78 |
|
|
79 |
|
void SimSetup::createSim( void ){ |
80 |
|
|
81 |
– |
MakeStamps *the_stamps; |
82 |
– |
Globals* the_globals; |
81 |
|
int i, j, k, globalAtomIndex; |
82 |
|
|
83 |
< |
int ensembleCase; |
86 |
< |
int ffCase; |
83 |
> |
// gather all of the information from the Bass file |
84 |
|
|
85 |
+ |
gatherInfo(); |
86 |
+ |
|
87 |
+ |
// creation of complex system objects |
88 |
+ |
|
89 |
+ |
sysObjectsCreation(); |
90 |
+ |
|
91 |
+ |
// check on the post processing info |
92 |
+ |
|
93 |
+ |
finalInfoCheck(); |
94 |
+ |
|
95 |
+ |
// initialize the system coordinates |
96 |
+ |
|
97 |
+ |
initSystemCoords(); |
98 |
+ |
|
99 |
+ |
|
100 |
+ |
// make the output filenames |
101 |
+ |
|
102 |
+ |
makeOutNames(); |
103 |
+ |
|
104 |
+ |
// make the integrator |
105 |
+ |
|
106 |
+ |
makeIntegrator(); |
107 |
+ |
|
108 |
+ |
#ifdef IS_MPI |
109 |
+ |
mpiSim->mpiRefresh(); |
110 |
+ |
#endif |
111 |
+ |
|
112 |
+ |
// initialize the Fortran |
113 |
+ |
|
114 |
+ |
initFortran(); |
115 |
+ |
|
116 |
+ |
|
117 |
+ |
|
118 |
+ |
} |
119 |
+ |
|
120 |
+ |
|
121 |
+ |
void SimSetup::makeMolecules( void ){ |
122 |
+ |
|
123 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
124 |
+ |
molInit molInfo; |
125 |
+ |
DirectionalAtom* dAtom; |
126 |
+ |
LinkedAssign* extras; |
127 |
+ |
LinkedAssign* current_extra; |
128 |
+ |
AtomStamp* currentAtom; |
129 |
+ |
BondStamp* currentBond; |
130 |
+ |
BendStamp* currentBend; |
131 |
+ |
TorsionStamp* currentTorsion; |
132 |
+ |
|
133 |
+ |
bond_pair* theBonds; |
134 |
+ |
bend_set* theBends; |
135 |
+ |
torsion_set* theTorsions; |
136 |
+ |
|
137 |
+ |
|
138 |
+ |
//init the forceField paramters |
139 |
+ |
|
140 |
+ |
the_ff->readParams(); |
141 |
+ |
|
142 |
+ |
|
143 |
+ |
// init the atoms |
144 |
+ |
|
145 |
+ |
double ux, uy, uz, u, uSqr; |
146 |
+ |
|
147 |
+ |
atomOffset = 0; |
148 |
+ |
excludeOffset = 0; |
149 |
+ |
for(i=0; i<info->n_mol; i++){ |
150 |
+ |
|
151 |
+ |
stampID = the_molecules[i].getStampID(); |
152 |
+ |
|
153 |
+ |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
154 |
+ |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
155 |
+ |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
156 |
+ |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 |
+ |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
158 |
+ |
|
159 |
+ |
molInfo.myAtoms = &the_atoms[atomOffset]; |
160 |
+ |
molInfo.myExcludes = &the_excludes[excludeOffset]; |
161 |
+ |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
162 |
+ |
molInfo.myBends = new Bend*[molInfo.nBends]; |
163 |
+ |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
164 |
+ |
|
165 |
+ |
theBonds = new bond_pair[molInfo.nBonds]; |
166 |
+ |
theBends = new bend_set[molInfo.nBends]; |
167 |
+ |
theTorsions = new torsion_set[molInfo.nTorsions]; |
168 |
+ |
|
169 |
+ |
// make the Atoms |
170 |
+ |
|
171 |
+ |
for(j=0; j<molInfo.nAtoms; j++){ |
172 |
+ |
|
173 |
+ |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
174 |
+ |
if( currentAtom->haveOrientation() ){ |
175 |
+ |
|
176 |
+ |
dAtom = new DirectionalAtom(j + atomOffset); |
177 |
+ |
info->n_oriented++; |
178 |
+ |
molInfo.myAtoms[j] = dAtom; |
179 |
+ |
|
180 |
+ |
ux = currentAtom->getOrntX(); |
181 |
+ |
uy = currentAtom->getOrntY(); |
182 |
+ |
uz = currentAtom->getOrntZ(); |
183 |
+ |
|
184 |
+ |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
185 |
+ |
|
186 |
+ |
u = sqrt( uSqr ); |
187 |
+ |
ux = ux / u; |
188 |
+ |
uy = uy / u; |
189 |
+ |
uz = uz / u; |
190 |
+ |
|
191 |
+ |
dAtom->setSUx( ux ); |
192 |
+ |
dAtom->setSUy( uy ); |
193 |
+ |
dAtom->setSUz( uz ); |
194 |
+ |
} |
195 |
+ |
else{ |
196 |
+ |
molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
197 |
+ |
} |
198 |
+ |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
199 |
+ |
|
200 |
+ |
#ifdef IS_MPI |
201 |
+ |
|
202 |
+ |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
203 |
+ |
|
204 |
+ |
#endif // is_mpi |
205 |
+ |
} |
206 |
+ |
|
207 |
+ |
// make the bonds |
208 |
+ |
for(j=0; j<molInfo.nBonds; j++){ |
209 |
+ |
|
210 |
+ |
currentBond = comp_stamps[stampID]->getBond( j ); |
211 |
+ |
theBonds[j].a = currentBond->getA() + atomOffset; |
212 |
+ |
theBonds[j].b = currentBond->getB() + atomOffset; |
213 |
+ |
|
214 |
+ |
exI = theBonds[j].a; |
215 |
+ |
exJ = theBonds[j].b; |
216 |
+ |
|
217 |
+ |
// exclude_I must always be the smaller of the pair |
218 |
+ |
if( exI > exJ ){ |
219 |
+ |
tempEx = exI; |
220 |
+ |
exI = exJ; |
221 |
+ |
exJ = tempEx; |
222 |
+ |
} |
223 |
+ |
#ifdef IS_MPI |
224 |
+ |
tempEx = exI; |
225 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
226 |
+ |
tempEx = exJ; |
227 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
228 |
+ |
|
229 |
+ |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
230 |
+ |
#else // isn't MPI |
231 |
+ |
|
232 |
+ |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
233 |
+ |
#endif //is_mpi |
234 |
+ |
} |
235 |
+ |
excludeOffset += molInfo.nBonds; |
236 |
+ |
|
237 |
+ |
//make the bends |
238 |
+ |
for(j=0; j<molInfo.nBends; j++){ |
239 |
+ |
|
240 |
+ |
currentBend = comp_stamps[stampID]->getBend( j ); |
241 |
+ |
theBends[j].a = currentBend->getA() + atomOffset; |
242 |
+ |
theBends[j].b = currentBend->getB() + atomOffset; |
243 |
+ |
theBends[j].c = currentBend->getC() + atomOffset; |
244 |
+ |
|
245 |
+ |
if( currentBend->haveExtras() ){ |
246 |
+ |
|
247 |
+ |
extras = currentBend->getExtras(); |
248 |
+ |
current_extra = extras; |
249 |
+ |
|
250 |
+ |
while( current_extra != NULL ){ |
251 |
+ |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
252 |
+ |
|
253 |
+ |
switch( current_extra->getType() ){ |
254 |
+ |
|
255 |
+ |
case 0: |
256 |
+ |
theBends[j].ghost = |
257 |
+ |
current_extra->getInt() + atomOffset; |
258 |
+ |
theBends[j].isGhost = 1; |
259 |
+ |
break; |
260 |
+ |
|
261 |
+ |
case 1: |
262 |
+ |
theBends[j].ghost = |
263 |
+ |
(int)current_extra->getDouble() + atomOffset; |
264 |
+ |
theBends[j].isGhost = 1; |
265 |
+ |
break; |
266 |
+ |
|
267 |
+ |
default: |
268 |
+ |
sprintf( painCave.errMsg, |
269 |
+ |
"SimSetup Error: ghostVectorSource was neither a " |
270 |
+ |
"double nor an int.\n" |
271 |
+ |
"-->Bend[%d] in %s\n", |
272 |
+ |
j, comp_stamps[stampID]->getID() ); |
273 |
+ |
painCave.isFatal = 1; |
274 |
+ |
simError(); |
275 |
+ |
} |
276 |
+ |
} |
277 |
+ |
|
278 |
+ |
else{ |
279 |
+ |
|
280 |
+ |
sprintf( painCave.errMsg, |
281 |
+ |
"SimSetup Error: unhandled bend assignment:\n" |
282 |
+ |
" -->%s in Bend[%d] in %s\n", |
283 |
+ |
current_extra->getlhs(), |
284 |
+ |
j, comp_stamps[stampID]->getID() ); |
285 |
+ |
painCave.isFatal = 1; |
286 |
+ |
simError(); |
287 |
+ |
} |
288 |
+ |
|
289 |
+ |
current_extra = current_extra->getNext(); |
290 |
+ |
} |
291 |
+ |
} |
292 |
+ |
|
293 |
+ |
if( !theBends[j].isGhost ){ |
294 |
+ |
|
295 |
+ |
exI = theBends[j].a; |
296 |
+ |
exJ = theBends[j].c; |
297 |
+ |
} |
298 |
+ |
else{ |
299 |
+ |
|
300 |
+ |
exI = theBends[j].a; |
301 |
+ |
exJ = theBends[j].b; |
302 |
+ |
} |
303 |
+ |
|
304 |
+ |
// exclude_I must always be the smaller of the pair |
305 |
+ |
if( exI > exJ ){ |
306 |
+ |
tempEx = exI; |
307 |
+ |
exI = exJ; |
308 |
+ |
exJ = tempEx; |
309 |
+ |
} |
310 |
+ |
#ifdef IS_MPI |
311 |
+ |
tempEx = exI; |
312 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
313 |
+ |
tempEx = exJ; |
314 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
315 |
+ |
|
316 |
+ |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
317 |
+ |
#else // isn't MPI |
318 |
+ |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
319 |
+ |
#endif //is_mpi |
320 |
+ |
} |
321 |
+ |
excludeOffset += molInfo.nBends; |
322 |
+ |
|
323 |
+ |
for(j=0; j<molInfo.nTorsions; j++){ |
324 |
+ |
|
325 |
+ |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
326 |
+ |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
327 |
+ |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
328 |
+ |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
329 |
+ |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
330 |
+ |
|
331 |
+ |
exI = theTorsions[j].a; |
332 |
+ |
exJ = theTorsions[j].d; |
333 |
+ |
|
334 |
+ |
// exclude_I must always be the smaller of the pair |
335 |
+ |
if( exI > exJ ){ |
336 |
+ |
tempEx = exI; |
337 |
+ |
exI = exJ; |
338 |
+ |
exJ = tempEx; |
339 |
+ |
} |
340 |
+ |
#ifdef IS_MPI |
341 |
+ |
tempEx = exI; |
342 |
+ |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
343 |
+ |
tempEx = exJ; |
344 |
+ |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
345 |
+ |
|
346 |
+ |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
347 |
+ |
#else // isn't MPI |
348 |
+ |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 |
+ |
#endif //is_mpi |
350 |
+ |
} |
351 |
+ |
excludeOffset += molInfo.nTorsions; |
352 |
+ |
|
353 |
+ |
|
354 |
+ |
// send the arrays off to the forceField for init. |
355 |
+ |
|
356 |
+ |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
357 |
+ |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
358 |
+ |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
359 |
+ |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
360 |
+ |
|
361 |
+ |
|
362 |
+ |
the_molecules[i].initialize( molInfo ); |
363 |
+ |
|
364 |
+ |
|
365 |
+ |
