205 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
206 |
< |
|
207 |
< |
u = sqrt( uSqr ); |
208 |
< |
ux = ux / u; |
209 |
< |
uy = uy / u; |
210 |
< |
uz = uz / u; |
211 |
< |
|
212 |
< |
dAtom->setSUx( ux ); |
213 |
< |
dAtom->setSUy( uy ); |
214 |
< |
dAtom->setSUz( uz ); |
215 |
< |
} |
216 |
< |
else{ |
217 |
< |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
218 |
< |
info[k].getConfiguration() ); |
219 |
< |
} |
220 |
< |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
192 |
> |
|
193 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
194 |
> |
if( currentAtom->haveOrientation() ){ |
195 |
|
|
196 |
+ |
dAtom = new DirectionalAtom( (j + atomOffset), |
197 |
+ |
info[k].getConfiguration() ); |
198 |
+ |
info[k].n_oriented++; |
199 |
+ |
molInfo.myAtoms[j] = dAtom; |
200 |
+ |
|
201 |
+ |
ux = currentAtom->getOrntX(); |
202 |
+ |
uy = currentAtom->getOrntY(); |
203 |
+ |
uz = currentAtom->getOrntZ(); |
204 |
+ |
|
205 |
+ |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
206 |
+ |
|
207 |
+ |
u = sqrt( uSqr ); |
208 |
+ |
ux = ux / u; |
209 |
+ |
uy = uy / u; |
210 |
+ |
uz = uz / u; |
211 |
+ |
|
212 |
+ |
dAtom->setSUx( ux ); |
213 |
+ |
dAtom->setSUy( uy ); |
214 |
+ |
dAtom->setSUz( uz ); |
215 |
+ |
} |
216 |
+ |
else{ |
217 |
+ |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
218 |
+ |
info[k].getConfiguration() ); |
219 |
+ |
} |
220 |
+ |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
221 |
+ |
|
222 |
|
#ifdef IS_MPI |
223 |
|
|
224 |
< |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
224 |
> |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
225 |
|
|
226 |
|
#endif // is_mpi |
227 |
|
} |
229 |
|
// make the bonds |
230 |
|
for(j=0; j<molInfo.nBonds; j++){ |
231 |
|
|
232 |
< |
currentBond = comp_stamps[stampID]->getBond( j ); |
233 |
< |
theBonds[j].a = currentBond->getA() + atomOffset; |
234 |
< |
theBonds[j].b = currentBond->getB() + atomOffset; |
235 |
< |
|
236 |
< |
exI = theBonds[j].a; |
237 |
< |
exJ = theBonds[j].b; |
238 |
< |
|
239 |
< |
// exclude_I must always be the smaller of the pair |
240 |
< |
if( exI > exJ ){ |
241 |
< |
tempEx = exI; |
242 |
< |
exI = exJ; |
243 |
< |
exJ = tempEx; |
244 |
< |
} |
245 |
< |
#ifdef IS_MPI |
246 |
< |
tempEx = exI; |
247 |
< |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
248 |
< |
tempEx = exJ; |
249 |
< |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
250 |
< |
|
251 |
< |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
232 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
233 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
234 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
235 |
> |
|
236 |
> |
exI = theBonds[j].a; |
237 |
> |
exJ = theBonds[j].b; |
238 |
> |
|
239 |
> |
// exclude_I must always be the smaller of the pair |
240 |
> |
if( exI > exJ ){ |
241 |
> |
tempEx = exI; |
242 |
> |
exI = exJ; |
243 |
> |
exJ = tempEx; |
244 |
> |
} |
245 |
> |
#ifdef IS_MPI |
246 |
> |
tempEx = exI; |
247 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
248 |
> |
tempEx = exJ; |
249 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
250 |
> |
|
251 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
252 |
|
#else // isn't MPI |
253 |
< |
|
254 |
< |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
253 |
> |
|
254 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
255 |
|
#endif //is_mpi |
256 |
|
} |
257 |
|
excludeOffset += molInfo.nBonds; |
258 |
|
|
259 |
|
//make the bends |
260 |
|
for(j=0; j<molInfo.nBends; j++){ |
261 |
< |
|
262 |
< |
currentBend = comp_stamps[stampID]->getBend( j ); |
263 |
< |
theBends[j].a = currentBend->getA() + atomOffset; |
264 |
< |
theBends[j].b = currentBend->getB() + atomOffset; |
265 |
< |
theBends[j].c = currentBend->getC() + atomOffset; |
266 |
< |
|
267 |
< |
if( currentBend->haveExtras() ){ |
268 |
< |
|
269 |
< |
extras = currentBend->getExtras(); |
270 |
< |
current_extra = extras; |
271 |
< |
|
272 |
< |
while( current_extra != NULL ){ |
273 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
274 |
< |
|
275 |
< |
switch( current_extra->getType() ){ |
276 |
< |
|
277 |
< |
case 0: |
278 |
< |
theBends[j].ghost = |
279 |
< |
current_extra->getInt() + atomOffset; |
280 |
< |
theBends[j].isGhost = 1; |
281 |
< |
break; |
282 |
< |
|
283 |
< |
case 1: |
284 |
< |
theBends[j].ghost = |
285 |
< |
(int)current_extra->getDouble() + atomOffset; |
286 |
< |
theBends[j].isGhost = 1; |
287 |
< |
break; |
288 |
< |
|
289 |
< |
default: |
290 |
< |
sprintf( painCave.errMsg, |
291 |
< |
"SimSetup Error: ghostVectorSource was neither a " |
292 |
< |
"double nor an int.\n" |
293 |
< |
"-->Bend[%d] in %s\n", |
294 |
< |
j, comp_stamps[stampID]->getID() ); |
295 |
< |
painCave.isFatal = 1; |
296 |
< |
simError(); |
297 |
< |
} |
298 |
< |
} |
299 |
< |
|
300 |
< |
else{ |
301 |
< |
|
302 |
< |
sprintf( painCave.errMsg, |
303 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
304 |
< |
" -->%s in Bend[%d] in %s\n", |
305 |
< |
current_extra->getlhs(), |
306 |
< |
j, comp_stamps[stampID]->getID() ); |
307 |
< |
painCave.isFatal = 1; |
308 |
< |
simError(); |
309 |
< |
} |
310 |
< |
|
311 |
< |
current_extra = current_extra->getNext(); |
312 |
< |
} |
313 |
< |
} |
314 |
< |
|
315 |
< |
if( !theBends[j].isGhost ){ |
316 |
< |
|
317 |
< |
exI = theBends[j].a; |
318 |
< |
exJ = theBends[j].c; |
319 |
< |
} |
320 |
< |
else{ |
321 |
< |
|
322 |
< |
exI = theBends[j].a; |
323 |
< |
exJ = theBends[j].b; |
324 |
< |
} |
325 |
< |
|
326 |
< |
// exclude_I must always be the smaller of the pair |
327 |
< |
if( exI > exJ ){ |
328 |
< |
tempEx = exI; |
329 |
< |
exI = exJ; |
330 |
< |
exJ = tempEx; |
331 |
< |
} |
261 |
> |
|
262 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
263 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
264 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
265 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
266 |
> |
|
267 |
> |
if( currentBend->haveExtras() ){ |
268 |
> |
|
269 |
> |
extras = currentBend->getExtras(); |
270 |
> |
current_extra = extras; |
271 |
> |
|
272 |
> |
while( current_extra != NULL ){ |
273 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
274 |
> |
|
275 |
> |
switch( current_extra->getType() ){ |
276 |
> |
|
277 |
> |
case 0: |
278 |
> |
theBends[j].ghost = |
279 |
> |
current_extra->getInt() + atomOffset; |
280 |
> |
theBends[j].isGhost = 1; |
281 |
> |
break; |
282 |
> |
|
283 |
> |
case 1: |
284 |
> |
theBends[j].ghost = |
285 |
> |
