# | 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 "ReadWrite.hpp" |
9 | #include "parse_me.h" | |
10 | #include "Integrator.hpp" | |
11 | #include "simError.h" | |
# | Line 14 | Line 17 | |
17 | ||
18 | // some defines for ensemble and Forcefield cases | |
19 | ||
20 | < | #define NVE_ENS 0 |
21 | < | #define NVT_ENS 1 |
22 | < | #define NPTi_ENS 2 |
23 | < | #define NPTf_ENS 3 |
20 | > | #define NVE_ENS 0 |
21 | > | #define NVT_ENS 1 |
22 | > | #define NPTi_ENS 2 |
23 | > | #define NPTf_ENS 3 |
24 | > | #define NPTim_ENS 4 |
25 | > | #define NPTfm_ENS 5 |
26 | ||
22 | – | |
27 | #define FF_DUFF 0 | |
28 | #define FF_LJ 1 | |
29 | + | #define FF_EAM 2 |
30 | ||
31 | + | using namespace std; |
32 | ||
33 | SimSetup::SimSetup(){ | |
34 | + | |
35 | + | isInfoArray = 0; |
36 | + | nInfo = 1; |
37 | + | |
38 | stamps = new MakeStamps(); | |
39 | globals = new Globals(); | |
40 | ||
41 | + | |
42 | #ifdef IS_MPI | |
43 | strcpy( checkPointMsg, "SimSetup creation successful" ); | |
44 | MPIcheckPoint(); | |
# | Line 39 | Line 50 | SimSetup::~SimSetup(){ | |
50 | delete globals; | |
51 | } | |
52 | ||
53 | + | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
54 | + | info = the_info; |
55 | + | nInfo = theNinfo; |
56 | + | isInfoArray = 1; |
57 | + | } |
58 | + | |
59 | + | |
60 | void SimSetup::parseFile( char* fileName ){ | |
61 | ||
62 | #ifdef IS_MPI | |
# | Line 74 | Line 92 | void SimSetup::receiveParse(void){ | |
92 | ||
93 | #endif // is_mpi | |
94 | ||
95 | < | void SimSetup::createSim( void ){ |
95 | > | void SimSetup::createSim(void){ |
96 | ||
79 | – | MakeStamps *the_stamps; |
80 | – | Globals* the_globals; |
97 | int i, j, k, globalAtomIndex; | |
98 | ||
99 | < | int ensembleCase; |
100 | < | int ffCase; |
99 | > | // gather all of the information from the Bass file |
100 | > | |
101 | > | std::cerr << "gathering info\n"; |
102 | > | |
103 | > | gatherInfo(); |
104 | > | |
105 | > | // creation of complex system objects |
106 | > | |
107 | > | std::cerr << "creating system objects\n"; |
108 | > | |
109 | > | sysObjectsCreation(); |
110 | > | |
111 | > | // check on the post processing info |
112 | ||
113 | < | ensembleCase = -1; |
87 | < | ffCase = -1; |
113 | > | std::cerr << "performing final info check.\n"; |
114 | ||
115 | < | // get the stamps and globals; |
90 | < | the_stamps = stamps; |
91 | < | the_globals = globals; |
115 | > | finalInfoCheck(); |
116 | ||
117 | < | // set the easy ones first |
94 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
95 | < | simnfo->dt = the_globals->getDt(); |
96 | < | simnfo->run_time = the_globals->getRunTime(); |
117 | > | // initialize the system coordinates |
118 | ||
119 | < | // get the ones we know are there, yet still may need some work. |
99 | < | n_components = the_globals->getNComponents(); |
100 | < | strcpy( force_field, the_globals->getForceField() ); |
119 | > | std::cerr << "about to init coords\n"; |
120 | ||
121 | + | if( !isInfoArray ) initSystemCoords(); |
122 | + | |
123 | + | // make the output filenames |
124 | + | |
125 | + | makeOutNames(); |
126 | + | |
127 | + | // make the integrator |
128 | + | |
129 | + | makeIntegrator(); |
130 | + | |
131 | + | #ifdef IS_MPI |
132 | + | mpiSim->mpiRefresh(); |
133 | + | #endif |
134 | + | |
135 | + | // initialize the Fortran |
136 | + | |
137 | + | initFortran(); |
138 | + | |
139 | + | |
140 | + | |
141 | + | } |
142 | + | |
143 | + | |
144 | + | void SimSetup::makeMolecules( void ){ |
145 | + | |
146 | + | int k,l; |
147 | + | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
148 | + | molInit molInfo; |
149 | + | DirectionalAtom* dAtom; |
150 | + | LinkedAssign* extras; |
151 | + | LinkedAssign* current_extra; |
152 | + | AtomStamp* currentAtom; |
153 | + | BondStamp* currentBond; |
154 | + | BendStamp* currentBend; |
155 | + | TorsionStamp* currentTorsion; |
156 | + | |
157 | + | bond_pair* theBonds; |
158 | + | bend_set* theBends; |
159 | + | torsion_set* theTorsions; |
160 | + | |
161 | + | |
162 | + | //init the forceField paramters |
163 | + | |
164 | + | the_ff->readParams(); |
165 | + | |
166 | + | |
167 | + | // init the atoms |
168 | + | |
169 | + | double ux, uy, uz, u, uSqr; |
170 | + | |
171 | + | for(k=0; k<nInfo; k++){ |
172 | + | |
173 | + | the_ff->setSimInfo( &(info[k]) ); |
174 | + | |
175 | + | atomOffset = 0; |
176 | + | excludeOffset = 0; |
177 | + | for(i=0; i<info[k].n_mol; i++){ |
178 | + | |
179 | + | stampID = info[k].molecules[i].getStampID(); |
180 | + | |
181 | + | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
182 | + | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
183 | + | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
184 | + | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
185 | + | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
186 | + | |
187 | + | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
188 | + | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
189 | + | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
190 | + | molInfo.myBends = new Bend*[molInfo.nBends]; |
191 | + | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
192 | + | |
193 | + | theBonds = new bond_pair[molInfo.nBonds]; |
194 | + | theBends = new bend_set[molInfo.nBends]; |
195 | + | theTorsions = new torsion_set[molInfo.nTorsions]; |
196 | + | |
197 | + | // make the Atoms |
198 | + | |
199 | + | for(j=0; j<molInfo.nAtoms; j++){ |
200 | + | |
201 | + | currentAtom = comp_stamps[stampID]->getAtom( j ); |
202 | + | if( currentAtom->haveOrientation() ){ |
203 | + | |
204 | + | dAtom = new DirectionalAtom( (j + atomOffset), |
205 | + | info[k].getConfiguration() ); |
206 | + | info[k].n_oriented++; |
207 | + | molInfo.myAtoms[j] = dAtom; |
208 | + | |
209 | + | ux = currentAtom->getOrntX(); |
210 | + | uy = currentAtom->getOrntY(); |
211 | + | uz = currentAtom->getOrntZ(); |
212 | + | |
213 | + | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
214 | + | |
215 | + | u = sqrt( uSqr ); |
216 | + | ux = ux / u; |
217 | + | uy = uy / u; |
218 | + | uz = uz / u; |
219 | + | |
220 | + | dAtom->setSUx( ux ); |
221 | + | dAtom->setSUy( uy ); |
222 | + | dAtom->setSUz( uz ); |
223 | + | } |
224 | + | else{ |
225 | + | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
226 | + | info[k].getConfiguration() ); |
227 | + | } |
228 | + | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
229 | + | |
230 | + | #ifdef IS_MPI |
231 | + | |
232 | + | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
233 | + | |
234 | + | #endif // is_mpi |
235 | + | } |
236 | + | |
237 | + | // make the bonds |
238 | + | for(j=0; j<molInfo.nBonds; j++){ |
239 | + | |
240 | + | currentBond = comp_stamps[stampID]->getBond( j ); |
241 | + | theBonds[j].a = currentBond->getA() + atomOffset; |
242 | + | theBonds[j].b = currentBond->getB() + atomOffset; |
243 | + | |
244 | + | exI = theBonds[j].a; |
245 | + | exJ = theBonds[j].b; |
246 | + | |
247 | + | // exclude_I must always be the smaller of the pair |
248 | + | if( exI > exJ ){ |
249 | + | tempEx = exI; |
250 | + | exI = exJ; |
251 | + | exJ = tempEx; |
252 | + | } |
253 | + | #ifdef IS_MPI |
254 | + | tempEx = exI; |
255 | + | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
256 | + | tempEx = exJ; |
257 | + | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
258 | + | |
259 | + | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
260 | + | #else // isn't MPI |
261 | + | |
262 | + | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
263 | + | #endif //is_mpi |
264 | + | } |
265 | + | excludeOffset += molInfo.nBonds; |
266 | + | |
267 | + | //make the bends |
268 | + | for(j=0; j<molInfo.nBends; j++){ |
269 | + | |
270 | + | currentBend = comp_stamps[stampID]->getBend( j ); |
271 | + | theBends[j].a = currentBend->getA() + atomOffset; |
272 | + | theBends[j].b = currentBend->getB() + atomOffset; |
273 | + | theBends[j].c = currentBend->getC() + atomOffset; |
274 | + | |
275 | + | if( currentBend->haveExtras() ){ |
276 | + | |
277 | + | extras = currentBend->getExtras(); |
278 | + | current_extra = extras; |
279 | + | |
280 | + | while( current_extra != NULL ){ |
281 | + | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
282 | + | |
283 | + | switch( current_extra->getType() ){ |
284 | + | |
285 | + | case 0: |
286 | + | theBends[j].ghost = |
287 | + | current_extra->getInt() + atomOffset; |
288 | + | theBends[j].isGhost = 1; |
289 | + | break; |
290 | + | |
291 | + | case 1: |
292 | + | theBends[j].ghost = |
293 | + | (int)current_extra->getDouble() + atomOffset; |
294 | + | theBends[j].isGhost = 1; |
295 | + | break; |
296 | + | |
297 | + | default: |
298 | + | sprintf( painCave.errMsg, |
299 | + | "SimSetup Error: ghostVectorSource was neither a " |
300 | + | "double nor an int.\n" |
301 | + | "-->Bend[%d] in %s\n", |
302 | + | j, comp_stamps[stampID]->getID() ); |
303 | + | painCave.isFatal = 1; |
304 | + | simError(); |
305 | + | } |
306 | + | } |
307 | + | |
308 | + | else{ |
309 | + | |
310 | + | sprintf( painCave.errMsg, |
311 | + | "SimSetup Error: unhandled bend assignment:\n" |
312 | + | " -->%s in Bend[%d] in %s\n", |
313 | + | current_extra->getlhs(), |
314 | + | j, comp_stamps[stampID]->getID() ); |
315 | + | painCave.isFatal = 1; |
316 | + | simError(); |
317 | + | } |
318 | + | |
319 | + | current_extra = current_extra->getNext(); |
320 | + | } |
321 | + | } |
322 | + | |
323 | + | if( !theBends[j].isGhost ){ |
324 | + | |
325 | + | exI = theBends[j].a; |
326 | + | exJ = theBends[j].c; |
327 | + | } |
328 | + | else{ |
329 | + | |
330 | + | exI = theBends[j].a; |
331 | + | exJ = theBends[j].b; |
332 | + | } |
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 = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
343 | + | tempEx = exJ; |
344 | + | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
345 | + | |
346 | + | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
347 | + | #else // isn't MPI |
348 | + | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 | + | #endif //is_mpi |
350 | + | } |
351 | + | excludeOffset += molInfo.nBends; |
352 | + | |
353 | + | for(j=0; j<molInfo.nTorsions; j++){ |
354 | + | |
355 | + | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
356 | + | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
357 | + | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
358 | + | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
359 | + | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
360 | + | |
361 | + | exI = theTorsions[j].a; |
362 | + | exJ = theTorsions[j].d; |
363 | + | |
364 | + | // exclude_I must always be the smaller of the pair |
365 | + | if( exI > exJ ){ |
366 | + | tempEx = exI; |
367 | + | exI = exJ; |
368 | + | exJ = tempEx; |
369 | + | } |
370 | + | #ifdef IS_MPI |
371 | + | tempEx = exI; |
372 | + | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
373 | + | tempEx = exJ; |
374 | + | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
375 | + | |
376 | + | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
377 | + | #else // isn't MPI |
378 | + | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
379 | + | #endif //is_mpi |
380 | + | } |
381 | + | excludeOffset += molInfo.nTorsions; |
382 | + | |
383 | + | |
384 | + | // send the arrays off to the forceField for init. |
