# | Line 1 | Line 1 | |
---|---|---|
1 | + | #include <algorithm> |
2 | #include <cstdlib> | |
3 | #include <iostream> | |
4 | #include <cmath> | |
5 | + | #include <string> |
6 | ||
7 | #include "SimSetup.hpp" | |
8 | #include "parse_me.h" | |
# | Line 14 | Line 16 | |
16 | ||
17 | // some defines for ensemble and Forcefield cases | |
18 | ||
19 | < | #define NVE_ENS 0 |
20 | < | #define NVT_ENS 1 |
21 | < | #define NPT_ENS 2 |
19 | > | #define NVE_ENS 0 |
20 | > | #define NVT_ENS 1 |
21 | > | #define NPTi_ENS 2 |
22 | > | #define NPTf_ENS 3 |
23 | > | #define NPTim_ENS 4 |
24 | > | #define NPTfm_ENS 5 |
25 | ||
26 | #define FF_DUFF 0 | |
27 | #define FF_LJ 1 | |
28 | + | #define FF_EAM 2 |
29 | ||
30 | + | using namespace std; |
31 | ||
32 | SimSetup::SimSetup(){ | |
33 | + | |
34 | + | isInfoArray = 0; |
35 | + | nInfo = 1; |
36 | + | |
37 | stamps = new MakeStamps(); | |
38 | globals = new Globals(); | |
39 | ||
40 | + | |
41 | #ifdef IS_MPI | |
42 | strcpy( checkPointMsg, "SimSetup creation successful" ); | |
43 | MPIcheckPoint(); | |
# | Line 37 | Line 49 | SimSetup::~SimSetup(){ | |
49 | delete globals; | |
50 | } | |
51 | ||
52 | + | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
53 | + | info = the_info; |
54 | + | nInfo = theNinfo; |
55 | + | isInfoArray = 1; |
56 | + | } |
57 | + | |
58 | + | |
59 | void SimSetup::parseFile( char* fileName ){ | |
60 | ||
61 | #ifdef IS_MPI | |
# | Line 72 | Line 91 | void SimSetup::receiveParse(void){ | |
91 | ||
92 | #endif // is_mpi | |
93 | ||
94 | < | void SimSetup::createSim( void ){ |
94 | > | void SimSetup::createSim(void){ |
95 | ||
77 | – | MakeStamps *the_stamps; |
78 | – | Globals* the_globals; |
96 | int i, j, k, globalAtomIndex; | |
97 | ||
98 | < | int ensembleCase; |
82 | < | int ffCase; |
98 | > | // gather all of the information from the Bass file |
99 | ||
100 | < | ensembleCase = -1; |
85 | < | ffCase = -1; |
100 | > | gatherInfo(); |
101 | ||
102 | < | // get the stamps and globals; |
88 | < | the_stamps = stamps; |
89 | < | the_globals = globals; |
102 | > | // creation of complex system objects |
103 | ||
104 | < | // set the easy ones first |
92 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
93 | < | simnfo->dt = the_globals->getDt(); |
94 | < | simnfo->run_time = the_globals->getRunTime(); |
104 | > | sysObjectsCreation(); |
105 | ||
106 | < | // get the ones we know are there, yet still may need some work. |
107 | < | n_components = the_globals->getNComponents(); |
108 | < | strcpy( force_field, the_globals->getForceField() ); |
106 | > | // check on the post processing info |
107 | > | |
108 | > | finalInfoCheck(); |
109 | > | |
110 | > | // initialize the system coordinates |
111 | > | |
112 | > | if( !isInfoArray ) initSystemCoords(); |
113 | > | |
114 | > | // make the output filenames |
115 | > | |
116 | > | makeOutNames(); |
117 | > | |
118 | > | // make the integrator |
119 | > | |
120 | > | makeIntegrator(); |
121 | > | |
122 | > | #ifdef IS_MPI |
123 | > | mpiSim->mpiRefresh(); |
124 | > | #endif |
125 | > | |
126 | > | // initialize the Fortran |
127 | > | |
128 | > | initFortran(); |
129 | > | |
130 | > | |
131 | > | |
132 | > | } |
133 | > | |
134 | > | |
135 | > | void SimSetup::makeMolecules( void ){ |
136 | > | |
137 | > | int k,l; |
138 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
139 | > | molInit molInfo; |
140 | > | DirectionalAtom* dAtom; |
141 | > | LinkedAssign* extras; |
142 | > | LinkedAssign* current_extra; |
143 | > | AtomStamp* currentAtom; |
144 | > | BondStamp* currentBond; |
145 | > | BendStamp* currentBend; |
146 | > | TorsionStamp* currentTorsion; |
147 | > | |
148 | > | bond_pair* theBonds; |
149 | > | bend_set* theBends; |
150 | > | torsion_set* theTorsions; |
151 | > | |
152 | > | |
153 | > | //init the forceField paramters |
154 | > | |
155 | > | the_ff->readParams(); |
156 | > | |
157 | > | |
158 | > | // init the atoms |
159 | > | |
160 | > | double ux, uy, uz, u, uSqr; |
161 | > | |
162 | > | for(k=0; k<nInfo; k++){ |
163 | > | |
164 | > | the_ff->setSimInfo( &(info[k]) ); |
165 | > | |
166 | > | atomOffset = 0; |
167 | > | excludeOffset = 0; |
168 | > | for(i=0; i<info[k].n_mol; i++){ |
169 | > | |
170 | > | stampID = info[k].molecules[i].getStampID(); |
171 | > | |
172 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
173 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
174 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
175 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
176 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
177 | > | |
178 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
179 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
180 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
181 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
182 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
183 | > | |
184 | > | theBonds = new bond_pair[molInfo.nBonds]; |
185 | > | theBends = new bend_set[molInfo.nBends]; |
186 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
187 | > | |
188 | > | // make the Atoms |
189 | > | |
190 | > | for(j=0; j<molInfo.nAtoms; j++){ |
191 | > | |
192 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
193 | > | if( currentAtom->haveOrientation() ){ |
194 | > | |
195 | > | dAtom = new DirectionalAtom( (j + atomOffset), |
196 | > | info[k].getConfiguration() ); |
197 | > | info[k].n_oriented++; |
198 | > | molInfo.myAtoms[j] = dAtom; |
199 | > | |
200 | > | ux = currentAtom->getOrntX(); |
201 | > | uy = currentAtom->getOrntY(); |
202 | > | uz = currentAtom->getOrntZ(); |
203 | > | |
204 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
205 | > | |
206 | > | u = sqrt( uSqr ); |
207 | > | ux = ux / u; |
208 | > | uy = uy / u; |
209 | > | uz = uz / u; |
210 | > | |
211 | > | dAtom->setSUx( ux ); |
212 | > | dAtom->setSUy( uy ); |
213 | > | dAtom->setSUz( uz ); |
214 | > | } |
215 | > | else{ |
216 | > | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
217 | > | info[k].getConfiguration() ); |
218 | > | } |
219 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
220 | > | |
221 | > | #ifdef IS_MPI |
222 | > | |
223 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
224 | > | |
225 | > | #endif // is_mpi |
226 | > | } |
227 | > | |
228 | > | // make the bonds |
229 | > | for(j=0; j<molInfo.nBonds; j++){ |
230 | > | |
231 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
232 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
233 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
234 | > | |
235 | > | exI = theBonds[j].a; |
236 | > | exJ = theBonds[j].b; |
237 | > | |
238 | > | // exclude_I must always be the smaller of the pair |
239 | > | if( exI > exJ ){ |
240 | > | tempEx = exI; |
241 | > | exI = exJ; |
242 | > | exJ = tempEx; |
243 | > | } |
244 | > | #ifdef IS_MPI |
245 | > | tempEx = exI; |
246 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
247 | > | tempEx = exJ; |
248 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
249 | > | |
250 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
251 | > | #else // isn't MPI |
252 | > | |
253 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
254 | > | #endif //is_mpi |
255 | > | } |
256 | > | excludeOffset += molInfo.nBonds; |
257 | > | |
258 | > | //make the bends |
259 | > | for(j=0; j<molInfo.nBends; j++){ |
260 | > | |
261 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
262 | > | theBends[j].a = currentBend->getA() + atomOffset; |
263 | > | theBends[j].b = currentBend->getB() + atomOffset; |
264 | > | theBends[j].c = currentBend->getC() + atomOffset; |
265 | > | |
266 | > | if( currentBend->haveExtras() ){ |
267 | > | |
268 | > | extras = currentBend->getExtras(); |
269 | > | current_extra = extras; |
270 | > | |
271 | > | while( current_extra != NULL ){ |
272 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
273 | > | |
274 | > | switch( current_extra->getType() ){ |
275 | > | |
276 | > | case 0: |
277 | > | theBends[j].ghost = |
278 | > | current_extra->getInt() + atomOffset; |
279 | > | theBends[j].isGhost = 1; |
280 | > | break; |
281 | > | |
282 | > | case 1: |
283 | > | theBends[j].ghost = |
284 | > | (int)current_extra->getDouble() + atomOffset; |
285 | > | theBends[j].isGhost = 1; |
286 | > | break; |
287 | > | |
288 | > | default: |
289 | > | sprintf( painCave.errMsg, |
290 | > | "SimSetup Error: ghostVectorSource was neither a " |
291 | > | "double nor an int.\n" |
292 | > | "-->Bend[%d] in %s\n", |
293 | > | j, comp_stamps[stampID]->getID() ); |
294 | > | painCave.isFatal = 1; |
295 | > | simError(); |
296 | > | } |
297 | > | } |
298 | > | |
299 | > | else{ |
300 | > | |
301 | > | sprintf( painCave.errMsg, |
302 | > | "SimSetup Error: unhandled bend assignment:\n" |
303 | > | " -->%s in Bend[%d] in %s\n", |
304 | > | current_extra->getlhs(), |
305 | > | j, comp_stamps[stampID]->getID() ); |
306 | > | painCave.isFatal = 1; |
307 | > | simError(); |
308 | > | } |
309 | > | |
310 | > | current_extra = current_extra->getNext(); |
311 | > | } |
312 | > | } |
313 | > | |
314 | > | if( !theBends[j].isGhost ){ |
315 | > | |
316 | > | exI = theBends[j].a; |
317 | > | exJ = theBends[j].c; |
318 | > | } |
319 | > | else{ |
320 | > | |
321 | > | exI = theBends[j].a; |
322 | > | exJ = theBends[j].b; |
323 | > | } |
324 | > | |
325 | > | // exclude_I must always be the smaller of the pair |
326 | > | if( exI > exJ ){ |
327 | > | tempEx = exI; |
328 | > | exI = exJ; |
329 | > | exJ = tempEx; |
330 | > | } |
331 | > | #ifdef IS_MPI |
332 | > | tempEx = exI; |
333 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
334 | > | tempEx = exJ; |
335 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
336 | > | |
337 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
338 | > | #else // isn't MPI |
339 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
340 | > | #endif //is_mpi |
341 | > | } |
342 | > | excludeOffset += molInfo.nBends; |
343 | > | |
344 | > | for(j=0; j<molInfo.nTorsions; j++){ |
345 | > | |
346 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
347 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
348 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
349 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
350 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
351 | > | |
352 | > | exI = theTorsions[j].a; |
353 | > | exJ = theTorsions[j].d; |
354 | > | |
355 | > | // exclude_I must always be the smaller of the pair |
356 | > | if( exI > exJ ){ |
357 | > | tempEx = exI; |
358 | > | exI = exJ; |
359 | > | exJ = tempEx; |
360 | > | } |
361 | > | #ifdef IS_MPI |
362 | > | tempEx = exI; |
363 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
364 | > | tempEx = exJ; |
365 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
366 | > | |
367 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
368 | > | #else // isn't MPI |
369 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