(int)current_extra->getDouble() + atomOffset; |
286 |
> |
theBends[j].isGhost = 1; |
287 |
> |
break; |
288 |
> |
|
289 |
> |
default: |
290 |
> |
sprintf( painCave.errMsg, |
291 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
292 |
> |
"double nor an int.\n" |
293 |
> |
"-->Bend[%d] in %s\n", |
294 |
> |
j, comp_stamps[stampID]->getID() ); |
295 |
> |
painCave.isFatal = 1; |
296 |
> |
simError(); |
297 |
> |
} |
298 |
> |
} |
299 |
> |
|
300 |
> |
else{ |
301 |
> |
|
302 |
> |
sprintf( painCave.errMsg, |
303 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
304 |
> |
" -->%s in Bend[%d] in %s\n", |
305 |
> |
current_extra->getlhs(), |
306 |
> |
j, comp_stamps[stampID]->getID() ); |
307 |
> |
painCave.isFatal = 1; |
308 |
> |
simError(); |
309 |
> |
} |
310 |
> |
|
311 |
> |
current_extra = current_extra->getNext(); |
312 |
> |
} |
313 |
> |
} |
314 |
> |
|
315 |
> |
if( !theBends[j].isGhost ){ |
316 |
> |
|
317 |
> |
exI = theBends[j].a; |
318 |
> |
exJ = theBends[j].c; |
319 |
> |
} |
320 |
> |
else{ |
321 |
> |
|
322 |
> |
exI = theBends[j].a; |
323 |
> |
exJ = theBends[j].b; |
324 |
> |
} |
325 |
> |
|
326 |
> |
// exclude_I must always be the smaller of the pair |
327 |
> |
if( exI > exJ ){ |
328 |
> |
tempEx = exI; |
329 |
> |
exI = exJ; |
330 |
> |
exJ = tempEx; |
331 |
> |
} |
332 |
|
#ifdef IS_MPI |
333 |
< |
tempEx = exI; |
334 |
< |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
335 |
< |
tempEx = exJ; |
336 |
< |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
333 |
> |
tempEx = exI; |
334 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
335 |
> |
tempEx = exJ; |
336 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
337 |
|
|
338 |
< |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
338 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
339 |
|
#else // isn't MPI |
340 |
< |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
340 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
341 |
|
#endif //is_mpi |
342 |
|
} |
343 |
|
excludeOffset += molInfo.nBends; |
344 |
|
|
345 |
|
for(j=0; j<molInfo.nTorsions; j++){ |
346 |
< |
|
347 |
< |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
348 |
< |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
349 |
< |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
350 |
< |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
351 |
< |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
352 |
< |
|
353 |
< |
exI = theTorsions[j].a; |
354 |
< |
exJ = theTorsions[j].d; |
355 |
< |
|
356 |
< |
// exclude_I must always be the smaller of the pair |
357 |
< |
if( exI > exJ ){ |
358 |
< |
tempEx = exI; |
359 |
< |
exI = exJ; |
360 |
< |
exJ = tempEx; |
361 |
< |
} |
346 |
> |
|
347 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
348 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
349 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
350 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
351 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
352 |
> |
|
353 |
> |
exI = theTorsions[j].a; |
354 |
> |
exJ = theTorsions[j].d; |
355 |
> |
|
356 |
> |
// exclude_I must always be the smaller of the pair |
357 |
> |
if( exI > exJ ){ |
358 |
> |
tempEx = exI; |
359 |
> |
exI = exJ; |
360 |
> |
exJ = tempEx; |
361 |
> |
} |
362 |
|
#ifdef IS_MPI |
363 |
< |
tempEx = exI; |
364 |
< |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
365 |
< |
tempEx = exJ; |
366 |
< |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
367 |
< |
|
368 |
< |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
363 |
> |
tempEx = exI; |
364 |
> |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
365 |
> |
tempEx = exJ; |
366 |
> |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
367 |
> |
|
368 |
> |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
369 |
|
#else // isn't MPI |
370 |
< |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
370 |
> |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
371 |
|
#endif //is_mpi |
372 |
|
} |
373 |
|
excludeOffset += molInfo.nTorsions; |
436 |
|
|
437 |
|
if( n_per_extra > 4){ |
438 |
|
sprintf( painCave.errMsg, |
439 |
< |
"SimSetup error. There has been an error in constructing" |
440 |
< |
" the non-complete lattice.\n" ); |
439 |
> |
"SimSetup error. There has been an error in constructing" |
440 |
> |
" the non-complete lattice.\n" ); |
441 |
|
painCave.isFatal = 1; |
442 |
|
simError(); |
443 |
|
} |
458 |
|
for( j=0; j < n_cells; j++ ){ |
459 |
|
for( k=0; k < n_cells; k++ ){ |
460 |
|
|
461 |
< |
makeElement( i * cellx, |
462 |
< |
j * celly, |
463 |
< |
k * cellz ); |
461 |
> |
makeElement( i * cellx, |
462 |
> |
j * celly, |
463 |
> |
k * cellz ); |
464 |
|
|
465 |
< |
makeElement( i * cellx + 0.5 * cellx, |
466 |
< |
j * celly + 0.5 * celly, |
467 |
< |
k * cellz ); |
465 |
> |
makeElement( i * cellx + 0.5 * cellx, |
466 |
> |
j * celly + 0.5 * celly, |
467 |
> |
k * cellz ); |
468 |
|
|
469 |
< |
makeElement( i * cellx, |
470 |
< |
j * celly + 0.5 * celly, |
471 |
< |
k * cellz + 0.5 * cellz ); |
469 |
> |
makeElement( i * cellx, |
470 |
> |
j * celly + 0.5 * celly, |
471 |
> |
k * cellz + 0.5 * cellz ); |
472 |
|
|
473 |
< |
makeElement( i * cellx + 0.5 * cellx, |
474 |
< |
j * celly, |
475 |
< |
k * cellz + 0.5 * cellz ); |
473 |
> |
makeElement( i * cellx + 0.5 * cellx, |
474 |
> |
j * celly, |
475 |
> |
k * cellz + 0.5 * cellz ); |
476 |
|
} |
477 |
|
} |
478 |
|
} |
484 |
|
for( i=0; i < (n_cells+1) && !done; i++ ){ |
485 |
|
for( j=0; j < (n_cells+1) && !done; j++ ){ |
486 |
|
|
487 |
< |
if( i < n_cells ){ |
487 |
> |
if( i < n_cells ){ |
488 |
|
|
489 |
< |
if( j < n_cells ){ |
490 |
< |
start_ndx = n_cells; |
491 |
< |
} |
492 |
< |
else start_ndx = 0; |
493 |
< |
} |
494 |
< |
else start_ndx = 0; |
489 |
> |
if( j < n_cells ){ |
490 |
> |
start_ndx = n_cells; |
491 |
> |
} |
492 |
> |
else start_ndx = 0; |
493 |
> |
} |
494 |
> |
else start_ndx = 0; |
495 |
|
|
496 |
< |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
496 |
> |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
497 |
|
|
498 |
< |
makeElement( i * cellx, |
499 |
< |
j * celly, |
500 |
< |
k * cellz ); |
501 |
< |
done = ( current_mol >= tot_nmol ); |
498 |
> |
makeElement( i * cellx, |
499 |
> |
j * celly, |
500 |
> |
k * cellz ); |
501 |
> |
done = ( current_mol >= tot_nmol ); |
502 |
|
|
503 |
< |
if( !done && n_per_extra > 1 ){ |
504 |
< |
makeElement( i * cellx + 0.5 * cellx, |
505 |
< |
j * celly + 0.5 * celly, |
506 |
< |
k * cellz ); |
507 |
< |
done = ( current_mol >= tot_nmol ); |