385 | + | |
386 | + | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
387 | + | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
388 | + | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
389 | + | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
390 | + | |
391 | + | |
392 | + | info[k].molecules[i].initialize( molInfo ); |
393 | + | |
394 | + | |
395 | + | atomOffset += molInfo.nAtoms; |
396 | + | delete[] theBonds; |
397 | + | delete[] theBends; |
398 | + | delete[] theTorsions; |
399 | + | } |
400 | + | } |
401 | + | |
402 | + | #ifdef IS_MPI |
403 | + | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
404 | + | MPIcheckPoint(); |
405 | + | #endif // is_mpi |
406 | + | |
407 | + | // clean up the forcefield |
408 | + | |
409 | + | the_ff->calcRcut(); |
410 | + | the_ff->cleanMe(); |
411 | + | |
412 | + | } |
413 | + | |
414 | + | void SimSetup::initFromBass( void ){ |
415 | + | |
416 | + | int i, j, k; |
417 | + | int n_cells; |
418 | + | double cellx, celly, cellz; |
419 | + | double temp1, temp2, temp3; |
420 | + | int n_per_extra; |
421 | + | int n_extra; |
422 | + | int have_extra, done; |
423 | + | |
424 | + | double vel[3]; |
425 | + | vel[0] = 0.0; |
426 | + | vel[1] = 0.0; |
427 | + | vel[2] = 0.0; |
428 | + | |
429 | + | temp1 = (double)tot_nmol / 4.0; |
430 | + | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
431 | + | temp3 = ceil( temp2 ); |
432 | + | |
433 | + | have_extra =0; |
434 | + | if( temp2 < temp3 ){ // we have a non-complete lattice |
435 | + | have_extra =1; |
436 | + | |
437 | + | n_cells = (int)temp3 - 1; |
438 | + | cellx = info[0].boxL[0] / temp3; |
439 | + | celly = info[0].boxL[1] / temp3; |
440 | + | cellz = info[0].boxL[2] / temp3; |
441 | + | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
442 | + | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
443 | + | n_per_extra = (int)ceil( temp1 ); |
444 | + | |
445 | + | if( n_per_extra > 4){ |
446 | + | sprintf( painCave.errMsg, |
447 | + | "SimSetup error. There has been an error in constructing" |
448 | + | " the non-complete lattice.\n" ); |
449 | + | painCave.isFatal = 1; |
450 | + | simError(); |
451 | + | } |
452 | + | } |
453 | + | else{ |
454 | + | n_cells = (int)temp3; |
455 | + | cellx = info[0].boxL[0] / temp3; |
456 | + | celly = info[0].boxL[1] / temp3; |
457 | + | cellz = info[0].boxL[2] / temp3; |
458 | + | } |
459 | + | |
460 | + | current_mol = 0; |
461 | + | current_comp_mol = 0; |
462 | + | current_comp = 0; |
463 | + | current_atom_ndx = 0; |
464 | + | |
465 | + | for( i=0; i < n_cells ; i++ ){ |
466 | + | for( j=0; j < n_cells; j++ ){ |
467 | + | for( k=0; k < n_cells; k++ ){ |
468 | + | |
469 | + | makeElement( i * cellx, |
470 | + | j * celly, |
471 | + | k * cellz ); |
472 | + | |
473 | + | makeElement( i * cellx + 0.5 * cellx, |
474 | + | j * celly + 0.5 * celly, |
475 | + | k * cellz ); |
476 | + | |
477 | + | makeElement( i * cellx, |
478 | + | j * celly + 0.5 * celly, |
479 | + | k * cellz + 0.5 * cellz ); |
480 | + | |
481 | + | makeElement( i * cellx + 0.5 * cellx, |
482 | + | j * celly, |
483 | + | k * cellz + 0.5 * cellz ); |
484 | + | } |
485 | + | } |
486 | + | } |
487 | + | |
488 | + | if( have_extra ){ |
489 | + | done = 0; |
490 | + | |
491 | + | int start_ndx; |
492 | + | for( i=0; i < (n_cells+1) && !done; i++ ){ |
493 | + | for( j=0; j < (n_cells+1) && !done; j++ ){ |
494 | + | |
495 | + | if( i < n_cells ){ |
496 | + | |
497 | + | if( j < n_cells ){ |
498 | + | start_ndx = n_cells; |
499 | + | } |
500 | + | else start_ndx = 0; |
501 | + | } |
502 | + | else start_ndx = 0; |
503 | + | |
504 | + | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
505 | + | |
506 | + | makeElement( i * cellx, |
507 | + | j * celly, |
508 | + | k * cellz ); |
509 | + | done = ( current_mol >= tot_nmol ); |
510 | + | |
511 | + | if( !done && n_per_extra > 1 ){ |
512 | + | makeElement( i * cellx + 0.5 * cellx, |
513 | + | j * celly + 0.5 * celly, |
514 | + | k * cellz ); |
515 | + | done = ( current_mol >= tot_nmol ); |
516 | + | } |
517 | + | |
518 | + | if( !done && n_per_extra > 2){ |
519 | + | makeElement( i * cellx, |
520 | + | j * celly + 0.5 * celly, |
521 | + | k * cellz + 0.5 * cellz ); |
522 | + | done = ( current_mol >= tot_nmol ); |
523 | + | } |
524 | + | |
525 | + | if( !done && n_per_extra > 3){ |
526 | + | makeElement( i * cellx + 0.5 * cellx, |
527 | + | j * celly, |
528 | + | k * cellz + 0.5 * cellz ); |
529 | + | done = ( current_mol >= tot_nmol ); |
530 | + | } |
531 | + | } |
532 | + | } |
533 | + | } |
534 | + | } |
535 | + | |
536 | + | for( i=0; i<info[0].n_atoms; i++ ){ |
537 | + | info[0].atoms[i]->setVel( vel ); |
538 | + | } |
539 | + | } |
540 | + | |
541 | + | void SimSetup::makeElement( double x, double y, double z ){ |
542 | + | |
543 | + | int k; |
544 | + | AtomStamp* current_atom; |
545 | + | DirectionalAtom* dAtom; |
546 | + | double rotMat[3][3]; |
547 | + | double pos[3]; |
548 | + | |
549 | + | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
550 | + | |
551 | + | current_atom = comp_stamps[current_comp]->getAtom( k ); |
552 | + | if( !current_atom->havePosition() ){ |
553 | + | sprintf( painCave.errMsg, |
554 | + | "SimSetup:initFromBass error.\n" |
555 | + | "\tComponent %s, atom %s does not have a position specified.\n" |
556 | + | "\tThe initialization routine is unable to give a start" |
557 | + | " position.\n", |
558 | + | comp_stamps[current_comp]->getID(), |
559 | + | current_atom->getType() ); |
560 | + | painCave.isFatal = 1; |
561 | + | simError(); |
562 | + | } |
563 | + | |
564 | + | pos[0] = x + current_atom->getPosX(); |
565 | + | pos[1] = y + current_atom->getPosY(); |
566 | + | pos[2] = z + current_atom->getPosZ(); |
567 | + | |
568 | + | info[0].atoms[current_atom_ndx]->setPos( pos ); |
569 | + | |
570 | + | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
571 | + | |
572 | + | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
573 | + | |
574 | + | rotMat[0][0] = 1.0; |
575 | + | rotMat[0][1] = 0.0; |
576 | + | rotMat[0][2] = 0.0; |
577 | + | |
578 | + | rotMat[1][0] = 0.0; |
579 | + | rotMat[1][1] = 1.0; |
580 | + | rotMat[1][2] = 0.0; |
581 | + | |
582 | + | rotMat[2][0] = 0.0; |
583 | + | rotMat[2][1] = 0.0; |
584 | + | rotMat[2][2] = 1.0; |
585 | + | |
586 | + | dAtom->setA( rotMat ); |
587 | + | } |
588 | + | |
589 | + | current_atom_ndx++; |
590 | + | } |
591 | + | |
592 | + | current_mol++; |
593 | + | current_comp_mol++; |
594 | + | |
595 | + | if( current_comp_mol >= components_nmol[current_comp] ){ |
596 | + | |
597 | + | current_comp_mol = 0; |
598 | + | current_comp++; |
599 | + | } |
600 | + | } |
601 | + | |
602 | + | |
603 | + | void SimSetup::gatherInfo( void ){ |
604 | + | int i,j,k; |
605 | + | |
606 | + | ensembleCase = -1; |
607 | + | ffCase = -1; |
608 | + | |
609 | + | // set the easy ones first |
610 | + | |
611 | + | for( i=0; i<nInfo; i++){ |
612 | + | info[i].target_temp = globals->getTargetTemp(); |
613 | + | info[i].dt = globals->getDt(); |
614 | + | info[i].run_time = globals->getRunTime(); |
615 | + | } |
616 | + | n_components = globals->getNComponents(); |
617 | + | |
618 | + | |
619 | + | // get the forceField |
620 | + | |
621 | + | strcpy( force_field, globals->getForceField() ); |
622 | + | |
623 | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; | |
624 | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; | |
625 | + | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
626 | else{ | |
627 | sprintf( painCave.errMsg, | |
628 | "SimSetup Error. Unrecognized force field -> %s\n", | |
# | Line 109 | Line 631 | void SimSetup::createSim( void ){ | |
631 | simError(); | |
632 | } | |
633 | ||
634 | < | // get the ensemble: |
113 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
634 | > | // get the ensemble |
635 | ||
636 | + | strcpy( ensemble, globals->getEnsemble() ); |
637 | + | |
638 | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; | |
639 | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; | |
640 | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) | |
641 | ensembleCase = NPTi_ENS; | |
642 | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; | |
643 | + | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
644 | + | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
645 | else{ | |
646 | sprintf( painCave.errMsg, | |
647 | "SimSetup Warning. Unrecognized Ensemble -> %s, " | |
# | Line 127 | Line 652 | void SimSetup::createSim( void ){ | |
652 | strcpy( ensemble, "NVE" ); | |
653 | ensembleCase = NVE_ENS; | |
654 | } | |
655 | < | strcpy( simnfo->ensemble, ensemble ); |
655 | > | |
656 | > | for(i=0; i<nInfo; i++){ |
657 | > | |
658 | > | strcpy( info[i].ensemble, ensemble ); |
659 | ||
660 | + | // get the mixing rule |
661 | ||
662 | < | // if( !strcasecmp( ensemble, "NPT" ) ) { |
663 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
135 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
136 | < | // if (the_globals->haveTargetPressure()) |
137 | < | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
138 | < | // else { |
139 | < | // sprintf( painCave.errMsg, |
140 | < | // "SimSetup error: If you use the constant pressure\n" |
141 | < | // " ensemble, you must set targetPressure.\n" |
142 | < | // " This was found in the BASS file.\n"); |
143 | < | // painCave.isFatal = 1; |
144 | < | // simError(); |
145 | < | // } |
146 | < | |
147 | < | // if (the_globals->haveTauThermostat()) |
148 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
149 | < | // else if (the_globals->haveQmass()) |
150 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
151 | < | // else { |
152 | < | // sprintf( painCave.errMsg, |
153 | < | // "SimSetup error: If you use one of the constant temperature\n" |
154 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
155 | < | // " Neither of these was found in the BASS file.\n"); |
156 | < | // painCave.isFatal = 1; |
157 | < | // simError(); |
158 | < | // } |
159 | < | |
160 | < | // if (the_globals->haveTauBarostat()) |
161 | < | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
162 | < | // else { |
163 | < | // sprintf( painCave.errMsg, |
164 | < | // "SimSetup error: If you use the constant pressure\n" |
165 | < | // " ensemble, you must set tauBarostat.\n" |
166 | < | // " This was found in the BASS file.\n"); |
167 | < | // painCave.isFatal = 1; |
168 | < | // simError(); |
169 | < | // } |
170 | < | |
171 | < | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
172 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
173 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
174 | < | |
175 | < | // if (the_globals->haveTauThermostat()) |
176 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
177 | < | // else if (the_globals->haveQmass()) |
178 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
179 | < | // else { |
180 | < | // sprintf( painCave.errMsg, |
181 | < | // "SimSetup error: If you use one of the constant temperature\n" |
182 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
183 | < | // " Neither of these was found in the BASS file.\n"); |
184 | < | // painCave.isFatal = 1; |
185 | < | // simError(); |
186 | < | // } |
187 | < | |
188 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
189 | < | simnfo->usePBC = the_globals->getPBC(); |
