# | Line 3 | Line 3 | |
---|---|---|
3 | #include <iostream> | |
4 | #include <cmath> | |
5 | #include <string> | |
6 | + | #include <sys/time.h> |
7 | ||
8 | #include "SimSetup.hpp" | |
9 | #include "ReadWrite.hpp" | |
# | Line 189 | Line 190 | void SimSetup::makeMolecules( void ){ | |
190 | // make the Atoms | |
191 | ||
192 | for(j=0; j<molInfo.nAtoms; j++){ | |
193 | < | |
194 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
195 | < | 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() ); |
193 | > | |
194 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
195 | > | if( currentAtom->haveOrientation() ){ |
196 | ||
197 | + | dAtom = new DirectionalAtom( (j + atomOffset), |
198 | + | info[k].getConfiguration() ); |
199 | + | info[k].n_oriented++; |
200 | + | molInfo.myAtoms[j] = dAtom; |
201 | + | |
202 | + | ux = currentAtom->getOrntX(); |
203 | + | uy = currentAtom->getOrntY(); |
204 | + | uz = currentAtom->getOrntZ(); |
205 | + | |
206 | + | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
207 | + | |
208 | + | u = sqrt( uSqr ); |
209 | + | ux = ux / u; |
210 | + | uy = uy / u; |
211 | + | uz = uz / u; |
212 | + | |
213 | + | dAtom->setSUx( ux ); |
214 | + | dAtom->setSUy( uy ); |
215 | + | dAtom->setSUz( uz ); |
216 | + | } |
217 | + | else{ |
218 | + | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
219 | + | info[k].getConfiguration() ); |
220 | + | } |
221 | + | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
222 | + | |
223 | #ifdef IS_MPI | |
224 | ||
225 | < | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
225 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
226 | ||
227 | #endif // is_mpi | |
228 | } | |
# | Line 229 | Line 230 | void SimSetup::makeMolecules( void ){ | |
230 | // make the bonds | |
231 | for(j=0; j<molInfo.nBonds; j++){ | |
232 | ||
233 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
234 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
235 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
236 | < | |
237 | < | exI = theBonds[j].a; |
238 | < | exJ = theBonds[j].b; |
239 | < | |
240 | < | // exclude_I must always be the smaller of the pair |
241 | < | if( exI > exJ ){ |
242 | < | tempEx = exI; |
243 | < | exI = exJ; |
244 | < | exJ = tempEx; |
245 | < | } |
246 | < | #ifdef IS_MPI |
247 | < | tempEx = exI; |
248 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
249 | < | tempEx = exJ; |
250 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
251 | < | |
252 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
233 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
234 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
235 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
236 | > | |
237 | > | exI = theBonds[j].a; |
238 | > | exJ = theBonds[j].b; |
239 | > | |
240 | > | // exclude_I must always be the smaller of the pair |
241 | > | if( exI > exJ ){ |
242 | > | tempEx = exI; |
243 | > | exI = exJ; |
244 | > | exJ = tempEx; |
245 | > | } |
246 | > | #ifdef IS_MPI |
247 | > | tempEx = exI; |
248 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
249 | > | tempEx = exJ; |
250 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
251 | > | |
252 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
253 | #else // isn't MPI | |
254 | < | |
255 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
254 | > | |
255 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
256 | #endif //is_mpi | |
257 | } | |
258 | excludeOffset += molInfo.nBonds; | |
259 | ||
260 | //make the bends | |
261 | for(j=0; j<molInfo.nBends; j++){ | |
262 | < | |
263 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
264 | < | theBends[j].a = currentBend->getA() + atomOffset; |
265 | < | theBends[j].b = currentBend->getB() + atomOffset; |
266 | < | theBends[j].c = currentBend->getC() + atomOffset; |
267 | < | |
268 | < | if( currentBend->haveExtras() ){ |
269 | < | |
270 | < | extras = currentBend->getExtras(); |
271 | < | current_extra = extras; |
272 | < | |
273 | < | while( current_extra != NULL ){ |
274 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
275 | < | |
276 | < | switch( current_extra->getType() ){ |
277 | < | |
278 | < | case 0: |
279 | < | theBends[j].ghost = |
280 | < | current_extra->getInt() + atomOffset; |
281 | < | theBends[j].isGhost = 1; |
282 | < | break; |
283 | < | |
284 | < | case 1: |
285 | < | theBends[j].ghost = |
286 | < | (int)current_extra->getDouble() + atomOffset; |
287 | < | theBends[j].isGhost = 1; |
288 | < | break; |
289 | < | |
290 | < | default: |
291 | < | sprintf( painCave.errMsg, |
292 | < | "SimSetup Error: ghostVectorSource was neither a " |
293 | < | "double nor an int.\n" |
294 | < | "-->Bend[%d] in %s\n", |
295 | < | j, comp_stamps[stampID]->getID() ); |
296 | < | painCave.isFatal = 1; |
297 | < | simError(); |
298 | < | } |
299 | < | } |
300 | < | |
301 | < | else{ |
302 | < | |
303 | < | sprintf( painCave.errMsg, |
304 | < | "SimSetup Error: unhandled bend assignment:\n" |
305 | < | " -->%s in Bend[%d] in %s\n", |
306 | < | current_extra->getlhs(), |
307 | < | j, comp_stamps[stampID]->getID() ); |
308 | < | painCave.isFatal = 1; |
309 | < | simError(); |
310 | < | } |
311 | < | |
312 | < | current_extra = current_extra->getNext(); |
313 | < | } |
314 | < | } |
315 | < | |
316 | < | if( !theBends[j].isGhost ){ |
317 | < | |
318 | < | exI = theBends[j].a; |
319 | < | exJ = theBends[j].c; |
320 | < | } |
321 | < | else{ |
322 | < | |
323 | < | exI = theBends[j].a; |
324 | < | exJ = theBends[j].b; |
325 | < | } |
326 | < | |
327 | < | // exclude_I must always be the smaller of the pair |
328 | < | if( exI > exJ ){ |
329 | < | tempEx = exI; |
330 | < | exI = exJ; |
331 | < | exJ = tempEx; |
332 | < | } |
262 | > | |
263 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
264 | > | theBends[j].a = currentBend->getA() + atomOffset; |
265 | > | theBends[j].b = currentBend->getB() + atomOffset; |
266 | > | theBends[j].c = currentBend->getC() + atomOffset; |
267 | > | |
268 | > | if( currentBend->haveExtras() ){ |
269 | > | |
270 | > | extras = currentBend->getExtras(); |
271 | > | current_extra = extras; |
272 | > | |
273 | > | while( current_extra != NULL ){ |
274 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
275 | > | |
276 | > | switch( current_extra->getType() ){ |
277 | > | |
278 | > | case 0: |
279 | > | theBends[j].ghost = |
280 | > | current_extra->getInt() + atomOffset; |
281 | > | theBends[j].isGhost = 1; |
282 | > | break; |
283 | > | |
284 | > | case 1: |
285 | > | theBends[j].ghost = |
286 | > | (int)current_extra->getDouble() + atomOffset; |
287 | > | theBends[j].isGhost = 1; |
288 | > | break; |
289 | > | |
290 | > | default: |
291 | > | sprintf( painCave.errMsg, |
292 | > | "SimSetup Error: ghostVectorSource was neither a " |
293 | > | "double nor an int.\n" |