508 |
< |
} |
503 |
> |
if( !done && n_per_extra > 1 ){ |
504 |
> |
makeElement( i * cellx + 0.5 * cellx, |
505 |
> |
j * celly + 0.5 * celly, |
506 |
> |
k * cellz ); |
507 |
> |
done = ( current_mol >= tot_nmol ); |
508 |
> |
} |
509 |
|
|
510 |
< |
if( !done && n_per_extra > 2){ |
511 |
< |
makeElement( i * cellx, |
512 |
< |
j * celly + 0.5 * celly, |
513 |
< |
k * cellz + 0.5 * cellz ); |
514 |
< |
done = ( current_mol >= tot_nmol ); |
515 |
< |
} |
510 |
> |
if( !done && n_per_extra > 2){ |
511 |
> |
makeElement( i * cellx, |
512 |
> |
j * celly + 0.5 * celly, |
513 |
> |
k * cellz + 0.5 * cellz ); |
514 |
> |
done = ( current_mol >= tot_nmol ); |
515 |
> |
} |
516 |
|
|
517 |
< |
if( !done && n_per_extra > 3){ |
518 |
< |
makeElement( i * cellx + 0.5 * cellx, |
519 |
< |
j * celly, |
520 |
< |
k * cellz + 0.5 * cellz ); |
521 |
< |
done = ( current_mol >= tot_nmol ); |
522 |
< |
} |
523 |
< |
} |
517 |
> |
if( !done && n_per_extra > 3){ |
518 |
> |
makeElement( i * cellx + 0.5 * cellx, |
519 |
> |
j * celly, |
520 |
> |
k * cellz + 0.5 * cellz ); |
521 |
> |
done = ( current_mol >= tot_nmol ); |
522 |
> |
} |
523 |
> |
} |
524 |
|
} |
525 |
|
} |
526 |
|
} |
543 |
|
current_atom = comp_stamps[current_comp]->getAtom( k ); |
544 |
|
if( !current_atom->havePosition() ){ |
545 |
|
sprintf( painCave.errMsg, |
546 |
< |
"SimSetup:initFromBass error.\n" |
547 |
< |
"\tComponent %s, atom %s does not have a position specified.\n" |
548 |
< |
"\tThe initialization routine is unable to give a start" |
549 |
< |
" position.\n", |
550 |
< |
comp_stamps[current_comp]->getID(), |
551 |
< |
current_atom->getType() ); |
546 |
> |
"SimSetup:initFromBass error.\n" |
547 |
> |
"\tComponent %s, atom %s does not have a position specified.\n" |
548 |
> |
"\tThe initialization routine is unable to give a start" |
549 |
> |
" position.\n", |
550 |
> |
comp_stamps[current_comp]->getID(), |
551 |
> |
current_atom->getType() ); |
552 |
|
painCave.isFatal = 1; |
553 |
|
simError(); |
554 |
|
} |
617 |
|
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
618 |
|
else{ |
619 |
|
sprintf( painCave.errMsg, |
620 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
621 |
< |
force_field ); |
620 |
> |
"SimSetup Error. Unrecognized force field -> %s\n", |
621 |
> |
force_field ); |
622 |
|
painCave.isFatal = 1; |
623 |
|
simError(); |
624 |
|
} |
636 |
|
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
637 |
|
else{ |
638 |
|
sprintf( painCave.errMsg, |
639 |
< |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
639 |
> |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
640 |
|
"reverting to NVE for this simulation.\n", |
641 |
< |
ensemble ); |
641 |
> |
ensemble ); |
642 |
|
painCave.isFatal = 0; |
643 |
|
simError(); |
644 |
|
strcpy( ensemble, "NVE" ); |
669 |
|
for( i=0; i<n_components; i++ ){ |
670 |
|
|
671 |
|
if( !the_components[i]->haveNMol() ){ |
672 |
< |
// we have a problem |
673 |
< |
sprintf( painCave.errMsg, |
674 |
< |
"SimSetup Error. No global NMol or component NMol" |
675 |
< |
" given. Cannot calculate the number of atoms.\n" ); |
676 |
< |
painCave.isFatal = 1; |
677 |
< |
simError(); |
672 |
> |
// we have a problem |
673 |
> |
sprintf( painCave.errMsg, |
674 |
> |
"SimSetup Error. No global NMol or component NMol" |
675 |
> |
" given. Cannot calculate the number of atoms.\n" ); |
676 |
> |
painCave.isFatal = 1; |
677 |
> |
simError(); |
678 |
|
} |
679 |
|
|
680 |
|
tot_nmol += the_components[i]->getNMol(); |
683 |
|
} |
684 |
|
else{ |
685 |
|
sprintf( painCave.errMsg, |
686 |
< |
"SimSetup error.\n" |
687 |
< |
"\tSorry, the ability to specify total" |
688 |
< |
" nMols and then give molfractions in the components\n" |
689 |
< |
"\tis not currently supported." |
690 |
< |
" Please give nMol in the components.\n" ); |
686 |
> |
"SimSetup error.\n" |
687 |
> |
"\tSorry, the ability to specify total" |
688 |
> |
" nMols and then give molfractions in the components\n" |
689 |
> |
"\tis not currently supported." |
690 |
> |
" Please give nMol in the components.\n" ); |
691 |
|
painCave.isFatal = 1; |
692 |
|
simError(); |
693 |
|
} |
741 |
|
} |
742 |
|
else{ |
743 |
|
if( !globals->haveBoxX() ){ |
744 |
< |
sprintf( painCave.errMsg, |
745 |
< |
"SimSetup error, no periodic BoxX size given.\n" ); |
746 |
< |
painCave.isFatal = 1; |
747 |
< |
simError(); |
744 |
> |
sprintf( painCave.errMsg, |
745 |
> |
"SimSetup error, no periodic BoxX size given.\n" ); |
746 |
> |
painCave.isFatal = 1; |
747 |
> |
simError(); |
748 |
|
} |
749 |
|
boxVector[0] = globals->getBoxX(); |
750 |
|
|
751 |
|
if( !globals->haveBoxY() ){ |
752 |
< |
sprintf( painCave.errMsg, |
753 |
< |
"SimSetup error, no periodic BoxY size given.\n" ); |
754 |
< |
painCave.isFatal = 1; |
755 |
< |
simError(); |
752 |
> |
sprintf( painCave.errMsg, |
753 |
> |
"SimSetup error, no periodic BoxY size given.\n" ); |
754 |
> |
painCave.isFatal = 1; |
755 |
> |
simError(); |
756 |
|
} |
757 |
|
boxVector[1] = globals->getBoxY(); |
758 |
|
|
759 |
|
if( !globals->haveBoxZ() ){ |
760 |
< |
sprintf( painCave.errMsg, |
761 |
< |
"SimSetup error, no periodic BoxZ size given.\n" ); |
762 |
< |
painCave.isFatal = 1; |
763 |
< |
simError(); |
760 |
> |
sprintf( painCave.errMsg, |
761 |
> |
"SimSetup error, no periodic BoxZ size given.\n" ); |
762 |
> |
painCave.isFatal = 1; |
763 |
> |
simError(); |
764 |
|
} |
765 |
|
boxVector[2] = globals->getBoxZ(); |
766 |
|
|
803 |
|
info[i].useReactionField = 1; |
804 |
|
|
805 |
|
if( !globals->haveECR() ){ |
806 |
< |
sprintf( painCave.errMsg, |
807 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
808 |
< |
"box length for the electrostaticCutoffRadius.\n" |
809 |
< |
"I hope you have a very fast processor!\n"); |
810 |
< |
painCave.isFatal = 0; |
811 |
< |
simError(); |
812 |
< |
double smallest; |
813 |
< |
smallest = info[i].boxL[0]; |
814 |
< |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
815 |
< |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
816 |
< |
theEcr = 0.5 * smallest; |
806 |
> |
sprintf( painCave.errMsg, |
807 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
808 |
> |
"box length for the electrostaticCutoffRadius.\n" |
809 |
> |
"I hope you have a very fast processor!\n"); |
810 |
> |
painCave.isFatal = 0; |
811 |
> |
simError(); |
812 |
> |
double smallest; |
813 |
> |
smallest = info[i].boxL[0]; |
814 |
> |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
815 |
> |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
816 |
> |
theEcr = 0.5 * smallest; |
817 |
|
} else { |