atomOffset += molInfo.nAtoms; |
366 |
+ |
delete[] theBonds; |
367 |
+ |
delete[] theBends; |
368 |
+ |
delete[] theTorsions; |
369 |
+ |
} |
370 |
+ |
|
371 |
+ |
#ifdef IS_MPI |
372 |
+ |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
373 |
+ |
MPIcheckPoint(); |
374 |
+ |
#endif // is_mpi |
375 |
+ |
|
376 |
+ |
// clean up the forcefield |
377 |
+ |
the_ff->calcRcut(); |
378 |
+ |
the_ff->cleanMe(); |
379 |
+ |
|
380 |
+ |
} |
381 |
+ |
|
382 |
+ |
void SimSetup::initFromBass( void ){ |
383 |
+ |
|
384 |
+ |
int i, j, k; |
385 |
+ |
int n_cells; |
386 |
+ |
double cellx, celly, cellz; |
387 |
+ |
double temp1, temp2, temp3; |
388 |
+ |
int n_per_extra; |
389 |
+ |
int n_extra; |
390 |
+ |
int have_extra, done; |
391 |
+ |
|
392 |
+ |
temp1 = (double)tot_nmol / 4.0; |
393 |
+ |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
394 |
+ |
temp3 = ceil( temp2 ); |
395 |
+ |
|
396 |
+ |
have_extra =0; |
397 |
+ |
if( temp2 < temp3 ){ // we have a non-complete lattice |
398 |
+ |
have_extra =1; |
399 |
+ |
|
400 |
+ |
n_cells = (int)temp3 - 1; |
401 |
+ |
cellx = info->boxL[0] / temp3; |
402 |
+ |
celly = info->boxL[1] / temp3; |
403 |
+ |
cellz = info->boxL[2] / temp3; |
404 |
+ |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
405 |
+ |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
406 |
+ |
n_per_extra = (int)ceil( temp1 ); |
407 |
+ |
|
408 |
+ |
if( n_per_extra > 4){ |
409 |
+ |
sprintf( painCave.errMsg, |
410 |
+ |
"SimSetup error. There has been an error in constructing" |
411 |
+ |
" the non-complete lattice.\n" ); |
412 |
+ |
painCave.isFatal = 1; |
413 |
+ |
simError(); |
414 |
+ |
} |
415 |
+ |
} |
416 |
+ |
else{ |
417 |
+ |
n_cells = (int)temp3; |
418 |
+ |
cellx = info->boxL[0] / temp3; |
419 |
+ |
celly = info->boxL[1] / temp3; |
420 |
+ |
cellz = info->boxL[2] / temp3; |
421 |
+ |
} |
422 |
+ |
|
423 |
+ |
current_mol = 0; |
424 |
+ |
current_comp_mol = 0; |
425 |
+ |
current_comp = 0; |
426 |
+ |
current_atom_ndx = 0; |
427 |
+ |
|
428 |
+ |
for( i=0; i < n_cells ; i++ ){ |
429 |
+ |
for( j=0; j < n_cells; j++ ){ |
430 |
+ |
for( k=0; k < n_cells; k++ ){ |
431 |
+ |
|
432 |
+ |
makeElement( i * cellx, |
433 |
+ |
j * celly, |
434 |
+ |
k * cellz ); |
435 |
+ |
|
436 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
437 |
+ |
j * celly + 0.5 * celly, |
438 |
+ |
k * cellz ); |
439 |
+ |
|
440 |
+ |
makeElement( i * cellx, |
441 |
+ |
j * celly + 0.5 * celly, |
442 |
+ |
k * cellz + 0.5 * cellz ); |
443 |
+ |
|
444 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
445 |
+ |
j * celly, |
446 |
+ |
k * cellz + 0.5 * cellz ); |
447 |
+ |
} |
448 |
+ |
} |
449 |
+ |
} |
450 |
+ |
|
451 |
+ |
if( have_extra ){ |
452 |
+ |
done = 0; |
453 |
+ |
|
454 |
+ |
int start_ndx; |
455 |
+ |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
456 |
+ |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
457 |
+ |
|
458 |
+ |
if( i < n_cells ){ |
459 |
+ |
|
460 |
+ |
if( j < n_cells ){ |
461 |
+ |
start_ndx = n_cells; |
462 |
+ |
} |
463 |
+ |
else start_ndx = 0; |
464 |
+ |
} |
465 |
+ |
else start_ndx = 0; |
466 |
+ |
|
467 |
+ |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
468 |
+ |
|
469 |
+ |
makeElement( i * cellx, |
470 |
+ |
j * celly, |
471 |
+ |
k * cellz ); |
472 |
+ |
done = ( current_mol >= tot_nmol ); |
473 |
+ |
|
474 |
+ |
if( !done && n_per_extra > 1 ){ |
475 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
476 |
+ |
j * celly + 0.5 * celly, |
477 |
+ |
k * cellz ); |
478 |
+ |
done = ( current_mol >= tot_nmol ); |
479 |
+ |
} |
480 |
+ |
|
481 |
+ |
if( !done && n_per_extra > 2){ |
482 |
+ |
makeElement( i * cellx, |
483 |
+ |
j * celly + 0.5 * celly, |
484 |
+ |
k * cellz + 0.5 * cellz ); |
485 |
+ |
done = ( current_mol >= tot_nmol ); |
486 |
+ |
} |
487 |
+ |
|
488 |
+ |
if( !done && n_per_extra > 3){ |
489 |
+ |
makeElement( i * cellx + 0.5 * cellx, |
490 |
+ |
j * celly, |
491 |
+ |
k * cellz + 0.5 * cellz ); |
492 |
+ |
done = ( current_mol >= tot_nmol ); |
493 |
+ |
} |
494 |
+ |
} |
495 |
+ |
} |
496 |
+ |
} |
497 |
+ |
} |
498 |
+ |
|
499 |
+ |
|
500 |
+ |
for( i=0; i<info->n_atoms; i++ ){ |
501 |
+ |
info->atoms[i]->set_vx( 0.0 ); |
502 |
+ |
info->atoms[i]->set_vy( 0.0 ); |
503 |
+ |
info->atoms[i]->set_vz( 0.0 ); |
504 |
+ |
} |
505 |
+ |
} |
506 |
+ |
|
507 |
+ |
void SimSetup::makeElement( double x, double y, double z ){ |
508 |
+ |
|
509 |
+ |
int k; |
510 |
+ |
AtomStamp* current_atom; |
511 |
+ |
DirectionalAtom* dAtom; |
512 |
+ |
double rotMat[3][3]; |
513 |
+ |
|
514 |
+ |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
515 |
+ |
|
516 |
+ |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
517 |
+ |
if( !current_atom->havePosition() ){ |
518 |
+ |
sprintf( painCave.errMsg, |
519 |
+ |
"SimSetup:initFromBass error.\n" |
520 |
+ |
"\tComponent %s, atom %s does not have a position specified.\n" |
521 |
+ |
"\tThe initialization routine is unable to give a start" |
522 |
+ |
" position.\n", |
523 |
+ |
comp_stamps[current_comp]->getID(), |
524 |
+ |
current_atom->getType() ); |
525 |
+ |
painCave.isFatal = 1; |
526 |
+ |
simError(); |
527 |
+ |
} |
528 |
+ |
|
529 |
+ |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
530 |
+ |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
531 |
+ |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
532 |
+ |
|
533 |
+ |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
534 |
+ |
|
535 |
+ |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
536 |
+ |
|
537 |
+ |
rotMat[0][0] = 1.0; |
538 |
+ |
rotMat[0][1] = 0.0; |
539 |
+ |
rotMat[0][2] = 0.0; |
540 |
+ |
|
541 |
+ |
rotMat[1][0] = 0.0; |
542 |
+ |
rotMat[1][1] = 1.0; |
543 |
+ |
rotMat[1][2] = 0.0; |
544 |
+ |
|
545 |
+ |
rotMat[2][0] = 0.0; |
546 |
+ |
rotMat[2][1] = 0.0; |
547 |
+ |
rotMat[2][2] = 1.0; |
548 |
+ |
|
549 |
+ |
dAtom->setA( rotMat ); |
550 |
+ |
} |
551 |
+ |
|
552 |
+ |
current_atom_ndx++; |
553 |
+ |
} |
554 |
+ |
|
555 |
+ |
current_mol++; |
556 |
+ |
current_comp_mol++; |
557 |
+ |
|
558 |
+ |
if( current_comp_mol >= components_nmol[current_comp] ){ |
559 |
+ |
|
560 |
+ |
current_comp_mol = 0; |
561 |
+ |
current_comp++; |
562 |
+ |
} |
563 |
+ |
} |
564 |
+ |
|
565 |
+ |
|
566 |
+ |
void SimSetup::gatherInfo( void ){ |
567 |
+ |
int i,j,k; |
568 |
+ |
|
569 |
|
ensembleCase = -1; |
570 |
|
ffCase = -1; |
571 |
|
|
572 |
|
// get the stamps and globals; |
573 |
< |
the_stamps = stamps; |
574 |
< |
the_globals = globals; |
573 |
> |
stamps = stamps; |
574 |
> |
globals = globals; |
575 |
|
|
576 |
|
// set the easy ones first |
577 |
< |
simnfo->target_temp = the_globals->getTargetTemp(); |
578 |
< |
simnfo->dt = the_globals->getDt(); |
579 |
< |
simnfo->run_time = the_globals->getRunTime(); |
577 |
> |
info->target_temp = globals->getTargetTemp(); |
578 |
> |
info->dt = globals->getDt(); |
579 |
> |
info->run_time = globals->getRunTime(); |
580 |
> |
n_components = globals->getNComponents(); |
581 |
|
|
100 |
– |
// get the ones we know are there, yet still may need some work. |
101 |
– |
n_components = the_globals->getNComponents(); |
102 |
– |
strcpy( force_field, the_globals->getForceField() ); |
582 |
|
|
583 |
+ |
// get the forceField |
584 |
+ |
|
585 |
+ |
strcpy( force_field, globals->getForceField() ); |
586 |
+ |
|
587 |
|
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
588 |
|
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
589 |
|
else{ |
594 |
|
simError(); |
595 |
|
} |
596 |
|
|
597 |
< |
// get the ensemble: |
115 |
< |
strcpy( ensemble, the_globals->getEnsemble() ); |
597 |
> |
// get the ensemble |
598 |
|
|
599 |
+ |
strcpy( ensemble, globals->getEnsemble() ); |
600 |
+ |
|
601 |
|
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
602 |
|
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
603 |
|
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
615 |
|
strcpy( ensemble, "NVE" ); |
616 |
|
ensembleCase = NVE_ENS; |
617 |
|
} |
618 |
< |
strcpy( simnfo->ensemble, ensemble ); |
618 |
> |
strcpy( info->ensemble, ensemble ); |
619 |
|
|
620 |
+ |
// get the mixing rule |
621 |
|
|
622 |
< |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
623 |
< |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
624 |
< |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
625 |
< |
// if (the_globals->haveTargetPressure()) |
141 |
< |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
142 |
< |
// else { |
143 |
< |
// sprintf( painCave.errMsg, |
144 |
< |
// "SimSetup error: If you use the constant pressure\n" |
145 |
< |
// " ensemble, you must set targetPressure.\n" |
146 |
< |
// " This was found in the BASS file.\n"); |
147 |
< |
// painCave.isFatal = 1; |
148 |
< |
// simError(); |
149 |
< |
// } |
150 |
< |
|
151 |
< |
// if (the_globals->haveTauThermostat()) |
152 |
< |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
153 |
< |
// else if (the_globals->haveQmass()) |
154 |
< |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
155 |
< |
// else { |
156 |
< |
// sprintf( painCave.errMsg, |
157 |
< |
// "SimSetup error: If you use one of the constant temperature\n" |
158 |
< |
// " ensembles, you must set either tauThermostat or qMass.\n" |
159 |
< |
// " Neither of these was found in the BASS file.\n"); |
160 |
< |
// painCave.isFatal = 1; |
161 |
< |