190 | < | |
191 | < | int usesDipoles = 0; |
192 | < | switch( ffCase ){ |
193 | < | |
194 | < | case FF_DUFF: |
195 | < | the_ff = new DUFF(); |
196 | < | usesDipoles = 1; |
197 | < | break; |
198 | < | |
199 | < | case FF_LJ: |
200 | < | the_ff = new LJFF(); |
201 | < | break; |
202 | < | |
203 | < | default: |
204 | < | sprintf( painCave.errMsg, |
205 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
206 | < | painCave.isFatal = 1; |
207 | < | simError(); |
662 | > | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
663 | > | info[i].usePBC = globals->getPBC(); |
664 | } | |
665 | < | |
210 | < | #ifdef IS_MPI |
211 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
212 | < | MPIcheckPoint(); |
213 | < | #endif // is_mpi |
214 | < | |
665 | > | |
666 | // get the components and calculate the tot_nMol and indvidual n_mol | |
667 | < | the_components = the_globals->getComponents(); |
667 | > | |
668 | > | the_components = globals->getComponents(); |
669 | components_nmol = new int[n_components]; | |
218 | – | comp_stamps = new MoleculeStamp*[n_components]; |
670 | ||
671 | < | if( !the_globals->haveNMol() ){ |
671 | > | |
672 | > | if( !globals->haveNMol() ){ |
673 | // we don't have the total number of molecules, so we assume it is | |
674 | // given in each component | |
675 | ||
# | Line 246 | Line 698 | void SimSetup::createSim( void ){ | |
698 | " Please give nMol in the components.\n" ); | |
699 | painCave.isFatal = 1; | |
700 | simError(); | |
249 | – | |
250 | – | |
251 | – | // tot_nmol = the_globals->getNMol(); |
252 | – | |
253 | – | // //we have the total number of molecules, now we check for molfractions |
254 | – | // for( i=0; i<n_components; i++ ){ |
255 | – | |
256 | – | // if( !the_components[i]->haveMolFraction() ){ |
257 | – | |
258 | – | // if( !the_components[i]->haveNMol() ){ |
259 | – | // //we have a problem |
260 | – | // std::cerr << "SimSetup error. Neither molFraction nor " |
261 | – | // << " nMol was given in component |
262 | – | |
701 | } | |
702 | ||
703 | < | #ifdef IS_MPI |
266 | < | strcpy( checkPointMsg, "Have the number of components" ); |
267 | < | MPIcheckPoint(); |
268 | < | #endif // is_mpi |
269 | < | |
270 | < | // make an array of molecule stamps that match the components used. |
271 | < | // also extract the used stamps out into a separate linked list |
272 | < | |
273 | < | simnfo->nComponents = n_components; |
274 | < | simnfo->componentsNmol = components_nmol; |
275 | < | simnfo->compStamps = comp_stamps; |
276 | < | simnfo->headStamp = new LinkedMolStamp(); |
703 | > | // set the status, sample, and thermal kick times |
704 | ||
705 | < | char* id; |
279 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
280 | < | LinkedMolStamp* currentStamp = NULL; |
281 | < | for( i=0; i<n_components; i++ ){ |
705 | > | for(i=0; i<nInfo; i++){ |
706 | ||
707 | < | id = the_components[i]->getType(); |
708 | < | comp_stamps[i] = NULL; |
707 | > | if( globals->haveSampleTime() ){ |
708 | > | info[i].sampleTime = globals->getSampleTime(); |
709 | > | info[i].statusTime = info[i].sampleTime; |
710 | > | info[i].thermalTime = info[i].sampleTime; |
711 | > | } |
712 | > | else{ |
713 | > | info[i].sampleTime = globals->getRunTime(); |
714 | > | info[i].statusTime = info[i].sampleTime; |
715 | > | info[i].thermalTime = info[i].sampleTime; |
716 | > | } |
717 | ||
718 | < | // check to make sure the component isn't already in the list |
718 | > | if( globals->haveStatusTime() ){ |
719 | > | info[i].statusTime = globals->getStatusTime(); |
720 | > | } |
721 | > | |
722 | > | if( globals->haveThermalTime() ){ |
723 | > | info[i].thermalTime = globals->getThermalTime(); |
724 | > | } |
725 | ||
726 | < | comp_stamps[i] = headStamp->match( id ); |
727 | < | if( comp_stamps[i] == NULL ){ |
726 | > | // check for the temperature set flag |
727 | > | |
728 | > | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
729 | > | |
730 | > | // get some of the tricky things that may still be in the globals |
731 | > | |
732 | > | double boxVector[3]; |
733 | > | if( globals->haveBox() ){ |
734 | > | boxVector[0] = globals->getBox(); |
735 | > | boxVector[1] = globals->getBox(); |
736 | > | boxVector[2] = globals->getBox(); |
737 | ||
738 | < | // extract the component from the list; |
738 | > | info[i].setBox( boxVector ); |
739 | > | } |
740 | > | else if( globals->haveDensity() ){ |
741 | ||
742 | < | currentStamp = the_stamps->extractMolStamp( id ); |
743 | < | if( currentStamp == NULL ){ |
742 | > | double vol; |
743 | > | vol = (double)tot_nmol / globals->getDensity(); |
744 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
745 | > | boxVector[1] = boxVector[0]; |
746 | > | boxVector[2] = boxVector[0]; |
747 | > | |
748 | > | info[i].setBox( boxVector ); |
749 | > | } |
750 | > | else{ |
751 | > | if( !globals->haveBoxX() ){ |
752 | sprintf( painCave.errMsg, | |
753 | < | "SimSetup error: Component \"%s\" was not found in the " |
297 | < | "list of declared molecules\n", |
298 | < | id ); |
753 | > | "SimSetup error, no periodic BoxX size given.\n" ); |
754 | painCave.isFatal = 1; | |
755 | simError(); | |
756 | } | |
757 | + | boxVector[0] = globals->getBoxX(); |
758 | ||
759 | < | headStamp->add( currentStamp ); |
760 | < | comp_stamps[i] = headStamp->match( id ); |
759 | > | if( !globals->haveBoxY() ){ |
760 | > | sprintf( painCave.errMsg, |
761 | > | "SimSetup error, no periodic BoxY size given.\n" ); |
762 | > | painCave.isFatal = 1; |
763 | > | simError(); |
764 | > | } |
765 | > | boxVector[1] = globals->getBoxY(); |
766 | > | |
767 | > | if( !globals->haveBoxZ() ){ |
768 | > | sprintf( painCave.errMsg, |
769 | > | "SimSetup error, no periodic BoxZ size given.\n" ); |
770 | > | painCave.isFatal = 1; |
771 | > | simError(); |
772 | > | } |
773 | > | boxVector[2] = globals->getBoxZ(); |
774 | > | |
775 | > | info[i].setBox( boxVector ); |
776 | } | |
306 | – | } |
777 | ||
778 | + | } |
779 | + | |
780 | #ifdef IS_MPI | |
781 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
781 | > | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
782 | MPIcheckPoint(); | |
783 | #endif // is_mpi | |
312 | – | |
784 | ||
785 | + | } |
786 | ||
787 | ||
788 | < | // caclulate the number of atoms, bonds, bends and torsions |
788 | > | void SimSetup::finalInfoCheck( void ){ |
789 | > | int index; |
790 | > | int usesDipoles; |
791 | > | int i; |
792 | ||
793 | < | tot_atoms = 0; |
794 | < | tot_bonds = 0; |
320 | < | tot_bends = 0; |
321 | < | tot_torsions = 0; |
322 | < | for( i=0; i<n_components; i++ ){ |
793 | > | for(i=0; i<nInfo; i++){ |
794 | > | // check electrostatic parameters |
795 | ||
796 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
797 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
798 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
799 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
796 | > | index = 0; |
797 | > | usesDipoles = 0; |
798 | > | while( (index < info[i].n_atoms) && !usesDipoles ){ |
799 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
800 | > | index++; |
801 | > | } |
802 | > | |
803 | > | #ifdef IS_MPI |
804 | > | int myUse = usesDipoles; |
805 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
806 | > | #endif //is_mpi |
807 | > | |
808 | > | double theEcr, theEst; |
809 | > | |
810 | > | if (globals->getUseRF() ) { |
811 | > | info[i].useReactionField = 1; |
812 | > | |
813 | > | if( !globals->haveECR() ){ |
814 | > | sprintf( painCave.errMsg, |
815 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
816 | > | "box length for the electrostaticCutoffRadius.\n" |
817 | > | "I hope you have a very fast processor!\n"); |
818 | > | painCave.isFatal = 0; |
819 | > | simError(); |
820 | > | double smallest; |
821 | > | smallest = info[i].boxL[0]; |
822 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
823 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
824 | > | theEcr = 0.5 * smallest; |
825 | > | } else { |
826 | > | theEcr = globals->getECR(); |
827 | > | } |
828 | > | |
829 | > | if( !globals->haveEST() ){ |
830 | > | sprintf( painCave.errMsg, |
831 | > | "SimSetup Warning: using default value of 0.05 * the " |
832 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
833 | > | ); |
834 | > | painCave.isFatal = 0; |
835 | > | simError(); |
836 | > | theEst = 0.05 * theEcr; |
837 | > | } else { |
838 | > | theEst= globals->getEST(); |
839 | > | } |
840 | > | |
841 | > | info[i].setEcr( theEcr, theEst ); |
842 | > | |
843 | > | if(!globals->haveDielectric() ){ |
844 | > | sprintf( painCave.errMsg, |
845 | > | "SimSetup Error: You are trying to use Reaction Field without" |
846 | > | "setting a dielectric constant!\n" |
847 | > | ); |
848 | > | painCave.isFatal = 1; |
849 | > | simError(); |
850 | > | } |
851 | > | info[i].dielectric = globals->getDielectric(); |
852 | > | } |
853 | > | else { |
854 | > | if (usesDipoles) { |
855 | > | |
856 | > | if( !globals->haveECR() ){ |
857 | > | sprintf( painCave.errMsg, |
858 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
859 | > | "box length for the electrostaticCutoffRadius.\n" |
860 | > | "I hope you have a very fast processor!\n"); |
861 | > | painCave.isFatal = 0; |
862 | > | simError(); |
863 | > | double smallest; |
864 | > | smallest = info[i].boxL[0]; |
865 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
866 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
867 | > | theEcr = 0.5 * smallest; |
868 | > | } else { |
869 | > | theEcr = globals->getECR(); |
870 | > | } |
871 | > | |
872 | > | if( !globals->haveEST() ){ |
873 | > | sprintf( painCave.errMsg, |
874 | > | "SimSetup Warning: using default value of 0.05 * the " |
875 | > | "electrostaticCutoffRadius for the " |
876 | > | "electrostaticSkinThickness\n" |
877 | > | ); |
878 | > | painCave.isFatal = 0; |
879 | > | simError(); |
880 | > | theEst = 0.05 * theEcr; |
881 | > | } else { |
882 | > | theEst= globals->getEST(); |
883 | > | } |
884 | > | |
885 | > | info[i].setEcr( theEcr, theEst ); |
886 | > | } |
887 | > | } |
888 | } | |
889 | ||
330 | – | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
331 | – | |
332 | – | simnfo->n_atoms = tot_atoms; |
333 | – | simnfo->n_bonds = tot_bonds; |
334 | – | simnfo->n_bends = tot_bends; |
335 | – | simnfo->n_torsions = tot_torsions; |
336 | – | simnfo->n_SRI = tot_SRI; |
337 | – | simnfo->n_mol = tot_nmol; |
338 | – | |
339 | – | simnfo->molMembershipArray = new int[tot_atoms]; |
340 | – | |
890 | #ifdef IS_MPI | |
891 | + | strcpy( checkPointMsg, "post processing checks out" ); |
892 | + | MPIcheckPoint(); |
893 | + | #endif // is_mpi |
894 | ||
895 | < | // divide the molecules among processors here. |
344 | < | |
345 | < | mpiSim = new mpiSimulation( simnfo ); |
346 | < | |
347 | < | globalIndex = mpiSim->divideLabor(); |
895 | > | } |
896 | ||
897 | < | // set up the local variables |
897 | > | void SimSetup::initSystemCoords( void ){ |
898 | > | int i; |
899 | ||
900 | < | int localMol, allMol; |
352 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
900 | > | char* inName; |
901 | ||
902 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
355 | < | int* molCompType = mpiSim->getMolComponentType(); |
356 | < | |
357 | < | allMol = 0; |
358 | < | localMol = 0; |
359 | < | local_atoms = 0; |