818 |
< |
theEcr = globals->getECR(); |
818 |
> |
theEcr = globals->getECR(); |
819 |
|
} |
820 |
|
|
821 |
|
if( !globals->haveEST() ){ |
822 |
< |
sprintf( painCave.errMsg, |
823 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
824 |
< |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 |
< |
); |
826 |
< |
painCave.isFatal = 0; |
827 |
< |
simError(); |
828 |
< |
theEst = 0.05 * theEcr; |
822 |
> |
sprintf( painCave.errMsg, |
823 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
824 |
> |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 |
> |
); |
826 |
> |
painCave.isFatal = 0; |
827 |
> |
simError(); |
828 |
> |
theEst = 0.05 * theEcr; |
829 |
|
} else { |
830 |
< |
theEst= globals->getEST(); |
830 |
> |
theEst= globals->getEST(); |
831 |
|
} |
832 |
|
|
833 |
|
info[i].setEcr( theEcr, theEst ); |
834 |
|
|
835 |
|
if(!globals->haveDielectric() ){ |
836 |
< |
sprintf( painCave.errMsg, |
837 |
< |
"SimSetup Error: You are trying to use Reaction Field without" |
838 |
< |
"setting a dielectric constant!\n" |
839 |
< |
); |
840 |
< |
painCave.isFatal = 1; |
841 |
< |
simError(); |
836 |
> |
sprintf( painCave.errMsg, |
837 |
> |
"SimSetup Error: You are trying to use Reaction Field without" |
838 |
> |
"setting a dielectric constant!\n" |
839 |
> |
); |
840 |
> |
painCave.isFatal = 1; |
841 |
> |
simError(); |
842 |
|
} |
843 |
|
info[i].dielectric = globals->getDielectric(); |
844 |
|
} |
845 |
|
else { |
846 |
|
if (usesDipoles) { |
847 |
< |
|
848 |
< |
if( !globals->haveECR() ){ |
849 |
< |
sprintf( painCave.errMsg, |
850 |
< |
"SimSetup Warning: using default value of 1/2 the smallest " |
851 |
< |
"box length for the electrostaticCutoffRadius.\n" |
852 |
< |
"I hope you have a very fast processor!\n"); |
853 |
< |
painCave.isFatal = 0; |
854 |
< |
simError(); |
855 |
< |
double smallest; |
856 |
< |
smallest = info[i].boxL[0]; |
857 |
< |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
858 |
< |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
859 |
< |
theEcr = 0.5 * smallest; |
860 |
< |
} else { |
861 |
< |
theEcr = globals->getECR(); |
862 |
< |
} |
863 |
< |
|
864 |
< |
if( !globals->haveEST() ){ |
865 |
< |
sprintf( painCave.errMsg, |
866 |
< |
"SimSetup Warning: using default value of 0.05 * the " |
867 |
< |
"electrostaticCutoffRadius for the " |
868 |
< |
"electrostaticSkinThickness\n" |
869 |
< |
); |
870 |
< |
painCave.isFatal = 0; |
871 |
< |
simError(); |
872 |
< |
theEst = 0.05 * theEcr; |
873 |
< |
} else { |
874 |
< |
theEst= globals->getEST(); |
875 |
< |
} |
876 |
< |
|
877 |
< |
info[i].setEcr( theEcr, theEst ); |
847 |
> |
|
848 |
> |
if( !globals->haveECR() ){ |
849 |
> |
sprintf( painCave.errMsg, |
850 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
851 |
> |
"box length for the electrostaticCutoffRadius.\n" |
852 |
> |
"I hope you have a very fast processor!\n"); |
853 |
> |
painCave.isFatal = 0; |
854 |
> |
simError(); |
855 |
> |
double smallest; |
856 |
> |
smallest = info[i].boxL[0]; |
857 |
> |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
858 |
> |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
859 |
> |
theEcr = 0.5 * smallest; |
860 |
> |
} else { |
861 |
> |
theEcr = globals->getECR(); |
862 |
> |
} |
863 |
> |
|
864 |
> |
if( !globals->haveEST() ){ |
865 |
> |
sprintf( painCave.errMsg, |
866 |
> |
"SimSetup Warning: using default value of 0.05 * the " |
867 |
> |
"electrostaticCutoffRadius for the " |
868 |
> |
"electrostaticSkinThickness\n" |
869 |
> |
); |
870 |
> |
painCave.isFatal = 0; |
871 |
> |
simError(); |
872 |
> |
theEst = 0.05 * theEcr; |
873 |
> |
} else { |
874 |
> |
theEst= globals->getEST(); |
875 |
> |
} |
876 |
> |
|
877 |
> |
info[i].setEcr( theEcr, theEst ); |
878 |
|
} |
879 |
|
} |
880 |
|
} |
891 |
|
|
892 |
|
char* inName; |
893 |
|
|
894 |
– |
|
894 |
|
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
895 |
< |
|
895 |
> |
|
896 |
|
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
897 |
|
|
898 |
|
if( globals->haveInitialConfig() ){ |
902 |
|
if( worldRank == 0 ){ |
903 |
|
#endif //is_mpi |
904 |
|
inName = globals->getInitialConfig(); |
905 |
+ |
double* tempDouble = new double[1000000]; |
906 |
|
fileInit = new InitializeFromFile( inName ); |
907 |
|
#ifdef IS_MPI |
908 |
|
}else fileInit = new InitializeFromFile( NULL ); |
918 |
|
// no init from bass |
919 |
|
|
920 |
|
sprintf( painCave.errMsg, |
921 |
< |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
921 |
> |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
922 |
|
painCave.isFatal; |
923 |
|
simError(); |
924 |
|
|
950 |
|
#endif // is_mpi |
951 |
|
|
952 |
|
if( globals->haveFinalConfig() ){ |
953 |
< |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
953 |
> |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
954 |
|
} |
955 |
|
else{ |
956 |
< |
strcpy( info[k].finalName, inFileName ); |
957 |
< |
char* endTest; |
958 |
< |
int nameLength = strlen( info[k].finalName ); |
959 |
< |
endTest = &(info[k].finalName[nameLength - 5]); |
960 |
< |
if( !strcmp( endTest, ".bass" ) ){ |
961 |
< |
strcpy( endTest, ".eor" ); |
962 |
< |
} |
963 |
< |
else if( !strcmp( endTest, ".BASS" ) ){ |
964 |
< |
strcpy( endTest, ".eor" ); |
965 |
< |
} |
966 |
< |
else{ |
967 |
< |
endTest = &(info[k].finalName[nameLength - 4]); |
968 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
969 |
< |
strcpy( endTest, ".eor" ); |
970 |
< |
} |
971 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
972 |
< |
strcpy( endTest, ".eor" ); |
973 |
< |
} |
974 |
< |
else{ |
975 |
< |
strcat( info[k].finalName, ".eor" ); |
976 |
< |
} |
977 |
< |
} |
956 |
> |
strcpy( info[k].finalName, inFileName ); |
957 |
> |
char* endTest; |
958 |
> |
int nameLength = strlen( info[k].finalName ); |
959 |
> |
endTest = &(info[k].finalName[nameLength - 5]); |
960 |
> |
if( !strcmp( endTest, ".bass" ) ){ |
961 |
> |
strcpy( endTest, ".eor" ); |
962 |
> |
} |
963 |
> |
else if( !strcmp( endTest, ".BASS" ) ){ |
964 |
> |
strcpy( endTest, ".eor" ); |
965 |
> |
} |
966 |
> |
else{ |
967 |
> |
endTest = &(info[k].finalName[nameLength - 4]); |
968 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
969 |
> |
strcpy( endTest, ".eor" ); |
970 |
> |
} |
971 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
972 |
> |
strcpy( endTest, ".eor" ); |
973 |
> |
} |
974 |
> |
else{ |
975 |
> |
strcat( info[k].finalName, ".eor" ); |
976 |
> |
} |
977 |
> |
} |
978 |
|
} |
979 |
|
|
980 |
|
// make the sample and status out names |
984 |
|
int nameLength = strlen( info[k].sampleName ); |