// simError(); |
162 |
< |
// } |
163 |
< |
|
164 |
< |
// if (the_globals->haveTauBarostat()) |
165 |
< |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
166 |
< |
// else { |
167 |
< |
// sprintf( painCave.errMsg, |
168 |
< |
// "SimSetup error: If you use the constant pressure\n" |
169 |
< |
// " ensemble, you must set tauBarostat.\n" |
170 |
< |
// " This was found in the BASS file.\n"); |
171 |
< |
// painCave.isFatal = 1; |
172 |
< |
// simError(); |
173 |
< |
// } |
174 |
< |
|
175 |
< |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
176 |
< |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
177 |
< |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
178 |
< |
|
179 |
< |
// if (the_globals->haveTauThermostat()) |
180 |
< |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
181 |
< |
// else if (the_globals->haveQmass()) |
182 |
< |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
183 |
< |
// else { |
184 |
< |
// sprintf( painCave.errMsg, |
185 |
< |
// "SimSetup error: If you use one of the constant temperature\n" |
186 |
< |
// " ensembles, you must set either tauThermostat or qMass.\n" |
187 |
< |
// " Neither of these was found in the BASS file.\n"); |
188 |
< |
// painCave.isFatal = 1; |
189 |
< |
// simError(); |
190 |
< |
// } |
191 |
< |
|
192 |
< |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
193 |
< |
simnfo->usePBC = the_globals->getPBC(); |
194 |
< |
|
195 |
< |
int usesDipoles = 0; |
196 |
< |
switch( ffCase ){ |
197 |
< |
|
198 |
< |
case FF_DUFF: |
199 |
< |
the_ff = new DUFF(); |
200 |
< |
usesDipoles = 1; |
201 |
< |
break; |
202 |
< |
|
203 |
< |
case FF_LJ: |
204 |
< |
the_ff = new LJFF(); |
205 |
< |
break; |
206 |
< |
|
207 |
< |
default: |
208 |
< |
sprintf( painCave.errMsg, |
209 |
< |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
210 |
< |
painCave.isFatal = 1; |
211 |
< |
simError(); |
212 |
< |
} |
213 |
< |
|
214 |
< |
#ifdef IS_MPI |
215 |
< |
strcpy( checkPointMsg, "ForceField creation successful" ); |
216 |
< |
MPIcheckPoint(); |
217 |
< |
#endif // is_mpi |
218 |
< |
|
622 |
> |
strcpy( info->mixingRule, globals->getMixingRule() ); |
623 |
> |
info->usePBC = globals->getPBC(); |
624 |
> |
|
625 |
> |
|
626 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
627 |
< |
the_components = the_globals->getComponents(); |
627 |
> |
|
628 |
> |
the_components = globals->getComponents(); |
629 |
|
components_nmol = new int[n_components]; |
222 |
– |
comp_stamps = new MoleculeStamp*[n_components]; |
630 |
|
|
631 |
< |
if( !the_globals->haveNMol() ){ |
631 |
> |
|
632 |
> |
if( !globals->haveNMol() ){ |
633 |
|
// we don't have the total number of molecules, so we assume it is |
634 |
|
// given in each component |
635 |
|
|
658 |
|
" Please give nMol in the components.\n" ); |
659 |
|
painCave.isFatal = 1; |
660 |
|
simError(); |
253 |
– |
|
254 |
– |
|
255 |
– |
// tot_nmol = the_globals->getNMol(); |
256 |
– |
|
257 |
– |
// //we have the total number of molecules, now we check for molfractions |
258 |
– |
// for( i=0; i<n_components; i++ ){ |
259 |
– |
|
260 |
– |
// if( !the_components[i]->haveMolFraction() ){ |
261 |
– |
|
262 |
– |
// if( !the_components[i]->haveNMol() ){ |
263 |
– |
// //we have a problem |
264 |
– |
// std::cerr << "SimSetup error. Neither molFraction nor " |
265 |
– |
// << " nMol was given in component |
266 |
– |
|
661 |
|
} |
662 |
|
|
663 |
< |
#ifdef IS_MPI |
270 |
< |
strcpy( checkPointMsg, "Have the number of components" ); |
271 |
< |
MPIcheckPoint(); |
272 |
< |
#endif // is_mpi |
273 |
< |
|
274 |
< |
// make an array of molecule stamps that match the components used. |
275 |
< |
// also extract the used stamps out into a separate linked list |
276 |
< |
|
277 |
< |
simnfo->nComponents = n_components; |
278 |
< |
simnfo->componentsNmol = components_nmol; |
279 |
< |
simnfo->compStamps = comp_stamps; |
280 |
< |
simnfo->headStamp = new LinkedMolStamp(); |
663 |
> |
// set the status, sample, and thermal kick times |
664 |
|
|
665 |
< |
char* id; |
666 |
< |
LinkedMolStamp* headStamp = simnfo->headStamp; |
667 |
< |
LinkedMolStamp* currentStamp = NULL; |
668 |
< |
for( i=0; i<n_components; i++ ){ |
286 |
< |
|
287 |
< |
id = the_components[i]->getType(); |
288 |
< |
comp_stamps[i] = NULL; |
289 |
< |
|
290 |
< |
// check to make sure the component isn't already in the list |
291 |
< |
|
292 |
< |
comp_stamps[i] = headStamp->match( id ); |
293 |
< |
if( comp_stamps[i] == NULL ){ |
294 |
< |
|
295 |
< |
// extract the component from the list; |
296 |
< |
|
297 |
< |
currentStamp = the_stamps->extractMolStamp( id ); |
298 |
< |
if( currentStamp == NULL ){ |
299 |
< |
sprintf( painCave.errMsg, |
300 |
< |
"SimSetup error: Component \"%s\" was not found in the " |
301 |
< |
"list of declared molecules\n", |
302 |
< |
id ); |
303 |
< |
painCave.isFatal = 1; |
304 |
< |
simError(); |
305 |
< |
} |
306 |
< |
|
307 |
< |
headStamp->add( currentStamp ); |
308 |
< |
comp_stamps[i] = headStamp->match( id ); |
309 |
< |
} |
665 |
> |
if( globals->haveSampleTime() ){ |
666 |
> |
info->sampleTime = globals->getSampleTime(); |
667 |
> |
info->statusTime = info->sampleTime; |
668 |
> |
info->thermalTime = info->sampleTime; |
669 |
|
} |
670 |
+ |
else{ |
671 |
+ |
info->sampleTime = globals->getRunTime(); |
672 |
+ |
info->statusTime = info->sampleTime; |
673 |
+ |
info->thermalTime = info->sampleTime; |
674 |
+ |
} |
675 |
|
|
676 |
< |
#ifdef IS_MPI |
677 |
< |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
314 |
< |
MPIcheckPoint(); |
315 |
< |
#endif // is_mpi |
316 |
< |
|
317 |
< |
|
318 |
< |
|
319 |
< |
|
320 |
< |
// caclulate the number of atoms, bonds, bends and torsions |
321 |
< |
|
322 |
< |
tot_atoms = 0; |
323 |
< |
tot_bonds = 0; |
324 |
< |
tot_bends = 0; |
325 |
< |
tot_torsions = 0; |
326 |
< |
for( i=0; i<n_components; i++ ){ |
327 |
< |
|
328 |
< |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
329 |
< |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
330 |
< |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
331 |
< |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
676 |
> |
if( globals->haveStatusTime() ){ |
677 |
> |
info->statusTime = globals->getStatusTime(); |
678 |
|
} |
679 |
|
|
680 |
< |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
681 |
< |
|
682 |
< |
simnfo->n_atoms = tot_atoms; |
337 |
< |
simnfo->n_bonds = tot_bonds; |
338 |
< |
simnfo->n_bends = tot_bends; |
339 |
< |
simnfo->n_torsions = tot_torsions; |
340 |
< |
simnfo->n_SRI = tot_SRI; |
341 |
< |
simnfo->n_mol = tot_nmol; |
342 |
< |
|
343 |
< |
simnfo->molMembershipArray = new int[tot_atoms]; |
344 |
< |
|
345 |
< |
#ifdef IS_MPI |
346 |
< |
|
347 |
< |
// divide the molecules among processors here. |
348 |
< |
|
349 |
< |
mpiSim = new mpiSimulation( simnfo ); |
350 |
< |
|
351 |
< |
globalIndex = mpiSim->divideLabor(); |
352 |
< |
|
353 |
< |
// set up the local variables |
354 |
< |
|
355 |
< |
int localMol, allMol; |
356 |
< |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
357 |
< |
|
358 |
< |
int* mol2proc = mpiSim->getMolToProcMap(); |
359 |
< |
int* molCompType = mpiSim->getMolComponentType(); |
360 |
< |
|
361 |
< |
allMol = 0; |
362 |
< |
localMol = 0; |
363 |
< |
local_atoms = 0; |
364 |
< |
local_bonds = 0; |
365 |
< |
local_bends = 0; |
366 |
< |
local_torsions = 0; |
367 |
< |
globalAtomIndex = 0; |
680 |
> |
if( globals->haveThermalTime() ){ |
681 |
> |
info->thermalTime = globals->getThermalTime(); |
682 |
> |
} |
683 |
|
|
684 |
+ |
// check for the temperature set flag |
685 |
|
|
686 |
< |
for( i=0; i<n_components; i++ ){ |
686 |
> |
if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
687 |
|
|
372 |
– |
for( j=0; j<components_nmol[i]; j++ ){ |
373 |
– |
|
374 |
– |
if( mol2proc[allMol] == worldRank ){ |
375 |
– |
|
376 |
– |
local_atoms += comp_stamps[i]->getNAtoms(); |
377 |
– |
local_bonds += comp_stamps[i]->getNBonds(); |
378 |
– |
local_bends += comp_stamps[i]->getNBends(); |
379 |
– |
local_torsions += comp_stamps[i]->getNTorsions(); |
380 |
– |
localMol++; |
381 |
– |
} |
382 |
– |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
383 |
– |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
384 |
– |
globalAtomIndex++; |
385 |
– |
} |
386 |
– |
|
387 |
– |
allMol++; |
388 |
– |
} |
389 |
– |
} |
390 |
– |
local_SRI = local_bonds + local_bends + local_torsions; |
391 |
– |
|
392 |
– |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
393 |
– |
|
394 |
– |
if( local_atoms != simnfo->n_atoms ){ |
395 |
– |
sprintf( painCave.errMsg, |
396 |
– |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
397 |
– |
" localAtom (%d) are not equal.\n", |
398 |
– |
simnfo->n_atoms, |
399 |
– |
local_atoms ); |
400 |
– |
painCave.isFatal = 1; |
401 |
– |
simError(); |
402 |
– |
} |
403 |
– |
|
404 |
– |
simnfo->n_bonds = local_bonds; |
405 |
– |
simnfo->n_bends = local_bends; |
406 |
– |
simnfo->n_torsions = local_torsions; |
407 |
– |
simnfo->n_SRI = local_SRI; |
408 |
– |
simnfo->n_mol = localMol; |
409 |
– |
|
410 |
– |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
411 |
– |
MPIcheckPoint(); |
412 |
– |
|
413 |
– |
|
414 |
– |
#endif // is_mpi |
415 |
– |
|
416 |
– |
|
417 |
– |
// create the atom and short range interaction arrays |
418 |
– |
|
419 |
– |