360 | < | local_bonds = 0; |
361 | < | local_bends = 0; |
362 | < | local_torsions = 0; |
363 | < | globalAtomIndex = 0; |
902 | > | std::cerr << "Setting atom Coords\n"; |
903 | ||
904 | < | |
366 | < | for( i=0; i<n_components; i++ ){ |
367 | < | |
368 | < | for( j=0; j<components_nmol[i]; j++ ){ |
369 | < | |
370 | < | if( mol2proc[allMol] == worldRank ){ |
371 | < | |
372 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
373 | < | local_bonds += comp_stamps[i]->getNBonds(); |
374 | < | local_bends += comp_stamps[i]->getNBends(); |
375 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
376 | < | localMol++; |
377 | < | } |
378 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
379 | < | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
380 | < | globalAtomIndex++; |
381 | < | } |
382 | < | |
383 | < | allMol++; |
384 | < | } |
385 | < | } |
386 | < | local_SRI = local_bonds + local_bends + local_torsions; |
904 | > | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
905 | ||
906 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
906 | > | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
907 | ||
908 | < | if( local_atoms != simnfo->n_atoms ){ |
908 | > | if( globals->haveInitialConfig() ){ |
909 | > | |
910 | > | InitializeFromFile* fileInit; |
911 | > | #ifdef IS_MPI // is_mpi |
912 | > | if( worldRank == 0 ){ |
913 | > | #endif //is_mpi |
914 | > | inName = globals->getInitialConfig(); |
915 | > | fileInit = new InitializeFromFile( inName ); |
916 | > | #ifdef IS_MPI |
917 | > | }else fileInit = new InitializeFromFile( NULL ); |
918 | > | #endif |
919 | > | fileInit->readInit( info ); // default velocities on |
920 | > | |
921 | > | delete fileInit; |
922 | > | } |
923 | > | else{ |
924 | > | |
925 | > | #ifdef IS_MPI |
926 | > | |
927 | > | // no init from bass |
928 | > | |
929 | sprintf( painCave.errMsg, | |
930 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
931 | < | " localAtom (%d) are not equal.\n", |
394 | < | simnfo->n_atoms, |
395 | < | local_atoms ); |
396 | < | painCave.isFatal = 1; |
930 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
931 | > | painCave.isFatal; |
932 | simError(); | |
933 | + | |
934 | + | #else |
935 | + | |
936 | + | initFromBass(); |
937 | + | |
938 | + | |
939 | + | #endif |
940 | } | |
399 | – | |
400 | – | simnfo->n_bonds = local_bonds; |
401 | – | simnfo->n_bends = local_bends; |
402 | – | simnfo->n_torsions = local_torsions; |
403 | – | simnfo->n_SRI = local_SRI; |
404 | – | simnfo->n_mol = localMol; |
405 | – | |
406 | – | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
407 | – | MPIcheckPoint(); |
941 | ||
942 | < | |
942 | > | #ifdef IS_MPI |
943 | > | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
944 | > | MPIcheckPoint(); |
945 | #endif // is_mpi | |
946 | ||
947 | + | } |
948 | ||
413 | – | // create the atom and short range interaction arrays |
949 | ||
950 | < | Atom::createArrays(simnfo->n_atoms); |
416 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
417 | < | the_molecules = new Molecule[simnfo->n_mol]; |
418 | < | int molIndex; |
419 | < | |
420 | < | // initialize the molecule's stampID's |
421 | < | |
422 | < | #ifdef IS_MPI |
950 | > | void SimSetup::makeOutNames( void ){ |
951 | ||
952 | + | int k; |
953 | ||
425 | – | molIndex = 0; |
426 | – | for(i=0; i<mpiSim->getTotNmol(); i++){ |
427 | – | |
428 | – | if(mol2proc[i] == worldRank ){ |
429 | – | the_molecules[molIndex].setStampID( molCompType[i] ); |
430 | – | the_molecules[molIndex].setMyIndex( molIndex ); |
431 | – | the_molecules[molIndex].setGlobalIndex( i ); |
432 | – | molIndex++; |
433 | – | } |
434 | – | } |
435 | – | |
436 | – | #else // is_mpi |
954 | ||
955 | < | molIndex = 0; |
956 | < | globalAtomIndex = 0; |
957 | < | for(i=0; i<n_components; i++){ |
958 | < | for(j=0; j<components_nmol[i]; j++ ){ |
959 | < | the_molecules[molIndex].setStampID( i ); |
960 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
961 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
962 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
446 | < | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
447 | < | globalAtomIndex++; |
955 | > | for(k=0; k<nInfo; k++){ |
956 | > | |
957 | > | #ifdef IS_MPI |
958 | > | if( worldRank == 0 ){ |
959 | > | #endif // is_mpi |
960 | > | |
961 | > | if( globals->haveFinalConfig() ){ |
962 | > | strcpy( info[k].finalName, globals->getFinalConfig() ); |
963 | } | |
964 | < | molIndex++; |
964 | > | else{ |
965 | > | strcpy( info[k].finalName, inFileName ); |
966 | > | char* endTest; |
967 | > | int nameLength = strlen( info[k].finalName ); |
968 | > | endTest = &(info[k].finalName[nameLength - 5]); |
969 | > | if( !strcmp( endTest, ".bass" ) ){ |
970 | > | strcpy( endTest, ".eor" ); |
971 | > | } |
972 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
973 | > | strcpy( endTest, ".eor" ); |
974 | > | } |
975 | > | else{ |
976 | > | endTest = &(info[k].finalName[nameLength - 4]); |
977 | > | if( !strcmp( endTest, ".bss" ) ){ |
978 | > | strcpy( endTest, ".eor" ); |
979 | > | } |
980 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
981 | > | strcpy( endTest, ".eor" ); |
982 | > | } |
983 | > | else{ |
984 | > | strcat( info[k].finalName, ".eor" ); |
985 | > | } |
986 | > | } |
987 | > | } |
988 | > | |
989 | > | // make the sample and status out names |
990 | > | |
991 | > | strcpy( info[k].sampleName, inFileName ); |
992 | > | char* endTest; |
993 | > | int nameLength = strlen( info[k].sampleName ); |
994 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
995 | > | if( !strcmp( endTest, ".bass" ) ){ |
996 | > | strcpy( endTest, ".dump" ); |
997 | > | } |
998 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
999 | > | strcpy( endTest, ".dump" ); |
1000 | > | } |
1001 | > | else{ |
1002 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1003 | > | if( !strcmp( endTest, ".bss" ) ){ |
1004 | > | strcpy( endTest, ".dump" ); |
1005 | > | } |
1006 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1007 | > | strcpy( endTest, ".dump" ); |
1008 | > | } |
1009 | > | else{ |
1010 | > | strcat( info[k].sampleName, ".dump" ); |
1011 | > | } |
1012 | > | } |
1013 | > | |
1014 | > | strcpy( info[k].statusName, inFileName ); |
1015 | > | nameLength = strlen( info[k].statusName ); |
1016 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1017 | > | if( !strcmp( endTest, ".bass" ) ){ |
1018 | > | strcpy( endTest, ".stat" ); |
1019 | > | } |
1020 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
1021 | > | strcpy( endTest, ".stat" ); |
1022 | > | } |
1023 | > | else{ |
1024 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1025 | > | if( !strcmp( endTest, ".bss" ) ){ |
1026 | > | strcpy( endTest, ".stat" ); |
1027 | > | } |
1028 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1029 | > | strcpy( endTest, ".stat" ); |
1030 | > | } |
1031 | > | else{ |
1032 | > | strcat( info[k].statusName, ".stat" ); |
1033 | > | } |
1034 | > | } |
1035 | > | |
1036 | > | #ifdef IS_MPI |
1037 | } | |
1038 | + | #endif // is_mpi |
1039 | } | |
1040 | < | |
1040 | > | } |
1041 | ||
454 | – | #endif // is_mpi |
1042 | ||
1043 | + | void SimSetup::sysObjectsCreation( void ){ |
1044 | + | |
1045 | + | int i,k; |
1046 | + | |
1047 | + | // create the forceField |
1048 | ||
1049 | < | if( simnfo->n_SRI ){ |
458 | < | |
459 | < | Exclude::createArray(simnfo->n_SRI); |
460 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
461 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
462 | < | simnfo->globalExcludes = new int; |
463 | < | simnfo->n_exclude = simnfo->n_SRI; |
464 | < | } |
465 | < | else{ |
466 | < | |
467 | < | Exclude::createArray( 1 ); |
468 | < | the_excludes = new Exclude*; |
469 | < | the_excludes[0] = new Exclude(0); |
470 | < | the_excludes[0]->setPair( 0,0 ); |
471 | < | simnfo->globalExcludes = new int; |
472 | < | simnfo->globalExcludes[0] = 0; |
473 | < | simnfo->n_exclude = 0; |
474 | < | } |
1049 | > | createFF(); |
1050 | ||
1051 | < | // set the arrays into the SimInfo object |
1051 | > | // extract componentList |
1052 | ||
1053 | < | simnfo->atoms = the_atoms; |
479 | < | simnfo->molecules = the_molecules; |
480 | < | simnfo->nGlobalExcludes = 0; |
481 | < | simnfo->excludes = the_excludes; |
1053 | > | compList(); |
1054 | ||
1055 | + | // calc the number of atoms, bond, bends, and torsions |
1056 | ||
1057 | < | // get some of the tricky things that may still be in the globals |
1057 | > | calcSysValues(); |
1058 | ||
1059 | < | double boxVector[3]; |
1060 | < | if( the_globals->haveBox() ){ |
1061 | < | boxVector[0] = the_globals->getBox(); |
1062 | < | boxVector[1] = the_globals->getBox(); |
1063 | < | boxVector[2] = the_globals->getBox(); |
1064 | < | |
1065 | < | simnfo->setBox( boxVector ); |
1059 | > | #ifdef IS_MPI |
1060 | > | // divide the molecules among the processors |
1061 | > | |
1062 | > | mpiMolDivide(); |
1063 | > | #endif //is_mpi |
1064 | > | |
1065 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1066 | > | |
1067 | > | makeSysArrays(); |
1068 | > | |
1069 | > | // make and initialize the molecules (all but atomic coordinates) |
1070 | > | |
1071 | > | makeMolecules(); |
1072 | > | |
1073 | > | for(k=0; k<nInfo; k++){ |
1074 | > | info[k].identArray = new int[info[k].n_atoms]; |
1075 | > | for(i=0; i<info[k].n_atoms; i++){ |
1076 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1077 | > | } |
1078 | } | |
1079 | < | else if( the_globals->haveDensity() ){ |
1079 | > | } |
1080 | ||
496 | – | double vol; |
497 | – | vol = (double)tot_nmol / the_globals->getDensity(); |
498 | – | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
499 | – | boxVector[1] = boxVector[0]; |
500 | – | boxVector[2] = boxVector[0]; |
1081 | ||
1082 | < | simnfo->setBox( boxVector ); |
503 | < | } |
504 | < | else{ |
505 | < | if( !the_globals->haveBoxX() ){ |
506 | < | sprintf( painCave.errMsg, |
507 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
508 | < | painCave.isFatal = 1; |
509 | < | simError(); |
510 | < | } |
511 | < | boxVector[0] = the_globals->getBoxX(); |
1082 | > | void SimSetup::createFF( void ){ |
1083 | ||
1084 | < | if( !the_globals->haveBoxY() ){ |
514 | < | sprintf( painCave.errMsg, |
515 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
516 | < | painCave.isFatal = 1; |
517 | < | simError(); |
518 | < | } |
519 | < | boxVector[1] = the_globals->getBoxY(); |
1084 | > | switch( ffCase ){ |
1085 | ||
1086 | < | if( !the_globals->haveBoxZ() ){ |
1087 | < | sprintf( painCave.errMsg, |
1088 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
524 | < | painCave.isFatal = 1; |
525 | < | simError(); |
526 | < | } |
527 | < | boxVector[2] = the_globals->getBoxZ(); |
1086 | > | case FF_DUFF: |
1087 | > | the_ff = new DUFF(); |
1088 | > | break; |
1089 | ||
1090 | < | simnfo->setBox( boxVector ); |
1090 | > | case FF_LJ: |
1091 | > | the_ff = new LJFF(); |
1092 | > | break; |
1093 | > | |
1094 | > | case FF_EAM: |
1095 | > | the_ff = new EAM_FF(); |
1096 | > | break; |
1097 | > | |
1098 | > | default: |
1099 | > | sprintf( painCave.errMsg, |
1100 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1101 | > | painCave.isFatal = 1; |
1102 | > | simError(); |
1103 | } | |
1104 | ||
1105 | #ifdef IS_MPI | |