370 | > | #endif //is_mpi |
371 | > | } |
372 | > | excludeOffset += molInfo.nTorsions; |
373 | > | |
374 | > | |
375 | > | // send the arrays off to the forceField for init. |
376 | > | |
377 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
378 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
379 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
380 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
381 | > | |
382 | > | |
383 | > | info[k].molecules[i].initialize( molInfo ); |
384 | ||
385 | + | |
386 | + | atomOffset += molInfo.nAtoms; |
387 | + | delete[] theBonds; |
388 | + | delete[] theBends; |
389 | + | delete[] theTorsions; |
390 | + | } |
391 | + | } |
392 | + | |
393 | + | #ifdef IS_MPI |
394 | + | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
395 | + | MPIcheckPoint(); |
396 | + | #endif // is_mpi |
397 | + | |
398 | + | // clean up the forcefield |
399 | + | |
400 | + | the_ff->calcRcut(); |
401 | + | the_ff->cleanMe(); |
402 | + | |
403 | + | } |
404 | + | |
405 | + | void SimSetup::initFromBass( void ){ |
406 | + | |
407 | + | int i, j, k; |
408 | + | int n_cells; |
409 | + | double cellx, celly, cellz; |
410 | + | double temp1, temp2, temp3; |
411 | + | int n_per_extra; |
412 | + | int n_extra; |
413 | + | int have_extra, done; |
414 | + | |
415 | + | double vel[3]; |
416 | + | vel[0] = 0.0; |
417 | + | vel[1] = 0.0; |
418 | + | vel[2] = 0.0; |
419 | + | |
420 | + | temp1 = (double)tot_nmol / 4.0; |
421 | + | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
422 | + | temp3 = ceil( temp2 ); |
423 | + | |
424 | + | have_extra =0; |
425 | + | if( temp2 < temp3 ){ // we have a non-complete lattice |
426 | + | have_extra =1; |
427 | + | |
428 | + | n_cells = (int)temp3 - 1; |
429 | + | cellx = info[0].boxL[0] / temp3; |
430 | + | celly = info[0].boxL[1] / temp3; |
431 | + | cellz = info[0].boxL[2] / temp3; |
432 | + | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
433 | + | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
434 | + | n_per_extra = (int)ceil( temp1 ); |
435 | + | |
436 | + | if( n_per_extra > 4){ |
437 | + | sprintf( painCave.errMsg, |
438 | + | "SimSetup error. There has been an error in constructing" |
439 | + | " the non-complete lattice.\n" ); |
440 | + | painCave.isFatal = 1; |
441 | + | simError(); |
442 | + | } |
443 | + | } |
444 | + | else{ |
445 | + | n_cells = (int)temp3; |
446 | + | cellx = info[0].boxL[0] / temp3; |
447 | + | celly = info[0].boxL[1] / temp3; |
448 | + | cellz = info[0].boxL[2] / temp3; |
449 | + | } |
450 | + | |
451 | + | current_mol = 0; |
452 | + | current_comp_mol = 0; |
453 | + | current_comp = 0; |
454 | + | current_atom_ndx = 0; |
455 | + | |
456 | + | for( i=0; i < n_cells ; i++ ){ |
457 | + | for( j=0; j < n_cells; j++ ){ |
458 | + | for( k=0; k < n_cells; k++ ){ |
459 | + | |
460 | + | makeElement( i * cellx, |
461 | + | j * celly, |
462 | + | k * cellz ); |
463 | + | |
464 | + | makeElement( i * cellx + 0.5 * cellx, |
465 | + | j * celly + 0.5 * celly, |
466 | + | k * cellz ); |
467 | + | |
468 | + | makeElement( i * cellx, |
469 | + | j * celly + 0.5 * celly, |
470 | + | k * cellz + 0.5 * cellz ); |
471 | + | |
472 | + | makeElement( i * cellx + 0.5 * cellx, |
473 | + | j * celly, |
474 | + | k * cellz + 0.5 * cellz ); |
475 | + | } |
476 | + | } |
477 | + | } |
478 | + | |
479 | + | if( have_extra ){ |
480 | + | done = 0; |
481 | + | |
482 | + | int start_ndx; |
483 | + | for( i=0; i < (n_cells+1) && !done; i++ ){ |
484 | + | for( j=0; j < (n_cells+1) && !done; j++ ){ |
485 | + | |
486 | + | if( i < n_cells ){ |
487 | + | |
488 | + | if( j < n_cells ){ |
489 | + | start_ndx = n_cells; |
490 | + | } |
491 | + | else start_ndx = 0; |
492 | + | } |
493 | + | else start_ndx = 0; |
494 | + | |
495 | + | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
496 | + | |
497 | + | makeElement( i * cellx, |
498 | + | j * celly, |
499 | + | k * cellz ); |
500 | + | done = ( current_mol >= tot_nmol ); |
501 | + | |
502 | + | if( !done && n_per_extra > 1 ){ |
503 | + | makeElement( i * cellx + 0.5 * cellx, |
504 | + | j * celly + 0.5 * celly, |
505 | + | k * cellz ); |
506 | + | done = ( current_mol >= tot_nmol ); |
507 | + | } |
508 | + | |
509 | + | if( !done && n_per_extra > 2){ |
510 | + | makeElement( i * cellx, |
511 | + | j * celly + 0.5 * celly, |
512 | + | k * cellz + 0.5 * cellz ); |
513 | + | done = ( current_mol >= tot_nmol ); |
514 | + | } |
515 | + | |
516 | + | if( !done && n_per_extra > 3){ |
517 | + | makeElement( i * cellx + 0.5 * cellx, |
518 | + | j * celly, |
519 | + | k * cellz + 0.5 * cellz ); |
520 | + | done = ( current_mol >= tot_nmol ); |
521 | + | } |
522 | + | } |
523 | + | } |
524 | + | } |
525 | + | } |
526 | + | |
527 | + | for( i=0; i<info[0].n_atoms; i++ ){ |
528 | + | info[0].atoms[i]->setVel( vel ); |
529 | + | } |
530 | + | } |
531 | + | |
532 | + | void SimSetup::makeElement( double x, double y, double z ){ |
533 | + | |
534 | + | int k; |
535 | + | AtomStamp* current_atom; |
536 | + | DirectionalAtom* dAtom; |
537 | + | double rotMat[3][3]; |
538 | + | double pos[3]; |
539 | + | |
540 | + | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
541 | + | |
542 | + | current_atom = comp_stamps[current_comp]->getAtom( k ); |
543 | + | if( !current_atom->havePosition() ){ |
544 | + | sprintf( painCave.errMsg, |
545 | + | "SimSetup:initFromBass error.\n" |
546 | + | "\tComponent %s, atom %s does not have a position specified.\n" |
547 | + | "\tThe initialization routine is unable to give a start" |
548 | + | " position.\n", |
549 | + | comp_stamps[current_comp]->getID(), |
550 | + | current_atom->getType() ); |
551 | + | painCave.isFatal = 1; |
552 | + | simError(); |
553 | + | } |
554 | + | |
555 | + | pos[0] = x + current_atom->getPosX(); |
556 | + | pos[1] = y + current_atom->getPosY(); |
557 | + | pos[2] = z + current_atom->getPosZ(); |
558 | + | |
559 | + | info[0].atoms[current_atom_ndx]->setPos( pos ); |
560 | + | |
561 | + | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
562 | + | |
563 | + | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
564 | + | |
565 | + | rotMat[0][0] = 1.0; |
566 | + | rotMat[0][1] = 0.0; |
567 | + | rotMat[0][2] = 0.0; |
568 | + | |
569 | + | rotMat[1][0] = 0.0; |
570 | + | rotMat[1][1] = 1.0; |
571 | + | rotMat[1][2] = 0.0; |
572 | + | |
573 | + | rotMat[2][0] = 0.0; |
574 | + | rotMat[2][1] = 0.0; |
575 | + | rotMat[2][2] = 1.0; |
576 | + | |
577 | + | dAtom->setA( rotMat ); |
578 | + | } |
579 | + | |
580 | + | current_atom_ndx++; |
581 | + | } |
582 | + | |
583 | + | current_mol++; |
584 | + | current_comp_mol++; |
585 | + | |
586 | + | if( current_comp_mol >= components_nmol[current_comp] ){ |
587 | + | |
588 | + | current_comp_mol = 0; |
589 | + | current_comp++; |
590 | + | } |
591 | + | } |
592 | + | |
593 | + | |
594 | + | void SimSetup::gatherInfo( void ){ |
595 | + | int i,j,k; |
596 | + | |
597 | + | ensembleCase = -1; |
598 | + | ffCase = -1; |
599 | + | |
600 | + | // set the easy ones first |
601 | + | |
602 | + | for( i=0; i<nInfo; i++){ |
603 | + | info[i].target_temp = globals->getTargetTemp(); |
604 | + | info[i].dt = globals->getDt(); |
605 | + | info[i].run_time = globals->getRunTime(); |
606 | + | } |
607 | + | n_components = globals->getNComponents(); |
608 | + | |
609 | + | |
610 | + | // get the forceField |
611 | + | |
612 | + | strcpy( force_field, globals->getForceField() ); |
613 | + | |
614 | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; | |
615 | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; | |
616 | + | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
617 | else{ | |
618 | sprintf( painCave.errMsg, | |
619 | "SimSetup Error. Unrecognized force field -> %s\n", | |
# | Line 107 | Line 622 | void SimSetup::createSim( void ){ | |
622 | simError(); | |
623 | } | |
624 | ||
625 | < | // get the ensemble: |
111 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
625 | > | // get the ensemble |
626 | ||
627 | + | strcpy( ensemble, globals->getEnsemble() ); |
628 | + | |
629 | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; | |
630 | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; | |
631 | < | else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS; |
631 | > | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
632 | > | ensembleCase = NPTi_ENS; |
633 | > | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
634 | > | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
635 | > | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
636 | else{ | |
637 | sprintf( painCave.errMsg, | |
638 | "SimSetup Warning. Unrecognized Ensemble -> %s, " | |
# | Line 123 | Line 643 | void SimSetup::createSim( void ){ | |
643 | strcpy( ensemble, "NVE" ); | |
644 | ensembleCase = NVE_ENS; | |
645 | } | |
646 | < | strcpy( simnfo->ensemble, ensemble ); |
646 | > | |
647 | > | for(i=0; i<nInfo; i++){ |
648 | > | |
649 | > | strcpy( info[i].ensemble, ensemble ); |
650 | ||
651 | + | // get the mixing rule |
652 | ||
653 | < | // if( !strcasecmp( ensemble, "NPT" ) ) { |
654 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
131 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
132 | < | // if (the_globals->haveTargetPressure()) |
133 | < | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
134 | < | // else { |
135 | < | // sprintf( painCave.errMsg, |
136 | < | // "SimSetup error: If you use the constant pressure\n" |
137 | < | // " ensemble, you must set targetPressure.\n" |
138 | < | // " This was found in the BASS file.\n"); |
139 | < | // painCave.isFatal = 1; |
140 | < | // simError(); |
141 | < | // } |
142 | < | |
143 | < | // if (the_globals->haveTauThermostat()) |
144 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
145 | < | // else if (the_globals->haveQmass()) |
146 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
147 | < | // else { |
148 | < | // sprintf( painCave.errMsg, |
149 | < | // "SimSetup error: If you use one of the constant temperature\n" |
150 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
151 | < | // " Neither of these was found in the BASS file.\n"); |
152 | < | // painCave.isFatal = 1; |
153 | < | // simError(); |
154 | < | // } |
155 | < | |
156 | < | // if (the_globals->haveTauBarostat()) |
157 | < | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
158 | < | // else { |
159 | < | // sprintf( painCave.errMsg, |
160 | < | // "SimSetup error: If you use the constant pressure\n" |
161 | < | // " ensemble, you must set tauBarostat.\n" |
162 | < | // " This was found in the BASS file.\n"); |
163 | < | // painCave.isFatal = 1; |
164 | < | // simError(); |
165 | < | // } |
166 | < | |
167 | < | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
168 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
169 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
170 | < | |
171 | < | // if (the_globals->haveTauThermostat()) |
172 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