Atom::createArrays(simnfo->n_atoms); |
420 |
– |
the_atoms = new Atom*[simnfo->n_atoms]; |
421 |
– |
the_molecules = new Molecule[simnfo->n_mol]; |
422 |
– |
int molIndex; |
423 |
– |
|
424 |
– |
// initialize the molecule's stampID's |
425 |
– |
|
426 |
– |
#ifdef IS_MPI |
427 |
– |
|
428 |
– |
|
429 |
– |
molIndex = 0; |
430 |
– |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
431 |
– |
|
432 |
– |
if(mol2proc[i] == worldRank ){ |
433 |
– |
the_molecules[molIndex].setStampID( molCompType[i] ); |
434 |
– |
the_molecules[molIndex].setMyIndex( molIndex ); |
435 |
– |
the_molecules[molIndex].setGlobalIndex( i ); |
436 |
– |
molIndex++; |
437 |
– |
} |
438 |
– |
} |
439 |
– |
|
440 |
– |
#else // is_mpi |
441 |
– |
|
442 |
– |
molIndex = 0; |
443 |
– |
globalAtomIndex = 0; |
444 |
– |
for(i=0; i<n_components; i++){ |
445 |
– |
for(j=0; j<components_nmol[i]; j++ ){ |
446 |
– |
the_molecules[molIndex].setStampID( i ); |
447 |
– |
the_molecules[molIndex].setMyIndex( molIndex ); |
448 |
– |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
449 |
– |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
450 |
– |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
451 |
– |
globalAtomIndex++; |
452 |
– |
} |
453 |
– |
molIndex++; |
454 |
– |
} |
455 |
– |
} |
456 |
– |
|
457 |
– |
|
458 |
– |
#endif // is_mpi |
459 |
– |
|
460 |
– |
|
461 |
– |
if( simnfo->n_SRI ){ |
462 |
– |
|
463 |
– |
Exclude::createArray(simnfo->n_SRI); |
464 |
– |
the_excludes = new Exclude*[simnfo->n_SRI]; |
465 |
– |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
466 |
– |
simnfo->globalExcludes = new int; |
467 |
– |
simnfo->n_exclude = simnfo->n_SRI; |
468 |
– |
} |
469 |
– |
else{ |
470 |
– |
|
471 |
– |
Exclude::createArray( 1 ); |
472 |
– |
the_excludes = new Exclude*; |
473 |
– |
the_excludes[0] = new Exclude(0); |
474 |
– |
the_excludes[0]->setPair( 0,0 ); |
475 |
– |
simnfo->globalExcludes = new int; |
476 |
– |
simnfo->globalExcludes[0] = 0; |
477 |
– |
simnfo->n_exclude = 0; |
478 |
– |
} |
479 |
– |
|
480 |
– |
// set the arrays into the SimInfo object |
481 |
– |
|
482 |
– |
simnfo->atoms = the_atoms; |
483 |
– |
simnfo->molecules = the_molecules; |
484 |
– |
simnfo->nGlobalExcludes = 0; |
485 |
– |
simnfo->excludes = the_excludes; |
486 |
– |
|
487 |
– |
|
688 |
|
// get some of the tricky things that may still be in the globals |
689 |
|
|
690 |
|
double boxVector[3]; |
691 |
< |
if( the_globals->haveBox() ){ |
692 |
< |
boxVector[0] = the_globals->getBox(); |
693 |
< |
boxVector[1] = the_globals->getBox(); |
694 |
< |
boxVector[2] = the_globals->getBox(); |
691 |
> |
if( globals->haveBox() ){ |
692 |
> |
boxVector[0] = globals->getBox(); |
693 |
> |
boxVector[1] = globals->getBox(); |
694 |
> |
boxVector[2] = globals->getBox(); |
695 |
|
|
696 |
< |
simnfo->setBox( boxVector ); |
696 |
> |
info->setBox( boxVector ); |
697 |
|
} |
698 |
< |
else if( the_globals->haveDensity() ){ |
698 |
> |
else if( globals->haveDensity() ){ |
699 |
|
|
700 |
|
double vol; |
701 |
< |
vol = (double)tot_nmol / the_globals->getDensity(); |
701 |
> |
vol = (double)tot_nmol / globals->getDensity(); |
702 |
|
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
703 |
|
boxVector[1] = boxVector[0]; |
704 |
|
boxVector[2] = boxVector[0]; |
705 |
|
|
706 |
< |
simnfo->setBox( boxVector ); |
706 |
> |
info->setBox( boxVector ); |
707 |
|
} |
708 |
|
else{ |
709 |
< |
if( !the_globals->haveBoxX() ){ |
709 |
> |
if( !globals->haveBoxX() ){ |
710 |
|
sprintf( painCave.errMsg, |
711 |
|
"SimSetup error, no periodic BoxX size given.\n" ); |
712 |
|
painCave.isFatal = 1; |
713 |
|
simError(); |
714 |
|
} |
715 |
< |
boxVector[0] = the_globals->getBoxX(); |
715 |
> |
boxVector[0] = globals->getBoxX(); |
716 |
|
|
717 |
< |
if( !the_globals->haveBoxY() ){ |
717 |
> |
if( !globals->haveBoxY() ){ |
718 |
|
sprintf( painCave.errMsg, |
719 |
|
"SimSetup error, no periodic BoxY size given.\n" ); |
720 |
|
painCave.isFatal = 1; |
721 |
|
simError(); |
722 |
|
} |
723 |
< |
boxVector[1] = the_globals->getBoxY(); |
723 |
> |
boxVector[1] = globals->getBoxY(); |
724 |
|
|
725 |
< |
if( !the_globals->haveBoxZ() ){ |
725 |
> |
if( !globals->haveBoxZ() ){ |
726 |
|
sprintf( painCave.errMsg, |
727 |
|
"SimSetup error, no periodic BoxZ size given.\n" ); |
728 |
|
painCave.isFatal = 1; |
729 |
|
simError(); |
730 |
|
} |
731 |
< |
boxVector[2] = the_globals->getBoxZ(); |
731 |
> |
boxVector[2] = globals->getBoxZ(); |
732 |
|
|
733 |
< |
simnfo->setBox( boxVector ); |
733 |
> |
info->setBox( boxVector ); |
734 |
|
} |
735 |
|
|
736 |
+ |
|
737 |
+ |
|
738 |
|
#ifdef IS_MPI |
739 |
< |
strcpy( checkPointMsg, "Box size set up" ); |
739 |
> |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
740 |
|
MPIcheckPoint(); |
741 |
|
#endif // is_mpi |
742 |
|
|
743 |
+ |
} |
744 |
|
|
542 |
– |
// initialize the arrays |
745 |
|
|
746 |
< |
the_ff->setSimInfo( simnfo ); |
746 |
> |
void SimSetup::finalInfoCheck( void ){ |
747 |
> |
int index; |
748 |
> |
int usesDipoles; |
749 |
> |
|
750 |
|
|
751 |
< |
makeMolecules(); |
752 |
< |
simnfo->identArray = new int[simnfo->n_atoms]; |
753 |
< |
for(i=0; i<simnfo->n_atoms; i++){ |
754 |
< |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
751 |
> |
// check electrostatic parameters |
752 |
> |
|
753 |
> |
index = 0; |
754 |
> |
usesDipoles = 0; |
755 |
> |
while( (index < info->n_atoms) && !usesDipoles ){ |
756 |
> |
usesDipoles = ((info->atoms)[index])->hasDipole(); |
757 |
> |
index++; |
758 |
|
} |
759 |
|
|
760 |
< |
if (the_globals->getUseRF() ) { |
761 |
< |
simnfo->useReactionField = 1; |
762 |
< |
|
763 |
< |
if( !the_globals->haveECR() ){ |
760 |
> |
#ifdef IS_MPI |
761 |
> |
int myUse = usesDipoles; |
762 |
> |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
763 |
> |
#endif //is_mpi |
764 |
> |
|
765 |
> |
|
766 |
> |
if (globals->getUseRF() ) { |
767 |
> |
info->useReactionField = 1; |
768 |
> |
|
769 |
> |
if( !globals->haveECR() ){ |
770 |
|
sprintf( painCave.errMsg, |
771 |
|
"SimSetup Warning: using default value of 1/2 the smallest " |
772 |
|
"box length for the electrostaticCutoffRadius.\n" |
774 |
|
painCave.isFatal = 0; |
775 |
|
simError(); |
776 |
|
double smallest; |
777 |
< |
smallest = simnfo->boxLx; |
778 |
< |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
779 |
< |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
780 |
< |
simnfo->ecr = 0.5 * smallest; |
777 |
> |
smallest = info->boxL[0]; |
778 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
779 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
780 |
> |
info->ecr = 0.5 * smallest; |
781 |
|
} else { |
782 |
< |
simnfo->ecr = the_globals->getECR(); |
782 |
> |
info->ecr = globals->getECR(); |
783 |
|
} |
784 |
|
|
785 |
< |
if( !the_globals->haveEST() ){ |
785 |
> |
if( !globals->haveEST() ){ |
786 |
|
sprintf( painCave.errMsg, |
787 |
|
"SimSetup Warning: using default value of 0.05 * the " |
788 |
|
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
789 |
|
); |
790 |
|
painCave.isFatal = 0; |
791 |
|
simError(); |
792 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
792 |
> |
info->est = 0.05 * info->ecr; |
793 |
|
} else { |
794 |
< |
simnfo->est = the_globals->getEST(); |
794 |
> |
info->est = globals->getEST(); |
795 |
|
} |
796 |
|
|
797 |
< |
if(!the_globals->haveDielectric() ){ |
797 |
> |
if(!globals->haveDielectric() ){ |
798 |
|
sprintf( painCave.errMsg, |
799 |
|
"SimSetup Error: You are trying to use Reaction Field without" |
800 |
|
"setting a dielectric constant!\n" |
802 |
|
painCave.isFatal = 1; |
803 |
|
simError(); |
804 |
|
} |
805 |
< |
simnfo->dielectric = the_globals->getDielectric(); |
806 |
< |
} else { |
805 |
> |
info->dielectric = globals->getDielectric(); |
806 |
> |
} |
807 |
> |
else { |
808 |
|
if (usesDipoles) { |
809 |
|
|
810 |
< |
if( !the_globals->haveECR() ){ |
810 |
> |
if( !globals->haveECR() ){ |
811 |
|
sprintf( painCave.errMsg, |
812 |
|
"SimSetup Warning: using default value of 1/2 the smallest " |
813 |
|
"box length for the electrostaticCutoffRadius.\n" |
815 |
|
painCave.isFatal = 0; |
816 |
|
simError(); |
817 |
|
double smallest; |
818 |
< |
smallest = simnfo->boxLx; |
819 |
< |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
820 |
< |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
821 |
< |
simnfo->ecr = 0.5 * smallest; |
818 |
> |
smallest = info->boxL[0]; |
819 |
> |
if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
820 |
> |
if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
821 |
> |
info->ecr = 0.5 * smallest; |
822 |
|
} else { |
823 |
< |
simnfo->ecr = the_globals->getECR(); |
823 |
> |
info->ecr = globals->getECR(); |
824 |
|
} |
825 |
|
|
826 |
< |
if( !the_globals->haveEST() ){ |
826 |
> |
if( !globals->haveEST() ){ |
827 |
|
sprintf( painCave.errMsg, |
828 |
|
"SimSetup Warning: using default value of 5%% of the " |
829 |
|
"electrostaticCutoffRadius for the " |
831 |
|
); |
832 |
|
painCave.isFatal = 0; |
833 |
|
simError(); |
834 |
< |
simnfo->est = 0.05 * simnfo->ecr; |
834 |
> |
info->est = 0.05 * info->ecr; |
835 |
|
} else { |
836 |
< |
simnfo->est = the_globals->getEST(); |
836 |
> |
info->est = globals->getEST(); |
837 |
|
} |
838 |
|
} |
839 |
|
} |
840 |
|
|
841 |
|
#ifdef IS_MPI |
842 |