1106 | < | strcpy( checkPointMsg, "Box size set up" ); |
1106 | > | strcpy( checkPointMsg, "ForceField creation successful" ); |
1107 | MPIcheckPoint(); | |
1108 | #endif // is_mpi | |
1109 | ||
1110 | + | } |
1111 | ||
538 | – | // initialize the arrays |
1112 | ||
1113 | < | the_ff->setSimInfo( simnfo ); |
1113 | > | void SimSetup::compList( void ){ |
1114 | ||
1115 | < | makeMolecules(); |
1116 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
1117 | < | for(i=0; i<simnfo->n_atoms; i++){ |
1118 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
1119 | < | } |
1115 | > | int i; |
1116 | > | char* id; |
1117 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1118 | > | LinkedMolStamp* currentStamp = NULL; |
1119 | > | comp_stamps = new MoleculeStamp*[n_components]; |
1120 | ||
1121 | < | if (the_globals->getUseRF() ) { |
1122 | < | simnfo->useReactionField = 1; |
1121 | > | // make an array of molecule stamps that match the components used. |
1122 | > | // also extract the used stamps out into a separate linked list |
1123 | ||
1124 | < | if( !the_globals->haveECR() ){ |
1125 | < | sprintf( painCave.errMsg, |
1126 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
1127 | < | "box length for the electrostaticCutoffRadius.\n" |
1128 | < | "I hope you have a very fast processor!\n"); |
1129 | < | painCave.isFatal = 0; |
1130 | < | simError(); |
558 | < | double smallest; |
559 | < | smallest = simnfo->boxLx; |
560 | < | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
561 | < | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
562 | < | simnfo->ecr = 0.5 * smallest; |
563 | < | } else { |
564 | < | simnfo->ecr = the_globals->getECR(); |
565 | < | } |
1124 | > | for(i=0; i<nInfo; i++){ |
1125 | > | info[i].nComponents = n_components; |
1126 | > | info[i].componentsNmol = components_nmol; |
1127 | > | info[i].compStamps = comp_stamps; |
1128 | > | info[i].headStamp = headStamp; |
1129 | > | } |
1130 | > | |
1131 | ||
1132 | < | if( !the_globals->haveEST() ){ |
1133 | < | sprintf( painCave.errMsg, |
1134 | < | "SimSetup Warning: using default value of 0.05 * the " |
1135 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
571 | < | ); |
572 | < | painCave.isFatal = 0; |
573 | < | simError(); |
574 | < | simnfo->est = 0.05 * simnfo->ecr; |
575 | < | } else { |
576 | < | simnfo->est = the_globals->getEST(); |
577 | < | } |
1132 | > | for( i=0; i<n_components; i++ ){ |
1133 | > | |
1134 | > | id = the_components[i]->getType(); |
1135 | > | comp_stamps[i] = NULL; |
1136 | ||
1137 | < | if(!the_globals->haveDielectric() ){ |
1138 | < | sprintf( painCave.errMsg, |
1139 | < | "SimSetup Error: You are trying to use Reaction Field without" |
1140 | < | "setting a dielectric constant!\n" |
583 | < | ); |
584 | < | painCave.isFatal = 1; |
585 | < | simError(); |
586 | < | } |
587 | < | simnfo->dielectric = the_globals->getDielectric(); |
588 | < | } else { |
589 | < | if (usesDipoles) { |
1137 | > | // check to make sure the component isn't already in the list |
1138 | > | |
1139 | > | comp_stamps[i] = headStamp->match( id ); |
1140 | > | if( comp_stamps[i] == NULL ){ |
1141 | ||
1142 | < | if( !the_globals->haveECR() ){ |
592 | < | sprintf( painCave.errMsg, |
593 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
594 | < | "box length for the electrostaticCutoffRadius.\n" |
595 | < | "I hope you have a very fast processor!\n"); |
596 | < | painCave.isFatal = 0; |
597 | < | simError(); |
598 | < | double smallest; |
599 | < | smallest = simnfo->boxLx; |
600 | < | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
601 | < | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
602 | < | simnfo->ecr = 0.5 * smallest; |
603 | < | } else { |
604 | < | simnfo->ecr = the_globals->getECR(); |
605 | < | } |
1142 | > | // extract the component from the list; |
1143 | ||
1144 | < | if( !the_globals->haveEST() ){ |
1145 | < | sprintf( painCave.errMsg, |
1146 | < | "SimSetup Warning: using default value of 5%% of the " |
1147 | < | "electrostaticCutoffRadius for the " |
1148 | < | "electrostaticSkinThickness\n" |
1149 | < | ); |
1150 | < | painCave.isFatal = 0; |
1151 | < | simError(); |
615 | < | simnfo->est = 0.05 * simnfo->ecr; |
616 | < | } else { |
617 | < | simnfo->est = the_globals->getEST(); |
1144 | > | currentStamp = stamps->extractMolStamp( id ); |
1145 | > | if( currentStamp == NULL ){ |
1146 | > | sprintf( painCave.errMsg, |
1147 | > | "SimSetup error: Component \"%s\" was not found in the " |
1148 | > | "list of declared molecules\n", |
1149 | > | id ); |
1150 | > | painCave.isFatal = 1; |
1151 | > | simError(); |
1152 | } | |
1153 | + | |
1154 | + | headStamp->add( currentStamp ); |
1155 | + | comp_stamps[i] = headStamp->match( id ); |
1156 | } | |
1157 | < | } |
1157 | > | } |
1158 | ||
1159 | #ifdef IS_MPI | |
1160 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
1160 | > | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1161 | MPIcheckPoint(); | |
1162 | #endif // is_mpi | |
1163 | ||
627 | – | if( the_globals->haveInitialConfig() ){ |
628 | – | |
629 | – | InitializeFromFile* fileInit; |
630 | – | #ifdef IS_MPI // is_mpi |
631 | – | if( worldRank == 0 ){ |
632 | – | #endif //is_mpi |
633 | – | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
634 | – | #ifdef IS_MPI |
635 | – | }else fileInit = new InitializeFromFile( NULL ); |
636 | – | #endif |
637 | – | fileInit->read_xyz( simnfo ); // default velocities on |
1164 | ||
1165 | < | delete fileInit; |
640 | < | } |
641 | < | else{ |
1165 | > | } |
1166 | ||
1167 | < | #ifdef IS_MPI |
1168 | < | |
645 | < | // no init from bass |
1167 | > | void SimSetup::calcSysValues( void ){ |
1168 | > | int i, j, k; |
1169 | ||
1170 | < | sprintf( painCave.errMsg, |
648 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
649 | < | painCave.isFatal; |
650 | < | simError(); |
1170 | > | int *molMembershipArray; |
1171 | ||
1172 | < | #else |
1172 | > | tot_atoms = 0; |
1173 | > | tot_bonds = 0; |
1174 | > | tot_bends = 0; |
1175 | > | tot_torsions = 0; |
1176 | > | for( i=0; i<n_components; i++ ){ |
1177 | > | |
1178 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1179 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1180 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1181 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1182 | > | } |
1183 | > | |
1184 | > | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1185 | > | molMembershipArray = new int[tot_atoms]; |
1186 | > | |
1187 | > | for(i=0; i<nInfo; i++){ |
1188 | > | info[i].n_atoms = tot_atoms; |
1189 | > | info[i].n_bonds = tot_bonds; |
1190 | > | info[i].n_bends = tot_bends; |
1191 | > | info[i].n_torsions = tot_torsions; |
1192 | > | info[i].n_SRI = tot_SRI; |
1193 | > | info[i].n_mol = tot_nmol; |
1194 | > | |
1195 | > | info[i].molMembershipArray = molMembershipArray; |
1196 | > | } |
1197 | > | } |
1198 | ||
654 | – | initFromBass(); |
655 | – | |
656 | – | |
657 | – | #endif |
658 | – | } |
659 | – | |
1199 | #ifdef IS_MPI | |
1200 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
1200 | > | |
1201 | > | void SimSetup::mpiMolDivide( void ){ |
1202 | > | |
1203 | > | int i, j, k; |
1204 | > | int localMol, allMol; |
1205 | > | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1206 | > | |
1207 | > | mpiSim = new mpiSimulation( info ); |
1208 | > | |
1209 | > | globalIndex = mpiSim->divideLabor(); |
1210 | > | |
1211 | > | // set up the local variables |
1212 | > | |
1213 | > | mol2proc = mpiSim->getMolToProcMap(); |
1214 | > | molCompType = mpiSim->getMolComponentType(); |
1215 | > | |
1216 | > | allMol = 0; |
1217 | > | localMol = 0; |
1218 | > | local_atoms = 0; |
1219 | > | local_bonds = 0; |
1220 | > | local_bends = 0; |
1221 | > | local_torsions = 0; |
1222 | > | globalAtomIndex = 0; |
1223 | > | |
1224 | > | |
1225 | > | for( i=0; i<n_components; i++ ){ |
1226 | > | |
1227 | > | for( j=0; j<components_nmol[i]; j++ ){ |
1228 | > | |
1229 | > | if( mol2proc[allMol] == worldRank ){ |
1230 | > | |
1231 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1232 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1233 | > | local_bends += comp_stamps[i]->getNBends(); |
1234 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1235 | > | localMol++; |
1236 | > | } |
1237 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1238 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1239 | > | globalAtomIndex++; |
1240 | > | } |
1241 | > | |
1242 | > | allMol++; |
1243 | > | } |
1244 | > | } |
1245 | > | local_SRI = local_bonds + local_bends + local_torsions; |
1246 | > | |
1247 | > | info[0].n_atoms = mpiSim->getMyNlocal(); |
1248 | > | |
1249 | > | if( local_atoms != info[0].n_atoms ){ |
1250 | > | sprintf( painCave.errMsg, |
1251 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1252 | > | " localAtom (%d) are not equal.\n", |
1253 | > | info[0].n_atoms, |
1254 | > | local_atoms ); |
1255 | > | painCave.isFatal = 1; |
1256 | > | simError(); |
1257 | > | } |
1258 | > | |
1259 | > | info[0].n_bonds = local_bonds; |
1260 | > | info[0].n_bends = local_bends; |
1261 | > | info[0].n_torsions = local_torsions; |
1262 | > | info[0].n_SRI = local_SRI; |
1263 | > | info[0].n_mol = localMol; |
1264 | > | |
1265 | > | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1266 | MPIcheckPoint(); | |
1267 | + | } |
1268 | + | |
1269 | #endif // is_mpi | |
1270 | ||
1271 | ||
1272 | < | |
1273 | < | |
668 | < | |
1272 | > | void SimSetup::makeSysArrays( void ){ |
1273 | > | int i, j, k, l; |
1274 | ||
1275 | + | Atom** the_atoms; |
1276 | + | Molecule* the_molecules; |
1277 | + | Exclude** the_excludes; |
1278 | + | |
1279 | ||
1280 | + | for(l=0; l<nInfo; l++){ |
1281 | + | |
1282 | + | // create the atom and short range interaction arrays |
1283 | + | |
1284 | + | the_atoms = new Atom*[info[l].n_atoms]; |
1285 | + | the_molecules = new Molecule[info[l].n_mol]; |
1286 | + | int molIndex; |
1287 | + | |
1288 | + | // initialize the molecule's stampID's |
1289 | + | |
1290 | #ifdef IS_MPI | |
672 | – | if( worldRank == 0 ){ |
673 | – | #endif // is_mpi |
1291 | ||
675 | – | if( the_globals->haveFinalConfig() ){ |
676 | – | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
677 | – | } |
678 | – | else{ |
679 | – | strcpy( simnfo->finalName, inFileName ); |
680 | – | char* endTest; |
681 | – | int nameLength = strlen( simnfo->finalName ); |
682 | – | endTest = &(simnfo->finalName[nameLength - 5]); |
683 | – | if( !strcmp( endTest, ".bass" ) ){ |
684 | – | strcpy( endTest, ".eor" ); |
685 | – | } |
686 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
687 | – | strcpy( endTest, ".eor" ); |
688 | – | } |
689 | – | else{ |
690 | – | endTest = &(simnfo->finalName[nameLength - 4]); |
691 | – | if( !strcmp( endTest, ".bss" ) ){ |
692 | – | strcpy( endTest, ".eor" ); |
693 | – | } |
694 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
695 | – | strcpy( endTest, ".eor" ); |
696 | – | } |
697 | – | else{ |
698 | – | strcat( simnfo->finalName, ".eor" ); |
699 | – | } |
700 | – | } |
701 | – | } |
1292 | ||
1293 | < | // make the sample and status out names |
1293 | > | molIndex = 0; |
1294 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1295 | ||
1296 | < | strcpy( simnfo->sampleName, inFileName ); |
1297 | < | char* endTest; |
1298 | < | int nameLength = strlen( simnfo->sampleName ); |