985 |
|
endTest = &(info[k].sampleName[nameLength - 5]); |
986 |
|
if( !strcmp( endTest, ".bass" ) ){ |
987 |
< |
strcpy( endTest, ".dump" ); |
987 |
> |
strcpy( endTest, ".dump" ); |
988 |
|
} |
989 |
|
else if( !strcmp( endTest, ".BASS" ) ){ |
990 |
< |
strcpy( endTest, ".dump" ); |
990 |
> |
strcpy( endTest, ".dump" ); |
991 |
|
} |
992 |
|
else{ |
993 |
< |
endTest = &(info[k].sampleName[nameLength - 4]); |
994 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
995 |
< |
strcpy( endTest, ".dump" ); |
996 |
< |
} |
997 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
998 |
< |
strcpy( endTest, ".dump" ); |
999 |
< |
} |
1000 |
< |
else{ |
1001 |
< |
strcat( info[k].sampleName, ".dump" ); |
1002 |
< |
} |
993 |
> |
endTest = &(info[k].sampleName[nameLength - 4]); |
994 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
995 |
> |
strcpy( endTest, ".dump" ); |
996 |
> |
} |
997 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
998 |
> |
strcpy( endTest, ".dump" ); |
999 |
> |
} |
1000 |
> |
else{ |
1001 |
> |
strcat( info[k].sampleName, ".dump" ); |
1002 |
> |
} |
1003 |
|
} |
1004 |
|
|
1005 |
|
strcpy( info[k].statusName, inFileName ); |
1006 |
|
nameLength = strlen( info[k].statusName ); |
1007 |
|
endTest = &(info[k].statusName[nameLength - 5]); |
1008 |
|
if( !strcmp( endTest, ".bass" ) ){ |
1009 |
< |
strcpy( endTest, ".stat" ); |
1009 |
> |
strcpy( endTest, ".stat" ); |
1010 |
|
} |
1011 |
|
else if( !strcmp( endTest, ".BASS" ) ){ |
1012 |
< |
strcpy( endTest, ".stat" ); |
1012 |
> |
strcpy( endTest, ".stat" ); |
1013 |
|
} |
1014 |
|
else{ |
1015 |
< |
endTest = &(info[k].statusName[nameLength - 4]); |
1016 |
< |
if( !strcmp( endTest, ".bss" ) ){ |
1017 |
< |
strcpy( endTest, ".stat" ); |
1018 |
< |
} |
1019 |
< |
else if( !strcmp( endTest, ".mdl" ) ){ |
1020 |
< |
strcpy( endTest, ".stat" ); |
1021 |
< |
} |
1022 |
< |
else{ |
1023 |
< |
strcat( info[k].statusName, ".stat" ); |
1024 |
< |
} |
1015 |
> |
endTest = &(info[k].statusName[nameLength - 4]); |
1016 |
> |
if( !strcmp( endTest, ".bss" ) ){ |
1017 |
> |
strcpy( endTest, ".stat" ); |
1018 |
> |
} |
1019 |
> |
else if( !strcmp( endTest, ".mdl" ) ){ |
1020 |
> |
strcpy( endTest, ".stat" ); |
1021 |
> |
} |
1022 |
> |
else{ |
1023 |
> |
strcat( info[k].statusName, ".stat" ); |
1024 |
> |
} |
1025 |
|
} |
1026 |
|
|
1027 |
|
#ifdef IS_MPI |
1088 |
|
|
1089 |
|
default: |
1090 |
|
sprintf( painCave.errMsg, |
1091 |
< |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1091 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1092 |
|
painCave.isFatal = 1; |
1093 |
|
simError(); |
1094 |
|
} |
1134 |
|
|
1135 |
|
currentStamp = stamps->extractMolStamp( id ); |
1136 |
|
if( currentStamp == NULL ){ |
1137 |
< |
sprintf( painCave.errMsg, |
1138 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
1139 |
< |
"list of declared molecules\n", |
1140 |
< |
id ); |
1141 |
< |
painCave.isFatal = 1; |
1142 |
< |
simError(); |
1137 |
> |
sprintf( painCave.errMsg, |
1138 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1139 |
> |
"list of declared molecules\n", |
1140 |
> |
id ); |
1141 |
> |
painCave.isFatal = 1; |
1142 |
> |
simError(); |
1143 |
|
} |
1144 |
|
|
1145 |
|
headStamp->add( currentStamp ); |
1218 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
1219 |
|
|
1220 |
|
if( mol2proc[allMol] == worldRank ){ |
1221 |
< |
|
1222 |
< |
local_atoms += comp_stamps[i]->getNAtoms(); |
1223 |
< |
local_bonds += comp_stamps[i]->getNBonds(); |
1224 |
< |
local_bends += comp_stamps[i]->getNBends(); |
1225 |
< |
local_torsions += comp_stamps[i]->getNTorsions(); |
1226 |
< |
localMol++; |
1221 |
> |
|
1222 |
> |
local_atoms += comp_stamps[i]->getNAtoms(); |
1223 |
> |
local_bonds += comp_stamps[i]->getNBonds(); |
1224 |
> |
local_bends += comp_stamps[i]->getNBends(); |
1225 |
> |
local_torsions += comp_stamps[i]->getNTorsions(); |
1226 |
> |
localMol++; |
1227 |
|
} |
1228 |
|
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1229 |
|
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1239 |
|
|
1240 |
|
if( local_atoms != info[0].n_atoms ){ |
1241 |
|
sprintf( painCave.errMsg, |
1242 |
< |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1243 |
< |
" localAtom (%d) are not equal.\n", |
1244 |
< |
info[0].n_atoms, |
1245 |
< |
local_atoms ); |
1242 |
> |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1243 |
> |
" localAtom (%d) are not equal.\n", |
1244 |
> |
info[0].n_atoms, |
1245 |
> |
local_atoms ); |
1246 |
|
painCave.isFatal = 1; |
1247 |
|
simError(); |
1248 |
|
} |
1285 |
|
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1286 |
|
|
1287 |
|
if(mol2proc[i] == worldRank ){ |
1288 |
< |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1289 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1290 |
< |
the_molecules[molIndex].setGlobalIndex( i ); |
1291 |
< |
molIndex++; |
1288 |
> |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1289 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1290 |
> |
the_molecules[molIndex].setGlobalIndex( i ); |
1291 |
> |
molIndex++; |
1292 |
|
} |
1293 |
|
} |
1294 |
|
|
1298 |
|
globalAtomIndex = 0; |
1299 |
|
for(i=0; i<n_components; i++){ |
1300 |
|
for(j=0; j<components_nmol[i]; j++ ){ |
1301 |
< |
the_molecules[molIndex].setStampID( i ); |
1302 |
< |
the_molecules[molIndex].setMyIndex( molIndex ); |
1303 |
< |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1304 |
< |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1305 |
< |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1306 |
< |
globalAtomIndex++; |
1307 |
< |
} |
1308 |
< |
molIndex++; |
1301 |
> |
the_molecules[molIndex].setStampID( i ); |
1302 |
> |
the_molecules[molIndex].setMyIndex( molIndex ); |
1303 |
> |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1304 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1305 |
> |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1306 |
> |
globalAtomIndex++; |
1307 |
> |
} |
1308 |
> |
molIndex++; |
1309 |
|
} |
1310 |
|
} |
1311 |
|
|
1318 |
|
Exclude::createArray(info[l].n_SRI); |
1319 |
|
the_excludes = new Exclude*[info[l].n_SRI]; |
1320 |
|
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1321 |
< |
the_excludes[ex] = new Exclude(ex); |
1321 |
> |
the_excludes[ex] = new Exclude(ex); |
1322 |
|
} |
1323 |
|
info[l].globalExcludes = new int; |
1324 |
|
info[l].n_exclude = info[l].n_SRI; |
1361 |
|
switch( ensembleCase ){ |
1362 |
|
|
1363 |
|
case NVE_ENS: |
1364 |
< |
if (globals->haveZconstraints()){ |
1365 |
< |