< |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
842 |
> |
strcpy( checkPointMsg, "post processing checks out" ); |
843 |
|
MPIcheckPoint(); |
844 |
|
#endif // is_mpi |
845 |
|
|
846 |
< |
if( the_globals->haveInitialConfig() ){ |
846 |
> |
} |
847 |
> |
|
848 |
> |
void SimSetup::initSystemCoords( void ){ |
849 |
> |
|
850 |
> |
if( globals->haveInitialConfig() ){ |
851 |
|
|
852 |
|
InitializeFromFile* fileInit; |
853 |
|
#ifdef IS_MPI // is_mpi |
854 |
|
if( worldRank == 0 ){ |
855 |
|
#endif //is_mpi |
856 |
< |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
856 |
> |
fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
857 |
|
#ifdef IS_MPI |
858 |
|
}else fileInit = new InitializeFromFile( NULL ); |
859 |
|
#endif |
860 |
< |
fileInit->read_xyz( simnfo ); // default velocities on |
860 |
> |
fileInit->read_xyz( info ); // default velocities on |
861 |
|
|
862 |
|
delete fileInit; |
863 |
|
} |
885 |
|
MPIcheckPoint(); |
886 |
|
#endif // is_mpi |
887 |
|
|
888 |
+ |
} |
889 |
|
|
670 |
– |
|
671 |
– |
|
672 |
– |
|
890 |
|
|
891 |
< |
|
891 |
> |
void SimSetup::makeOutNames( void ){ |
892 |
> |
|
893 |
|
#ifdef IS_MPI |
894 |
|
if( worldRank == 0 ){ |
895 |
|
#endif // is_mpi |
896 |
|
|
897 |
< |
if( the_globals->haveFinalConfig() ){ |
898 |
< |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
897 |
> |
if( globals->haveFinalConfig() ){ |
898 |
> |
strcpy( info->finalName, globals->getFinalConfig() ); |
899 |
|
} |
900 |
|
else{ |
901 |
< |
strcpy( simnfo->finalName, inFileName ); |
901 |
> |
strcpy( info->finalName, inFileName ); |
902 |
|
char* endTest; |
903 |
< |
int nameLength = strlen( simnfo->finalName ); |
904 |
< |
endTest = &(simnfo->finalName[nameLength - 5]); |
903 |
> |
int nameLength = strlen( info->finalName ); |
904 |
> |
endTest = &(info->finalName[nameLength - 5]); |
905 |
|
if( !strcmp( endTest, ".bass" ) ){ |
906 |
|
strcpy( endTest, ".eor" ); |
907 |
|
} |
909 |
|
strcpy( endTest, ".eor" ); |
910 |
|
} |
911 |
|
else{ |
912 |
< |
endTest = &(simnfo->finalName[nameLength - 4]); |
912 |
> |
endTest = &(info->finalName[nameLength - 4]); |
913 |
|
if( !strcmp( endTest, ".bss" ) ){ |
914 |
|
strcpy( endTest, ".eor" ); |
915 |
|
} |
917 |
|
strcpy( endTest, ".eor" ); |
918 |
|
} |
919 |
|
else{ |
920 |
< |
strcat( simnfo->finalName, ".eor" ); |
920 |
> |
strcat( info->finalName, ".eor" ); |
921 |
|
} |
922 |
|
} |
923 |
|
} |
924 |
|
|
925 |
|
// make the sample and status out names |
926 |
|
|
927 |
< |
strcpy( simnfo->sampleName, inFileName ); |
927 |
> |
strcpy( info->sampleName, inFileName ); |
928 |
|
char* endTest; |
929 |
< |
int nameLength = strlen( simnfo->sampleName ); |
930 |
< |
endTest = &(simnfo->sampleName[nameLength - 5]); |
929 |
> |
int nameLength = strlen( info->sampleName ); |
930 |
> |
endTest = &(info->sampleName[nameLength - 5]); |
931 |
|
if( !strcmp( endTest, ".bass" ) ){ |
932 |
|
strcpy( endTest, ".dump" ); |
933 |
|
} |
935 |
|
strcpy( endTest, ".dump" ); |
936 |
|
} |
937 |
|
else{ |
938 |
< |
endTest = &(simnfo->sampleName[nameLength - 4]); |
938 |
> |
endTest = &(info->sampleName[nameLength - 4]); |
939 |
|
if( !strcmp( endTest, ".bss" ) ){ |
940 |
|
strcpy( endTest, ".dump" ); |
941 |
|
} |
943 |
|
strcpy( endTest, ".dump" ); |
944 |
|
} |
945 |
|
else{ |
946 |
< |
strcat( simnfo->sampleName, ".dump" ); |
946 |
> |
strcat( info->sampleName, ".dump" ); |
947 |
|
} |
948 |
|
} |
949 |
|
|
950 |
< |
strcpy( simnfo->statusName, inFileName ); |
951 |
< |
nameLength = strlen( simnfo->statusName ); |
952 |
< |
endTest = &(simnfo->statusName[nameLength - 5]); |
950 |
> |
strcpy( info->statusName, inFileName ); |
951 |
> |
nameLength = strlen( info->statusName ); |
952 |
> |
endTest = &(info->statusName[nameLength - 5]); |
953 |
|
if( !strcmp( endTest, ".bass" ) ){ |
954 |
|
strcpy( endTest, ".stat" ); |
955 |
|
} |
957 |
|
strcpy( endTest, ".stat" ); |
958 |
|
} |
959 |
|
else{ |
960 |
< |
endTest = &(simnfo->statusName[nameLength - 4]); |
960 |
> |
endTest = &(info->statusName[nameLength - 4]); |
961 |
|
if( !strcmp( endTest, ".bss" ) ){ |
962 |
|
strcpy( endTest, ".stat" ); |
963 |
|
} |
965 |
|
strcpy( endTest, ".stat" ); |
966 |
|
} |
967 |
|
else{ |
968 |
< |
strcat( simnfo->statusName, ".stat" ); |
968 |
> |
strcat( info->statusName, ".stat" ); |
969 |
|
} |
970 |
|
} |
971 |
|
|
972 |
|
#ifdef IS_MPI |
973 |
|
} |
974 |
|
#endif // is_mpi |
975 |
+ |
|
976 |
+ |
} |
977 |
+ |
|
978 |
+ |
|
979 |
+ |
void SimSetup::sysObjectsCreation( void ){ |
980 |
+ |
|
981 |
+ |
int i; |
982 |
+ |
|
983 |
+ |
// create the forceField |
984 |
+ |
|
985 |
+ |
createFF(); |
986 |
+ |
|
987 |
+ |
// extract componentList |
988 |
+ |
|
989 |
+ |
compList(); |
990 |
+ |
|
991 |
+ |
// calc the number of atoms, bond, bends, and torsions |
992 |
+ |
|
993 |
+ |
calcSysValues(); |
994 |
+ |
|
995 |
+ |
#ifdef IS_MPI |
996 |
+ |
// divide the molecules among the processors |
997 |
|
|
998 |
< |
// set the status, sample, and themal kick times |
998 |
> |
mpiMolDivide(); |
999 |
> |
#endif //is_mpi |
1000 |
|
|
1001 |
< |
if( the_globals->haveSampleTime() ){ |
1002 |
< |
simnfo->sampleTime = the_globals->getSampleTime(); |
1003 |
< |
simnfo->statusTime = simnfo->sampleTime; |
1004 |
< |
simnfo->thermalTime = simnfo->sampleTime; |
1001 |
> |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1002 |
> |
|
1003 |
> |
makeSysArrays(); |
1004 |
> |
|
1005 |
> |
// make and initialize the molecules (all but atomic coordinates) |
1006 |
> |
|
1007 |
> |
makeMolecules(); |
1008 |
> |
info->identArray = new int[info->n_atoms]; |
1009 |
> |
for(i=0; i<info->n_atoms; i++){ |
1010 |
> |
info->identArray[i] = the_atoms[i]->getIdent(); |
1011 |
|
} |
1012 |
< |
else{ |
1013 |
< |
simnfo->sampleTime = the_globals->getRunTime(); |
1014 |
< |
simnfo->statusTime = simnfo->sampleTime; |
1015 |
< |
simnfo->thermalTime = simnfo->sampleTime; |
1012 |
> |
|
1013 |
> |
|
1014 |
> |
|
1015 |
> |
} |
1016 |
> |
|
1017 |
> |
|
1018 |
> |
void SimSetup::createFF( void ){ |
1019 |
> |
|
1020 |
> |
switch( ffCase ){ |
1021 |
> |
|
1022 |
> |
case FF_DUFF: |
1023 |
> |
the_ff = new DUFF(); |
1024 |
> |
break; |
1025 |
> |
|
1026 |
> |
case FF_LJ: |
1027 |
> |
the_ff = new LJFF(); |
1028 |
> |
break; |
1029 |
> |
|
1030 |
> |
default: |
1031 |
> |
sprintf( painCave.errMsg, |
1032 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1033 |
> |
painCave.isFatal = 1; |
1034 |
> |
simError(); |
1035 |
|
} |
1036 |
|
|
1037 |
< |
if( the_globals->haveStatusTime() ){ |
1038 |
< |
simnfo->statusTime = the_globals->getStatusTime(); |
1037 |
> |
#ifdef IS_MPI |
1038 |
> |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1039 |
> |
MPIcheckPoint(); |
1040 |
> |
#endif // is_mpi |
1041 |
> |
|
1042 |
> |
} |
1043 |
> |
|
1044 |
> |
|
1045 |
> |
void SimSetup::compList( void ){ |
1046 |
> |
|
1047 |
> |
int i; |
1048 |
> |
|
1049 |
> |
comp_stamps = new MoleculeStamp*[n_components]; |
1050 |
> |
|
1051 |
> |
// make an array of molecule stamps that match the components used. |
1052 |
> |
// also extract the used stamps out into a separate linked list |
1053 |
> |
|
1054 |
> |
info->nComponents = n_components; |
1055 |
> |
info->componentsNmol = components_nmol; |
1056 |
> |
info->compStamps = comp_stamps; |
1057 |
> |
info->headStamp = new LinkedMolStamp(); |
1058 |
> |
|
1059 |
> |
char* id; |
1060 |
> |
LinkedMolStamp* headStamp = info->headStamp; |
1061 |
> |
LinkedMolStamp* currentStamp = NULL; |
1062 |
> |
for( i=0; i<n_components; i++ ){ |
1063 |
> |
|
1064 |
> |
id = the_components[i]->getType(); |
1065 |
> |
comp_stamps[i] = NULL; |
1066 |
> |
|
1067 |
> |
// check to make sure the component isn't already in the list |
1068 |
> |
|
1069 |
> |
comp_stamps[i] = headStamp->match( id ); |
1070 |
> |
if( comp_stamps[i] == NULL ){ |
1071 |
> |
|
1072 |
> |
// extract the component from the list; |
1073 |
> |
|
1074 |
> |
currentStamp = stamps->extractMolStamp( id ); |
1075 |
> |
if( currentStamp == NULL ){ |
1076 |
> |
sprintf( painCave.errMsg, |
1077 |
> |
"SimSetup error: Component \"%s\" was not found in the " |
1078 |
> |
"list of declared molecules\n", |
1079 |
> |
id ); |
1080 |
> |
painCave.isFatal = 1; |
1081 |
> |
simError(); |
1082 |
> |
} |
1083 |
> |
|
1084 |
> |
headStamp->add( currentStamp ); |
1085 |
> |
comp_stamps[i] = headStamp->match( id ); |
1086 |
> |
} |
1087 |
|
} |
1088 |
|
|
1089 |
< |
if( the_globals->haveThermalTime() ){ |
1090 |
< |
simnfo->thermalTime = the_globals->getThermalTime(); |
1089 |
> |
#ifdef IS_MPI |
1090 |
> |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1091 |
> |
MPIcheckPoint(); |
1092 |
> |
#endif // is_mpi |
1093 |
> |
|
1094 |
> |
|
1095 |
> |
} |
1096 |
> |
|
1097 |
> |
void SimSetup::calcSysValues( void ){ |
1098 |
> |
int i, j, k; |
1099 |
> |
|
1100 |
> |
|
1101 |
> |
tot_atoms = 0; |
1102 |
> |
tot_bonds = 0; |
1103 |
> |
tot_bends = 0; |
1104 |
> |
tot_torsions = 0; |
1105 |
> |
for( i=0; i<n_components; i++ ){ |
1106 |
> |
|
1107 |
> |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1108 |
> |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1109 |
> |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1110 |
> |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1111 |
|
} |
1112 |
|
|
1113 |
< |
// check for the temperature set flag |