1299 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
1300 | < | if( !strcmp( endTest, ".bass" ) ){ |
710 | < | strcpy( endTest, ".dump" ); |
711 | < | } |
712 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
713 | < | strcpy( endTest, ".dump" ); |
714 | < | } |
715 | < | else{ |
716 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
717 | < | if( !strcmp( endTest, ".bss" ) ){ |
718 | < | strcpy( endTest, ".dump" ); |
1296 | > | if(mol2proc[i] == worldRank ){ |
1297 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
1298 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1299 | > | the_molecules[molIndex].setGlobalIndex( i ); |
1300 | > | molIndex++; |
1301 | } | |
720 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
721 | – | strcpy( endTest, ".dump" ); |
722 | – | } |
723 | – | else{ |
724 | – | strcat( simnfo->sampleName, ".dump" ); |
725 | – | } |
1302 | } | |
1303 | ||
1304 | < | strcpy( simnfo->statusName, inFileName ); |
1305 | < | nameLength = strlen( simnfo->statusName ); |
1306 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
1307 | < | if( !strcmp( endTest, ".bass" ) ){ |
1308 | < | strcpy( endTest, ".stat" ); |
1309 | < | } |
1310 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
1311 | < | strcpy( endTest, ".stat" ); |
1312 | < | } |
1313 | < | else{ |
1314 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
1315 | < | if( !strcmp( endTest, ".bss" ) ){ |
1316 | < | strcpy( endTest, ".stat" ); |
1304 | > | #else // is_mpi |
1305 | > | |
1306 | > | molIndex = 0; |
1307 | > | globalAtomIndex = 0; |
1308 | > | for(i=0; i<n_components; i++){ |
1309 | > | for(j=0; j<components_nmol[i]; j++ ){ |
1310 | > | the_molecules[molIndex].setStampID( i ); |
1311 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1312 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1313 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1314 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1315 | > | globalAtomIndex++; |
1316 | > | } |
1317 | > | molIndex++; |
1318 | } | |
742 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
743 | – | strcpy( endTest, ".stat" ); |
744 | – | } |
745 | – | else{ |
746 | – | strcat( simnfo->statusName, ".stat" ); |
747 | – | } |
1319 | } | |
1320 | ||
1321 | < | #ifdef IS_MPI |
751 | < | } |
1321 | > | |
1322 | #endif // is_mpi | |
753 | – | |
754 | – | // set the status, sample, and themal kick times |
755 | – | |
756 | – | if( the_globals->haveSampleTime() ){ |
757 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
758 | – | simnfo->statusTime = simnfo->sampleTime; |
759 | – | simnfo->thermalTime = simnfo->sampleTime; |
760 | – | } |
761 | – | else{ |
762 | – | simnfo->sampleTime = the_globals->getRunTime(); |
763 | – | simnfo->statusTime = simnfo->sampleTime; |
764 | – | simnfo->thermalTime = simnfo->sampleTime; |
765 | – | } |
1323 | ||
767 | – | if( the_globals->haveStatusTime() ){ |
768 | – | simnfo->statusTime = the_globals->getStatusTime(); |
769 | – | } |
1324 | ||
1325 | < | if( the_globals->haveThermalTime() ){ |
1326 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
1327 | < | } |
1325 | > | if( info[l].n_SRI ){ |
1326 | > | |
1327 | > | Exclude::createArray(info[l].n_SRI); |
1328 | > | the_excludes = new Exclude*[info[l].n_SRI]; |
1329 | > | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1330 | > | the_excludes[ex] = new Exclude(ex); |
1331 | > | } |
1332 | > | info[l].globalExcludes = new int; |
1333 | > | info[l].n_exclude = info[l].n_SRI; |
1334 | > | } |
1335 | > | else{ |
1336 | > | |
1337 | > | Exclude::createArray( 1 ); |
1338 | > | the_excludes = new Exclude*; |
1339 | > | the_excludes[0] = new Exclude(0); |
1340 | > | the_excludes[0]->setPair( 0,0 ); |
1341 | > | info[l].globalExcludes = new int; |
1342 | > | info[l].globalExcludes[0] = 0; |
1343 | > | info[l].n_exclude = 0; |
1344 | > | } |
1345 | ||
1346 | < | // check for the temperature set flag |
1346 | > | // set the arrays into the SimInfo object |
1347 | ||
1348 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
1348 | > | info[l].atoms = the_atoms; |
1349 | > | info[l].molecules = the_molecules; |
1350 | > | info[l].nGlobalExcludes = 0; |
1351 | > | info[l].excludes = the_excludes; |
1352 | ||
1353 | + | the_ff->setSimInfo( info ); |
1354 | + | |
1355 | + | } |
1356 | + | } |
1357 | ||
1358 | < | // make the integrator |
781 | < | |
782 | < | |
783 | < | NVT* myNVT = NULL; |
784 | < | NPTi* myNPTi = NULL; |
785 | < | NPTf* myNPTf = NULL; |
786 | < | switch( ensembleCase ){ |
1358 | > | void SimSetup::makeIntegrator( void ){ |
1359 | ||
1360 | < | case NVE_ENS: |
789 | < | new NVE( simnfo, the_ff ); |
790 | < | break; |
1360 | > | int k; |
1361 | ||
1362 | < | case NVT_ENS: |
1363 | < | myNVT = new NVT( simnfo, the_ff ); |
1364 | < | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
1362 | > | NVT<RealIntegrator>* myNVT = NULL; |
1363 | > | NPTi<RealIntegrator>* myNPTi = NULL; |
1364 | > | NPTf<RealIntegrator>* myNPTf = NULL; |
1365 | > | NPTim<RealIntegrator>* myNPTim = NULL; |
1366 | > | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1367 | > | |
1368 | > | for(k=0; k<nInfo; k++){ |
1369 | > | |
1370 | > | switch( ensembleCase ){ |
1371 | > | |
1372 | > | case NVE_ENS: |
1373 | > | if (globals->haveZconstraints()){ |
1374 | > | setupZConstraint(info[k]); |
1375 | > | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1376 | > | } |
1377 | ||
1378 | < | if (the_globals->haveTauThermostat()) |
1379 | < | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
1378 | > | else |
1379 | > | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1380 | > | break; |
1381 | > | |
1382 | > | case NVT_ENS: |
1383 | > | if (globals->haveZconstraints()){ |
1384 | > | setupZConstraint(info[k]); |
1385 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1386 | > | } |
1387 | > | else |
1388 | > | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1389 | ||
1390 | < | else { |
1391 | < | sprintf( painCave.errMsg, |
1392 | < | "SimSetup error: If you use the NVT\n" |
1393 | < | " ensemble, you must set tauThermostat.\n"); |
1394 | < | painCave.isFatal = 1; |
1395 | < | simError(); |
1396 | < | } |
1397 | < | break; |
1390 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1391 | > | |
1392 | > | if (globals->haveTauThermostat()) |
1393 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1394 | > | |
1395 | > | else { |
1396 | > | sprintf( painCave.errMsg, |
1397 | > | "SimSetup error: If you use the NVT\n" |
1398 | > | " ensemble, you must set tauThermostat.\n"); |
1399 | > | painCave.isFatal = 1; |
1400 | > | simError(); |
1401 | > | } |
1402 | > | break; |
1403 | > | |
1404 | > | case NPTi_ENS: |
1405 | > | if (globals->haveZconstraints()){ |
1406 | > | setupZConstraint(info[k]); |
1407 | > | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1408 | > | } |
1409 | > | else |
1410 | > | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1411 | ||
1412 | < | case NPTi_ENS: |
1413 | < | myNPTi = new NPTi( simnfo, the_ff ); |
1414 | < | myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
1415 | < | |
1416 | < | if (the_globals->haveTargetPressure()) |
1417 | < | myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
1418 | < | else { |
1419 | < | sprintf( painCave.errMsg, |
1420 | < | "SimSetup error: If you use a constant pressure\n" |
1421 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1422 | < | painCave.isFatal = 1; |
1423 | < | simError(); |
1424 | < | } |
1425 | < | |
1426 | < | if( the_globals->haveTauThermostat() ) |
1427 | < | myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
1428 | < | else{ |
1429 | < | sprintf( painCave.errMsg, |
1430 | < | "SimSetup error: If you use an NPT\n" |
1431 | < | " ensemble, you must set tauThermostat.\n"); |
1432 | < | painCave.isFatal = 1; |
1433 | < | simError(); |
1434 | < | } |
1412 | > | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1413 | > | |
1414 | > | if (globals->haveTargetPressure()) |
1415 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1416 | > | else { |
1417 | > | sprintf( painCave.errMsg, |
1418 | > | "SimSetup error: If you use a constant pressure\n" |
1419 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1420 | > | painCave.isFatal = 1; |
1421 | > | simError(); |
1422 | > | } |
1423 | > | |
1424 | > | if( globals->haveTauThermostat() ) |
1425 | > | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1426 | > | else{ |
1427 | > | sprintf( painCave.errMsg, |
1428 | > | "SimSetup error: If you use an NPT\n" |
1429 | > | " ensemble, you must set tauThermostat.\n"); |
1430 | > | painCave.isFatal = 1; |
1431 | > | simError(); |
1432 | > | } |
1433 | > | |
1434 | > | if( globals->haveTauBarostat() ) |
1435 | > | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1436 | > | else{ |
1437 | > | sprintf( painCave.errMsg, |
1438 | > | "SimSetup error: If you use an NPT\n" |
1439 | > | " ensemble, you must set tauBarostat.\n"); |
1440 | > | painCave.isFatal = 1; |
1441 | > | simError(); |
1442 | > | } |
1443 | > | break; |
1444 | > | |
1445 | > | case NPTf_ENS: |
1446 | > | if (globals->haveZconstraints()){ |
1447 | > | setupZConstraint(info[k]); |
1448 | > | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1449 | > | } |
1450 | > | else |
1451 | > | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1452 | ||
1453 | < | if( the_globals->haveTauBarostat() ) |
1454 | < | myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
1455 | < | else{ |
1453 | > | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1454 | > | |
1455 | > | if (globals->haveTargetPressure()) |
1456 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1457 | > | else { |
1458 | > | sprintf( painCave.errMsg, |
1459 | > | "SimSetup error: If you use a constant pressure\n" |
1460 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1461 | > | painCave.isFatal = 1; |
1462 | > | simError(); |
1463 | > | } |
1464 | > | |
1465 | > | if( globals->haveTauThermostat() ) |
1466 | > | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1467 | > | else{ |
1468 | > | sprintf( painCave.errMsg, |
1469 | > | "SimSetup error: If you use an NPT\n" |
1470 | > | " ensemble, you must set tauThermostat.\n"); |
1471 | > | painCave.isFatal = 1; |
1472 | > | simError(); |
1473 | > | } |
1474 | > | |
1475 | > | if( globals->haveTauBarostat() ) |
1476 | > | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1477 | > | else{ |
1478 | > | sprintf( painCave.errMsg, |
1479 | > | "SimSetup error: If you use an NPT\n" |
1480 | > | " ensemble, you must set tauBarostat.\n"); |
1481 | > | painCave.isFatal = 1; |
1482 | > | simError(); |
1483 | > | } |
1484 | > | break; |
1485 | > | |
1486 | > | case NPTim_ENS: |
1487 | > | if (globals->haveZconstraints()){ |
1488 | > | setupZConstraint(info[k]); |
1489 | > | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1490 | > | } |
1491 | > | else |
1492 | > | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1493 | > | |
1494 | > | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1495 | > | |
1496 | > | if (globals->haveTargetPressure()) |
1497 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1498 | > | else { |
1499 | > | sprintf( painCave.errMsg, |
1500 | > | "SimSetup error: If you use a constant pressure\n" |