294 | > | "-->Bend[%d] in %s\n", |
295 | > | j, comp_stamps[stampID]->getID() ); |
296 | > | painCave.isFatal = 1; |
297 | > | simError(); |
298 | > | } |
299 | > | } |
300 | > | |
301 | > | else{ |
302 | > | |
303 | > | sprintf( painCave.errMsg, |
304 | > | "SimSetup Error: unhandled bend assignment:\n" |
305 | > | " -->%s in Bend[%d] in %s\n", |
306 | > | current_extra->getlhs(), |
307 | > | j, comp_stamps[stampID]->getID() ); |
308 | > | painCave.isFatal = 1; |
309 | > | simError(); |
310 | > | } |
311 | > | |
312 | > | current_extra = current_extra->getNext(); |
313 | > | } |
314 | > | } |
315 | > | |
316 | > | if( !theBends[j].isGhost ){ |
317 | > | |
318 | > | exI = theBends[j].a; |
319 | > | exJ = theBends[j].c; |
320 | > | } |
321 | > | else{ |
322 | > | |
323 | > | exI = theBends[j].a; |
324 | > | exJ = theBends[j].b; |
325 | > | } |
326 | > | |
327 | > | // exclude_I must always be the smaller of the pair |
328 | > | if( exI > exJ ){ |
329 | > | tempEx = exI; |
330 | > | exI = exJ; |
331 | > | exJ = tempEx; |
332 | > | } |
333 | #ifdef IS_MPI | |
334 | < | tempEx = exI; |
335 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
336 | < | tempEx = exJ; |
337 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
334 | > | tempEx = exI; |
335 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
336 | > | tempEx = exJ; |
337 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
338 | ||
339 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
339 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
340 | #else // isn't MPI | |
341 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
341 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
342 | #endif //is_mpi | |
343 | } | |
344 | excludeOffset += molInfo.nBends; | |
345 | ||
346 | for(j=0; j<molInfo.nTorsions; j++){ | |
347 | < | |
348 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
349 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
350 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
351 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
352 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
353 | < | |
354 | < | exI = theTorsions[j].a; |
355 | < | exJ = theTorsions[j].d; |
356 | < | |
357 | < | // exclude_I must always be the smaller of the pair |
358 | < | if( exI > exJ ){ |
359 | < | tempEx = exI; |
360 | < | exI = exJ; |
361 | < | exJ = tempEx; |
362 | < | } |
347 | > | |
348 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
349 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
350 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
351 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
352 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
353 | > | |
354 | > | exI = theTorsions[j].a; |
355 | > | exJ = theTorsions[j].d; |
356 | > | |
357 | > | // exclude_I must always be the smaller of the pair |
358 | > | if( exI > exJ ){ |
359 | > | tempEx = exI; |
360 | > | exI = exJ; |
361 | > | exJ = tempEx; |
362 | > | } |
363 | #ifdef IS_MPI | |
364 | < | tempEx = exI; |
365 | < | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
366 | < | tempEx = exJ; |
367 | < | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
368 | < | |
369 | < | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
364 | > | tempEx = exI; |
365 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
366 | > | tempEx = exJ; |
367 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
368 | > | |
369 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
370 | #else // isn't MPI | |
371 | < | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
371 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
372 | #endif //is_mpi | |
373 | } | |
374 | excludeOffset += molInfo.nTorsions; | |
# | Line 436 | Line 437 | void SimSetup::initFromBass( void ){ | |
437 | ||
438 | if( n_per_extra > 4){ | |
439 | sprintf( painCave.errMsg, | |
440 | < | "SimSetup error. There has been an error in constructing" |
441 | < | " the non-complete lattice.\n" ); |
440 | > | "SimSetup error. There has been an error in constructing" |
441 | > | " the non-complete lattice.\n" ); |
442 | painCave.isFatal = 1; | |
443 | simError(); | |
444 | } | |
# | Line 458 | Line 459 | void SimSetup::initFromBass( void ){ | |
459 | for( j=0; j < n_cells; j++ ){ | |
460 | for( k=0; k < n_cells; k++ ){ | |
461 | ||
462 | < | makeElement( i * cellx, |
463 | < | j * celly, |
464 | < | k * cellz ); |
462 | > | makeElement( i * cellx, |
463 | > | j * celly, |
464 | > | k * cellz ); |
465 | ||
466 | < | makeElement( i * cellx + 0.5 * cellx, |
467 | < | j * celly + 0.5 * celly, |
468 | < | k * cellz ); |
466 | > | makeElement( i * cellx + 0.5 * cellx, |
467 | > | j * celly + 0.5 * celly, |
468 | > | k * cellz ); |
469 | ||
470 | < | makeElement( i * cellx, |
471 | < | j * celly + 0.5 * celly, |
472 | < | k * cellz + 0.5 * cellz ); |
470 | > | makeElement( i * cellx, |
471 | > | j * celly + 0.5 * celly, |
472 | > | k * cellz + 0.5 * cellz ); |
473 | ||
474 | < | makeElement( i * cellx + 0.5 * cellx, |
475 | < | j * celly, |
476 | < | k * cellz + 0.5 * cellz ); |
474 | > | makeElement( i * cellx + 0.5 * cellx, |
475 | > | j * celly, |
476 | > | k * cellz + 0.5 * cellz ); |
477 | } | |
478 | } | |
479 | } | |
# | Line 484 | Line 485 | void SimSetup::initFromBass( void ){ | |
485 | for( i=0; i < (n_cells+1) && !done; i++ ){ | |
486 | for( j=0; j < (n_cells+1) && !done; j++ ){ | |
487 | ||
488 | < | if( i < n_cells ){ |
488 | > | if( i < n_cells ){ |
489 | ||
490 | < | if( j < n_cells ){ |
491 | < | start_ndx = n_cells; |
492 | < | } |
493 | < | else start_ndx = 0; |
494 | < | } |
495 | < | else start_ndx = 0; |
490 | > | if( j < n_cells ){ |
491 | > | start_ndx = n_cells; |
492 | > | } |
493 | > | else start_ndx = 0; |
494 | > | } |
495 | > | else start_ndx = 0; |
496 | ||
497 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
497 | > | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
498 | ||
499 | < | makeElement( i * cellx, |
500 | < | j * celly, |
501 | < | k * cellz ); |
502 | < | done = ( current_mol >= tot_nmol ); |
499 | > | makeElement( i * cellx, |
500 | > | j * celly, |
501 | > | k * cellz ); |
502 | > | done = ( current_mol >= tot_nmol ); |
503 | ||
504 | < | if( !done && n_per_extra > 1 ){ |
505 | < | makeElement( i * cellx + 0.5 * cellx, |
506 | < | j * celly + 0.5 * celly, |
507 | < | k * cellz ); |
508 | < | done = ( current_mol >= tot_nmol ); |
509 | < | } |
504 | > | if( !done && n_per_extra > 1 ){ |
505 | > | makeElement( i * cellx + 0.5 * cellx, |
506 | > | j * celly + 0.5 * celly, |
507 | > | k * cellz ); |
508 | > | done = ( current_mol >= tot_nmol ); |
509 | > | } |
510 | ||
511 | < | if( !done && n_per_extra > 2){ |
512 | < | makeElement( i * cellx, |
513 | < | j * celly + 0.5 * celly, |
514 | < | k * cellz + 0.5 * cellz ); |
515 | < | done = ( current_mol >= tot_nmol ); |