1113 |
> |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1114 |
|
|
1115 |
< |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
1115 |
> |
info->n_atoms = tot_atoms; |
1116 |
> |
info->n_bonds = tot_bonds; |
1117 |
> |
info->n_bends = tot_bends; |
1118 |
> |
info->n_torsions = tot_torsions; |
1119 |
> |
info->n_SRI = tot_SRI; |
1120 |
> |
info->n_mol = tot_nmol; |
1121 |
> |
|
1122 |
> |
info->molMembershipArray = new int[tot_atoms]; |
1123 |
> |
} |
1124 |
|
|
1125 |
|
|
1126 |
< |
// make the integrator |
1126 |
> |
#ifdef IS_MPI |
1127 |
> |
|
1128 |
> |
void SimSetup::mpiMolDivide( void ){ |
1129 |
|
|
1130 |
+ |
int i, j, k; |
1131 |
+ |
int localMol, allMol; |
1132 |
+ |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1133 |
+ |
|
1134 |
+ |
mpiSim = new mpiSimulation( info ); |
1135 |
|
|
1136 |
+ |
globalIndex = mpiSim->divideLabor(); |
1137 |
+ |
|
1138 |
+ |
// set up the local variables |
1139 |
+ |
|
1140 |
+ |
mol2proc = mpiSim->getMolToProcMap(); |
1141 |
+ |
molCompType = mpiSim->getMolComponentType(); |
1142 |
+ |
|
1143 |
+ |
allMol = 0; |
1144 |
+ |
localMol = 0; |
1145 |
+ |
local_atoms = 0; |
1146 |
+ |
local_bonds = 0; |
1147 |
+ |
local_bends = 0; |
1148 |
+ |
local_torsions = 0; |
1149 |
+ |
globalAtomIndex = 0; |
1150 |
+ |
|
1151 |
+ |
|
1152 |
+ |
for( i=0; i<n_components; i++ ){ |
1153 |
+ |
|
1154 |
+ |
for( j=0; j<components_nmol[i]; j++ ){ |
1155 |
+ |
|
1156 |
+ |
if( mol2proc[allMol] == worldRank ){ |
1157 |
+ |
|
1158 |
+ |
local_atoms += comp_stamps[i]->getNAtoms(); |
1159 |
+ |
local_bonds += comp_stamps[i]->getNBonds(); |
1160 |
+ |
local_bends += comp_stamps[i]->getNBends(); |
1161 |
+ |
local_torsions += comp_stamps[i]->getNTorsions(); |
1162 |
+ |
localMol++; |
1163 |
+ |
} |
1164 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1165 |
+ |
info->molMembershipArray[globalAtomIndex] = allMol; |
1166 |
+ |
globalAtomIndex++; |
1167 |
+ |
} |
1168 |
+ |
|
1169 |
+ |
allMol++; |
1170 |
+ |
} |
1171 |
+ |
} |
1172 |
+ |
local_SRI = local_bonds + local_bends + local_torsions; |
1173 |
+ |
|
1174 |
+ |
info->n_atoms = mpiSim->getMyNlocal(); |
1175 |
+ |
|
1176 |
+ |
if( local_atoms != info->n_atoms ){ |
1177 |
+ |
sprintf( painCave.errMsg, |
1178 |
+ |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1179 |
+ |
" localAtom (%d) are not equal.\n", |
1180 |
+ |
info->n_atoms, |
1181 |
+ |
local_atoms ); |
1182 |
+ |
painCave.isFatal = 1; |
1183 |
+ |
simError(); |
1184 |
+ |
} |
1185 |
+ |
|
1186 |
+ |
info->n_bonds = local_bonds; |
1187 |
+ |
info->n_bends = local_bends; |
1188 |
+ |
info->n_torsions = local_torsions; |
1189 |
+ |
info->n_SRI = local_SRI; |
1190 |
+ |
info->n_mol = localMol; |
1191 |
+ |
|
1192 |
+ |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1193 |
+ |
MPIcheckPoint(); |
1194 |
+ |
} |
1195 |
+ |
|
1196 |
+ |
#endif // is_mpi |
1197 |
+ |
|
1198 |
+ |
|
1199 |
+ |
void SimSetup::makeSysArrays( void ){ |
1200 |
+ |
int i, j, k; |
1201 |
+ |
|
1202 |
+ |
|
1203 |
+ |
// create the atom and short range interaction arrays |
1204 |
+ |
|
1205 |
+ |
Atom::createArrays(info->n_atoms); |
1206 |
+ |
the_atoms = new Atom*[info->n_atoms]; |
1207 |
+ |
the_molecules = new Molecule[info->n_mol]; |
1208 |
+ |
int molIndex; |
1209 |
+ |
|
1210 |
+ |
// initialize the molecule's stampID's |
1211 |
+ |
|
1212 |
+ |
#ifdef IS_MPI |
1213 |
+ |
|
1214 |
+ |
|
1215 |
+ |
molIndex = 0; |
1216 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1217 |
+ |
|
1218 |
+ |
if(mol2proc[i] == worldRank ){ |
1219 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1220 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1221 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
1222 |
+ |
molIndex++; |
1223 |
+ |
} |
1224 |
+ |
} |
1225 |
+ |
|
1226 |
+ |
#else // is_mpi |
1227 |
+ |
|
1228 |
+ |
molIndex = 0; |
1229 |
+ |
globalAtomIndex = 0; |
1230 |
+ |
for(i=0; i<n_components; i++){ |
1231 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
1232 |
+ |
the_molecules[molIndex].setStampID( i ); |
1233 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
1234 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1235 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1236 |
+ |
info->molMembershipArray[globalAtomIndex] = molIndex; |
1237 |
+ |
globalAtomIndex++; |
1238 |
+ |
} |
1239 |
+ |
molIndex++; |
1240 |
+ |
} |
1241 |
+ |
} |
1242 |
+ |
|
1243 |
+ |
|
1244 |
+ |
#endif // is_mpi |
1245 |
+ |
|
1246 |
+ |
|
1247 |
+ |
if( info->n_SRI ){ |
1248 |
+ |
|
1249 |
+ |
Exclude::createArray(info->n_SRI); |
1250 |
+ |
the_excludes = new Exclude*[info->n_SRI]; |
1251 |
+ |
for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1252 |
+ |
info->globalExcludes = new int; |
1253 |
+ |
info->n_exclude = info->n_SRI; |
1254 |
+ |
} |
1255 |
+ |
else{ |
1256 |
+ |
|
1257 |
+ |
Exclude::createArray( 1 ); |
1258 |
+ |
the_excludes = new Exclude*; |
1259 |
+ |
the_excludes[0] = new Exclude(0); |
1260 |
+ |
the_excludes[0]->setPair( 0,0 ); |
1261 |
+ |
info->globalExcludes = new int; |
1262 |
+ |
info->globalExcludes[0] = 0; |
1263 |
+ |
info->n_exclude = 0; |
1264 |
+ |
} |
1265 |
+ |
|
1266 |
+ |
// set the arrays into the SimInfo object |
1267 |
+ |
|
1268 |
+ |
info->atoms = the_atoms; |
1269 |
+ |
info->molecules = the_molecules; |
1270 |
+ |
info->nGlobalExcludes = 0; |
1271 |
+ |
info->excludes = the_excludes; |
1272 |
+ |
|
1273 |
+ |
the_ff->setSimInfo( info ); |
1274 |
+ |
|
1275 |
+ |
} |
1276 |
+ |
|
1277 |
+ |
void SimSetup::makeIntegrator( void ){ |
1278 |
+ |
|
1279 |
|
NVT* myNVT = NULL; |
1280 |
|
NPTi* myNPTi = NULL; |
1281 |
|
NPTf* myNPTf = NULL; |
1285 |
|
switch( ensembleCase ){ |
1286 |
|
|
1287 |
|
case NVE_ENS: |
1288 |
< |
new NVE( simnfo, the_ff ); |
1288 |
> |
new NVE( info, the_ff ); |
1289 |
|
break; |
1290 |
|
|
1291 |
|
case NVT_ENS: |
1292 |
< |
myNVT = new NVT( simnfo, the_ff ); |
1293 |
< |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
1292 |
> |
myNVT = new NVT( info, the_ff ); |
1293 |
> |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1294 |
|
|
1295 |
< |
if (the_globals->haveTauThermostat()) |
1296 |
< |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
1295 |
> |
if (globals->haveTauThermostat()) |
1296 |
> |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1297 |
|
|
1298 |
|
else { |
1299 |
|
sprintf( painCave.errMsg, |
1305 |
|
break; |
1306 |
|
|
1307 |
|
case NPTi_ENS: |
1308 |
< |
myNPTi = new NPTi( simnfo, the_ff ); |
1309 |
< |
myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
1308 |
> |
myNPTi = new NPTi( info, the_ff ); |
1309 |
> |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1310 |
|
|
1311 |
< |
if (the_globals->haveTargetPressure()) |
1312 |
< |
myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
1311 |
> |
if (globals->haveTargetPressure()) |
1312 |
> |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1313 |
|
else { |
1314 |
|
sprintf( painCave.errMsg, |
1315 |
|
"SimSetup error: If you use a constant pressure\n" |
1318 |
|
simError(); |
1319 |
|
} |
1320 |
|
|
1321 |
< |
if( the_globals->haveTauThermostat() ) |
1322 |
< |
myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
1321 |
> |
if( globals->haveTauThermostat() ) |
1322 |
> |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1323 |
|
else{ |
1324 |
|
sprintf( painCave.errMsg, |
1325 |
|
"SimSetup error: If you use an NPT\n" |
1328 |
|
simError(); |
1329 |
|
} |
1330 |
|
|
1331 |
< |
if( the_globals->haveTauBarostat() ) |
1332 |
< |
myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
1331 |
> |
if( globals->haveTauBarostat() ) |
1332 |
> |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1333 |
|
else{ |
1334 |
|
sprintf( painCave.errMsg, |
1335 |
|
"SimSetup error: If you use an NPT\n" |
1340 |
|
break; |
1341 |
|
|
1342 |
|
case NPTf_ENS: |
1343 |
< |
myNPTf = new NPTf( simnfo, the_ff ); |
1344 |
< |
myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
1343 |
> |
myNPTf = new NPTf( info, the_ff ); |
1344 |
> |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1345 |
|
|
1346 |
< |
if (the_globals->haveTargetPressure()) |
1347 |
< |
myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
1346 |
> |
if (globals->haveTargetPressure()) |
1347 |
> |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1348 |
|
else { |
1349 |
|
sprintf( painCave.errMsg, |
1350 |
|
"SimSetup error: If you use a constant pressure\n" |
1353 |
|
simError(); |
1354 |
|
} |
1355 |
|
|
1356 |
< |
if( the_globals->haveTauThermostat() ) |
1357 |
< |
myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
1356 |
> |
if( globals->haveTauThermostat() ) |
1357 |
> |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1358 |
|
else{ |
1359 |
|
sprintf( painCave.errMsg, |
1360 |
|
"SimSetup error: If you use an NPT\n" |
1363 |
|
simError(); |
1364 |
|
} |
1365 |
|
|
1366 |
< |
if( the_globals->haveTauBarostat() ) |
1367 |
< |
myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
1366 |
> |
if( globals->haveTauBarostat() ) |
1367 |
> |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1368 |
|
else{ |
1369 |
|
sprintf( painCave.errMsg, |
1370 |
|
"SimSetup error: If you use an NPT\n" |
1375 |
|
break; |
1376 |
|
|
1377 |
|
case NPTim_ENS: |
1378 |
< |
myNPTim = new NPTim( simnfo, the_ff ); |
1379 |
< |
myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
1378 |
> |
myNPTim = new NPTim( info, the_ff ); |
1379 |
> |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1380 |
|
|
1381 |
< |
if (the_globals->haveTargetPressure()) |
1382 |
< |
myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
1381 |
> |
if (globals->haveTargetPressure()) |
1382 |
> |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1383 |
|
else { |
1384 |
|
sprintf( painCave.errMsg, |
1385 |
|
"SimSetup error: If you use a constant pressure\n" |
1388 |
|
simError(); |
1389 |
|
} |
1390 |
|
|
1391 |
< |
if( the_globals->haveTauThermostat() ) |
1392 |
< |
myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
1391 |
> |
if( globals->haveTauThermostat() ) |
1392 |
> |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1393 |
|
else{ |
1394 |
|
sprintf( painCave.errMsg, |
1395 |
|
"SimSetup error: If you use an NPT\n" |
1398 |
|
simError(); |
1399 |
|
} |
1400 |
|
|
1401 |
< |
if( the_globals->haveTauBarostat() ) |
1402 |
< |
myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
1401 |
> |
if( globals->haveTauBarostat() ) |
1402 |
> |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1403 |
|
else{ |
1404 |
|
sprintf( painCave.errMsg, |
1405 |
|
"SimSetup error: If you use an NPT\n" |
1410 |
|
break; |
1411 |
|
|
1412 |
|
case NPTfm_ENS: |
1413 |
< |
myNPTfm = new NPTfm( simnfo, the_ff ); |
1414 |
< |
myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
1413 |
> |
myNPTfm = new NPTfm( info, the_ff ); |
1414 |
> |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1415 |
|
|
1416 |
< |
if (the_globals->haveTargetPressure()) |
1417 |
< |
myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
1416 |
> |
if (globals->haveTargetPressure()) |
1417 |
> |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1418 |
|
else { |
1419 |
|
sprintf( painCave.errMsg, |
1420 |
|
"SimSetup error: If you use a constant pressure\n" |
1423 |
|
simError(); |
1424 |
|
} |
1425 |
|
|
1426 |
< |
if( the_globals->haveTauThermostat() ) |
1427 |
< |
myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
1426 |
> |
if( globals->haveTauThermostat() ) |
1427 |
> |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1428 |
|
else{ |
1429 |
|
sprintf( painCave.errMsg, |
1430 |
|
"SimSetup error: If you use an NPT\n" |
1433 |
|
simError(); |
1434 |
|
} |
1435 |
|
|
1436 |
< |
if( the_globals->haveTauBarostat() ) |
1437 |
< |
myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
1436 |
> |
if( globals->haveTauBarostat() ) |
1437 |
> |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1438 |
|
else{ |
1439 |
|
sprintf( painCave.errMsg, |
1440 |
|
"SimSetup error: If you use an NPT\n" |
1451 |
|
simError(); |
1452 |
|
} |
1453 |
|
|
1454 |
+ |
} |
1455 |
|
|
1456 |
< |
#ifdef IS_MPI |
964 |
< |
mpiSim->mpiRefresh(); |
965 |
< |
#endif |
1456 |
> |
void SimSetup::initFortran( void ){ |
1457 |
|
|
1458 |
< |
// initialize the Fortran |
968 |
< |
|
969 |
< |
|
970 |
< |
simnfo->refreshSim(); |
1458 |
> |
info->refreshSim(); |
1459 |
|
|
1460 |
< |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
1460 |
> |
if( !strcmp( info->mixingRule, "standard") ){ |
1461 |
|
the_ff->initForceField( LB_MIXING_RULE ); |
1462 |
|
} |
1463 |
< |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
1463 |
> |
else if( !strcmp( info->mixingRule, "explicit") ){ |
1464 |
|
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1465 |
|
} |
1466 |
|
else{ |
1467 |
|
sprintf( painCave.errMsg, |
1468 |
|
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1469 |
< |
simnfo->mixingRule ); |
1469 |
> |
info->mixingRule ); |
1470 |
|
painCave.isFatal = 1; |
1471 |
|
simError(); |
1472 |
|
} |
1477 |
|
"Successfully intialized the mixingRule for Fortran." ); |
1478 |
|
MPIcheckPoint(); |
1479 |
|
#endif // is_mpi |
992 |
– |
} |
1480 |
|
|
994 |
– |
|
995 |
– |
void SimSetup::makeMolecules( void ){ |
996 |
– |
|
997 |
– |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
998 |
– |
molInit info; |
999 |
– |
DirectionalAtom* dAtom; |
1000 |
– |
LinkedAssign* extras; |
1001 |
– |
LinkedAssign* current_extra; |
1002 |
– |
AtomStamp* currentAtom; |
1003 |
– |
BondStamp* currentBond; |
1004 |
– |
BendStamp* currentBend; |
1005 |
– |
TorsionStamp* currentTorsion; |
1006 |
– |
|
1007 |
– |
bond_pair* theBonds; |
1008 |
– |
bend_set* theBends; |
1009 |
– |
torsion_set* theTorsions; |
1010 |
– |
|
1011 |
– |
|
1012 |
– |
//init the forceField paramters |
1013 |
– |
|
1014 |
– |
the_ff->readParams(); |
1015 |
– |
|
1016 |
– |
|
1017 |
– |
// init the atoms |
1018 |
– |
|
1019 |
– |
double ux, uy, uz, u, uSqr; |
1020 |
– |
|
1021 |
– |
atomOffset = 0; |
1022 |
– |
excludeOffset = 0; |
1023 |
– |
for(i=0; i<simnfo->n_mol; i++){ |
1024 |
– |
|
1025 |
– |
stampID = the_molecules[i].getStampID(); |
1026 |
– |
|
1027 |
– |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
1028 |
– |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
1029 |
– |
info.nBends = comp_stamps[stampID]->getNBends(); |
1030 |
– |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
1031 |
– |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
1032 |
– |
|
1033 |
– |
info.myAtoms = &the_atoms[atomOffset]; |
1034 |
– |
info.myExcludes = &the_excludes[excludeOffset]; |
1035 |
– |
info.myBonds = new Bond*[info.nBonds]; |
1036 |
– |
info.myBends = new Bend*[info.nBends]; |
1037 |
– |
info.myTorsions = new Torsion*[info.nTorsions]; |
1038 |
– |
|
1039 |
– |
theBonds = new bond_pair[info.nBonds]; |
1040 |
– |
theBends = new bend_set[info.nBends]; |
1041 |
– |
theTorsions = new torsion_set[info.nTorsions]; |
1042 |
– |
|
1043 |
– |
// make the Atoms |
1044 |
– |
|
1045 |
– |
for(j=0; j<info.nAtoms; j++){ |
1046 |
– |
|
1047 |
– |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
1048 |
– |
if( currentAtom->haveOrientation() ){ |
1049 |
– |
|
1050 |
– |
dAtom = new DirectionalAtom(j + atomOffset); |
1051 |
– |
simnfo->n_oriented++; |
1052 |
– |
info.myAtoms[j] = dAtom; |
1053 |
– |
|
1054 |
– |
ux = currentAtom->getOrntX(); |
1055 |
– |
uy = currentAtom->getOrntY(); |
1056 |
– |
uz = currentAtom->getOrntZ(); |
1057 |
– |
|
1058 |
– |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
1059 |
– |
|
1060 |
– |
u = sqrt( uSqr ); |
1061 |
– |
ux = ux / u; |
1062 |
– |
uy = uy / u; |
1063 |
– |
uz = uz / u; |
1064 |
– |
|
1065 |
– |
dAtom->setSUx( ux ); |
1066 |
– |
dAtom->setSUy( uy ); |
1067 |
– |
dAtom->setSUz( uz ); |
1068 |
– |
} |
1069 |
– |
else{ |
1070 |
– |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
1071 |
– |
} |
1072 |
– |
info.myAtoms[j]->setType( currentAtom->getType() ); |
1073 |
– |
|
1074 |
– |
#ifdef IS_MPI |
1075 |
– |
|
1076 |
– |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1077 |
– |
|
1078 |
– |
#endif // is_mpi |
1079 |
– |
} |
1080 |
– |
|
1081 |
– |
// make the bonds |
1082 |
– |
for(j=0; j<info.nBonds; j++){ |
1083 |
– |
|
1084 |
– |
currentBond = comp_stamps[stampID]->getBond( j ); |
1085 |
– |
theBonds[j].a = currentBond->getA() + atomOffset; |
1086 |
– |
theBonds[j].b = currentBond->getB() + atomOffset; |
1087 |
– |
|
1088 |
– |
exI = theBonds[j].a; |
1089 |
– |
exJ = theBonds[j].b; |
1090 |
– |
|
1091 |
– |
// exclude_I must always be the smaller of the pair |
1092 |
– |
if( exI > exJ ){ |
1093 |
– |
tempEx = exI; |
1094 |
– |
exI = exJ; |
1095 |
– |
exJ = tempEx; |
1096 |
– |
} |
1097 |
– |
#ifdef IS_MPI |
1098 |
– |
tempEx = exI; |
1099 |
– |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1100 |
– |
tempEx = exJ; |
1101 |
– |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1102 |
– |
|
1103 |
– |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1104 |
– |
#else // isn't MPI |
1105 |
– |
|
1106 |
– |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1107 |
– |
#endif //is_mpi |
1108 |
– |
} |
1109 |
– |
excludeOffset += info.nBonds; |
1110 |
– |
|
1111 |
– |
//make the bends |
1112 |
– |
for(j=0; j<info.nBends; j++){ |
1113 |
– |
|
1114 |
– |
currentBend = comp_stamps[stampID]->getBend( j ); |
1115 |
– |
theBends[j].a = currentBend->getA() + atomOffset; |
1116 |
– |
theBends[j].b = currentBend->getB() + atomOffset; |
1117 |
– |
theBends[j].c = currentBend->getC() + atomOffset; |
1118 |
– |
|
1119 |
– |
if( currentBend->haveExtras() ){ |
1120 |
– |
|
1121 |
– |
extras = currentBend->getExtras(); |
1122 |
– |
current_extra = extras; |
1123 |
– |
|
1124 |
– |
while( current_extra != NULL ){ |
1125 |
– |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1126 |
– |
|
1127 |
– |
switch( current_extra->getType() ){ |
1128 |
– |
|
1129 |
– |
case 0: |
1130 |
– |
theBends[j].ghost = |
1131 |
– |
current_extra->getInt() + atomOffset; |
1132 |
– |
theBends[j].isGhost = 1; |
1133 |
– |
break; |
1134 |
– |
|
1135 |
– |
case 1: |
1136 |
– |
theBends[j].ghost = |
1137 |
– |
(int)current_extra->getDouble() + atomOffset; |
1138 |
– |
theBends[j].isGhost = 1; |
1139 |
– |
break; |
1140 |
– |
|
1141 |
– |
default: |
1142 |
– |
sprintf( painCave.errMsg, |
1143 |
– |
"SimSetup Error: ghostVectorSource was neither a " |
1144 |
– |
"double nor an int.\n" |
1145 |
– |
"-->Bend[%d] in %s\n", |
1146 |
– |
j, comp_stamps[stampID]->getID() ); |
1147 |
– |
painCave.isFatal = 1; |
1148 |
– |
simError(); |
1149 |
– |
} |
1150 |
– |
} |
1151 |
– |
|
1152 |
– |
else{ |
1153 |
– |
|
1154 |
– |
sprintf( painCave.errMsg, |