setupZConstraint(info[k]); |
1366 |
< |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1367 |
< |
} |
1364 |
> |
if (globals->haveZconstraints()){ |
1365 |
> |
setupZConstraint(info[k]); |
1366 |
> |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1367 |
> |
} |
1368 |
|
|
1369 |
< |
else |
1369 |
> |
else |
1370 |
|
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1371 |
|
break; |
1372 |
|
|
1373 |
|
case NVT_ENS: |
1374 |
< |
if (globals->haveZconstraints()){ |
1375 |
< |
setupZConstraint(info[k]); |
1376 |
< |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1377 |
< |
} |
1378 |
< |
else |
1374 |
> |
if (globals->haveZconstraints()){ |
1375 |
> |
setupZConstraint(info[k]); |
1376 |
> |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1377 |
> |
} |
1378 |
> |
else |
1379 |
|
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1380 |
|
|
1381 |
< |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1381 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1382 |
|
|
1383 |
< |
if (globals->haveTauThermostat()) |
1384 |
< |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1383 |
> |
if (globals->haveTauThermostat()) |
1384 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1385 |
|
|
1386 |
< |
else { |
1387 |
< |
sprintf( painCave.errMsg, |
1388 |
< |
"SimSetup error: If you use the NVT\n" |
1389 |
< |
" ensemble, you must set tauThermostat.\n"); |
1390 |
< |
painCave.isFatal = 1; |
1391 |
< |
simError(); |
1392 |
< |
} |
1393 |
< |
break; |
1386 |
> |
else { |
1387 |
> |
sprintf( painCave.errMsg, |
1388 |
> |
"SimSetup error: If you use the NVT\n" |
1389 |
> |
" ensemble, you must set tauThermostat.\n"); |
1390 |
> |
painCave.isFatal = 1; |
1391 |
> |
simError(); |
1392 |
> |
} |
1393 |
> |
break; |
1394 |
|
|
1395 |
|
case NPTi_ENS: |
1396 |
< |
if (globals->haveZconstraints()){ |
1397 |
< |
setupZConstraint(info[k]); |
1398 |
< |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1399 |
< |
} |
1400 |
< |
else |
1396 |
> |
if (globals->haveZconstraints()){ |
1397 |
> |
setupZConstraint(info[k]); |
1398 |
> |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1399 |
> |
} |
1400 |
> |
else |
1401 |
|
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1402 |
|
|
1403 |
< |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1404 |
< |
|
1403 |
> |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1404 |
> |
|
1405 |
|
if (globals->haveTargetPressure()) |
1406 |
< |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1406 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1407 |
|
else { |
1408 |
< |
sprintf( painCave.errMsg, |
1409 |
< |
"SimSetup error: If you use a constant pressure\n" |
1410 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1411 |
< |
painCave.isFatal = 1; |
1412 |
< |
simError(); |
1408 |
> |
sprintf( painCave.errMsg, |
1409 |
> |
"SimSetup error: If you use a constant pressure\n" |
1410 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1411 |
> |
painCave.isFatal = 1; |
1412 |
> |
simError(); |
1413 |
|
} |
1414 |
< |
|
1414 |
> |
|
1415 |
|
if( globals->haveTauThermostat() ) |
1416 |
< |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1416 |
> |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1417 |
|
else{ |
1418 |
< |
sprintf( painCave.errMsg, |
1419 |
< |
"SimSetup error: If you use an NPT\n" |
1420 |
< |
" ensemble, you must set tauThermostat.\n"); |
1421 |
< |
painCave.isFatal = 1; |
1422 |
< |
simError(); |
1418 |
> |
sprintf( painCave.errMsg, |
1419 |
> |
"SimSetup error: If you use an NPT\n" |
1420 |
> |
" ensemble, you must set tauThermostat.\n"); |
1421 |
> |
painCave.isFatal = 1; |
1422 |
> |
simError(); |
1423 |
|
} |
1424 |
< |
|
1424 |
> |
|
1425 |
|
if( globals->haveTauBarostat() ) |
1426 |
< |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1426 |
> |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1427 |
|
else{ |
1428 |
< |
sprintf( painCave.errMsg, |
1429 |
< |
"SimSetup error: If you use an NPT\n" |
1430 |
< |
" ensemble, you must set tauBarostat.\n"); |
1431 |
< |
painCave.isFatal = 1; |
1432 |
< |
simError(); |
1433 |
< |
} |
1434 |
< |
break; |
1428 |
> |
sprintf( painCave.errMsg, |
1429 |
> |
"SimSetup error: If you use an NPT\n" |
1430 |
> |
" ensemble, you must set tauBarostat.\n"); |
1431 |
> |
painCave.isFatal = 1; |
1432 |
> |
simError(); |
1433 |
> |
} |
1434 |
> |
break; |
1435 |
|
|
1436 |
|
case NPTf_ENS: |
1437 |
< |
if (globals->haveZconstraints()){ |
1438 |
< |
setupZConstraint(info[k]); |
1439 |
< |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1440 |
< |
} |
1441 |
< |
else |
1437 |
> |
if (globals->haveZconstraints()){ |
1438 |
> |
setupZConstraint(info[k]); |
1439 |
> |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1440 |
> |
} |
1441 |
> |
else |
1442 |
|
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1443 |
|
|
1444 |
|
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1445 |
< |
|
1445 |
> |
|
1446 |
|
if (globals->haveTargetPressure()) |
1447 |
< |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1447 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1448 |
|
else { |
1449 |
< |
sprintf( painCave.errMsg, |
1450 |
< |
"SimSetup error: If you use a constant pressure\n" |
1451 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1452 |
< |
painCave.isFatal = 1; |
1453 |
< |
simError(); |
1449 |
> |
sprintf( painCave.errMsg, |
1450 |
> |
"SimSetup error: If you use a constant pressure\n" |
1451 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1452 |
> |
painCave.isFatal = 1; |
1453 |
> |
simError(); |
1454 |
|
} |
1455 |
< |
|
1455 |
> |
|
1456 |
|
if( globals->haveTauThermostat() ) |
1457 |
< |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1457 |
> |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1458 |
|
else{ |
1459 |
< |
sprintf( painCave.errMsg, |
1460 |
< |
"SimSetup error: If you use an NPT\n" |
1461 |
< |
" ensemble, you must set tauThermostat.\n"); |
1462 |
< |
painCave.isFatal = 1; |
1463 |
< |
simError(); |
1459 |
> |
sprintf( painCave.errMsg, |
1460 |
> |
"SimSetup error: If you use an NPT\n" |
1461 |
> |
" ensemble, you must set tauThermostat.\n"); |
1462 |
> |
painCave.isFatal = 1; |
1463 |
> |
simError(); |
1464 |
|
} |
1465 |
< |
|
1465 |
> |
|
1466 |
|
if( globals->haveTauBarostat() ) |
1467 |
< |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1467 |
> |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1468 |
|
else{ |
1469 |
< |
sprintf( painCave.errMsg, |
1470 |
< |
"SimSetup error: If you use an NPT\n" |
1471 |
< |