516 | < | } |
511 | > | if( !done && n_per_extra > 2){ |
512 | > | makeElement( i * cellx, |
513 | > | j * celly + 0.5 * celly, |
514 | > | k * cellz + 0.5 * cellz ); |
515 | > | done = ( current_mol >= tot_nmol ); |
516 | > | } |
517 | ||
518 | < | if( !done && n_per_extra > 3){ |
519 | < | makeElement( i * cellx + 0.5 * cellx, |
520 | < | j * celly, |
521 | < | k * cellz + 0.5 * cellz ); |
522 | < | done = ( current_mol >= tot_nmol ); |
523 | < | } |
524 | < | } |
518 | > | if( !done && n_per_extra > 3){ |
519 | > | makeElement( i * cellx + 0.5 * cellx, |
520 | > | j * celly, |
521 | > | k * cellz + 0.5 * cellz ); |
522 | > | done = ( current_mol >= tot_nmol ); |
523 | > | } |
524 | > | } |
525 | } | |
526 | } | |
527 | } | |
# | Line 543 | Line 544 | void SimSetup::makeElement( double x, double y, double | |
544 | current_atom = comp_stamps[current_comp]->getAtom( k ); | |
545 | if( !current_atom->havePosition() ){ | |
546 | sprintf( painCave.errMsg, | |
547 | < | "SimSetup:initFromBass error.\n" |
548 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
549 | < | "\tThe initialization routine is unable to give a start" |
550 | < | " position.\n", |
551 | < | comp_stamps[current_comp]->getID(), |
552 | < | current_atom->getType() ); |
547 | > | "SimSetup:initFromBass error.\n" |
548 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
549 | > | "\tThe initialization routine is unable to give a start" |
550 | > | " position.\n", |
551 | > | comp_stamps[current_comp]->getID(), |
552 | > | current_atom->getType() ); |
553 | painCave.isFatal = 1; | |
554 | simError(); | |
555 | } | |
# | Line 617 | Line 618 | void SimSetup::gatherInfo( void ){ | |
618 | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; | |
619 | else{ | |
620 | sprintf( painCave.errMsg, | |
621 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
622 | < | force_field ); |
621 | > | "SimSetup Error. Unrecognized force field -> %s\n", |
622 | > | force_field ); |
623 | painCave.isFatal = 1; | |
624 | simError(); | |
625 | } | |
# | Line 636 | Line 637 | void SimSetup::gatherInfo( void ){ | |
637 | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; | |
638 | else{ | |
639 | sprintf( painCave.errMsg, | |
640 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
640 | > | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
641 | "reverting to NVE for this simulation.\n", | |
642 | < | ensemble ); |
642 | > | ensemble ); |
643 | painCave.isFatal = 0; | |
644 | simError(); | |
645 | strcpy( ensemble, "NVE" ); | |
# | Line 669 | Line 670 | void SimSetup::gatherInfo( void ){ | |
670 | for( i=0; i<n_components; i++ ){ | |
671 | ||
672 | if( !the_components[i]->haveNMol() ){ | |
673 | < | // we have a problem |
674 | < | sprintf( painCave.errMsg, |
675 | < | "SimSetup Error. No global NMol or component NMol" |
676 | < | " given. Cannot calculate the number of atoms.\n" ); |
677 | < | painCave.isFatal = 1; |
678 | < | simError(); |
673 | > | // we have a problem |
674 | > | sprintf( painCave.errMsg, |
675 | > | "SimSetup Error. No global NMol or component NMol" |
676 | > | " given. Cannot calculate the number of atoms.\n" ); |
677 | > | painCave.isFatal = 1; |
678 | > | simError(); |
679 | } | |
680 | ||
681 | tot_nmol += the_components[i]->getNMol(); | |
# | Line 683 | Line 684 | void SimSetup::gatherInfo( void ){ | |
684 | } | |
685 | else{ | |
686 | sprintf( painCave.errMsg, | |
687 | < | "SimSetup error.\n" |
688 | < | "\tSorry, the ability to specify total" |
689 | < | " nMols and then give molfractions in the components\n" |
690 | < | "\tis not currently supported." |
691 | < | " Please give nMol in the components.\n" ); |
687 | > | "SimSetup error.\n" |
688 | > | "\tSorry, the ability to specify total" |
689 | > | " nMols and then give molfractions in the components\n" |
690 | > | "\tis not currently supported." |
691 | > | " Please give nMol in the components.\n" ); |
692 | painCave.isFatal = 1; | |
693 | simError(); | |
694 | } | |
# | Line 741 | Line 742 | void SimSetup::gatherInfo( void ){ | |
742 | } | |
743 | else{ | |
744 | if( !globals->haveBoxX() ){ | |
745 | < | sprintf( painCave.errMsg, |
746 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
747 | < | painCave.isFatal = 1; |
748 | < | simError(); |
745 | > | sprintf( painCave.errMsg, |
746 | > | "SimSetup error, no periodic BoxX size given.\n" ); |
747 | > | painCave.isFatal = 1; |
748 | > | simError(); |
749 | } | |
750 | boxVector[0] = globals->getBoxX(); | |
751 | ||
752 | if( !globals->haveBoxY() ){ | |
753 | < | sprintf( painCave.errMsg, |
754 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
755 | < | painCave.isFatal = 1; |
756 | < | simError(); |
753 | > | sprintf( painCave.errMsg, |
754 | > | "SimSetup error, no periodic BoxY size given.\n" ); |
755 | > | painCave.isFatal = 1; |
756 | > | simError(); |
757 | } | |
758 | boxVector[1] = globals->getBoxY(); | |
759 | ||
760 | if( !globals->haveBoxZ() ){ | |
761 | < | sprintf( painCave.errMsg, |
762 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
763 | < | painCave.isFatal = 1; |
764 | < | simError(); |
761 | > | sprintf( painCave.errMsg, |
762 | > | "SimSetup error, no periodic BoxZ size given.\n" ); |
763 | > | painCave.isFatal = 1; |
764 | > | simError(); |
765 | } | |
766 | boxVector[2] = globals->getBoxZ(); | |
767 | ||
768 | info[i].setBox( boxVector ); | |
769 | } | |
770 | + | } |
771 | ||
772 | + | int seedValue; |
773 | + | struct timeval now_time_val; |
774 | + | struct timezone time_zone; |
775 | + | |
776 | + | if(globals->haveSeed()){ |
777 | + | seedValue = globals->getSeed(); |
778 | } | |
779 | < | |
779 | > | else{ |
780 | > | #ifndef IS_MPI |
781 | > | gettimeofday(&now_time_val, &time_zone); // get the time now |
782 | > | seedValue = (int) now_time_val.tv_sec; // convert to epoch time |
783 | > | #else |
784 | > | if(worldRank == 0){ |
785 | > | gettimeofday(&now_time_val, &time_zone); // get the time now |
786 | > | seedValue = (int) now_time_val.tv_sec; // convert to epoch time |
787 | > | } |
788 | > | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
789 | > | #endif |
790 | > | } |
791 | > | |
792 | > | for(int i = 0; i < nInfo; i++){ |
793 | > | info[i].setSeed(seedValue); |
794 | > | } |
795 | > | |
796 | #ifdef IS_MPI | |
797 | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); | |
798 | MPIcheckPoint(); | |
# | Line 803 | Line 827 | void SimSetup::finalInfoCheck( void ){ | |
827 | info[i].useReactionField = 1; | |
828 | ||
829 | if( !globals->haveECR() ){ | |
830 | < | sprintf( painCave.errMsg, |
831 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
832 | < | "box length for the electrostaticCutoffRadius.\n" |
833 | < | "I hope you have a very fast processor!\n"); |
834 | < | painCave.isFatal = 0; |
835 | < | simError(); |