173 | < | // else if (the_globals->haveQmass()) |
174 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
175 | < | // else { |
176 | < | // sprintf( painCave.errMsg, |
177 | < | // "SimSetup error: If you use one of the constant temperature\n" |
178 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
179 | < | // " Neither of these was found in the BASS file.\n"); |
180 | < | // painCave.isFatal = 1; |
181 | < | // simError(); |
182 | < | // } |
183 | < | |
184 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
185 | < | simnfo->usePBC = the_globals->getPBC(); |
186 | < | |
187 | < | int usesDipoles = 0; |
188 | < | switch( ffCase ){ |
189 | < | |
190 | < | case FF_DUFF: |
191 | < | the_ff = new DUFF(); |
192 | < | usesDipoles = 1; |
193 | < | break; |
194 | < | |
195 | < | case FF_LJ: |
196 | < | the_ff = new LJFF(); |
197 | < | break; |
198 | < | |
199 | < | default: |
200 | < | sprintf( painCave.errMsg, |
201 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
202 | < | painCave.isFatal = 1; |
203 | < | simError(); |
653 | > | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
654 | > | info[i].usePBC = globals->getPBC(); |
655 | } | |
656 | < | |
206 | < | #ifdef IS_MPI |
207 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
208 | < | MPIcheckPoint(); |
209 | < | #endif // is_mpi |
210 | < | |
656 | > | |
657 | // get the components and calculate the tot_nMol and indvidual n_mol | |
658 | < | the_components = the_globals->getComponents(); |
658 | > | |
659 | > | the_components = globals->getComponents(); |
660 | components_nmol = new int[n_components]; | |
214 | – | comp_stamps = new MoleculeStamp*[n_components]; |
661 | ||
662 | < | if( !the_globals->haveNMol() ){ |
662 | > | |
663 | > | if( !globals->haveNMol() ){ |
664 | // we don't have the total number of molecules, so we assume it is | |
665 | // given in each component | |
666 | ||
# | Line 242 | Line 689 | void SimSetup::createSim( void ){ | |
689 | " Please give nMol in the components.\n" ); | |
690 | painCave.isFatal = 1; | |
691 | simError(); | |
245 | – | |
246 | – | |
247 | – | // tot_nmol = the_globals->getNMol(); |
248 | – | |
249 | – | // //we have the total number of molecules, now we check for molfractions |
250 | – | // for( i=0; i<n_components; i++ ){ |
251 | – | |
252 | – | // if( !the_components[i]->haveMolFraction() ){ |
253 | – | |
254 | – | // if( !the_components[i]->haveNMol() ){ |
255 | – | // //we have a problem |
256 | – | // std::cerr << "SimSetup error. Neither molFraction nor " |
257 | – | // << " nMol was given in component |
258 | – | |
692 | } | |
693 | ||
694 | < | #ifdef IS_MPI |
262 | < | strcpy( checkPointMsg, "Have the number of components" ); |
263 | < | MPIcheckPoint(); |
264 | < | #endif // is_mpi |
265 | < | |
266 | < | // make an array of molecule stamps that match the components used. |
267 | < | // also extract the used stamps out into a separate linked list |
268 | < | |
269 | < | simnfo->nComponents = n_components; |
270 | < | simnfo->componentsNmol = components_nmol; |
271 | < | simnfo->compStamps = comp_stamps; |
272 | < | simnfo->headStamp = new LinkedMolStamp(); |
273 | < | |
274 | < | char* id; |
275 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
276 | < | LinkedMolStamp* currentStamp = NULL; |
277 | < | for( i=0; i<n_components; i++ ){ |
278 | < | |
279 | < | id = the_components[i]->getType(); |
280 | < | comp_stamps[i] = NULL; |
281 | < | |
282 | < | // check to make sure the component isn't already in the list |
283 | < | |
284 | < | comp_stamps[i] = headStamp->match( id ); |
285 | < | if( comp_stamps[i] == NULL ){ |
286 | < | |
287 | < | // extract the component from the list; |
288 | < | |
289 | < | currentStamp = the_stamps->extractMolStamp( id ); |
290 | < | if( currentStamp == NULL ){ |
291 | < | sprintf( painCave.errMsg, |
292 | < | "SimSetup error: Component \"%s\" was not found in the " |
293 | < | "list of declared molecules\n", |
294 | < | id ); |
295 | < | painCave.isFatal = 1; |
296 | < | simError(); |
297 | < | } |
298 | < | |
299 | < | headStamp->add( currentStamp ); |
300 | < | comp_stamps[i] = headStamp->match( id ); |
301 | < | } |
302 | < | } |
303 | < | |
304 | < | #ifdef IS_MPI |
305 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
306 | < | MPIcheckPoint(); |
307 | < | #endif // is_mpi |
308 | < | |
309 | < | |
310 | < | |
311 | < | |
312 | < | // caclulate the number of atoms, bonds, bends and torsions |
313 | < | |
314 | < | tot_atoms = 0; |
315 | < | tot_bonds = 0; |
316 | < | tot_bends = 0; |
317 | < | tot_torsions = 0; |
318 | < | for( i=0; i<n_components; i++ ){ |
319 | < | |
320 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
321 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
322 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
323 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
324 | < | } |
325 | < | |
326 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
327 | < | |
328 | < | simnfo->n_atoms = tot_atoms; |
329 | < | simnfo->n_bonds = tot_bonds; |
330 | < | simnfo->n_bends = tot_bends; |
331 | < | simnfo->n_torsions = tot_torsions; |
332 | < | simnfo->n_SRI = tot_SRI; |
333 | < | simnfo->n_mol = tot_nmol; |
334 | < | |
335 | < | simnfo->molMembershipArray = new int[tot_atoms]; |
336 | < | |
337 | < | #ifdef IS_MPI |
338 | < | |
339 | < | // divide the molecules among processors here. |
340 | < | |
341 | < | mpiSim = new mpiSimulation( simnfo ); |
342 | < | |
343 | < | globalIndex = mpiSim->divideLabor(); |
344 | < | |
345 | < | // set up the local variables |
346 | < | |
347 | < | int localMol, allMol; |
348 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
349 | < | |
350 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
351 | < | int* molCompType = mpiSim->getMolComponentType(); |
352 | < | |
353 | < | allMol = 0; |
354 | < | localMol = 0; |
355 | < | local_atoms = 0; |
356 | < | local_bonds = 0; |
357 | < | local_bends = 0; |
358 | < | local_torsions = 0; |
359 | < | globalAtomIndex = 0; |
360 | < | |
361 | < | |
362 | < | for( i=0; i<n_components; i++ ){ |
363 | < | |
364 | < | for( j=0; j<components_nmol[i]; j++ ){ |
365 | < | |
366 | < | if( mol2proc[allMol] == worldRank ){ |
367 | < | |
368 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
369 | < | local_bonds += comp_stamps[i]->getNBonds(); |
370 | < | local_bends += comp_stamps[i]->getNBends(); |
371 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
372 | < | localMol++; |
373 | < | } |
374 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
375 | < | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
376 | < | globalAtomIndex++; |
377 | < | } |
378 | < | |
379 | < | allMol++; |
380 | < | } |
381 | < | } |
382 | < | local_SRI = local_bonds + local_bends + local_torsions; |
383 | < | |
384 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 | < | |
386 | < | if( local_atoms != simnfo->n_atoms ){ |
387 | < | sprintf( painCave.errMsg, |
388 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
389 | < | " localAtom (%d) are not equal.\n", |
390 | < | simnfo->n_atoms, |
391 | < | local_atoms ); |
392 | < | painCave.isFatal = 1; |
393 | < | simError(); |
394 | < | } |
395 | < | |
396 | < | simnfo->n_bonds = local_bonds; |
397 | < | simnfo->n_bends = local_bends; |
398 | < | simnfo->n_torsions = local_torsions; |
399 | < | simnfo->n_SRI = local_SRI; |
400 | < | simnfo->n_mol = localMol; |
401 | < | |
402 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
403 | < | MPIcheckPoint(); |
404 | < | |
405 | < | |
406 | < | #endif // is_mpi |
407 | < | |
408 | < | |
409 | < | // create the atom and short range interaction arrays |
410 | < | |
411 | < | Atom::createArrays(simnfo->n_atoms); |
412 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
413 | < | the_molecules = new Molecule[simnfo->n_mol]; |
414 | < | int molIndex; |
415 | < | |
416 | < | // initialize the molecule's stampID's |
417 | < | |
418 | < | #ifdef IS_MPI |
694 | > | // set the status, sample, and thermal kick times |
695 | ||
696 | + | for(i=0; i<nInfo; i++){ |
697 | ||
698 | < | molIndex = 0; |
699 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
700 | < | |
701 | < | if(mol2proc[i] == worldRank ){ |
425 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
426 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
427 | < | the_molecules[molIndex].setGlobalIndex( i ); |
428 | < | molIndex++; |
698 | > | if( globals->haveSampleTime() ){ |
699 | > | info[i].sampleTime = globals->getSampleTime(); |
700 | > | info[i].statusTime = info[i].sampleTime; |
701 | > | info[i].thermalTime = info[i].sampleTime; |
702 | } | |
430 | – | } |
431 | – | |
432 | – | #else // is_mpi |
433 | – | |
434 | – | molIndex = 0; |
435 | – | globalAtomIndex = 0; |
436 | – | for(i=0; i<n_components; i++){ |
437 | – | for(j=0; j<components_nmol[i]; j++ ){ |
438 | – | the_molecules[molIndex].setStampID( i ); |
439 | – | the_molecules[molIndex].setMyIndex( molIndex ); |
440 | – | the_molecules[molIndex].setGlobalIndex( molIndex ); |
441 | – | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
442 | – | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
443 | – | globalAtomIndex++; |
444 | – | } |
445 | – | molIndex++; |
446 | – | } |
447 | – | } |
448 | – | |
449 | – | |
450 | – | #endif // is_mpi |
451 | – | |
452 | – | |
453 | – | if( simnfo->n_SRI ){ |
454 | – | |
455 | – | Exclude::createArray(simnfo->n_SRI); |
456 | – | the_excludes = new Exclude*[simnfo->n_SRI]; |
457 | – | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
458 | – | simnfo->globalExcludes = new int; |
459 | – | simnfo->n_exclude = simnfo->n_SRI; |
460 | – | } |
461 | – | else{ |
462 | – | |
463 | – | Exclude::createArray( 1 ); |
464 | – | the_excludes = new Exclude*; |
465 | – | the_excludes[0] = new Exclude(0); |
466 | – | the_excludes[0]->setPair( 0,0 ); |
467 | – | simnfo->globalExcludes = new int; |
468 | – | simnfo->globalExcludes[0] = 0; |
469 | – | simnfo->n_exclude = 0; |
470 | – | } |
471 | – | |
472 | – | // set the arrays into the SimInfo object |
473 | – | |
474 | – | simnfo->atoms = the_atoms; |
475 | – | simnfo->molecules = the_molecules; |
476 | – | simnfo->nGlobalExcludes = 0; |
477 | – | simnfo->excludes = the_excludes; |
478 | – | |
479 | – | |
480 | – | // get some of the tricky things that may still be in the globals |
481 | – | |
482 | – | double boxVector[3]; |
483 | – | if( the_globals->haveBox() ){ |
484 | – | boxVector[0] = the_globals->getBox(); |
485 | – | boxVector[1] = the_globals->getBox(); |
486 | – | boxVector[2] = the_globals->getBox(); |
487 | – | |
488 | – | simnfo->setBox( boxVector ); |
489 | – | } |
490 | – | else if( the_globals->haveDensity() ){ |
491 | – | |
492 | – | double vol; |
493 | – | vol = (double)tot_nmol / the_globals->getDensity(); |
494 | – | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
495 | – | boxVector[1] = boxVector[0]; |
496 | – | boxVector[2] = boxVector[0]; |