" ensemble, you must set tauBarostat.\n"); |
1472 |
< |
painCave.isFatal = 1; |
1473 |
< |
simError(); |
1469 |
> |
sprintf( painCave.errMsg, |
1470 |
> |
"SimSetup error: If you use an NPT\n" |
1471 |
> |
" ensemble, you must set tauBarostat.\n"); |
1472 |
> |
painCave.isFatal = 1; |
1473 |
> |
simError(); |
1474 |
|
} |
1475 |
|
break; |
1476 |
|
|
1477 |
|
case NPTim_ENS: |
1478 |
< |
if (globals->haveZconstraints()){ |
1479 |
< |
setupZConstraint(info[k]); |
1480 |
< |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1481 |
< |
} |
1482 |
< |
else |
1478 |
> |
if (globals->haveZconstraints()){ |
1479 |
> |
setupZConstraint(info[k]); |
1480 |
> |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1481 |
> |
} |
1482 |
> |
else |
1483 |
|
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1484 |
|
|
1485 |
< |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1486 |
< |
|
1485 |
> |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1486 |
> |
|
1487 |
|
if (globals->haveTargetPressure()) |
1488 |
< |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1488 |
> |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1489 |
|
else { |
1490 |
< |
sprintf( painCave.errMsg, |
1491 |
< |
"SimSetup error: If you use a constant pressure\n" |
1492 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1493 |
< |
painCave.isFatal = 1; |
1494 |
< |
simError(); |
1490 |
> |
sprintf( painCave.errMsg, |
1491 |
> |
"SimSetup error: If you use a constant pressure\n" |
1492 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1493 |
> |
painCave.isFatal = 1; |
1494 |
> |
simError(); |
1495 |
|
} |
1496 |
< |
|
1496 |
> |
|
1497 |
|
if( globals->haveTauThermostat() ) |
1498 |
< |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1498 |
> |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1499 |
|
else{ |
1500 |
< |
sprintf( painCave.errMsg, |
1501 |
< |
"SimSetup error: If you use an NPT\n" |
1502 |
< |
" ensemble, you must set tauThermostat.\n"); |
1503 |
< |
painCave.isFatal = 1; |
1504 |
< |
simError(); |
1500 |
> |
sprintf( painCave.errMsg, |
1501 |
> |
"SimSetup error: If you use an NPT\n" |
1502 |
> |
" ensemble, you must set tauThermostat.\n"); |
1503 |
> |
painCave.isFatal = 1; |
1504 |
> |
simError(); |
1505 |
|
} |
1506 |
< |
|
1506 |
> |
|
1507 |
|
if( globals->haveTauBarostat() ) |
1508 |
< |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1508 |
> |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1509 |
|
else{ |
1510 |
< |
sprintf( painCave.errMsg, |
1511 |
< |
"SimSetup error: If you use an NPT\n" |
1512 |
< |
" ensemble, you must set tauBarostat.\n"); |
1513 |
< |
painCave.isFatal = 1; |
1514 |
< |
simError(); |
1510 |
> |
sprintf( painCave.errMsg, |
1511 |
> |
"SimSetup error: If you use an NPT\n" |
1512 |
> |
" ensemble, you must set tauBarostat.\n"); |
1513 |
> |
painCave.isFatal = 1; |
1514 |
> |
simError(); |
1515 |
|
} |
1516 |
|
break; |
1517 |
|
|
1518 |
|
case NPTfm_ENS: |
1519 |
< |
if (globals->haveZconstraints()){ |
1520 |
< |
setupZConstraint(info[k]); |
1521 |
< |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1522 |
< |
} |
1523 |
< |
else |
1519 |
> |
if (globals->haveZconstraints()){ |
1520 |
> |
setupZConstraint(info[k]); |
1521 |
> |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1522 |
> |
} |
1523 |
> |
else |
1524 |
|
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1525 |
|
|
1526 |
< |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1527 |
< |
|
1526 |
> |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1527 |
> |
|
1528 |
|
if (globals->haveTargetPressure()) |
1529 |
< |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1529 |
> |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1530 |
|
else { |
1531 |
< |
sprintf( painCave.errMsg, |
1532 |
< |
"SimSetup error: If you use a constant pressure\n" |
1533 |
< |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1534 |
< |
painCave.isFatal = 1; |
1535 |
< |
simError(); |
1531 |
> |
sprintf( painCave.errMsg, |
1532 |
> |
"SimSetup error: If you use a constant pressure\n" |
1533 |
> |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1534 |
> |
painCave.isFatal = 1; |
1535 |
> |
simError(); |
1536 |
|
} |
1537 |
< |
|
1537 |
> |
|
1538 |
|
if( globals->haveTauThermostat() ) |
1539 |
< |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1539 |
> |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1540 |
|
else{ |
1541 |
< |
sprintf( painCave.errMsg, |
1542 |
< |
"SimSetup error: If you use an NPT\n" |
1543 |
< |
" ensemble, you must set tauThermostat.\n"); |
1544 |
< |
painCave.isFatal = 1; |
1545 |
< |
simError(); |
1541 |
> |
sprintf( painCave.errMsg, |
1542 |
> |
"SimSetup error: If you use an NPT\n" |
1543 |
> |
" ensemble, you must set tauThermostat.\n"); |
1544 |
> |
painCave.isFatal = 1; |
1545 |
> |
simError(); |
1546 |
|
} |
1547 |
< |
|
1547 |
> |
|
1548 |
|
if( globals->haveTauBarostat() ) |
1549 |
< |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1549 |
> |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1550 |
|
else{ |
1551 |
< |
sprintf( painCave.errMsg, |
1552 |
< |
"SimSetup error: If you use an NPT\n" |
1553 |
< |
" ensemble, you must set tauBarostat.\n"); |
1554 |
< |
painCave.isFatal = 1; |
1555 |
< |
simError(); |
1551 |
> |
sprintf( painCave.errMsg, |
1552 |
> |
"SimSetup error: If you use an NPT\n" |
1553 |
> |
" ensemble, you must set tauBarostat.\n"); |
1554 |
> |
painCave.isFatal = 1; |
1555 |
> |
simError(); |
1556 |
|
} |
1557 |
|
break; |
1558 |
|
|
1559 |
|
default: |
1560 |
|
sprintf( painCave.errMsg, |
1561 |
< |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1561 |
> |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1562 |
|
painCave.isFatal = 1; |
1563 |
|
simError(); |
1564 |
|
} |
1577 |
|
} |
1578 |
|
else{ |
1579 |
|
sprintf( painCave.errMsg, |
1580 |
< |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1581 |
< |
info[0].mixingRule ); |
1580 |
> |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1581 |
> |
info[0].mixingRule ); |
1582 |
|
painCave.isFatal = 1; |
1583 |
|
simError(); |
1584 |
|
} |
1586 |
|
|
1587 |
|
#ifdef IS_MPI |
1588 |
|
strcpy( checkPointMsg, |
1589 |
< |
"Successfully intialized the mixingRule for Fortran." ); |
1589 |
> |
"Successfully intialized the mixingRule for Fortran." ); |
1590 |
|
MPIcheckPoint(); |
1591 |
|
#endif // is_mpi |
1592 |
|
|
1594 |
|
|
1595 |
|
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1596 |
|
{ |
1597 |
< |
int nZConstraints; |
1598 |
< |
ZconStamp** zconStamp; |
1599 |
< |
|
1600 |
< |