836 | < | double smallest; |
837 | < | smallest = info[i].boxL[0]; |
838 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
839 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
840 | < | theEcr = 0.5 * smallest; |
830 | > | sprintf( painCave.errMsg, |
831 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
832 | > | "box length for the electrostaticCutoffRadius.\n" |
833 | > | "I hope you have a very fast processor!\n"); |
834 | > | painCave.isFatal = 0; |
835 | > | simError(); |
836 | > | double smallest; |
837 | > | smallest = info[i].boxL[0]; |
838 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
839 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
840 | > | theEcr = 0.5 * smallest; |
841 | } else { | |
842 | < | theEcr = globals->getECR(); |
842 | > | theEcr = globals->getECR(); |
843 | } | |
844 | ||
845 | if( !globals->haveEST() ){ | |
846 | < | sprintf( painCave.errMsg, |
847 | < | "SimSetup Warning: using default value of 0.05 * the " |
848 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
849 | < | ); |
850 | < | painCave.isFatal = 0; |
851 | < | simError(); |
852 | < | theEst = 0.05 * theEcr; |
846 | > | sprintf( painCave.errMsg, |
847 | > | "SimSetup Warning: using default value of 0.05 * the " |
848 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
849 | > | ); |
850 | > | painCave.isFatal = 0; |
851 | > | simError(); |
852 | > | theEst = 0.05 * theEcr; |
853 | } else { | |
854 | < | theEst= globals->getEST(); |
854 | > | theEst= globals->getEST(); |
855 | } | |
856 | ||
857 | info[i].setEcr( theEcr, theEst ); | |
858 | ||
859 | if(!globals->haveDielectric() ){ | |
860 | < | sprintf( painCave.errMsg, |
861 | < | "SimSetup Error: You are trying to use Reaction Field without" |
862 | < | "setting a dielectric constant!\n" |
863 | < | ); |
864 | < | painCave.isFatal = 1; |
865 | < | simError(); |
860 | > | sprintf( painCave.errMsg, |
861 | > | "SimSetup Error: You are trying to use Reaction Field without" |
862 | > | "setting a dielectric constant!\n" |
863 | > | ); |
864 | > | painCave.isFatal = 1; |
865 | > | simError(); |
866 | } | |
867 | info[i].dielectric = globals->getDielectric(); | |
868 | } | |
869 | else { | |
870 | if (usesDipoles) { | |
871 | < | |
872 | < | if( !globals->haveECR() ){ |
873 | < | sprintf( painCave.errMsg, |
874 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
875 | < | "box length for the electrostaticCutoffRadius.\n" |
876 | < | "I hope you have a very fast processor!\n"); |
877 | < | painCave.isFatal = 0; |
878 | < | simError(); |
879 | < | double smallest; |
880 | < | smallest = info[i].boxL[0]; |
881 | < | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
882 | < | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
883 | < | theEcr = 0.5 * smallest; |
884 | < | } else { |
885 | < | theEcr = globals->getECR(); |
886 | < | } |
887 | < | |
888 | < | if( !globals->haveEST() ){ |
889 | < | sprintf( painCave.errMsg, |
890 | < | "SimSetup Warning: using default value of 0.05 * the " |
891 | < | "electrostaticCutoffRadius for the " |
892 | < | "electrostaticSkinThickness\n" |
893 | < | ); |
894 | < | painCave.isFatal = 0; |
895 | < | simError(); |
896 | < | theEst = 0.05 * theEcr; |
897 | < | } else { |
898 | < | theEst= globals->getEST(); |
899 | < | } |
900 | < | |
901 | < | info[i].setEcr( theEcr, theEst ); |
871 | > | |
872 | > | if( !globals->haveECR() ){ |
873 | > | sprintf( painCave.errMsg, |
874 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
875 | > | "box length for the electrostaticCutoffRadius.\n" |
876 | > | "I hope you have a very fast processor!\n"); |
877 | > | painCave.isFatal = 0; |
878 | > | simError(); |
879 | > | double smallest; |
880 | > | smallest = info[i].boxL[0]; |
881 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
882 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
883 | > | theEcr = 0.5 * smallest; |
884 | > | } else { |
885 | > | theEcr = globals->getECR(); |
886 | > | } |
887 | > | |
888 | > | if( !globals->haveEST() ){ |
889 | > | sprintf( painCave.errMsg, |
890 | > | "SimSetup Warning: using default value of 0.05 * the " |
891 | > | "electrostaticCutoffRadius for the " |
892 | > | "electrostaticSkinThickness\n" |
893 | > | ); |
894 | > | painCave.isFatal = 0; |
895 | > | simError(); |
896 | > | theEst = 0.05 * theEcr; |
897 | > | } else { |
898 | > | theEst= globals->getEST(); |
899 | > | } |
900 | > | |
901 | > | info[i].setEcr( theEcr, theEst ); |
902 | } | |
903 | } | |
904 | } | |
# | Line 891 | Line 915 | void SimSetup::initSystemCoords( void ){ | |
915 | ||
916 | char* inName; | |
917 | ||
894 | – | |
918 | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); | |
919 | < | |
919 | > | |
920 | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); | |
921 | ||
922 | if( globals->haveInitialConfig() ){ | |
# | Line 919 | Line 942 | void SimSetup::initSystemCoords( void ){ | |
942 | // no init from bass | |
943 | ||
944 | sprintf( painCave.errMsg, | |
945 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
945 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
946 | painCave.isFatal; | |
947 | simError(); | |
948 | ||
# | Line 951 | Line 974 | void SimSetup::makeOutNames( void ){ | |
974 | #endif // is_mpi | |
975 | ||
976 | if( globals->haveFinalConfig() ){ | |
977 | < | strcpy( info[k].finalName, globals->getFinalConfig() ); |
977 | > | strcpy( info[k].finalName, globals->getFinalConfig() ); |
978 | } | |
979 | else{ | |
980 | < | strcpy( info[k].finalName, inFileName ); |
981 | < | char* endTest; |
982 | < | int nameLength = strlen( info[k].finalName ); |
983 | < | endTest = &(info[k].finalName[nameLength - 5]); |
984 | < | if( !strcmp( endTest, ".bass" ) ){ |
985 | < | strcpy( endTest, ".eor" ); |
986 | < | } |
987 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
988 | < | strcpy( endTest, ".eor" ); |
989 | < | } |
990 | < | else{ |
991 | < | endTest = &(info[k].finalName[nameLength - 4]); |
992 | < | if( !strcmp( endTest, ".bss" ) ){ |
993 | < | strcpy( endTest, ".eor" ); |
994 | < | } |
995 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
996 | < | strcpy( endTest, ".eor" ); |
997 | < | } |
998 | < | else{ |
999 | < | strcat( info[k].finalName, ".eor" ); |
1000 | < | } |
1001 | < | } |
980 | > | strcpy( info[k].finalName, inFileName ); |
981 | > | char* endTest; |
982 | > | int nameLength = strlen( info[k].finalName ); |
983 | > | endTest = &(info[k].finalName[nameLength - 5]); |
984 | > | if( !strcmp( endTest, ".bass" ) ){ |
985 | > | strcpy( endTest, ".eor" ); |
986 | > | } |
987 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
988 | > | strcpy( endTest, ".eor" ); |
989 | > | } |
990 | > | else{ |
991 | > | endTest = &(info[k].finalName[nameLength - 4]); |
992 | > | if( !strcmp( endTest, ".bss" ) ){ |
993 | > | strcpy( endTest, ".eor" ); |
994 | > | } |