497 | – | |
498 | – | simnfo->setBox( boxVector ); |
499 | – | } |
500 | – | else{ |
501 | – | if( !the_globals->haveBoxX() ){ |
502 | – | sprintf( painCave.errMsg, |
503 | – | "SimSetup error, no periodic BoxX size given.\n" ); |
504 | – | painCave.isFatal = 1; |
505 | – | simError(); |
506 | – | } |
507 | – | boxVector[0] = the_globals->getBoxX(); |
508 | – | |
509 | – | if( !the_globals->haveBoxY() ){ |
510 | – | sprintf( painCave.errMsg, |
511 | – | "SimSetup error, no periodic BoxY size given.\n" ); |
512 | – | painCave.isFatal = 1; |
513 | – | simError(); |
514 | – | } |
515 | – | boxVector[1] = the_globals->getBoxY(); |
516 | – | |
517 | – | if( !the_globals->haveBoxZ() ){ |
518 | – | sprintf( painCave.errMsg, |
519 | – | "SimSetup error, no periodic BoxZ size given.\n" ); |
520 | – | painCave.isFatal = 1; |
521 | – | simError(); |
522 | – | } |
523 | – | boxVector[2] = the_globals->getBoxZ(); |
524 | – | |
525 | – | simnfo->setBox( boxVector ); |
526 | – | } |
527 | – | |
528 | – | #ifdef IS_MPI |
529 | – | strcpy( checkPointMsg, "Box size set up" ); |
530 | – | MPIcheckPoint(); |
531 | – | #endif // is_mpi |
532 | – | |
533 | – | |
534 | – | // initialize the arrays |
535 | – | |
536 | – | the_ff->setSimInfo( simnfo ); |
537 | – | |
538 | – | makeMolecules(); |
539 | – | simnfo->identArray = new int[simnfo->n_atoms]; |
540 | – | for(i=0; i<simnfo->n_atoms; i++){ |
541 | – | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
542 | – | } |
543 | – | |
544 | – | if (the_globals->getUseRF() ) { |
545 | – | simnfo->useReactionField = 1; |
546 | – | |
547 | – | if( !the_globals->haveECR() ){ |
548 | – | sprintf( painCave.errMsg, |
549 | – | "SimSetup Warning: using default value of 1/2 the smallest " |
550 | – | "box length for the electrostaticCutoffRadius.\n" |
551 | – | "I hope you have a very fast processor!\n"); |
552 | – | painCave.isFatal = 0; |
553 | – | simError(); |
554 | – | double smallest; |
555 | – | smallest = simnfo->boxLx; |
556 | – | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
557 | – | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
558 | – | simnfo->ecr = 0.5 * smallest; |
559 | – | } else { |
560 | – | simnfo->ecr = the_globals->getECR(); |
561 | – | } |
562 | – | |
563 | – | if( !the_globals->haveEST() ){ |
564 | – | sprintf( painCave.errMsg, |
565 | – | "SimSetup Warning: using default value of 0.05 * the " |
566 | – | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
567 | – | ); |
568 | – | painCave.isFatal = 0; |
569 | – | simError(); |
570 | – | simnfo->est = 0.05 * simnfo->ecr; |
571 | – | } else { |
572 | – | simnfo->est = the_globals->getEST(); |
573 | – | } |
574 | – | |
575 | – | if(!the_globals->haveDielectric() ){ |
576 | – | sprintf( painCave.errMsg, |
577 | – | "SimSetup Error: You are trying to use Reaction Field without" |
578 | – | "setting a dielectric constant!\n" |
579 | – | ); |
580 | – | painCave.isFatal = 1; |
581 | – | simError(); |
582 | – | } |
583 | – | simnfo->dielectric = the_globals->getDielectric(); |
584 | – | } else { |
585 | – | if (usesDipoles) { |
586 | – | |
587 | – | if( !the_globals->haveECR() ){ |
588 | – | sprintf( painCave.errMsg, |
589 | – | "SimSetup Warning: using default value of 1/2 the smallest " |
590 | – | "box length for the electrostaticCutoffRadius.\n" |
591 | – | "I hope you have a very fast processor!\n"); |
592 | – | painCave.isFatal = 0; |
593 | – | simError(); |
594 | – | double smallest; |
595 | – | smallest = simnfo->boxLx; |
596 | – | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
597 | – | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
598 | – | simnfo->ecr = 0.5 * smallest; |
599 | – | } else { |
600 | – | simnfo->ecr = the_globals->getECR(); |
601 | – | } |
602 | – | |
603 | – | if( !the_globals->haveEST() ){ |
604 | – | sprintf( painCave.errMsg, |
605 | – | "SimSetup Warning: using default value of 5%% of the " |
606 | – | "electrostaticCutoffRadius for the " |
607 | – | "electrostaticSkinThickness\n" |
608 | – | ); |
609 | – | painCave.isFatal = 0; |
610 | – | simError(); |
611 | – | simnfo->est = 0.05 * simnfo->ecr; |
612 | – | } else { |
613 | – | simnfo->est = the_globals->getEST(); |
614 | – | } |
615 | – | } |
616 | – | } |
617 | – | |
618 | – | #ifdef IS_MPI |
619 | – | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
620 | – | MPIcheckPoint(); |
621 | – | #endif // is_mpi |
622 | – | |
623 | – | if( the_globals->haveInitialConfig() ){ |
624 | – | |
625 | – | InitializeFromFile* fileInit; |
626 | – | #ifdef IS_MPI // is_mpi |
627 | – | if( worldRank == 0 ){ |
628 | – | #endif //is_mpi |
629 | – | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
630 | – | #ifdef IS_MPI |
631 | – | }else fileInit = new InitializeFromFile( NULL ); |
632 | – | #endif |
633 | – | fileInit->read_xyz( simnfo ); // default velocities on |
634 | – | |
635 | – | delete fileInit; |
636 | – | } |
637 | – | else{ |
638 | – | |
639 | – | #ifdef IS_MPI |
640 | – | |
641 | – | // no init from bass |
642 | – | |
643 | – | sprintf( painCave.errMsg, |
644 | – | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
645 | – | painCave.isFatal; |
646 | – | simError(); |
647 | – | |
648 | – | #else |
649 | – | |
650 | – | initFromBass(); |
651 | – | |
652 | – | |
653 | – | #endif |
654 | – | } |
655 | – | |
656 | – | #ifdef IS_MPI |
657 | – | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
658 | – | MPIcheckPoint(); |
659 | – | #endif // is_mpi |
660 | – | |
661 | – | |
662 | – | |
663 | – | |
664 | – | |
665 | – | |
666 | – | |
667 | – | #ifdef IS_MPI |
668 | – | if( worldRank == 0 ){ |
669 | – | #endif // is_mpi |
670 | – | |
671 | – | if( the_globals->haveFinalConfig() ){ |
672 | – | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
673 | – | } |
703 | else{ | |
704 | < | strcpy( simnfo->finalName, inFileName ); |
705 | < | char* endTest; |
706 | < | int nameLength = strlen( simnfo->finalName ); |
678 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
679 | < | if( !strcmp( endTest, ".bass" ) ){ |
680 | < | strcpy( endTest, ".eor" ); |
681 | < | } |
682 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
683 | < | strcpy( endTest, ".eor" ); |
684 | < | } |
685 | < | else{ |
686 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
687 | < | if( !strcmp( endTest, ".bss" ) ){ |
688 | < | strcpy( endTest, ".eor" ); |
689 | < | } |
690 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
691 | < | strcpy( endTest, ".eor" ); |
692 | < | } |
693 | < | else{ |
694 | < | strcat( simnfo->finalName, ".eor" ); |
695 | < | } |
696 | < | } |
704 | > | info[i].sampleTime = globals->getRunTime(); |
705 | > | info[i].statusTime = info[i].sampleTime; |
706 | > | info[i].thermalTime = info[i].sampleTime; |
707 | } | |
708 | ||
709 | < | // make the sample and status out names |
709 | > | if( globals->haveStatusTime() ){ |
710 | > | info[i].statusTime = globals->getStatusTime(); |
711 | > | } |
712 | ||
713 | < | strcpy( simnfo->sampleName, inFileName ); |
714 | < | char* endTest; |
703 | < | int nameLength = strlen( simnfo->sampleName ); |
704 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
705 | < | if( !strcmp( endTest, ".bass" ) ){ |
706 | < | strcpy( endTest, ".dump" ); |
713 | > | if( globals->haveThermalTime() ){ |
714 | > | info[i].thermalTime = globals->getThermalTime(); |
715 | } | |
716 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
717 | < | strcpy( endTest, ".dump" ); |
718 | < | } |
719 | < | else{ |
712 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
713 | < | if( !strcmp( endTest, ".bss" ) ){ |
714 | < | strcpy( endTest, ".dump" ); |
715 | < | } |
716 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
717 | < | strcpy( endTest, ".dump" ); |
718 | < | } |
719 | < | else{ |
720 | < | strcat( simnfo->sampleName, ".dump" ); |
721 | < | } |
722 | < | } |
716 | > | |
717 | > | // check for the temperature set flag |
718 | > | |
719 | > | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
720 | ||
721 | < | strcpy( simnfo->statusName, inFileName ); |
722 | < | nameLength = strlen( simnfo->statusName ); |
723 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
724 | < | if( !strcmp( endTest, ".bass" ) ){ |
725 | < | strcpy( endTest, ".stat" ); |
721 | > | // get some of the tricky things that may still be in the globals |
722 | > | |
723 | > | double boxVector[3]; |
724 | > | if( globals->haveBox() ){ |
725 | > | boxVector[0] = globals->getBox(); |
726 | > | boxVector[1] = globals->getBox(); |
727 | > | boxVector[2] = globals->getBox(); |
728 | > | |
729 | > | info[i].setBox( boxVector ); |
730 | } | |
731 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
732 | < | strcpy( endTest, ".stat" ); |
733 | < | } |
731 | > | else if( globals->haveDensity() ){ |
732 | > | |
733 | > | double vol; |
734 | > | vol = (double)tot_nmol / globals->getDensity(); |
735 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
736 | > | boxVector[1] = boxVector[0]; |
737 | > | boxVector[2] = boxVector[0]; |
738 | > | |
739 | > | info[i].setBox( boxVector ); |
740 | > | } |
741 | else{ | |
742 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
743 | < | if( !strcmp( endTest, ".bss" ) ){ |
744 | < | strcpy( endTest, ".stat" ); |
742 | > | if( !globals->haveBoxX() ){ |
743 | > | sprintf( painCave.errMsg, |
744 | > | "SimSetup error, no periodic BoxX size given.\n" ); |
745 | > | painCave.isFatal = 1; |
746 | > | simError(); |
747 | } | |
748 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
749 | < | strcpy( endTest, ".stat" ); |
748 | > | boxVector[0] = globals->getBoxX(); |
749 | > | |
750 | > | if( !globals->haveBoxY() ){ |
751 | > | sprintf( painCave.errMsg, |
752 | > | "SimSetup error, no periodic BoxY size given.\n" ); |
753 | > | painCave.isFatal = 1; |
754 | > | simError(); |
755 | } | |
756 | < | else{ |
757 | < | strcat( simnfo->statusName, ".stat" ); |
756 | > | boxVector[1] = globals->getBoxY(); |
757 | > | |
758 | > | if( !globals->haveBoxZ() ){ |
759 | > | sprintf( painCave.errMsg, |
760 | > | "SimSetup error, no periodic BoxZ size given.\n" ); |
761 | > | painCave.isFatal = 1; |
762 | > | simError(); |
763 | } | |
764 | + | boxVector[2] = globals->getBoxZ(); |
765 | + | |
766 | + | info[i].setBox( boxVector ); |
767 | } | |
768 | + | |
769 | + | } |
770 | ||
771 | #ifdef IS_MPI | |
772 | < | } |
772 | > | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
773 | > | MPIcheckPoint(); |
774 | #endif // is_mpi | |
749 | – | |
750 | – | // set the status, sample, and themal kick times |
751 | – | |
752 | – | if( the_globals->haveSampleTime() ){ |
753 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
754 | – | simnfo->statusTime = simnfo->sampleTime; |
755 | – | simnfo->thermalTime = simnfo->sampleTime; |
756 | – | } |
757 | – | else{ |
758 | – | simnfo->sampleTime = the_globals->getRunTime(); |
759 | – | simnfo->statusTime = simnfo->sampleTime; |
760 | – | simnfo->thermalTime = simnfo->sampleTime; |