1501 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1502 | > | painCave.isFatal = 1; |
1503 | > | simError(); |
1504 | > | } |
1505 | > | |
1506 | > | if( globals->haveTauThermostat() ) |
1507 | > | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1508 | > | else{ |
1509 | > | sprintf( painCave.errMsg, |
1510 | > | "SimSetup error: If you use an NPT\n" |
1511 | > | " ensemble, you must set tauThermostat.\n"); |
1512 | > | painCave.isFatal = 1; |
1513 | > | simError(); |
1514 | > | } |
1515 | > | |
1516 | > | if( globals->haveTauBarostat() ) |
1517 | > | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1518 | > | else{ |
1519 | sprintf( painCave.errMsg, | |
1520 | "SimSetup error: If you use an NPT\n" | |
1521 | " ensemble, you must set tauBarostat.\n"); | |
1522 | painCave.isFatal = 1; | |
1523 | simError(); | |
1524 | < | } |
1525 | < | break; |
1524 | > | } |
1525 | > | break; |
1526 | > | |
1527 | > | case NPTfm_ENS: |
1528 | > | if (globals->haveZconstraints()){ |
1529 | > | setupZConstraint(info[k]); |
1530 | > | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1531 | > | } |
1532 | > | else |
1533 | > | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1534 | ||
1535 | < | case NPTf_ENS: |
1536 | < | myNPTf = new NPTf( simnfo, the_ff ); |
1537 | < | myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
1538 | < | |
1539 | < | if (the_globals->haveTargetPressure()) |
1540 | < | myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
1541 | < | else { |
1535 | > | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1536 | > | |
1537 | > | if (globals->haveTargetPressure()) |
1538 | > | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1539 | > | else { |
1540 | > | sprintf( painCave.errMsg, |
1541 | > | "SimSetup error: If you use a constant pressure\n" |
1542 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1543 | > | painCave.isFatal = 1; |
1544 | > | simError(); |
1545 | > | } |
1546 | > | |
1547 | > | if( globals->haveTauThermostat() ) |
1548 | > | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1549 | > | else{ |
1550 | > | sprintf( painCave.errMsg, |
1551 | > | "SimSetup error: If you use an NPT\n" |
1552 | > | " ensemble, you must set tauThermostat.\n"); |
1553 | > | painCave.isFatal = 1; |
1554 | > | simError(); |
1555 | > | } |
1556 | > | |
1557 | > | if( globals->haveTauBarostat() ) |
1558 | > | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1559 | > | else{ |
1560 | > | sprintf( painCave.errMsg, |
1561 | > | "SimSetup error: If you use an NPT\n" |
1562 | > | " ensemble, you must set tauBarostat.\n"); |
1563 | > | painCave.isFatal = 1; |
1564 | > | simError(); |
1565 | > | } |
1566 | > | break; |
1567 | > | |
1568 | > | default: |
1569 | sprintf( painCave.errMsg, | |
1570 | < | "SimSetup error: If you use a constant pressure\n" |
852 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1570 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1571 | painCave.isFatal = 1; | |
1572 | simError(); | |
855 | – | } |
856 | – | |
857 | – | if( the_globals->haveTauThermostat() ) |
858 | – | myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
859 | – | else{ |
860 | – | sprintf( painCave.errMsg, |
861 | – | "SimSetup error: If you use an NPT\n" |
862 | – | " ensemble, you must set tauThermostat.\n"); |
863 | – | painCave.isFatal = 1; |
864 | – | simError(); |
1573 | } | |
866 | – | |
867 | – | if( the_globals->haveTauBarostat() ) |
868 | – | myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
869 | – | else{ |
870 | – | sprintf( painCave.errMsg, |
871 | – | "SimSetup error: If you use an NPT\n" |
872 | – | " ensemble, you must set tauBarostat.\n"); |
873 | – | painCave.isFatal = 1; |
874 | – | simError(); |
875 | – | } |
876 | – | break; |
877 | – | |
878 | – | |
879 | – | |
880 | – | default: |
881 | – | sprintf( painCave.errMsg, |
882 | – | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
883 | – | painCave.isFatal = 1; |
884 | – | simError(); |
1574 | } | |
1575 | + | } |
1576 | ||
1577 | + | void SimSetup::initFortran( void ){ |
1578 | ||
1579 | < | #ifdef IS_MPI |
889 | < | mpiSim->mpiRefresh(); |
890 | < | #endif |
891 | < | |
892 | < | // initialize the Fortran |
893 | < | |
894 | < | |
895 | < | simnfo->refreshSim(); |
1579 | > | info[0].refreshSim(); |
1580 | ||
1581 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
1581 | > | if( !strcmp( info[0].mixingRule, "standard") ){ |
1582 | the_ff->initForceField( LB_MIXING_RULE ); | |
1583 | } | |
1584 | < | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
1584 | > | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1585 | the_ff->initForceField( EXPLICIT_MIXING_RULE ); | |
1586 | } | |
1587 | else{ | |
1588 | sprintf( painCave.errMsg, | |
1589 | "SimSetup Error: unknown mixing rule -> \"%s\"\n", | |
1590 | < | simnfo->mixingRule ); |
1590 | > | info[0].mixingRule ); |
1591 | painCave.isFatal = 1; | |
1592 | simError(); | |
1593 | } | |
# | Line 914 | Line 1598 | void SimSetup::createSim( void ){ | |
1598 | "Successfully intialized the mixingRule for Fortran." ); | |
1599 | MPIcheckPoint(); | |
1600 | #endif // is_mpi | |
1601 | + | |
1602 | } | |
1603 | ||
1604 | + | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1605 | + | { |
1606 | + | int nZConstraints; |
1607 | + | ZconStamp** zconStamp; |
1608 | + | |
1609 | + | if(globals->haveZconstraintTime()){ |
1610 | + | |
1611 | + | //add sample time of z-constraint into SimInfo's property list |
1612 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1613 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
1614 | + | zconsTimeProp->setData(globals->getZconsTime()); |
1615 | + | theInfo.addProperty(zconsTimeProp); |
1616 | + | } |
1617 | + | else{ |
1618 | + | sprintf( painCave.errMsg, |
1619 | + | "ZConstraint error: If you use an ZConstraint\n" |
1620 | + | " , you must set sample time.\n"); |
1621 | + | painCave.isFatal = 1; |
1622 | + | simError(); |
1623 | + | } |
1624 | ||
1625 | < | void SimSetup::makeMolecules( void ){ |
1625 | > | // |
1626 | > | nZConstraints = globals->getNzConstraints(); |
1627 | > | zconStamp = globals->getZconStamp(); |
1628 | > | ZConsParaItem tempParaItem; |
1629 | ||
1630 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
1631 | < | molInit info; |
1632 | < | DirectionalAtom* dAtom; |
1633 | < | LinkedAssign* extras; |
1634 | < | LinkedAssign* current_extra; |
1635 | < | AtomStamp* currentAtom; |
1636 | < | BondStamp* currentBond; |
1637 | < | BendStamp* currentBend; |
930 | < | TorsionStamp* currentTorsion; |
1630 | > | ZConsParaData* zconsParaData = new ZConsParaData(); |
1631 | > | zconsParaData->setID(ZCONSPARADATA_ID); |
1632 | > | |
1633 | > | for(int i = 0; i < nZConstraints; i++){ |
1634 | > | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1635 | > | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1636 | > | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1637 | > | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1638 | ||
1639 | < | bond_pair* theBonds; |
1640 | < | bend_set* theBends; |
934 | < | torsion_set* theTorsions; |
1639 | > | zconsParaData->addItem(tempParaItem); |
1640 | > | } |
1641 | ||
1642 | < | |
1643 | < | //init the forceField paramters |
1642 | > | //sort the parameters by index of molecules |
1643 | > | zconsParaData->sortByIndex(); |
1644 | > | |
1645 | > | //push data into siminfo, therefore, we can retrieve later |
1646 | > | theInfo.addProperty(zconsParaData); |
1647 | ||
1648 | < | the_ff->readParams(); |
1648 | > | //push zconsTol into siminfo, if user does not specify |
1649 | > | //value for zconsTol, a default value will be used |
1650 | > | DoubleData* zconsTol = new DoubleData(); |
1651 | > | zconsTol->setID(ZCONSTOL_ID); |
1652 | > | if(globals->haveZconsTol()){ |
1653 | > | zconsTol->setData(globals->getZconsTol()); |
1654 | > | } |
1655 | > | else{ |
1656 | > | double defaultZConsTol = 1E-6; |
1657 | > | sprintf( painCave.errMsg, |
1658 | > | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1659 | > | " , default value %f is used.\n", defaultZConsTol); |
1660 | > | painCave.isFatal = 0; |
1661 | > | simError(); |
1662 | ||
1663 | < | |
1664 | < | // init the atoms |
1665 | < | |
1666 | < | double ux, uy, uz, u, uSqr; |
1667 | < | |
1668 | < | atomOffset = 0; |
1669 | < | excludeOffset = 0; |
948 | < | for(i=0; i<simnfo->n_mol; i++){ |
1663 | > | zconsTol->setData(defaultZConsTol); |
1664 | > | } |
1665 | > | theInfo.addProperty(zconsTol); |
1666 | > | |
1667 | > | //Determine the name of ouput file and add it into SimInfo's property list |
1668 | > | //Be careful, do not use inFileName, since it is a pointer which |
1669 | > | //point to a string at master node, and slave nodes do not contain that string |
1670 | ||
1671 | < | stampID = the_molecules[i].getStampID(); |
951 | < | |
952 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
953 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
954 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
955 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
956 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
957 | < | |
958 | < | info.myAtoms = &the_atoms[atomOffset]; |
959 | < | info.myExcludes = &the_excludes[excludeOffset]; |
960 | < | info.myBonds = new Bond*[info.nBonds]; |
961 | < | info.myBends = new Bend*[info.nBends]; |
962 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
963 | < | |
964 | < | theBonds = new bond_pair[info.nBonds]; |
965 | < | theBends = new bend_set[info.nBends]; |
966 | < | theTorsions = new torsion_set[info.nTorsions]; |
1671 | > | string zconsOutput(theInfo.finalName); |
1672 | ||
1673 | < | // make the Atoms |
1673 | > | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1674 | ||
1675 | < | for(j=0; j<info.nAtoms; j++){ |
1676 | < | |
1677 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
973 | < | if( currentAtom->haveOrientation() ){ |
974 | < | |
975 | < | dAtom = new DirectionalAtom(j + atomOffset); |
976 | < | simnfo->n_oriented++; |
977 | < | info.myAtoms[j] = dAtom; |
978 | < | |
979 | < | ux = currentAtom->getOrntX(); |
980 | < | uy = currentAtom->getOrntY(); |
981 | < | uz = currentAtom->getOrntZ(); |
982 | < | |
983 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
984 | < | |
985 | < | u = sqrt( uSqr ); |
986 | < | ux = ux / u; |
987 | < | uy = uy / u; |
988 | < | uz = uz / u; |
989 | < | |
990 | < | dAtom->setSUx( ux ); |
991 | < | dAtom->setSUy( uy ); |
992 | < | dAtom->setSUz( uz ); |
993 | < | } |
994 | < | else{ |
995 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
996 | < | } |
997 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
1675 | > | StringData* zconsFilename = new StringData(); |
1676 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
1677 | > | zconsFilename->setData(zconsOutput); |
1678 | ||
1679 | < | #ifdef IS_MPI |
1000 | < | |
1001 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1002 | < | |
1003 | < | #endif // is_mpi |
1004 | < | } |
1005 | < | |
1006 | < | // make the bonds |
1007 | < | for(j=0; j<info.nBonds; j++){ |
1008 | < | |
1009 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
1010 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
1011 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
1012 | < | |
1013 | < | exI = theBonds[j].a; |
1014 | < | exJ = theBonds[j].b; |