995 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
996 | > | strcpy( endTest, ".eor" ); |
997 | > | } |
998 | > | else{ |
999 | > | strcat( info[k].finalName, ".eor" ); |
1000 | > | } |
1001 | > | } |
1002 | } | |
1003 | ||
1004 | // make the sample and status out names | |
# | Line 985 | Line 1008 | void SimSetup::makeOutNames( void ){ | |
1008 | int nameLength = strlen( info[k].sampleName ); | |
1009 | endTest = &(info[k].sampleName[nameLength - 5]); | |
1010 | if( !strcmp( endTest, ".bass" ) ){ | |
1011 | < | strcpy( endTest, ".dump" ); |
1011 | > | strcpy( endTest, ".dump" ); |
1012 | } | |
1013 | else if( !strcmp( endTest, ".BASS" ) ){ | |
1014 | < | strcpy( endTest, ".dump" ); |
1014 | > | strcpy( endTest, ".dump" ); |
1015 | } | |
1016 | else{ | |
1017 | < | endTest = &(info[k].sampleName[nameLength - 4]); |
1018 | < | if( !strcmp( endTest, ".bss" ) ){ |
1019 | < | strcpy( endTest, ".dump" ); |
1020 | < | } |
1021 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1022 | < | strcpy( endTest, ".dump" ); |
1023 | < | } |
1024 | < | else{ |
1025 | < | strcat( info[k].sampleName, ".dump" ); |
1026 | < | } |
1017 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1018 | > | if( !strcmp( endTest, ".bss" ) ){ |
1019 | > | strcpy( endTest, ".dump" ); |
1020 | > | } |
1021 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1022 | > | strcpy( endTest, ".dump" ); |
1023 | > | } |
1024 | > | else{ |
1025 | > | strcat( info[k].sampleName, ".dump" ); |
1026 | > | } |
1027 | } | |
1028 | ||
1029 | strcpy( info[k].statusName, inFileName ); | |
1030 | nameLength = strlen( info[k].statusName ); | |
1031 | endTest = &(info[k].statusName[nameLength - 5]); | |
1032 | if( !strcmp( endTest, ".bass" ) ){ | |
1033 | < | strcpy( endTest, ".stat" ); |
1033 | > | strcpy( endTest, ".stat" ); |
1034 | } | |
1035 | else if( !strcmp( endTest, ".BASS" ) ){ | |
1036 | < | strcpy( endTest, ".stat" ); |
1036 | > | strcpy( endTest, ".stat" ); |
1037 | } | |
1038 | else{ | |
1039 | < | endTest = &(info[k].statusName[nameLength - 4]); |
1040 | < | if( !strcmp( endTest, ".bss" ) ){ |
1041 | < | strcpy( endTest, ".stat" ); |
1042 | < | } |
1043 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
1044 | < | strcpy( endTest, ".stat" ); |
1045 | < | } |
1046 | < | else{ |
1047 | < | strcat( info[k].statusName, ".stat" ); |
1048 | < | } |
1039 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1040 | > | if( !strcmp( endTest, ".bss" ) ){ |
1041 | > | strcpy( endTest, ".stat" ); |
1042 | > | } |
1043 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1044 | > | strcpy( endTest, ".stat" ); |
1045 | > | } |
1046 | > | else{ |
1047 | > | strcat( info[k].statusName, ".stat" ); |
1048 | > | } |
1049 | } | |
1050 | ||
1051 | #ifdef IS_MPI | |
# | Line 1089 | Line 1112 | void SimSetup::createFF( void ){ | |
1112 | ||
1113 | default: | |
1114 | sprintf( painCave.errMsg, | |
1115 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1115 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1116 | painCave.isFatal = 1; | |
1117 | simError(); | |
1118 | } | |
# | Line 1135 | Line 1158 | void SimSetup::compList( void ){ | |
1158 | ||
1159 | currentStamp = stamps->extractMolStamp( id ); | |
1160 | if( currentStamp == NULL ){ | |
1161 | < | sprintf( painCave.errMsg, |
1162 | < | "SimSetup error: Component \"%s\" was not found in the " |
1163 | < | "list of declared molecules\n", |
1164 | < | id ); |
1165 | < | painCave.isFatal = 1; |
1166 | < | simError(); |
1161 | > | sprintf( painCave.errMsg, |
1162 | > | "SimSetup error: Component \"%s\" was not found in the " |
1163 | > | "list of declared molecules\n", |
1164 | > | id ); |
1165 | > | painCave.isFatal = 1; |
1166 | > | simError(); |
1167 | } | |
1168 | ||
1169 | headStamp->add( currentStamp ); | |
# | Line 1219 | Line 1242 | void SimSetup::mpiMolDivide( void ){ | |
1242 | for( j=0; j<components_nmol[i]; j++ ){ | |
1243 | ||
1244 | if( mol2proc[allMol] == worldRank ){ | |
1245 | < | |
1246 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
1247 | < | local_bonds += comp_stamps[i]->getNBonds(); |
1248 | < | local_bends += comp_stamps[i]->getNBends(); |
1249 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
1250 | < | localMol++; |
1245 | > | |
1246 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1247 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1248 | > | local_bends += comp_stamps[i]->getNBends(); |
1249 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1250 | > | localMol++; |
1251 | } | |
1252 | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { | |
1253 | info[0].molMembershipArray[globalAtomIndex] = allMol; | |
# | Line 1240 | Line 1263 | void SimSetup::mpiMolDivide( void ){ | |
1263 | ||
1264 | if( local_atoms != info[0].n_atoms ){ | |
1265 | sprintf( painCave.errMsg, | |
1266 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1267 | < | " localAtom (%d) are not equal.\n", |
1268 | < | info[0].n_atoms, |
1269 | < | local_atoms ); |
1266 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1267 | > | " localAtom (%d) are not equal.\n", |
1268 | > | info[0].n_atoms, |
1269 | > | local_atoms ); |
1270 | painCave.isFatal = 1; | |
1271 | simError(); | |
1272 | } | |
# | Line 1286 | Line 1309 | void SimSetup::makeSysArrays( void ){ | |
1309 | for(i=0; i<mpiSim->getTotNmol(); i++){ | |
1310 | ||
1311 | if(mol2proc[i] == worldRank ){ | |
1312 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
1313 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1314 | < | the_molecules[molIndex].setGlobalIndex( i ); |
1315 | < | molIndex++; |
1312 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
1313 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1314 | > | the_molecules[molIndex].setGlobalIndex( i ); |
1315 | > | molIndex++; |
1316 | } | |
1317 | } | |
1318 | ||
# | Line 1299 | Line 1322 | void SimSetup::makeSysArrays( void ){ | |
1322 | globalAtomIndex = 0; | |
1323 | for(i=0; i<n_components; i++){ | |
1324 | for(j=0; j<components_nmol[i]; j++ ){ | |
1325 | < | the_molecules[molIndex].setStampID( i ); |
1326 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
1327 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1328 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1329 | < | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1330 | < | globalAtomIndex++; |
1331 | < | } |
1332 | < | molIndex++; |
1325 | > | the_molecules[molIndex].setStampID( i ); |
1326 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1327 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1328 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1329 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1330 | > | globalAtomIndex++; |
1331 | > | } |
1332 | > | molIndex++; |
1333 | } | |
1334 | } | |
1335 | ||