761 | – | } |
775 | ||
776 | < | if( the_globals->haveStatusTime() ){ |
764 | < | simnfo->statusTime = the_globals->getStatusTime(); |
765 | < | } |
776 | > | } |
777 | ||
767 | – | if( the_globals->haveThermalTime() ){ |
768 | – | simnfo->thermalTime = the_globals->getThermalTime(); |
769 | – | } |
778 | ||
779 | < | // check for the temperature set flag |
779 | > | void SimSetup::finalInfoCheck( void ){ |
780 | > | int index; |
781 | > | int usesDipoles; |
782 | > | int i; |
783 | ||
784 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
785 | < | |
786 | < | |
787 | < | // make the integrator |
784 | > | for(i=0; i<nInfo; i++){ |
785 | > | // check electrostatic parameters |
786 | > | |
787 | > | index = 0; |
788 | > | usesDipoles = 0; |
789 | > | while( (index < info[i].n_atoms) && !usesDipoles ){ |
790 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
791 | > | index++; |
792 | > | } |
793 | > | |
794 | > | #ifdef IS_MPI |
795 | > | int myUse = usesDipoles; |
796 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
797 | > | #endif //is_mpi |
798 | > | |
799 | > | double theEcr, theEst; |
800 | ||
801 | < | |
802 | < | NVT* myNVT = NULL; |
803 | < | switch( ensembleCase ){ |
804 | < | |
805 | < | case NVE_ENS: |
806 | < | new NVE( simnfo, the_ff ); |
807 | < | break; |
808 | < | |
809 | < | case NVT_ENS: |
810 | < | myNVT = new NVT( simnfo, the_ff ); |
811 | < | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
812 | < | |
813 | < | if (the_globals->haveTauThermostat()) |
814 | < | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
815 | < | // else if (the_globals->haveQmass()) |
816 | < | // myNVT->setQmass(the_globals->getQmass()); |
801 | > | if (globals->getUseRF() ) { |
802 | > | info[i].useReactionField = 1; |
803 | > | |
804 | > | if( !globals->haveECR() ){ |
805 | > | sprintf( painCave.errMsg, |
806 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
807 | > | "box length for the electrostaticCutoffRadius.\n" |
808 | > | "I hope you have a very fast processor!\n"); |
809 | > | painCave.isFatal = 0; |
810 | > | simError(); |
811 | > | double smallest; |
812 | > | smallest = info[i].boxL[0]; |
813 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
814 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
815 | > | theEcr = 0.5 * smallest; |
816 | > | } else { |
817 | > | theEcr = globals->getECR(); |
818 | > | } |
819 | > | |
820 | > | if( !globals->haveEST() ){ |
821 | > | sprintf( painCave.errMsg, |
822 | > | "SimSetup Warning: using default value of 0.05 * the " |
823 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
824 | > | ); |
825 | > | painCave.isFatal = 0; |
826 | > | simError(); |
827 | > | theEst = 0.05 * theEcr; |
828 | > | } else { |
829 | > | theEst= globals->getEST(); |
830 | > | } |
831 | > | |
832 | > | info[i].setEcr( theEcr, theEst ); |
833 | > | |
834 | > | if(!globals->haveDielectric() ){ |
835 | > | sprintf( painCave.errMsg, |
836 | > | "SimSetup Error: You are trying to use Reaction Field without" |
837 | > | "setting a dielectric constant!\n" |
838 | > | ); |
839 | > | painCave.isFatal = 1; |
840 | > | simError(); |
841 | > | } |
842 | > | info[i].dielectric = globals->getDielectric(); |
843 | > | } |
844 | else { | |
845 | < | sprintf( painCave.errMsg, |
846 | < | "SimSetup error: If you use the NVT\n" |
847 | < | " ensemble, you must set either tauThermostat or qMass.\n" |
848 | < | " Neither of these was found in the BASS file.\n"); |
849 | < | painCave.isFatal = 1; |
850 | < | simError(); |
851 | < | } |
852 | < | break; |
853 | < | |
854 | < | default: |
855 | < | sprintf( painCave.errMsg, |
856 | < | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
857 | < | painCave.isFatal = 1; |
858 | < | simError(); |
845 | > | if (usesDipoles) { |
846 | > | |
847 | > | if( !globals->haveECR() ){ |
848 | > | sprintf( painCave.errMsg, |
849 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
850 | > | "box length for the electrostaticCutoffRadius.\n" |
851 | > | "I hope you have a very fast processor!\n"); |
852 | > | painCave.isFatal = 0; |
853 | > | simError(); |
854 | > | double smallest; |
855 | > | smallest = info[i].boxL[0]; |
856 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
857 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
858 | > | theEcr = 0.5 * smallest; |
859 | > | } else { |
860 | > | theEcr = globals->getECR(); |
861 | > | } |
862 | > | |
863 | > | if( !globals->haveEST() ){ |
864 | > | sprintf( painCave.errMsg, |
865 | > | "SimSetup Warning: using default value of 0.05 * the " |
866 | > | "electrostaticCutoffRadius for the " |
867 | > | "electrostaticSkinThickness\n" |
868 | > | ); |
869 | > | painCave.isFatal = 0; |
870 | > | simError(); |
871 | > | theEst = 0.05 * theEcr; |
872 | > | } else { |
873 | > | theEst= globals->getEST(); |
874 | > | } |
875 | > | |
876 | > | info[i].setEcr( theEcr, theEst ); |
877 | > | } |
878 | > | } |
879 | } | |
880 | ||
811 | – | |
881 | #ifdef IS_MPI | |
882 | < | mpiSim->mpiRefresh(); |
883 | < | #endif |
882 | > | strcpy( checkPointMsg, "post processing checks out" ); |
883 | > | MPIcheckPoint(); |
884 | > | #endif // is_mpi |
885 | ||
886 | < | // initialize the Fortran |
886 | > | } |
887 | ||
888 | + | void SimSetup::initSystemCoords( void ){ |
889 | + | int i; |
890 | + | |
891 | + | std::cerr << "Setting atom Coords\n"; |
892 | ||
893 | < | simnfo->refreshSim(); |
893 | > | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
894 | ||
895 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
896 | < | the_ff->initForceField( LB_MIXING_RULE ); |
895 | > | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
896 | > | |
897 | > | if( globals->haveInitialConfig() ){ |
898 | > | |
899 | > | InitializeFromFile* fileInit; |
900 | > | #ifdef IS_MPI // is_mpi |
901 | > | if( worldRank == 0 ){ |
902 | > | #endif //is_mpi |
903 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
904 | > | #ifdef IS_MPI |
905 | > | }else fileInit = new InitializeFromFile( NULL ); |
906 | > | #endif |
907 | > | fileInit->readInit( info ); // default velocities on |
908 | > | |
909 | > | delete fileInit; |
910 | } | |
824 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
825 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
826 | – | } |
911 | else{ | |
912 | + | |
913 | + | #ifdef IS_MPI |
914 | + | |
915 | + | // no init from bass |
916 | + | |
917 | sprintf( painCave.errMsg, | |
918 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
919 | < | simnfo->mixingRule ); |
831 | < | painCave.isFatal = 1; |
918 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
919 | > | painCave.isFatal; |
920 | simError(); | |
921 | + | |
922 | + | #else |
923 | + | |
924 | + | initFromBass(); |
925 | + | |
926 | + | |
927 | + | #endif |
928 | } | |
929 | < | |
835 | < | |
929 | > | |
930 | #ifdef IS_MPI | |
931 | < | strcpy( checkPointMsg, |
838 | < | "Successfully intialized the mixingRule for Fortran." ); |
931 | > | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
932 | MPIcheckPoint(); | |
933 | #endif // is_mpi | |
934 | + | |
935 | } | |
936 | ||
937 | ||
938 | < | void SimSetup::makeMolecules( void ){ |
845 | < | |
846 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
847 | < | molInit info; |
848 | < | DirectionalAtom* dAtom; |
849 | < | LinkedAssign* extras; |
850 | < | LinkedAssign* current_extra; |
851 | < | AtomStamp* currentAtom; |
852 | < | BondStamp* currentBond; |
853 | < | BendStamp* currentBend; |
854 | < | TorsionStamp* currentTorsion; |
855 | < | |
856 | < | bond_pair* theBonds; |
857 | < | bend_set* theBends; |
858 | < | torsion_set* theTorsions; |
859 | < | |
938 | > | void SimSetup::makeOutNames( void ){ |
939 | ||
940 | < | //init the forceField paramters |
940 | > | int k; |
941 | ||
863 | – | the_ff->readParams(); |
864 | – | |
942 | ||
943 | < | // init the atoms |
943 | > | for(k=0; k<nInfo; k++){ |
944 | ||
868 | – | double ux, uy, uz, u, uSqr; |
869 | – | |
870 | – | atomOffset = 0; |
871 | – | excludeOffset = 0; |
872 | – | for(i=0; i<simnfo->n_mol; i++){ |
873 | – | |
874 | – | stampID = the_molecules[i].getStampID(); |
875 | – | |
876 | – | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
877 | – | info.nBonds = comp_stamps[stampID]->getNBonds(); |
878 | – | info.nBends = comp_stamps[stampID]->getNBends(); |
879 | – | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
880 | – | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
881 | – | |
882 | – | info.myAtoms = &the_atoms[atomOffset]; |
883 | – | info.myExcludes = &the_excludes[excludeOffset]; |
884 | – | info.myBonds = new Bond*[info.nBonds]; |
885 | – | info.myBends = new Bend*[info.nBends]; |
886 | – | info.myTorsions = new Torsion*[info.nTorsions]; |
887 | – | |
888 | – | theBonds = new bond_pair[info.nBonds]; |
889 | – | theBends = new bend_set[info.nBends]; |
890 | – | theTorsions = new torsion_set[info.nTorsions]; |
891 | – | |
892 | – | // make the Atoms |
893 | – | |
894 | – | for(j=0; j<info.nAtoms; j++){ |
895 | – | |
896 | – | currentAtom = comp_stamps[stampID]->getAtom( j ); |
897 | – | if( currentAtom->haveOrientation() ){ |
898 | – | |
899 | – | dAtom = new DirectionalAtom(j + atomOffset); |
900 | – | simnfo->n_oriented++; |
901 | – | info.myAtoms[j] = dAtom; |
902 | – | |
903 | – | ux = currentAtom->getOrntX(); |
904 | – | uy = currentAtom->getOrntY(); |
905 | – | uz = currentAtom->getOrntZ(); |
906 | – | |
907 | – | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
908 | – | |
909 | – | u = sqrt( uSqr ); |
910 | – | ux = ux / u; |
911 | – | uy = uy / u; |
912 | – | uz = uz / u; |
913 | – | |
914 | – | dAtom->setSUx( ux ); |
915 | – | dAtom->setSUy( uy ); |
916 | – | dAtom->setSUz( uz ); |
917 | – | } |
918 | – | else{ |
919 | – | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
920 | – | } |
921 | – | info.myAtoms[j]->setType( currentAtom->getType() ); |
922 | – | |
945 | #ifdef IS_MPI | |
946 | < | |
925 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
926 | < | |
946 | > | if( worldRank == 0 ){ |
947 | #endif // is_mpi | |
928 | – | } |
929 | – | |
930 | – | // make the bonds |
931 | – | for(j=0; j<info.nBonds; j++){ |
948 | ||
949 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
950 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
935 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
936 | < | |
937 | < | exI = theBonds[j].a; |
938 | < | exJ = theBonds[j].b; |
939 | < | |
940 | < | // exclude_I must always be the smaller of the pair |
941 | < | if( exI > exJ ){ |
942 | < | tempEx = exI; |
943 | < | exI = exJ; |
944 | < | exJ = tempEx; |
949 | > | if( globals->haveFinalConfig() ){ |
950 | > | strcpy( info[k].finalName, globals->getFinalConfig() ); |
951 | } | |
952 | < | #ifdef IS_MPI |
953 | < | tempEx = exI; |
954 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
955 | < | tempEx = exJ; |
956 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
957 | < | |
958 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
959 | < | #else // isn't MPI |
960 | < | |
961 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
962 | < | #endif //is_mpi |
963 | < | } |
964 | < | excludeOffset += info.nBonds; |
965 | < | |
966 | < | //make the bends |
961 | < | for(j=0; j<info.nBends; j++){ |
962 | < | |
963 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
964 | < | theBends[j].a = currentBend->getA() + atomOffset; |
965 | < | theBends[j].b = currentBend->getB() + atomOffset; |
966 | < | theBends[j].c = currentBend->getC() + atomOffset; |
967 | < | |
968 | < | if( currentBend->haveExtras() ){ |
969 | < | |
970 | < | extras = currentBend->getExtras(); |
971 | < | current_extra = extras; |
972 | < | |
973 | < | while( current_extra != NULL ){ |
974 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
975 | < | |
976 | < | switch( current_extra->getType() ){ |
977 | < | |
978 | < | case 0: |
979 | < | theBends[j].ghost = |
980 | < | current_extra->getInt() + atomOffset; |
981 | < | theBends[j].isGhost = 1; |
982 | < | break; |
983 | < | |
984 | < | case 1: |
985 | < | theBends[j].ghost = |
986 | < | (int)current_extra->getDouble() + atomOffset; |
987 | < | theBends[j].isGhost = 1; |
988 | < | break; |
989 | < | |
990 | < | default: |
991 | < | sprintf( painCave.errMsg, |
992 | < | "SimSetup Error: ghostVectorSource was neither a " |
993 | < | "double nor an int.\n" |
994 | < | "-->Bend[%d] in %s\n", |
995 | < | j, comp_stamps[stampID]->getID() ); |
996 | < | painCave.isFatal = 1; |
997 | < | simError(); |
998 | < | } |
952 | > | else{ |
953 | > | strcpy( info[k].finalName, inFileName ); |
954 | > | char* endTest; |
955 | > | int nameLength = strlen( info[k].finalName ); |
956 | > | endTest = &(info[k].finalName[nameLength - 5]); |
957 | > | if( !strcmp( endTest, ".bass" ) ){ |
958 | > | strcpy( endTest, ".eor" ); |
959 | > | } |
960 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
961 | > | strcpy( endTest, ".eor" ); |
962 | > | } |
963 | > | else{ |
964 | > | endTest = &(info[k].finalName[nameLength - 4]); |
965 | > | if( !strcmp( endTest, ".bss" ) ){ |
966 | > | strcpy( endTest, ".eor" ); |
967 | } | |
968 | < | |
968 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
969 | > | strcpy( endTest, ".eor" ); |
970 | > | } |
971 | else{ | |
972 | < | |
1003 | < | sprintf( painCave.errMsg, |
1004 | < | "SimSetup Error: unhandled bend assignment:\n" |
1005 | < | " -->%s in Bend[%d] in %s\n", |
1006 | < | current_extra->getlhs(), |
1007 | < | j, comp_stamps[stampID]->getID() ); |
1008 | < | painCave.isFatal = 1; |
1009 | < | simError(); |
972 | > | strcat( info[k].finalName, ".eor" ); |
973 | } | |
1011 | – | |
1012 | – | current_extra = current_extra->getNext(); |
974 | } | |
975 | } | |
976 | < | |
977 | < | if( !theBends[j].isGhost ){ |
978 | < | |
979 | < | exI = theBends[j].a; |
980 | < | exJ = theBends[j].c; |
976 | > | |
977 | > | // make the sample and status out names |
978 | > | |
979 | > | strcpy( info[k].sampleName, inFileName ); |
980 | > | char* endTest; |
981 | > | int nameLength = strlen( info[k].sampleName ); |
982 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
983 | > | if( !strcmp( endTest, ".bass" ) ){ |
984 | > | strcpy( endTest, ".dump" ); |
985 | } | |
986 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
987 | + | strcpy( endTest, ".dump" ); |
988 | + | } |
989 | else{ | |
990 | < | |
991 | < | exI = theBends[j].a; |
992 | < | exJ = theBends[j].b; |
990 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
991 | > | if( !strcmp( endTest, ".bss" ) ){ |
992 | > | strcpy( endTest, ".dump" ); |
993 | > | } |
994 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
995 | > | strcpy( endTest, ".dump" ); |
996 | > | } |
997 | > | else{ |
998 | > | strcat( info[k].sampleName, ".dump" ); |
999 | > | } |
1000 | } | |
1001 | ||
1002 | < | // exclude_I must always be the smaller of the pair |
1003 | < | if( exI > exJ ){ |
1004 | < | tempEx = exI; |
1005 | < | exI = exJ; |
1006 | < | exJ = tempEx; |
1002 | > | strcpy( info[k].statusName, inFileName ); |
1003 | > | nameLength = strlen( info[k].statusName ); |
1004 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1005 | > | if( !strcmp( endTest, ".bass" ) ){ |
1006 | > | strcpy( endTest, ".stat" ); |
1007 | } | |
1008 | < | #ifdef IS_MPI |
1009 | < | tempEx = exI; |
1010 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1011 | < | tempEx = exJ; |
1012 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1008 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
1009 | > | strcpy( endTest, ".stat" ); |
1010 | > | } |
1011 | > | else{ |
1012 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1013 | > | if( !strcmp( endTest, ".bss" ) ){ |
1014 | > | strcpy( endTest, ".stat" ); |
1015 | > | } |
1016 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1017 | > | strcpy( endTest, ".stat" ); |
1018 | > | } |
1019 | > | else{ |
1020 | > | strcat( info[k].statusName, ".stat" ); |
1021 | > | } |
1022 | > | } |
1023 | ||
1024 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1040 | < | #else // isn't MPI |
1041 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1042 | < | #endif //is_mpi |
1024 | > | #ifdef IS_MPI |
1025 | } | |
1026 | < | excludeOffset += info.nBends; |
1026 | > | #endif // is_mpi |
1027 | > | } |
1028 | > | } |
1029 | ||
1046 | – | for(j=0; j<info.nTorsions; j++){ |
1047 | – | |
1048 | – | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1049 | – | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1050 | – | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1051 | – | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1052 | – | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1053 | – | |
1054 | – | exI = theTorsions[j].a; |
1055 | – | exJ = theTorsions[j].d; |
1030 | ||
1031 | < | // exclude_I must always be the smaller of the pair |
1032 | < | if( exI > exJ ){ |
1033 | < | tempEx = exI; |
1034 | < | exI = exJ; |
1035 | < | exJ = tempEx; |
1036 | < | } |
1031 | > | void SimSetup::sysObjectsCreation( void ){ |
1032 | > | |
1033 | > | int i,k; |
1034 | > | |
1035 | > | // create the forceField |
1036 | > | |
1037 | > | createFF(); |
1038 | > | |
1039 | > | // extract componentList |
1040 | > | |
1041 | > | compList(); |
1042 | > | |
1043 | > | // calc the number of atoms, bond, bends, and torsions |
1044 | > | |
1045 | > | calcSysValues(); |
1046 | > | |
1047 | #ifdef IS_MPI | |
1048 | < | tempEx = exI; |
1049 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1050 | < | tempEx = exJ; |
1051 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1052 | < | |
1053 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1054 | < | #else // isn't MPI |
1055 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1056 | < | #endif //is_mpi |
1048 | > | // divide the molecules among the processors |
1049 | > | |
1050 | > | mpiMolDivide(); |
1051 | > | #endif //is_mpi |
1052 | > | |
1053 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1054 | > | |
1055 | > | makeSysArrays(); |
1056 | > | |
1057 | > | // make and initialize the molecules (all but atomic coordinates) |
1058 | > | |
1059 | > | makeMolecules(); |
1060 | > | |
1061 | > | for(k=0; k<nInfo; k++){ |
1062 | > | info[k].identArray = new int[info[k].n_atoms]; |
1063 | > | for(i=0; i<info[k].n_atoms; i++){ |
1064 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1065 | } | |
1066 | < | excludeOffset += info.nTorsions; |
1066 | > | } |
1067 | > | } |
1068 | ||
1076 | – | |
1077 | – | // send the arrays off to the forceField for init. |
1069 | ||
1070 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1080 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1081 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1082 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1070 | > | void SimSetup::createFF( void ){ |
1071 | ||
1072 | + | switch( ffCase ){ |
1073 | ||
1074 | < | the_molecules[i].initialize( info ); |
1074 | > | case FF_DUFF: |
1075 | > | the_ff = new DUFF(); |
1076 | > | break; |
1077 | ||
1078 | + | case FF_LJ: |
1079 | + | the_ff = new LJFF(); |
1080 | + | break; |
1081 | ||
1082 | < | atomOffset += info.nAtoms; |
1083 | < | delete[] theBonds; |
1084 | < | delete[] theBends; |
1085 | < | delete[] theTorsions; |
1082 | > | case FF_EAM: |
1083 | > | the_ff = new EAM_FF(); |
1084 | > | break; |
1085 | > | |
1086 | > | default: |
1087 | > | sprintf( painCave.errMsg, |
1088 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1089 | > | painCave.isFatal = 1; |
1090 | > | simError(); |
1091 | } | |
1092 | ||
1093 | #ifdef IS_MPI | |
1094 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1094 | > | strcpy( checkPointMsg, "ForceField creation successful" ); |
1095 | MPIcheckPoint(); | |
1096 | #endif // is_mpi | |
1097 | ||
1099 | – | // clean up the forcefield |
1100 | – | the_ff->calcRcut(); |
1101 | – | the_ff->cleanMe(); |
1102 | – | |
1098 | } | |
1099 | ||
1105 | – | void SimSetup::initFromBass( void ){ |
1100 | ||
1101 | < | int i, j, k; |
1108 | < | int n_cells; |
1109 | < | double cellx, celly, cellz; |
1110 | < | double temp1, temp2, temp3; |
1111 | < | int n_per_extra; |
1112 | < | int n_extra; |
1113 | < | int have_extra, done; |
1101 | > | void SimSetup::compList( void ){ |
1102 | ||
1103 | < | temp1 = (double)tot_nmol / 4.0; |
1104 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1105 | < | temp3 = ceil( temp2 ); |
1103 | > | int i; |
1104 | > | char* id; |
1105 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1106 | > | LinkedMolStamp* currentStamp = NULL; |
1107 | > | comp_stamps = new MoleculeStamp*[n_components]; |
1108 | > | |
1109 | > | // make an array of molecule stamps that match the components used. |
1110 | > | // also extract the used stamps out into a separate linked list |
1111 | > | |
1112 | > | for(i=0; i<nInfo; i++){ |
1113 | > | info[i].nComponents = n_components; |
1114 | > | info[i].componentsNmol = components_nmol; |
1115 | > | info[i].compStamps = comp_stamps; |
1116 | > | info[i].headStamp = headStamp; |
1117 | > | } |
1118 | > | |
1119 | ||
1120 | < | have_extra =0; |
1120 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
1121 | < | have_extra =1; |
1120 | > | for( i=0; i<n_components; i++ ){ |
1121 | ||
1122 | < | n_cells = (int)temp3 - 1; |
1123 | < | cellx = simnfo->boxLx / temp3; |
1124 | < | celly = simnfo->boxLy / temp3; |
1125 | < | cellz = simnfo->boxLz / temp3; |
1127 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1128 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1129 | < | n_per_extra = (int)ceil( temp1 ); |
1122 | > | id = the_components[i]->getType(); |
1123 | > | comp_stamps[i] = NULL; |
1124 | > | |
1125 | > | // check to make sure the component isn't already in the list |
1126 | ||
1127 | < | if( n_per_extra > 4){ |
1128 | < | sprintf( painCave.errMsg, |
1129 | < | "SimSetup error. There has been an error in constructing" |