if(globals->haveZconstraintTime()){ |
1601 |
< |
|
1602 |
< |
//add sample time of z-constraint into SimInfo's property list |
1603 |
< |
DoubleData* zconsTimeProp = new DoubleData(); |
1604 |
< |
zconsTimeProp->setID(ZCONSTIME_ID); |
1605 |
< |
zconsTimeProp->setData(globals->getZconsTime()); |
1606 |
< |
theInfo.addProperty(zconsTimeProp); |
1607 |
< |
} |
1608 |
< |
else{ |
1609 |
< |
sprintf( painCave.errMsg, |
1610 |
< |
"ZConstraint error: If you use an ZConstraint\n" |
1611 |
< |
" , you must set sample time.\n"); |
1612 |
< |
painCave.isFatal = 1; |
1613 |
< |
simError(); |
1614 |
< |
} |
1597 |
> |
int nZConstraints; |
1598 |
> |
ZconStamp** zconStamp; |
1599 |
|
|
1600 |
< |
// |
1601 |
< |
nZConstraints = globals->getNzConstraints(); |
1602 |
< |
zconStamp = globals->getZconStamp(); |
1603 |
< |
ZConsParaItem tempParaItem; |
1600 |
> |
if(globals->haveZconstraintTime()){ |
1601 |
> |
|
1602 |
> |
//add sample time of z-constraint into SimInfo's property list |
1603 |
> |
DoubleData* zconsTimeProp = new DoubleData(); |
1604 |
> |
zconsTimeProp->setID(ZCONSTIME_ID); |
1605 |
> |
zconsTimeProp->setData(globals->getZconsTime()); |
1606 |
> |
theInfo.addProperty(zconsTimeProp); |
1607 |
> |
} |
1608 |
> |
else{ |
1609 |
> |
sprintf( painCave.errMsg, |
1610 |
> |
"ZConstraint error: If you use an ZConstraint\n" |
1611 |
> |
" , you must set sample time.\n"); |
1612 |
> |
painCave.isFatal = 1; |
1613 |
> |
simError(); |
1614 |
> |
} |
1615 |
|
|
1616 |
< |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1617 |
< |
zconsParaData->setID(ZCONSPARADATA_ID); |
1618 |
< |
|
1619 |
< |
for(int i = 0; i < nZConstraints; i++){ |
1616 |
> |
//push zconsTol into siminfo, if user does not specify |
1617 |
> |
//value for zconsTol, a default value will be used |
1618 |
> |
DoubleData* zconsTol = new DoubleData(); |
1619 |
> |
zconsTol->setID(ZCONSTOL_ID); |
1620 |
> |
if(globals->haveZconsTol()){ |
1621 |
> |
zconsTol->setData(globals->getZconsTol()); |
1622 |
> |
} |
1623 |
> |
else{ |
1624 |
> |
double defaultZConsTol = 0.01; |
1625 |
> |
sprintf( painCave.errMsg, |
1626 |
> |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1627 |
> |
" , default value %f is used.\n", defaultZConsTol); |
1628 |
> |
painCave.isFatal = 0; |
1629 |
> |
simError(); |
1630 |
> |
|
1631 |
> |
zconsTol->setData(defaultZConsTol); |
1632 |
> |
} |
1633 |
> |
theInfo.addProperty(zconsTol); |
1634 |
> |
|
1635 |
> |
//set Force Substraction Policy |
1636 |
> |
StringData* zconsForcePolicy = new StringData(); |
1637 |
> |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1638 |
> |
|
1639 |
> |
if(globals->haveZconsForcePolicy()){ |
1640 |
> |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1641 |
> |
} |
1642 |
> |
else{ |
1643 |
> |
sprintf( painCave.errMsg, |
1644 |
> |
"ZConstraint Warning: User does not set force substraction policy, " |
1645 |
> |
"average force substraction policy is used\n"); |
1646 |
> |
painCave.isFatal = 0; |
1647 |
> |
simError(); |
1648 |
> |
zconsForcePolicy->setData("BYNUMBER"); |
1649 |
> |
} |
1650 |
> |
|
1651 |
> |
theInfo.addProperty(zconsForcePolicy); |
1652 |
> |
|
1653 |
> |
//Determine the name of ouput file and add it into SimInfo's property list |
1654 |
> |
//Be careful, do not use inFileName, since it is a pointer which |
1655 |
> |
//point to a string at master node, and slave nodes do not contain that string |
1656 |
> |
|
1657 |
> |
string zconsOutput(theInfo.finalName); |
1658 |
> |
|
1659 |
> |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1660 |
> |
|
1661 |
> |
StringData* zconsFilename = new StringData(); |
1662 |
> |
zconsFilename->setID(ZCONSFILENAME_ID); |
1663 |
> |
zconsFilename->setData(zconsOutput); |
1664 |
> |
|
1665 |
> |
theInfo.addProperty(zconsFilename); |
1666 |
> |
|
1667 |
> |
//setup index, pos and other parameters of z-constraint molecules |
1668 |
> |
nZConstraints = globals->getNzConstraints(); |
1669 |
> |
theInfo.nZconstraints = nZConstraints; |
1670 |
> |
|
1671 |
> |
zconStamp = globals->getZconStamp(); |
1672 |
> |
ZConsParaItem tempParaItem; |
1673 |
> |
|
1674 |
> |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1675 |
> |
zconsParaData->setID(ZCONSPARADATA_ID); |
1676 |
> |
|
1677 |
> |
for(int i = 0; i < nZConstraints; i++){ |
1678 |
|
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1679 |
|
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1680 |
|
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1681 |
|
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1682 |
|
|
1683 |
|
zconsParaData->addItem(tempParaItem); |
1684 |
< |
} |
1684 |
> |
} |
1685 |
|
|
1686 |
< |
//sort the parameters by index of molecules |
1687 |
< |
zconsParaData->sortByIndex(); |
1688 |
< |
|
1689 |
< |
//push data into siminfo, therefore, we can retrieve later |
1690 |
< |
theInfo.addProperty(zconsParaData); |
1691 |
< |
|
1639 |
< |
//push zconsTol into siminfo, if user does not specify |
1640 |
< |
//value for zconsTol, a default value will be used |
1641 |
< |
DoubleData* zconsTol = new DoubleData(); |
1642 |
< |
zconsTol->setID(ZCONSTOL_ID); |
1643 |
< |
if(globals->haveZconsTol()){ |
1644 |
< |
zconsTol->setData(globals->getZconsTol()); |
1645 |
< |
} |
1646 |
< |
else{ |
1647 |
< |
double defaultZConsTol = 1E-6; |
1648 |
< |
sprintf( painCave.errMsg, |
1649 |
< |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1650 |
< |
" , default value %f is used.\n", defaultZConsTol); |
1651 |
< |
painCave.isFatal = 0; |
1652 |
< |
simError(); |
1653 |
< |
|
1654 |
< |
zconsTol->setData(defaultZConsTol); |
1655 |
< |
} |
1656 |
< |
theInfo.addProperty(zconsTol); |
1657 |
< |
|
1658 |
< |
//Determine the name of ouput file and add it into SimInfo's property list |
1659 |
< |
//Be careful, do not use inFileName, since it is a pointer which |
1660 |
< |
//point to a string at master node, and slave nodes do not contain that string |
1661 |
< |
|
1662 |
< |
string zconsOutput(theInfo.finalName); |
1663 |
< |
|
1664 |
< |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1665 |
< |
|
1666 |
< |
StringData* zconsFilename = new StringData(); |
1667 |
< |
zconsFilename->setID(ZCONSFILENAME_ID); |
1668 |
< |
zconsFilename->setData(zconsOutput); |
1669 |
< |
|
1670 |
< |
theInfo.addProperty(zconsFilename); |
1686 |
> |
//sort the parameters by index of molecules |
1687 |
> |
zconsParaData->sortByIndex(); |
1688 |
> |
|
1689 |
> |
//push data into siminfo, therefore, we can retrieve later |
1690 |
> |
theInfo.addProperty(zconsParaData); |
1691 |
> |
|
1692 |
|
} |