# | Line 1319 | Line 1342 | void SimSetup::makeSysArrays( void ){ | |
1342 | Exclude::createArray(info[l].n_SRI); | |
1343 | the_excludes = new Exclude*[info[l].n_SRI]; | |
1344 | for( int ex=0; ex<info[l].n_SRI; ex++){ | |
1345 | < | the_excludes[ex] = new Exclude(ex); |
1345 | > | the_excludes[ex] = new Exclude(ex); |
1346 | } | |
1347 | info[l].globalExcludes = new int; | |
1348 | info[l].n_exclude = info[l].n_SRI; | |
# | Line 1362 | Line 1385 | void SimSetup::makeIntegrator( void ){ | |
1385 | switch( ensembleCase ){ | |
1386 | ||
1387 | case NVE_ENS: | |
1388 | < | if (globals->haveZconstraints()){ |
1389 | < | setupZConstraint(info[k]); |
1390 | < | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1391 | < | } |
1388 | > | if (globals->haveZconstraints()){ |
1389 | > | setupZConstraint(info[k]); |
1390 | > | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1391 | > | } |
1392 | ||
1393 | < | else |
1393 | > | else |
1394 | new NVE<RealIntegrator>( &(info[k]), the_ff ); | |
1395 | break; | |
1396 | ||
1397 | case NVT_ENS: | |
1398 | < | if (globals->haveZconstraints()){ |
1399 | < | setupZConstraint(info[k]); |
1400 | < | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1401 | < | } |
1402 | < | else |
1398 | > | if (globals->haveZconstraints()){ |
1399 | > | setupZConstraint(info[k]); |
1400 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1401 | > | } |
1402 | > | else |
1403 | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); | |
1404 | ||
1405 | < | myNVT->setTargetTemp(globals->getTargetTemp()); |
1405 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1406 | ||
1407 | < | if (globals->haveTauThermostat()) |
1408 | < | myNVT->setTauThermostat(globals->getTauThermostat()); |
1407 | > | if (globals->haveTauThermostat()) |
1408 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1409 | ||
1410 | < | else { |
1411 | < | sprintf( painCave.errMsg, |
1412 | < | "SimSetup error: If you use the NVT\n" |
1413 | < | " ensemble, you must set tauThermostat.\n"); |
1414 | < | painCave.isFatal = 1; |
1415 | < | simError(); |
1416 | < | } |
1417 | < | break; |
1410 | > | else { |
1411 | > | sprintf( painCave.errMsg, |
1412 | > | "SimSetup error: If you use the NVT\n" |
1413 | > | " ensemble, you must set tauThermostat.\n"); |
1414 | > | painCave.isFatal = 1; |
1415 | > | simError(); |
1416 | > | } |
1417 | > | break; |
1418 | ||
1419 | case NPTi_ENS: | |
1420 | < | if (globals->haveZconstraints()){ |
1421 | < | setupZConstraint(info[k]); |
1422 | < | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1423 | < | } |
1424 | < | else |
1420 | > | if (globals->haveZconstraints()){ |
1421 | > | setupZConstraint(info[k]); |
1422 | > | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1423 | > | } |
1424 | > | else |
1425 | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); | |
1426 | ||
1427 | < | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1428 | < | |
1427 | > | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1428 | > | |
1429 | if (globals->haveTargetPressure()) | |
1430 | < | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1430 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1431 | else { | |
1432 | < | sprintf( painCave.errMsg, |
1433 | < | "SimSetup error: If you use a constant pressure\n" |
1434 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1435 | < | painCave.isFatal = 1; |
1436 | < | simError(); |
1432 | > | sprintf( painCave.errMsg, |
1433 | > | "SimSetup error: If you use a constant pressure\n" |
1434 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1435 | > | painCave.isFatal = 1; |
1436 | > | simError(); |
1437 | } | |
1438 | < | |
1438 | > | |
1439 | if( globals->haveTauThermostat() ) | |
1440 | < | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1440 | > | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1441 | else{ | |
1442 | < | sprintf( painCave.errMsg, |
1443 | < | "SimSetup error: If you use an NPT\n" |
1444 | < | " ensemble, you must set tauThermostat.\n"); |
1445 | < | painCave.isFatal = 1; |
1446 | < | simError(); |
1442 | > | sprintf( painCave.errMsg, |
1443 | > | "SimSetup error: If you use an NPT\n" |
1444 | > | " ensemble, you must set tauThermostat.\n"); |
1445 | > | painCave.isFatal = 1; |
1446 | > | simError(); |
1447 | } | |
1448 | < | |
1448 | > | |
1449 | if( globals->haveTauBarostat() ) | |
1450 | < | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1450 | > | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1451 | else{ | |
1452 | < | sprintf( painCave.errMsg, |
1453 | < | "SimSetup error: If you use an NPT\n" |
1454 | < | " ensemble, you must set tauBarostat.\n"); |
1455 | < | painCave.isFatal = 1; |
1456 | < | simError(); |
1457 | < | } |
1458 | < | break; |
1452 | > | sprintf( painCave.errMsg, |
1453 | > | "SimSetup error: If you use an NPT\n" |
1454 | > | " ensemble, you must set tauBarostat.\n"); |
1455 | > | painCave.isFatal = 1; |
1456 | > | simError(); |
1457 | > | } |
1458 | > | break; |
1459 | ||
1460 | case NPTf_ENS: | |
1461 | < | if (globals->haveZconstraints()){ |
1462 | < | setupZConstraint(info[k]); |
1463 | < | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1464 | < | } |
1465 | < | else |
1461 | > | if (globals->haveZconstraints()){ |
1462 | > | setupZConstraint(info[k]); |
1463 | > | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1464 | > | } |
1465 | > | else |
1466 | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); | |
1467 | ||
1468 | myNPTf->setTargetTemp( globals->getTargetTemp()); | |
1469 | < | |
1469 | > | |
1470 | if (globals->haveTargetPressure()) | |
1471 | < | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1471 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1472 | else { | |
1473 | < | sprintf( painCave.errMsg, |
1474 | < | "SimSetup error: If you use a constant pressure\n" |
1475 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1476 | < | painCave.isFatal = 1; |
1477 | < | simError(); |
1473 | > | sprintf( painCave.errMsg, |
1474 | > | "SimSetup error: If you use a constant pressure\n" |
1475 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1476 | > | painCave.isFatal = 1; |
1477 | > | simError(); |
1478 | } | |
1479 | < | |
1479 | > | |
1480 | if( globals->haveTauThermostat() ) | |
1481 | < | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1481 | > | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1482 | else{ | |
1483 | < | sprintf( painCave.errMsg, |
1484 | < | "SimSetup error: If you use an NPT\n" |
1485 | < | " ensemble, you must set tauThermostat.\n"); |
1486 | < | painCave.isFatal = 1; |
1487 | < | simError(); |
1483 | > | sprintf( painCave.errMsg, |
1484 | > | "SimSetup error: If you use an NPT\n" |
1485 | > | " ensemble, you must set tauThermostat.\n"); |
1486 | > | painCave.isFatal = 1; |
1487 | > | simError(); |
1488 | } | |
1489 | < | |
1489 | > | |
1490 | if( globals->haveTauBarostat() ) | |