1155 |
– |
"SimSetup Error: unhandled bend assignment:\n" |
1156 |
– |
" -->%s in Bend[%d] in %s\n", |
1157 |
– |
current_extra->getlhs(), |
1158 |
– |
j, comp_stamps[stampID]->getID() ); |
1159 |
– |
painCave.isFatal = 1; |
1160 |
– |
simError(); |
1161 |
– |
} |
1162 |
– |
|
1163 |
– |
current_extra = current_extra->getNext(); |
1164 |
– |
} |
1165 |
– |
} |
1166 |
– |
|
1167 |
– |
if( !theBends[j].isGhost ){ |
1168 |
– |
|
1169 |
– |
exI = theBends[j].a; |
1170 |
– |
exJ = theBends[j].c; |
1171 |
– |
} |
1172 |
– |
else{ |
1173 |
– |
|
1174 |
– |
exI = theBends[j].a; |
1175 |
– |
exJ = theBends[j].b; |
1176 |
– |
} |
1177 |
– |
|
1178 |
– |
// exclude_I must always be the smaller of the pair |
1179 |
– |
if( exI > exJ ){ |
1180 |
– |
tempEx = exI; |
1181 |
– |
exI = exJ; |
1182 |
– |
exJ = tempEx; |
1183 |
– |
} |
1184 |
– |
#ifdef IS_MPI |
1185 |
– |
tempEx = exI; |
1186 |
– |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1187 |
– |
tempEx = exJ; |
1188 |
– |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1189 |
– |
|
1190 |
– |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1191 |
– |
#else // isn't MPI |
1192 |
– |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1193 |
– |
#endif //is_mpi |
1194 |
– |
} |
1195 |
– |
excludeOffset += info.nBends; |
1196 |
– |
|
1197 |
– |
for(j=0; j<info.nTorsions; j++){ |
1198 |
– |
|
1199 |
– |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1200 |
– |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1201 |
– |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1202 |
– |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1203 |
– |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1204 |
– |
|
1205 |
– |
exI = theTorsions[j].a; |
1206 |
– |
exJ = theTorsions[j].d; |
1207 |
– |
|
1208 |
– |
// exclude_I must always be the smaller of the pair |
1209 |
– |
if( exI > exJ ){ |
1210 |
– |
tempEx = exI; |
1211 |
– |
exI = exJ; |
1212 |
– |
exJ = tempEx; |
1213 |
– |
} |
1214 |
– |
#ifdef IS_MPI |
1215 |
– |
tempEx = exI; |
1216 |
– |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1217 |
– |
tempEx = exJ; |
1218 |
– |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1219 |
– |
|
1220 |
– |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1221 |
– |
#else // isn't MPI |
1222 |
– |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1223 |
– |
#endif //is_mpi |
1224 |
– |
} |
1225 |
– |
excludeOffset += info.nTorsions; |
1226 |
– |
|
1227 |
– |
|
1228 |
– |
// send the arrays off to the forceField for init. |
1229 |
– |
|
1230 |
– |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1231 |
– |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1232 |
– |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1233 |
– |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1234 |
– |
|
1235 |
– |
|
1236 |
– |
the_molecules[i].initialize( info ); |
1237 |
– |
|
1238 |
– |
|
1239 |
– |
atomOffset += info.nAtoms; |
1240 |
– |
delete[] theBonds; |
1241 |
– |
delete[] theBends; |
1242 |
– |
delete[] theTorsions; |
1243 |
– |
} |
1244 |
– |
|
1245 |
– |
#ifdef IS_MPI |
1246 |
– |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1247 |
– |
MPIcheckPoint(); |
1248 |
– |
#endif // is_mpi |
1249 |
– |
|
1250 |
– |
// clean up the forcefield |
1251 |
– |
the_ff->calcRcut(); |
1252 |
– |
the_ff->cleanMe(); |
1253 |
– |
|
1481 |
|
} |
1255 |
– |
|
1256 |
– |
void SimSetup::initFromBass( void ){ |
1257 |
– |
|
1258 |
– |
int i, j, k; |
1259 |
– |
int n_cells; |
1260 |
– |
double cellx, celly, cellz; |
1261 |
– |
double temp1, temp2, temp3; |
1262 |
– |
int n_per_extra; |
1263 |
– |
int n_extra; |
1264 |
– |
int have_extra, done; |
1265 |
– |
|
1266 |
– |
temp1 = (double)tot_nmol / 4.0; |
1267 |
– |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1268 |
– |
temp3 = ceil( temp2 ); |
1269 |
– |
|
1270 |
– |
have_extra =0; |
1271 |
– |
if( temp2 < temp3 ){ // we have a non-complete lattice |
1272 |
– |
have_extra =1; |
1273 |
– |
|
1274 |
– |
n_cells = (int)temp3 - 1; |
1275 |
– |
cellx = simnfo->boxLx / temp3; |
1276 |
– |
celly = simnfo->boxLy / temp3; |
1277 |
– |
cellz = simnfo->boxLz / temp3; |
1278 |
– |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1279 |
– |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1280 |
– |
n_per_extra = (int)ceil( temp1 ); |
1281 |
– |
|
1282 |
– |
if( n_per_extra > 4){ |
1283 |
– |
sprintf( painCave.errMsg, |
1284 |
– |
"SimSetup error. There has been an error in constructing" |
1285 |
– |
" the non-complete lattice.\n" ); |
1286 |
– |
painCave.isFatal = 1; |
1287 |
– |
simError(); |
1288 |
– |
} |
1289 |
– |
} |
1290 |
– |
else{ |
1291 |
– |
n_cells = (int)temp3; |
1292 |
– |
cellx = simnfo->boxLx / temp3; |
1293 |
– |
celly = simnfo->boxLy / temp3; |
1294 |
– |
cellz = simnfo->boxLz / temp3; |
1295 |
– |
} |
1296 |
– |
|
1297 |
– |
current_mol = 0; |
1298 |
– |
current_comp_mol = 0; |
1299 |
– |
current_comp = 0; |
1300 |
– |
current_atom_ndx = 0; |
1301 |
– |
|
1302 |
– |
for( i=0; i < n_cells ; i++ ){ |
1303 |
– |
for( j=0; j < n_cells; j++ ){ |
1304 |
– |
for( k=0; k < n_cells; k++ ){ |
1305 |
– |
|
1306 |
– |
makeElement( i * cellx, |
1307 |
– |
j * celly, |
1308 |
– |
k * cellz ); |
1309 |
– |
|
1310 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1311 |
– |
j * celly + 0.5 * celly, |
1312 |
– |
k * cellz ); |
1313 |
– |
|
1314 |
– |
makeElement( i * cellx, |
1315 |
– |
j * celly + 0.5 * celly, |
1316 |
– |
k * cellz + 0.5 * cellz ); |
1317 |
– |
|
1318 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1319 |
– |
j * celly, |
1320 |
– |
k * cellz + 0.5 * cellz ); |
1321 |
– |
} |
1322 |
– |
} |
1323 |
– |
} |
1324 |
– |
|
1325 |
– |
if( have_extra ){ |
1326 |
– |
done = 0; |
1327 |
– |
|
1328 |
– |
int start_ndx; |
1329 |
– |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1330 |
– |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1331 |
– |
|
1332 |
– |
if( i < n_cells ){ |
1333 |
– |
|
1334 |
– |
if( j < n_cells ){ |
1335 |
– |
start_ndx = n_cells; |
1336 |
– |
} |
1337 |
– |
else start_ndx = 0; |
1338 |
– |
} |
1339 |
– |
else start_ndx = 0; |
1340 |
– |
|
1341 |
– |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1342 |
– |
|
1343 |
– |
makeElement( i * cellx, |
1344 |
– |
j * celly, |
1345 |
– |
k * cellz ); |
1346 |
– |
done = ( current_mol >= tot_nmol ); |
1347 |
– |
|
1348 |
– |
if( !done && n_per_extra > 1 ){ |
1349 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1350 |
– |
j * celly + 0.5 * celly, |
1351 |
– |
k * cellz ); |
1352 |
– |
done = ( current_mol >= tot_nmol ); |
1353 |
– |
} |
1354 |
– |
|
1355 |
– |
if( !done && n_per_extra > 2){ |
1356 |
– |
makeElement( i * cellx, |
1357 |
– |
j * celly + 0.5 * celly, |
1358 |
– |
k * cellz + 0.5 * cellz ); |
1359 |
– |
done = ( current_mol >= tot_nmol ); |
1360 |
– |
} |
1361 |
– |
|
1362 |
– |
if( !done && n_per_extra > 3){ |
1363 |
– |
makeElement( i * cellx + 0.5 * cellx, |
1364 |
– |
j * celly, |
1365 |
– |
k * cellz + 0.5 * cellz ); |
1366 |
– |
done = ( current_mol >= tot_nmol ); |
1367 |
– |
} |
1368 |
– |
} |
1369 |
– |
} |
1370 |
– |
} |
1371 |
– |
} |
1372 |
– |
|
1373 |
– |
|
1374 |
– |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1375 |
– |
simnfo->atoms[i]->set_vx( 0.0 ); |
1376 |
– |
simnfo->atoms[i]->set_vy( 0.0 ); |
1377 |
– |
simnfo->atoms[i]->set_vz( 0.0 ); |
1378 |
– |
} |
1379 |
– |
} |
1380 |
– |
|
1381 |
– |
void SimSetup::makeElement( double x, double y, double z ){ |
1382 |
– |
|
1383 |
– |
int k; |
1384 |
– |
AtomStamp* current_atom; |
1385 |
– |
DirectionalAtom* dAtom; |
1386 |
– |
double rotMat[3][3]; |
1387 |
– |
|
1388 |
– |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1389 |
– |
|
1390 |
– |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1391 |
– |
if( !current_atom->havePosition() ){ |
1392 |
– |
sprintf( painCave.errMsg, |
1393 |
– |
"SimSetup:initFromBass error.\n" |
1394 |
– |
"\tComponent %s, atom %s does not have a position specified.\n" |
1395 |
– |
"\tThe initialization routine is unable to give a start" |
1396 |
– |
" position.\n", |
1397 |
– |
comp_stamps[current_comp]->getID(), |
1398 |
– |
current_atom->getType() ); |
1399 |
– |
painCave.isFatal = 1; |
1400 |
– |
simError(); |
1401 |
– |
} |
1402 |
– |
|
1403 |
– |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1404 |
– |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1405 |
– |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1406 |
– |
|
1407 |
– |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1408 |
– |
|
1409 |
– |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1410 |
– |
|
1411 |
– |
rotMat[0][0] = 1.0; |
1412 |
– |
rotMat[0][1] = 0.0; |
1413 |
– |
rotMat[0][2] = 0.0; |
1414 |
– |
|
1415 |
– |
rotMat[1][0] = 0.0; |
1416 |
– |
rotMat[1][1] = 1.0; |
1417 |
– |
rotMat[1][2] = 0.0; |
1418 |
– |
|
1419 |
– |
rotMat[2][0] = 0.0; |
1420 |
– |
rotMat[2][1] = 0.0; |
1421 |
– |
rotMat[2][2] = 1.0; |
1422 |
– |
|
1423 |
– |
dAtom->setA( rotMat ); |
1424 |
– |
} |
1425 |
– |
|
1426 |
– |
current_atom_ndx++; |
1427 |
– |
} |
1428 |
– |
|
1429 |
– |
current_mol++; |
1430 |
– |
current_comp_mol++; |
1431 |
– |
|
1432 |
– |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1433 |
– |
|
1434 |
– |
current_comp_mol = 0; |
1435 |
– |
current_comp++; |
1436 |
– |
} |
1437 |
– |
} |