1015 | < | |
1016 | < | // exclude_I must always be the smaller of the pair |
1017 | < | if( exI > exJ ){ |
1018 | < | tempEx = exI; |
1019 | < | exI = exJ; |
1020 | < | exJ = tempEx; |
1021 | < | } |
1022 | < | #ifdef IS_MPI |
1023 | < | tempEx = exI; |
1024 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1025 | < | tempEx = exJ; |
1026 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1027 | < | |
1028 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1029 | < | #else // isn't MPI |
1030 | < | |
1031 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1032 | < | #endif //is_mpi |
1033 | < | } |
1034 | < | excludeOffset += info.nBonds; |
1035 | < | |
1036 | < | //make the bends |
1037 | < | for(j=0; j<info.nBends; j++){ |
1038 | < | |
1039 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
1040 | < | theBends[j].a = currentBend->getA() + atomOffset; |
1041 | < | theBends[j].b = currentBend->getB() + atomOffset; |
1042 | < | theBends[j].c = currentBend->getC() + atomOffset; |
1043 | < | |
1044 | < | if( currentBend->haveExtras() ){ |
1045 | < | |
1046 | < | extras = currentBend->getExtras(); |
1047 | < | current_extra = extras; |
1048 | < | |
1049 | < | while( current_extra != NULL ){ |
1050 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1051 | < | |
1052 | < | switch( current_extra->getType() ){ |
1053 | < | |
1054 | < | case 0: |
1055 | < | theBends[j].ghost = |
1056 | < | current_extra->getInt() + atomOffset; |
1057 | < | theBends[j].isGhost = 1; |
1058 | < | break; |
1059 | < | |
1060 | < | case 1: |
1061 | < | theBends[j].ghost = |
1062 | < | (int)current_extra->getDouble() + atomOffset; |
1063 | < | theBends[j].isGhost = 1; |
1064 | < | break; |
1065 | < | |
1066 | < | default: |
1067 | < | sprintf( painCave.errMsg, |
1068 | < | "SimSetup Error: ghostVectorSource was neither a " |
1069 | < | "double nor an int.\n" |
1070 | < | "-->Bend[%d] in %s\n", |
1071 | < | j, comp_stamps[stampID]->getID() ); |
1072 | < | painCave.isFatal = 1; |
1073 | < | simError(); |
1074 | < | } |
1075 | < | } |
1076 | < | |
1077 | < | else{ |
1078 | < | |
1079 | < | sprintf( painCave.errMsg, |
1080 | < | "SimSetup Error: unhandled bend assignment:\n" |
1081 | < | " -->%s in Bend[%d] in %s\n", |
1082 | < | current_extra->getlhs(), |
1083 | < | j, comp_stamps[stampID]->getID() ); |
1084 | < | painCave.isFatal = 1; |
1085 | < | simError(); |
1086 | < | } |
1087 | < | |
1088 | < | current_extra = current_extra->getNext(); |
1089 | < | } |
1090 | < | } |
1091 | < | |
1092 | < | if( !theBends[j].isGhost ){ |
1093 | < | |
1094 | < | exI = theBends[j].a; |
1095 | < | exJ = theBends[j].c; |
1096 | < | } |
1097 | < | else{ |
1098 | < | |
1099 | < | exI = theBends[j].a; |
1100 | < | exJ = theBends[j].b; |
1101 | < | } |
1102 | < | |
1103 | < | // exclude_I must always be the smaller of the pair |
1104 | < | if( exI > exJ ){ |
1105 | < | tempEx = exI; |
1106 | < | exI = exJ; |
1107 | < | exJ = tempEx; |
1108 | < | } |
1109 | < | #ifdef IS_MPI |
1110 | < | tempEx = exI; |
1111 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1112 | < | tempEx = exJ; |
1113 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1114 | < | |
1115 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1116 | < | #else // isn't MPI |
1117 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1118 | < | #endif //is_mpi |
1119 | < | } |
1120 | < | excludeOffset += info.nBends; |
1121 | < | |
1122 | < | for(j=0; j<info.nTorsions; j++){ |
1123 | < | |
1124 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1125 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1126 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1127 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1128 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1129 | < | |
1130 | < | exI = theTorsions[j].a; |
1131 | < | exJ = theTorsions[j].d; |
1132 | < | |
1133 | < | // exclude_I must always be the smaller of the pair |
1134 | < | if( exI > exJ ){ |
1135 | < | tempEx = exI; |
1136 | < | exI = exJ; |
1137 | < | exJ = tempEx; |
1138 | < | } |
1139 | < | #ifdef IS_MPI |
1140 | < | tempEx = exI; |
1141 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1142 | < | tempEx = exJ; |
1143 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1144 | < | |
1145 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1146 | < | #else // isn't MPI |
1147 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1148 | < | #endif //is_mpi |
1149 | < | } |
1150 | < | excludeOffset += info.nTorsions; |
1151 | < | |
1152 | < | |
1153 | < | // send the arrays off to the forceField for init. |
1154 | < | |
1155 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1156 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1157 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1158 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1159 | < | |
1160 | < | |
1161 | < | the_molecules[i].initialize( info ); |
1162 | < | |
1163 | < | |
1164 | < | atomOffset += info.nAtoms; |
1165 | < | delete[] theBonds; |
1166 | < | delete[] theBends; |
1167 | < | delete[] theTorsions; |
1168 | < | } |
1169 | < | |
1170 | < | #ifdef IS_MPI |
1171 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1172 | < | MPIcheckPoint(); |
1173 | < | #endif // is_mpi |
1174 | < | |
1175 | < | // clean up the forcefield |
1176 | < | the_ff->calcRcut(); |
1177 | < | the_ff->cleanMe(); |
1178 | < | |
1679 | > | theInfo.addProperty(zconsFilename); |
1680 | } | |
1180 | – | |
1181 | – | void SimSetup::initFromBass( void ){ |
1182 | – | |
1183 | – | int i, j, k; |
1184 | – | int n_cells; |
1185 | – | double cellx, celly, cellz; |
1186 | – | double temp1, temp2, temp3; |
1187 | – | int n_per_extra; |
1188 | – | int n_extra; |
1189 | – | int have_extra, done; |
1190 | – | |
1191 | – | temp1 = (double)tot_nmol / 4.0; |
1192 | – | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1193 | – | temp3 = ceil( temp2 ); |
1194 | – | |
1195 | – | have_extra =0; |
1196 | – | if( temp2 < temp3 ){ // we have a non-complete lattice |
1197 | – | have_extra =1; |
1198 | – | |
1199 | – | n_cells = (int)temp3 - 1; |
1200 | – | cellx = simnfo->boxLx / temp3; |
1201 | – | celly = simnfo->boxLy / temp3; |
1202 | – | cellz = simnfo->boxLz / temp3; |
1203 | – | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1204 | – | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1205 | – | n_per_extra = (int)ceil( temp1 ); |
1206 | – | |
1207 | – | if( n_per_extra > 4){ |
1208 | – | sprintf( painCave.errMsg, |
1209 | – | "SimSetup error. There has been an error in constructing" |
1210 | – | " the non-complete lattice.\n" ); |
1211 | – | painCave.isFatal = 1; |
1212 | – | simError(); |
1213 | – | } |
1214 | – | } |
1215 | – | else{ |
1216 | – | n_cells = (int)temp3; |
1217 | – | cellx = simnfo->boxLx / temp3; |
1218 | – | celly = simnfo->boxLy / temp3; |
1219 | – | cellz = simnfo->boxLz / temp3; |
1220 | – | } |
1221 | – | |
1222 | – | current_mol = 0; |
1223 | – | current_comp_mol = 0; |
1224 | – | current_comp = 0; |
1225 | – | current_atom_ndx = 0; |
1226 | – | |
1227 | – | for( i=0; i < n_cells ; i++ ){ |
1228 | – | for( j=0; j < n_cells; j++ ){ |
1229 | – | for( k=0; k < n_cells; k++ ){ |
1230 | – | |
1231 | – | makeElement( i * cellx, |
1232 | – | j * celly, |
1233 | – | k * cellz ); |
1234 | – | |
1235 | – | makeElement( i * cellx + 0.5 * cellx, |
1236 | – | j * celly + 0.5 * celly, |
1237 | – | k * cellz ); |
1238 | – | |
1239 | – | makeElement( i * cellx, |
1240 | – | j * celly + 0.5 * celly, |
1241 | – | k * cellz + 0.5 * cellz ); |
1242 | – | |
1243 | – | makeElement( i * cellx + 0.5 * cellx, |
1244 | – | j * celly, |
1245 | – | k * cellz + 0.5 * cellz ); |
1246 | – | } |
1247 | – | } |
1248 | – | } |
1249 | – | |
1250 | – | if( have_extra ){ |
1251 | – | done = 0; |
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++ ){ |
1256 | – | |
1257 | – | if( i < n_cells ){ |
1258 | – | |
1259 | – | if( j < n_cells ){ |
1260 | – | start_ndx = n_cells; |
1261 | – | } |
1262 | – | else start_ndx = 0; |
1263 | – | } |
1264 | – | else start_ndx = 0; |
1265 | – | |
1266 | – | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1267 | – | |
1268 | – | makeElement( i * cellx, |
1269 | – | j * celly, |
1270 | – | k * cellz ); |
1271 | – | done = ( current_mol >= tot_nmol ); |
1272 | – | |
1273 | – | if( !done && n_per_extra > 1 ){ |
1274 | – | makeElement( i * cellx + 0.5 * cellx, |
1275 | – | j * celly + 0.5 * celly, |
1276 | – | k * cellz ); |
1277 | – | done = ( current_mol >= tot_nmol ); |
1278 | – | } |
1279 | – | |
1280 | – | if( !done && n_per_extra > 2){ |
1281 | – | makeElement( i * cellx, |
1282 | – | j * celly + 0.5 * celly, |
1283 | – | k * cellz + 0.5 * cellz ); |
1284 | – | done = ( current_mol >= tot_nmol ); |
1285 | – | } |
1286 | – | |
1287 | – | if( !done && n_per_extra > 3){ |
1288 | – | makeElement( i * cellx + 0.5 * cellx, |
1289 | – | j * celly, |
1290 | – | k * cellz + 0.5 * cellz ); |
1291 | – | done = ( current_mol >= tot_nmol ); |
1292 | – | } |
1293 | – | } |
1294 | – | } |
1295 | – | } |
1296 | – | } |
1297 | – | |
1298 | – | |
1299 | – | for( i=0; i<simnfo->n_atoms; i++ ){ |
1300 | – | simnfo->atoms[i]->set_vx( 0.0 ); |
1301 | – | simnfo->atoms[i]->set_vy( 0.0 ); |
1302 | – | simnfo->atoms[i]->set_vz( 0.0 ); |
1303 | – | } |
1304 | – | } |
1305 | – | |
1306 | – | void SimSetup::makeElement( double x, double y, double z ){ |
1307 | – | |
1308 | – | int k; |
1309 | – | AtomStamp* current_atom; |
1310 | – | DirectionalAtom* dAtom; |
1311 | – | double rotMat[3][3]; |
1312 | – | |
1313 | – | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1314 | – | |
1315 | – | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1316 | – | if( !current_atom->havePosition() ){ |
1317 | – | sprintf( painCave.errMsg, |
1318 | – | "SimSetup:initFromBass error.\n" |
1319 | – | "\tComponent %s, atom %s does not have a position specified.\n" |
1320 | – | "\tThe initialization routine is unable to give a start" |
1321 | – | " position.\n", |
1322 | – | comp_stamps[current_comp]->getID(), |
1323 | – | current_atom->getType() ); |
1324 | – | painCave.isFatal = 1; |
1325 | – | simError(); |
1326 | – | } |
1327 | – | |
1328 | – | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1329 | – | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1330 | – | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1331 | – | |
1332 | – | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1333 | – | |
1334 | – | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1335 | – | |
1336 | – | rotMat[0][0] = 1.0; |
1337 | – | rotMat[0][1] = 0.0; |
1338 | – | rotMat[0][2] = 0.0; |
1339 | – | |
1340 | – | rotMat[1][0] = 0.0; |
1341 | – | rotMat[1][1] = 1.0; |
1342 | – | rotMat[1][2] = 0.0; |
1343 | – | |
1344 | – | rotMat[2][0] = 0.0; |
1345 | – | rotMat[2][1] = 0.0; |
1346 | – | rotMat[2][2] = 1.0; |
1347 | – | |
1348 | – | dAtom->setA( rotMat ); |
1349 | – | } |
1350 | – | |
1351 | – | current_atom_ndx++; |
1352 | – | } |
1353 | – | |
1354 | – | current_mol++; |
1355 | – | current_comp_mol++; |
1356 | – | |
1357 | – | if( current_comp_mol >= components_nmol[current_comp] ){ |
1358 | – | |
1359 | – | current_comp_mol = 0; |
1360 | – | current_comp++; |
1361 | – | } |
1362 | – | } |
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