1491 | < | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1491 | > | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1492 | else{ | |
1493 | < | sprintf( painCave.errMsg, |
1494 | < | "SimSetup error: If you use an NPT\n" |
1495 | < | " ensemble, you must set tauBarostat.\n"); |
1496 | < | painCave.isFatal = 1; |
1497 | < | simError(); |
1493 | > | sprintf( painCave.errMsg, |
1494 | > | "SimSetup error: If you use an NPT\n" |
1495 | > | " ensemble, you must set tauBarostat.\n"); |
1496 | > | painCave.isFatal = 1; |
1497 | > | simError(); |
1498 | } | |
1499 | break; | |
1500 | ||
1501 | case NPTim_ENS: | |
1502 | < | if (globals->haveZconstraints()){ |
1503 | < | setupZConstraint(info[k]); |
1504 | < | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1505 | < | } |
1506 | < | else |
1502 | > | if (globals->haveZconstraints()){ |
1503 | > | setupZConstraint(info[k]); |
1504 | > | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1505 | > | } |
1506 | > | else |
1507 | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); | |
1508 | ||
1509 | < | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1510 | < | |
1509 | > | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1510 | > | |
1511 | if (globals->haveTargetPressure()) | |
1512 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1512 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1513 | else { | |
1514 | < | sprintf( painCave.errMsg, |
1515 | < | "SimSetup error: If you use a constant pressure\n" |
1516 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1517 | < | painCave.isFatal = 1; |
1518 | < | simError(); |
1514 | > | sprintf( painCave.errMsg, |
1515 | > | "SimSetup error: If you use a constant pressure\n" |
1516 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1517 | > | painCave.isFatal = 1; |
1518 | > | simError(); |
1519 | } | |
1520 | < | |
1520 | > | |
1521 | if( globals->haveTauThermostat() ) | |
1522 | < | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1522 | > | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1523 | else{ | |
1524 | < | sprintf( painCave.errMsg, |
1525 | < | "SimSetup error: If you use an NPT\n" |
1526 | < | " ensemble, you must set tauThermostat.\n"); |
1527 | < | painCave.isFatal = 1; |
1528 | < | simError(); |
1524 | > | sprintf( painCave.errMsg, |
1525 | > | "SimSetup error: If you use an NPT\n" |
1526 | > | " ensemble, you must set tauThermostat.\n"); |
1527 | > | painCave.isFatal = 1; |
1528 | > | simError(); |
1529 | } | |
1530 | < | |
1530 | > | |
1531 | if( globals->haveTauBarostat() ) | |
1532 | < | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1532 | > | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1533 | else{ | |
1534 | < | sprintf( painCave.errMsg, |
1535 | < | "SimSetup error: If you use an NPT\n" |
1536 | < | " ensemble, you must set tauBarostat.\n"); |
1537 | < | painCave.isFatal = 1; |
1538 | < | simError(); |
1534 | > | sprintf( painCave.errMsg, |
1535 | > | "SimSetup error: If you use an NPT\n" |
1536 | > | " ensemble, you must set tauBarostat.\n"); |
1537 | > | painCave.isFatal = 1; |
1538 | > | simError(); |
1539 | } | |
1540 | break; | |
1541 | ||
1542 | case NPTfm_ENS: | |
1543 | < | if (globals->haveZconstraints()){ |
1544 | < | setupZConstraint(info[k]); |
1545 | < | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1546 | < | } |
1547 | < | else |
1543 | > | if (globals->haveZconstraints()){ |
1544 | > | setupZConstraint(info[k]); |
1545 | > | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1546 | > | } |
1547 | > | else |
1548 | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); | |
1549 | ||
1550 | < | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1551 | < | |
1550 | > | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1551 | > | |
1552 | if (globals->haveTargetPressure()) | |
1553 | < | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1553 | > | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1554 | else { | |
1555 | < | sprintf( painCave.errMsg, |
1556 | < | "SimSetup error: If you use a constant pressure\n" |
1557 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1558 | < | painCave.isFatal = 1; |
1559 | < | simError(); |
1555 | > | sprintf( painCave.errMsg, |
1556 | > | "SimSetup error: If you use a constant pressure\n" |
1557 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1558 | > | painCave.isFatal = 1; |
1559 | > | simError(); |
1560 | } | |
1561 | < | |
1561 | > | |
1562 | if( globals->haveTauThermostat() ) | |
1563 | < | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1563 | > | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1564 | else{ | |
1565 | < | sprintf( painCave.errMsg, |
1566 | < | "SimSetup error: If you use an NPT\n" |
1567 | < | " ensemble, you must set tauThermostat.\n"); |
1568 | < | painCave.isFatal = 1; |
1569 | < | simError(); |
1565 | > | sprintf( painCave.errMsg, |
1566 | > | "SimSetup error: If you use an NPT\n" |
1567 | > | " ensemble, you must set tauThermostat.\n"); |
1568 | > | painCave.isFatal = 1; |
1569 | > | simError(); |
1570 | } | |
1571 | < | |
1571 | > | |
1572 | if( globals->haveTauBarostat() ) | |
1573 | < | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1573 | > | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1574 | else{ | |
1575 | < | sprintf( painCave.errMsg, |
1576 | < | "SimSetup error: If you use an NPT\n" |
1577 | < | " ensemble, you must set tauBarostat.\n"); |
1578 | < | painCave.isFatal = 1; |
1579 | < | simError(); |
1575 | > | sprintf( painCave.errMsg, |
1576 | > | "SimSetup error: If you use an NPT\n" |
1577 | > | " ensemble, you must set tauBarostat.\n"); |
1578 | > | painCave.isFatal = 1; |
1579 | > | simError(); |
1580 | } | |
1581 | break; | |
1582 | ||
1583 | default: | |
1584 | sprintf( painCave.errMsg, | |
1585 | < | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1585 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1586 | painCave.isFatal = 1; | |
1587 | simError(); | |
1588 | } | |
# | Line 1578 | Line 1601 | void SimSetup::initFortran( void ){ | |
1601 | } | |
1602 | else{ | |
1603 | sprintf( painCave.errMsg, | |
1604 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1605 | < | info[0].mixingRule ); |
1604 | > | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1605 | > | info[0].mixingRule ); |
1606 | painCave.isFatal = 1; | |
1607 | simError(); | |
1608 | } | |
# | Line 1587 | Line 1610 | void SimSetup::initFortran( void ){ | |
1610 | ||
1611 | #ifdef IS_MPI | |
1612 | strcpy( checkPointMsg, | |
1613 | < | "Successfully intialized the mixingRule for Fortran." ); |
1613 | > | "Successfully intialized the mixingRule for Fortran." ); |
1614 | MPIcheckPoint(); | |
1615 | #endif // is_mpi | |
1616 | ||
# | Line 1595 | Line 1618 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1618 | ||
1619 | void SimSetup::setupZConstraint(SimInfo& theInfo) | |