1130 | < | " the non-complete lattice.\n" ); |
1131 | < | painCave.isFatal = 1; |
1132 | < | simError(); |
1127 | > | comp_stamps[i] = headStamp->match( id ); |
1128 | > | if( comp_stamps[i] == NULL ){ |
1129 | > | |
1130 | > | // extract the component from the list; |
1131 | > | |
1132 | > | currentStamp = stamps->extractMolStamp( id ); |
1133 | > | if( currentStamp == NULL ){ |
1134 | > | sprintf( painCave.errMsg, |
1135 | > | "SimSetup error: Component \"%s\" was not found in the " |
1136 | > | "list of declared molecules\n", |
1137 | > | id ); |
1138 | > | painCave.isFatal = 1; |
1139 | > | simError(); |
1140 | > | } |
1141 | > | |
1142 | > | headStamp->add( currentStamp ); |
1143 | > | comp_stamps[i] = headStamp->match( id ); |
1144 | } | |
1145 | } | |
1146 | < | else{ |
1147 | < | n_cells = (int)temp3; |
1148 | < | cellx = simnfo->boxLx / temp3; |
1149 | < | celly = simnfo->boxLy / temp3; |
1150 | < | cellz = simnfo->boxLz / temp3; |
1146 | > | |
1147 | > | #ifdef IS_MPI |
1148 | > | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1149 | > | MPIcheckPoint(); |
1150 | > | #endif // is_mpi |
1151 | > | |
1152 | > | |
1153 | > | } |
1154 | > | |
1155 | > | void SimSetup::calcSysValues( void ){ |
1156 | > | int i, j, k; |
1157 | > | |
1158 | > | int *molMembershipArray; |
1159 | > | |
1160 | > | tot_atoms = 0; |
1161 | > | tot_bonds = 0; |
1162 | > | tot_bends = 0; |
1163 | > | tot_torsions = 0; |
1164 | > | for( i=0; i<n_components; i++ ){ |
1165 | > | |
1166 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1167 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1168 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1169 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1170 | } | |
1171 | + | |
1172 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1173 | + | molMembershipArray = new int[tot_atoms]; |
1174 | + | |
1175 | + | for(i=0; i<nInfo; i++){ |
1176 | + | info[i].n_atoms = tot_atoms; |
1177 | + | info[i].n_bonds = tot_bonds; |
1178 | + | info[i].n_bends = tot_bends; |
1179 | + | info[i].n_torsions = tot_torsions; |
1180 | + | info[i].n_SRI = tot_SRI; |
1181 | + | info[i].n_mol = tot_nmol; |
1182 | + | |
1183 | + | info[i].molMembershipArray = molMembershipArray; |
1184 | + | } |
1185 | + | } |
1186 | ||
1187 | < | current_mol = 0; |
1147 | < | current_comp_mol = 0; |
1148 | < | current_comp = 0; |
1149 | < | current_atom_ndx = 0; |
1187 | > | #ifdef IS_MPI |
1188 | ||
1189 | < | for( i=0; i < n_cells ; i++ ){ |
1190 | < | for( j=0; j < n_cells; j++ ){ |
1191 | < | for( k=0; k < n_cells; k++ ){ |
1189 | > | void SimSetup::mpiMolDivide( void ){ |
1190 | > | |
1191 | > | int i, j, k; |
1192 | > | int localMol, allMol; |
1193 | > | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1194 | ||
1195 | < | makeElement( i * cellx, |
1196 | < | j * celly, |
1197 | < | k * cellz ); |
1195 | > | mpiSim = new mpiSimulation( info ); |
1196 | > | |
1197 | > | globalIndex = mpiSim->divideLabor(); |
1198 | ||
1199 | < | makeElement( i * cellx + 0.5 * cellx, |
1200 | < | j * celly + 0.5 * celly, |
1201 | < | k * cellz ); |
1199 | > | // set up the local variables |
1200 | > | |
1201 | > | mol2proc = mpiSim->getMolToProcMap(); |
1202 | > | molCompType = mpiSim->getMolComponentType(); |
1203 | > | |
1204 | > | allMol = 0; |
1205 | > | localMol = 0; |
1206 | > | local_atoms = 0; |
1207 | > | local_bonds = 0; |
1208 | > | local_bends = 0; |
1209 | > | local_torsions = 0; |
1210 | > | globalAtomIndex = 0; |
1211 | ||
1163 | – | makeElement( i * cellx, |
1164 | – | j * celly + 0.5 * celly, |
1165 | – | k * cellz + 0.5 * cellz ); |
1212 | ||
1213 | < | makeElement( i * cellx + 0.5 * cellx, |
1214 | < | j * celly, |
1215 | < | k * cellz + 0.5 * cellz ); |
1213 | > | for( i=0; i<n_components; i++ ){ |
1214 | > | |
1215 | > | for( j=0; j<components_nmol[i]; j++ ){ |
1216 | > | |
1217 | > | if( mol2proc[allMol] == worldRank ){ |
1218 | > | |
1219 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1220 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1221 | > | local_bends += comp_stamps[i]->getNBends(); |
1222 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1223 | > | localMol++; |
1224 | > | } |
1225 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1226 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1227 | > | globalAtomIndex++; |
1228 | } | |
1229 | + | |
1230 | + | allMol++; |
1231 | } | |
1232 | } | |
1233 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1234 | + | |
1235 | + | info[0].n_atoms = mpiSim->getMyNlocal(); |
1236 | + | |
1237 | + | if( local_atoms != info[0].n_atoms ){ |
1238 | + | sprintf( painCave.errMsg, |
1239 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1240 | + | " localAtom (%d) are not equal.\n", |
1241 | + | info[0].n_atoms, |
1242 | + | local_atoms ); |
1243 | + | painCave.isFatal = 1; |
1244 | + | simError(); |
1245 | + | } |
1246 | ||
1247 | < | if( have_extra ){ |
1248 | < | done = 0; |
1247 | > | info[0].n_bonds = local_bonds; |
1248 | > | info[0].n_bends = local_bends; |
1249 | > | info[0].n_torsions = local_torsions; |
1250 | > | info[0].n_SRI = local_SRI; |
1251 | > | info[0].n_mol = localMol; |
1252 | ||
1253 | < | int start_ndx; |
1254 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1255 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
1253 | > | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1254 | > | MPIcheckPoint(); |
1255 | > | } |
1256 | > | |
1257 | > | #endif // is_mpi |
1258 | ||
1181 | – | if( i < n_cells ){ |
1259 | ||
1260 | < | if( j < n_cells ){ |
1261 | < | start_ndx = n_cells; |
1185 | < | } |
1186 | < | else start_ndx = 0; |
1187 | < | } |
1188 | < | else start_ndx = 0; |
1260 | > | void SimSetup::makeSysArrays( void ){ |
1261 | > | int i, j, k, l; |
1262 | ||
1263 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1263 | > | Atom** the_atoms; |
1264 | > | Molecule* the_molecules; |
1265 | > | Exclude** the_excludes; |
1266 | ||
1267 | < | makeElement( i * cellx, |
1268 | < | j * celly, |
1269 | < | k * cellz ); |
1270 | < | done = ( current_mol >= tot_nmol ); |
1267 | > | |
1268 | > | for(l=0; l<nInfo; l++){ |
1269 | > | |
1270 | > | // create the atom and short range interaction arrays |
1271 | > | |
1272 | > | the_atoms = new Atom*[info[l].n_atoms]; |
1273 | > | the_molecules = new Molecule[info[l].n_mol]; |
1274 | > | int molIndex; |
1275 | ||
1276 | < | if( !done && n_per_extra > 1 ){ |
1277 | < | makeElement( i * cellx + 0.5 * cellx, |
1278 | < | j * celly + 0.5 * celly, |
1279 | < | k * cellz ); |
1280 | < | done = ( current_mol >= tot_nmol ); |
1281 | < | } |
1276 | > | // initialize the molecule's stampID's |
1277 | > | |
1278 | > | #ifdef IS_MPI |
1279 | > | |
1280 | > | |
1281 | > | molIndex = 0; |
1282 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1283 | > | |
1284 | > | if(mol2proc[i] == worldRank ){ |
1285 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
1286 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1287 | > | the_molecules[molIndex].setGlobalIndex( i ); |
1288 | > | molIndex++; |
1289 | > | } |
1290 | > | } |
1291 | > | |
1292 | > | #else // is_mpi |
1293 | > | |
1294 | > | molIndex = 0; |
1295 | > | globalAtomIndex = 0; |
1296 | > | for(i=0; i<n_components; i++){ |
1297 | > | for(j=0; j<components_nmol[i]; j++ ){ |
1298 | > | the_molecules[molIndex].setStampID( i ); |
1299 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1300 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1301 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1302 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1303 | > | globalAtomIndex++; |
1304 | > | } |
1305 | > | molIndex++; |
1306 | > | } |
1307 | > | } |
1308 | > | |
1309 | > | |
1310 | > | #endif // is_mpi |
1311 | ||
1204 | – | if( !done && n_per_extra > 2){ |
1205 | – | makeElement( i * cellx, |
1206 | – | j * celly + 0.5 * celly, |
1207 | – | k * cellz + 0.5 * cellz ); |
1208 | – | done = ( current_mol >= tot_nmol ); |
1209 | – | } |
1312 | ||
1313 | < | if( !done && n_per_extra > 3){ |
1314 | < | makeElement( i * cellx + 0.5 * cellx, |
1315 | < | j * celly, |
1316 | < | k * cellz + 0.5 * cellz ); |
1317 | < | done = ( current_mol >= tot_nmol ); |
1318 | < | } |
1217 | < | } |
1313 | > | if( info[l].n_SRI ){ |
1314 | > | |
1315 | > | Exclude::createArray(info[l].n_SRI); |
1316 | > | the_excludes = new Exclude*[info[l].n_SRI]; |
1317 | > | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1318 | > | the_excludes[ex] = new Exclude(ex); |
1319 | } | |
1320 | + | info[l].globalExcludes = new int; |
1321 | + | info[l].n_exclude = info[l].n_SRI; |
1322 | } | |
1323 | < | } |
1323 | > | else{ |
1324 | > | |
1325 | > | Exclude::createArray( 1 ); |
1326 | > | the_excludes = new Exclude*; |
1327 | > | the_excludes[0] = new Exclude(0); |
1328 | > | the_excludes[0]->setPair( 0,0 ); |
1329 | > | info[l].globalExcludes = new int; |
1330 | > | info[l].globalExcludes[0] = 0; |
1331 | > | info[l].n_exclude = 0; |
1332 | > | } |
1333 | ||
1334 | + | // set the arrays into the SimInfo object |
1335 | ||
1336 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1337 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1338 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1339 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
1336 | > | info[l].atoms = the_atoms; |
1337 | > | info[l].molecules = the_molecules; |
1338 | > | info[l].nGlobalExcludes = 0; |
1339 | > | info[l].excludes = the_excludes; |
1340 | > | |
1341 | > | the_ff->setSimInfo( info ); |
1342 | > | |
1343 | } | |
1344 | } | |
1345 | ||
1346 | < | void SimSetup::makeElement( double x, double y, double z ){ |
1346 | > | void SimSetup::makeIntegrator( void ){ |
1347 | ||
1348 | int k; | |
1233 | – | AtomStamp* current_atom; |
1234 | – | DirectionalAtom* dAtom; |
1235 | – | double rotMat[3][3]; |
1349 | ||
1350 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1351 | < | |
1352 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1353 | < | if( !current_atom->havePosition() ){ |
1350 | > | NVT<RealIntegrator>* myNVT = NULL; |
1351 | > | NPTi<RealIntegrator>* myNPTi = NULL; |
1352 | > | NPTf<RealIntegrator>* myNPTf = NULL; |
1353 | > | NPTim<RealIntegrator>* myNPTim = NULL; |
1354 | > | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1355 | > | |
1356 | > | for(k=0; k<nInfo; k++){ |
1357 | > | |
1358 | > | switch( ensembleCase ){ |
1359 | > | |
1360 | > | case NVE_ENS: |
1361 | > | if (haveZConstraint){ |
1362 | > | setupZConstraint(); |
1363 | > | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1364 | > | } |
1365 | > | |
1366 | > | else |
1367 | > | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1368 | > | break; |
1369 | > | |
1370 | > | case NVT_ENS: |
1371 | > | if (haveZConstraint){ |
1372 | > | setupZConstraint(); |
1373 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1374 | > | } |
1375 | > | else |
1376 | > | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1377 | > | |
1378 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1379 | > | |
1380 | > | if (globals->haveTauThermostat()) |
1381 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1382 | > | |
1383 | > | else { |
1384 | > | sprintf( painCave.errMsg, |
1385 | > | "SimSetup error: If you use the NVT\n" |
1386 | > | " ensemble, you must set tauThermostat.\n"); |
1387 | > | painCave.isFatal = 1; |
1388 | > | simError(); |
1389 | > | } |
1390 | > | break; |
1391 | > | |
1392 | > | case NPTi_ENS: |
1393 | > | if (haveZConstraint){ |
1394 | > | setupZConstraint(); |
1395 | > | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1396 | > | } |
1397 | > | else |
1398 | > | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1399 | > | |
1400 | > | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1401 | > | |
1402 | > | if (globals->haveTargetPressure()) |
1403 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1404 | > | else { |
1405 | > | sprintf( painCave.errMsg, |
1406 | > | "SimSetup error: If you use a constant pressure\n" |
1407 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1408 | > | painCave.isFatal = 1; |
1409 | > | simError(); |
1410 | > | } |
1411 | > | |
1412 | > | if( globals->haveTauThermostat() ) |
1413 | > | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1414 | > | else{ |
1415 | > | sprintf( painCave.errMsg, |
1416 | > | "SimSetup error: If you use an NPT\n" |
1417 | > | " ensemble, you must set tauThermostat.\n"); |
1418 | > | painCave.isFatal = 1; |
1419 | > | simError(); |
1420 | > | } |
1421 | > | |
1422 | > | if( globals->haveTauBarostat() ) |
1423 | > | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1424 | > | else{ |
1425 | > | sprintf( painCave.errMsg, |
1426 | > | "SimSetup error: If you use an NPT\n" |
1427 | > | " ensemble, you must set tauBarostat.\n"); |
1428 | > | painCave.isFatal = 1; |
1429 | > | simError(); |
1430 | > | } |
1431 | > | break; |
1432 | > | |
1433 | > | case NPTf_ENS: |
1434 | > | if (haveZConstraint){ |
1435 | > | setupZConstraint(); |
1436 | > | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1437 | > | } |
1438 | > | else |
1439 | > | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1440 | > | |
1441 | > | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1442 | > | |
1443 | > | if (globals->haveTargetPressure()) |
1444 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1445 | > | else { |
1446 | > | sprintf( painCave.errMsg, |
1447 | > | "SimSetup error: If you use a constant pressure\n" |
1448 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1449 | > | painCave.isFatal = 1; |
1450 | > | simError(); |
1451 | > | } |
1452 | > | |
1453 | > | if( globals->haveTauThermostat() ) |
1454 | > | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1455 | > | else{ |
1456 | > | sprintf( painCave.errMsg, |
1457 | > | "SimSetup error: If you use an NPT\n" |
1458 | > | " ensemble, you must set tauThermostat.\n"); |
1459 | > | painCave.isFatal = 1; |
1460 | > | simError(); |
1461 | > | } |
1462 | > | |
1463 | > | if( globals->haveTauBarostat() ) |
1464 | > | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1465 | > | else{ |
1466 | > | sprintf( painCave.errMsg, |
1467 | > | "SimSetup error: If you use an NPT\n" |
1468 | > | " ensemble, you must set tauBarostat.\n"); |
1469 | > | painCave.isFatal = 1; |
1470 | > | simError(); |
1471 | > | } |
1472 | > | break; |
1473 | > | |
1474 | > | case NPTim_ENS: |
1475 | > | if (haveZConstraint){ |
1476 | > | setupZConstraint(); |
1477 | > | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1478 | > | } |
1479 | > | else |
1480 | > | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1481 | > | |
1482 | > | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1483 | > | |
1484 | > | if (globals->haveTargetPressure()) |
1485 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1486 | > | else { |
1487 | > | sprintf( painCave.errMsg, |
1488 | > | "SimSetup error: If you use a constant pressure\n" |
1489 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1490 | > | painCave.isFatal = 1; |
1491 | > | simError(); |
1492 | > | } |
1493 | > | |
1494 | > | if( globals->haveTauThermostat() ) |
1495 | > | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1496 | > | else{ |
1497 | > | sprintf( painCave.errMsg, |
1498 | > | "SimSetup error: If you use an NPT\n" |
1499 | > | " ensemble, you must set tauThermostat.\n"); |
1500 | > | painCave.isFatal = 1; |
1501 | > | simError(); |
1502 | > | } |
1503 | > | |
1504 | > | if( globals->haveTauBarostat() ) |
1505 | > | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1506 | > | else{ |
1507 | sprintf( painCave.errMsg, | |
1508 | < | "SimSetup:initFromBass error.\n" |
1509 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
1244 | < | "\tThe initialization routine is unable to give a start" |
1245 | < | " position.\n", |
1246 | < | comp_stamps[current_comp]->getID(), |
1247 | < | current_atom->getType() ); |
1508 | > | "SimSetup error: If you use an NPT\n" |
1509 | > | " ensemble, you must set tauBarostat.\n"); |
1510 | painCave.isFatal = 1; | |
1511 | simError(); | |
1512 | + | } |
1513 | + | break; |
1514 | + | |
1515 | + | case NPTfm_ENS: |
1516 | + | if (haveZConstraint){ |
1517 | + | setupZConstraint(); |
1518 | + | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1519 | + | } |
1520 | + | else |
1521 | + | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1522 | + | |
1523 | + | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1524 | + | |
1525 | + | if (globals->haveTargetPressure()) |
1526 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1527 | + | else { |
1528 | + | sprintf( painCave.errMsg, |
1529 | + | "SimSetup error: If you use a constant pressure\n" |
1530 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1531 | + | painCave.isFatal = 1; |
1532 | + | simError(); |
1533 | + | } |
1534 | + | |
1535 | + | if( globals->haveTauThermostat() ) |
1536 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1537 | + | else{ |
1538 | + | sprintf( painCave.errMsg, |
1539 | + | "SimSetup error: If you use an NPT\n" |
1540 | + | " ensemble, you must set tauThermostat.\n"); |
1541 | + | painCave.isFatal = 1; |
1542 | + | simError(); |
1543 | + | } |
1544 | + | |
1545 | + | if( globals->haveTauBarostat() ) |
1546 | + | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1547 | + | else{ |
1548 | + | sprintf( painCave.errMsg, |
1549 | + | "SimSetup error: If you use an NPT\n" |
1550 | + | " ensemble, you must set tauBarostat.\n"); |
1551 | + | painCave.isFatal = 1; |
1552 | + | simError(); |
1553 | + | } |
1554 | + | break; |
1555 | + | |
1556 | + | default: |
1557 | + | sprintf( painCave.errMsg, |
1558 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1559 | + | painCave.isFatal = 1; |
1560 | + | simError(); |
1561 | } | |
1562 | + | } |
1563 | + | } |
1564 | ||
1565 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1253 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1254 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1565 | > | void SimSetup::initFortran( void ){ |
1566 | ||
1567 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1567 | > | info[0].refreshSim(); |
1568 | > | |
1569 | > | if( !strcmp( info[0].mixingRule, "standard") ){ |
1570 | > | the_ff->initForceField( LB_MIXING_RULE ); |
1571 | > | } |
1572 | > | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1573 | > | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1574 | > | } |
1575 | > | else{ |
1576 | > | sprintf( painCave.errMsg, |
1577 | > | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1578 | > | info[0].mixingRule ); |
1579 | > | painCave.isFatal = 1; |
1580 | > | simError(); |
1581 | > | } |
1582 | ||
1258 | – | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1583 | ||
1584 | < | rotMat[0][0] = 1.0; |
1585 | < | rotMat[0][1] = 0.0; |
1586 | < | rotMat[0][2] = 0.0; |
1584 | > | #ifdef IS_MPI |
1585 | > | strcpy( checkPointMsg, |
1586 | > | "Successfully intialized the mixingRule for Fortran." ); |
1587 | > | MPIcheckPoint(); |
1588 | > | #endif // is_mpi |
1589 | ||
1590 | < | rotMat[1][0] = 0.0; |
1265 | < | rotMat[1][1] = 1.0; |
1266 | < | rotMat[1][2] = 0.0; |
1590 | > | } |
1591 | ||
1592 | < | rotMat[2][0] = 0.0; |
1593 | < | rotMat[2][1] = 0.0; |
1594 | < | rotMat[2][2] = 1.0; |
1592 | > | void SimSetup::setupZConstraint() |
1593 | > | { |
1594 | > | int k; |
1595 | ||
1596 | < | dAtom->setA( rotMat ); |
1596 | > | for(k=0; k<nInfo; k++){ |
1597 | > | |
1598 | > | if(globals->haveZConsTime()){ |
1599 | > | |
1600 | > | //add sample time of z-constraint into SimInfo's property list |
1601 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1602 | > | zconsTimeProp->setID("zconstime"); |
1603 | > | zconsTimeProp->setData(globals->getZConsTime()); |
1604 | > | info[k].addProperty(zconsTimeProp); |
1605 | } | |
1606 | < | |
1607 | < | current_atom_ndx++; |
1606 | > | else{ |
1607 | > | sprintf( painCave.errMsg, |
1608 | > | "ZConstraint error: If you use an ZConstraint\n" |
1609 | > | " , you must set sample time.\n"); |
1610 | > | painCave.isFatal = 1; |
1611 | > | simError(); |
1612 | > | } |
1613 | > | |
1614 | > | if(globals->haveIndexOfAllZConsMols()){ |
1615 | > | |
1616 | > | //add index of z-constraint molecules into SimInfo's property list |
1617 | > | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1618 | > | |
1619 | > | //sort the index |
1620 | > | sort(tempIndex.begin(), tempIndex.end()); |
1621 | > | |
1622 | > | IndexData* zconsIndex = new IndexData(); |
1623 | > | zconsIndex->setID("zconsindex"); |
1624 | > | zconsIndex->setIndexData(tempIndex); |
1625 | > | info[k].addProperty(zconsIndex); |
1626 | > | } |
1627 | > | else{ |
1628 | > | sprintf( painCave.errMsg, |
1629 | > | "SimSetup error: If you use an ZConstraint\n" |
1630 | > | " , you must set index of z-constraint molecules.\n"); |
1631 | > | painCave.isFatal = 1; |
1632 | > | simError(); |
1633 | > | |
1634 | > | } |
1635 | > | |
1636 | > | //Determine the name of ouput file and add it into SimInfo's property list |
1637 | > | //Be careful, do not use inFileName, since it is a pointer which |
1638 | > | //point to a string at master node, and slave nodes do not contain that string |
1639 | > | |
1640 | > | string zconsOutput(info[k].finalName); |
1641 | > | |
1642 | > | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1643 | > | |
1644 | > | StringData* zconsFilename = new StringData(); |
1645 | > | zconsFilename->setID("zconsfilename"); |
1646 | > | zconsFilename->setData(zconsOutput); |
1647 | > | |
1648 | > | info[k].addProperty(zconsFilename); |
1649 | } | |
1277 | – | |
1278 | – | current_mol++; |
1279 | – | current_comp_mol++; |
1280 | – | |
1281 | – | if( current_comp_mol >= components_nmol[current_comp] ){ |
1282 | – | |
1283 | – | current_comp_mol = 0; |
1284 | – | current_comp++; |
1285 | – | } |
1650 | } |
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