1620 | { | |
1621 | < | int nZConstraints; |
1622 | < | ZconStamp** zconStamp; |
1600 | < | |
1601 | < | if(globals->haveZconstraintTime()){ |
1602 | < | |
1603 | < | //add sample time of z-constraint into SimInfo's property list |
1604 | < | DoubleData* zconsTimeProp = new DoubleData(); |
1605 | < | zconsTimeProp->setID(ZCONSTIME_ID); |
1606 | < | zconsTimeProp->setData(globals->getZconsTime()); |
1607 | < | theInfo.addProperty(zconsTimeProp); |
1608 | < | } |
1609 | < | else{ |
1610 | < | sprintf( painCave.errMsg, |
1611 | < | "ZConstraint error: If you use an ZConstraint\n" |
1612 | < | " , you must set sample time.\n"); |
1613 | < | painCave.isFatal = 1; |
1614 | < | simError(); |
1615 | < | } |
1621 | > | int nZConstraints; |
1622 | > | ZconStamp** zconStamp; |
1623 | ||
1624 | < | // |
1625 | < | nZConstraints = globals->getNzConstraints(); |
1626 | < | theInfo.nZconstraints = nZConstraints; |
1627 | < | |
1628 | < | zconStamp = globals->getZconStamp(); |
1629 | < | ZConsParaItem tempParaItem; |
1624 | > | if(globals->haveZconstraintTime()){ |
1625 | > | |
1626 | > | //add sample time of z-constraint into SimInfo's property list |
1627 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1628 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1629 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1630 | > | theInfo.addProperty(zconsTimeProp); |
1631 | > | } |
1632 | > | else{ |
1633 | > | sprintf( painCave.errMsg, |
1634 | > | "ZConstraint error: If you use an ZConstraint\n" |
1635 | > | " , you must set sample time.\n"); |
1636 | > | painCave.isFatal = 1; |
1637 | > | simError(); |
1638 | > | } |
1639 | ||
1640 | < | ZConsParaData* zconsParaData = new ZConsParaData(); |
1641 | < | zconsParaData->setID(ZCONSPARADATA_ID); |
1642 | < | |
1643 | < | for(int i = 0; i < nZConstraints; i++){ |
1640 | > | //push zconsTol into siminfo, if user does not specify |
1641 | > | //value for zconsTol, a default value will be used |
1642 | > | DoubleData* zconsTol = new DoubleData(); |
1643 | > | zconsTol->setID(ZCONSTOL_ID); |
1644 | > | if(globals->haveZconsTol()){ |
1645 | > | zconsTol->setData(globals->getZconsTol()); |
1646 | > | } |
1647 | > | else{ |
1648 | > | double defaultZConsTol = 0.01; |
1649 | > | sprintf( painCave.errMsg, |
1650 | > | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1651 | > | " , default value %f is used.\n", defaultZConsTol); |
1652 | > | painCave.isFatal = 0; |
1653 | > | simError(); |
1654 | > | |
1655 | > | zconsTol->setData(defaultZConsTol); |
1656 | > | } |
1657 | > | theInfo.addProperty(zconsTol); |
1658 | > | |
1659 | > | //set Force Substraction Policy |
1660 | > | StringData* zconsForcePolicy = new StringData(); |
1661 | > | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1662 | > | |
1663 | > | if(globals->haveZconsForcePolicy()){ |
1664 | > | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1665 | > | } |
1666 | > | else{ |
1667 | > | sprintf( painCave.errMsg, |
1668 | > | "ZConstraint Warning: User does not set force substraction policy, " |
1669 | > | "average force substraction policy is used\n"); |
1670 | > | painCave.isFatal = 0; |
1671 | > | simError(); |
1672 | > | zconsForcePolicy->setData("BYNUMBER"); |
1673 | > | } |
1674 | > | |
1675 | > | theInfo.addProperty(zconsForcePolicy); |
1676 | > | |
1677 | > | //Determine the name of ouput file and add it into SimInfo's property list |
1678 | > | //Be careful, do not use inFileName, since it is a pointer which |
1679 | > | //point to a string at master node, and slave nodes do not contain that string |
1680 | > | |
1681 | > | string zconsOutput(theInfo.finalName); |
1682 | > | |
1683 | > | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1684 | > | |
1685 | > | StringData* zconsFilename = new StringData(); |
1686 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
1687 | > | zconsFilename->setData(zconsOutput); |
1688 | > | |
1689 | > | theInfo.addProperty(zconsFilename); |
1690 | > | |
1691 | > | //setup index, pos and other parameters of z-constraint molecules |
1692 | > | nZConstraints = globals->getNzConstraints(); |
1693 | > | theInfo.nZconstraints = nZConstraints; |
1694 | > | |
1695 | > | zconStamp = globals->getZconStamp(); |
1696 | > | ZConsParaItem tempParaItem; |
1697 | > | |
1698 | > | ZConsParaData* zconsParaData = new ZConsParaData(); |
1699 | > | zconsParaData->setID(ZCONSPARADATA_ID); |
1700 | > | |
1701 | > | for(int i = 0; i < nZConstraints; i++){ |
1702 | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); | |
1703 | tempParaItem.zPos = zconStamp[i]->getZpos(); | |
1704 | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); | |
1705 | tempParaItem.kRatio = zconStamp[i]->getKratio(); | |
1706 | ||
1707 | zconsParaData->addItem(tempParaItem); | |
1708 | < | } |
1708 | > | } |
1709 | ||
1710 | < | //sort the parameters by index of molecules |
1711 | < | zconsParaData->sortByIndex(); |
1712 | < | |
1713 | < | //push data into siminfo, therefore, we can retrieve later |
1714 | < | theInfo.addProperty(zconsParaData); |
1715 | < | |
1642 | < | //push zconsTol into siminfo, if user does not specify |
1643 | < | //value for zconsTol, a default value will be used |
1644 | < | DoubleData* zconsTol = new DoubleData(); |
1645 | < | zconsTol->setID(ZCONSTOL_ID); |
1646 | < | if(globals->haveZconsTol()){ |
1647 | < | zconsTol->setData(globals->getZconsTol()); |
1648 | < | } |
1649 | < | else{ |
1650 | < | double defaultZConsTol = 1E-6; |
1651 | < | sprintf( painCave.errMsg, |
1652 | < | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1653 | < | " , default value %f is used.\n", defaultZConsTol); |
1654 | < | painCave.isFatal = 0; |
1655 | < | simError(); |
1656 | < | |
1657 | < | zconsTol->setData(defaultZConsTol); |
1658 | < | } |
1659 | < | theInfo.addProperty(zconsTol); |
1660 | < | |
1661 | < | //Determine the name of ouput file and add it into SimInfo's property list |
1662 | < | //Be careful, do not use inFileName, since it is a pointer which |
1663 | < | //point to a string at master node, and slave nodes do not contain that string |
1664 | < | |
1665 | < | string zconsOutput(theInfo.finalName); |
1666 | < | |
1667 | < | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1668 | < | |
1669 | < | StringData* zconsFilename = new StringData(); |
1670 | < | zconsFilename->setID(ZCONSFILENAME_ID); |
1671 | < | zconsFilename->setData(zconsOutput); |
1672 | < | |
1673 | < | theInfo.addProperty(zconsFilename); |
1710 | > | //sort the parameters by index of molecules |
1711 | > | zconsParaData->sortByIndex(); |
1712 | > | |
1713 | > | //push data into siminfo, therefore, we can retrieve later |
1714 | > | theInfo.addProperty(zconsParaData); |
1715 | > | |
1716 | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |