# | Line 78 | Line 78 | void SimSetup::createSim( void ){ | |
---|---|---|
78 | ||
79 | void SimSetup::createSim( void ){ | |
80 | ||
81 | – | MakeStamps *the_stamps; |
82 | – | Globals* the_globals; |
81 | int i, j, k, globalAtomIndex; | |
82 | ||
83 | < | int ensembleCase; |
86 | < | int ffCase; |
83 | > | // gather all of the information from the Bass file |
84 | ||
85 | + | gatherInfo(); |
86 | + | |
87 | + | // creation of complex system objects |
88 | + | |
89 | + | sysObjectsCreation(); |
90 | + | |
91 | + | // check on the post processing info |
92 | + | |
93 | + | finalInfoCheck(); |
94 | + | |
95 | + | // initialize the system coordinates |
96 | + | |
97 | + | initSystemCoords(); |
98 | + | |
99 | + | |
100 | + | // make the output filenames |
101 | + | |
102 | + | makeOutNames(); |
103 | + | |
104 | + | // make the integrator |
105 | + | |
106 | + | makeIntegrator(); |
107 | + | |
108 | + | #ifdef IS_MPI |
109 | + | mpiSim->mpiRefresh(); |
110 | + | #endif |
111 | + | |
112 | + | // initialize the Fortran |
113 | + | |
114 | + | initFortran(); |
115 | + | |
116 | + | |
117 | + | |
118 | + | } |
119 | + | |
120 | + | |
121 | + | void SimSetup::makeMolecules( void ){ |
122 | + | |
123 | + | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
124 | + | molInit molInfo; |
125 | + | DirectionalAtom* dAtom; |
126 | + | LinkedAssign* extras; |
127 | + | LinkedAssign* current_extra; |
128 | + | AtomStamp* currentAtom; |
129 | + | BondStamp* currentBond; |
130 | + | BendStamp* currentBend; |
131 | + | TorsionStamp* currentTorsion; |
132 | + | |
133 | + | bond_pair* theBonds; |
134 | + | bend_set* theBends; |
135 | + | torsion_set* theTorsions; |
136 | + | |
137 | + | |
138 | + | //init the forceField paramters |
139 | + | |
140 | + | the_ff->readParams(); |
141 | + | |
142 | + | |
143 | + | // init the atoms |
144 | + | |
145 | + | double ux, uy, uz, u, uSqr; |
146 | + | |
147 | + | atomOffset = 0; |
148 | + | excludeOffset = 0; |
149 | + | for(i=0; i<info->n_mol; i++){ |
150 | + | |
151 | + | stampID = the_molecules[i].getStampID(); |
152 | + | |
153 | + | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
154 | + | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
155 | + | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
156 | + | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 | + | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
158 | + | |
159 | + | molInfo.myAtoms = &the_atoms[atomOffset]; |
160 | + | molInfo.myExcludes = &the_excludes[excludeOffset]; |
161 | + | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
162 | + | molInfo.myBends = new Bend*[molInfo.nBends]; |
163 | + | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
164 | + | |
165 | + | theBonds = new bond_pair[molInfo.nBonds]; |
166 | + | theBends = new bend_set[molInfo.nBends]; |
167 | + | theTorsions = new torsion_set[molInfo.nTorsions]; |
168 | + | |
169 | + | // make the Atoms |
170 | + | |
171 | + | for(j=0; j<molInfo.nAtoms; j++){ |
172 | + | |
173 | + | currentAtom = comp_stamps[stampID]->getAtom( j ); |
174 | + | if( currentAtom->haveOrientation() ){ |
175 | + | |
176 | + | dAtom = new DirectionalAtom(j + atomOffset); |
177 | + | info->n_oriented++; |
178 | + | molInfo.myAtoms[j] = dAtom; |
179 | + | |
180 | + | ux = currentAtom->getOrntX(); |
181 | + | uy = currentAtom->getOrntY(); |
182 | + | uz = currentAtom->getOrntZ(); |
183 | + | |
184 | + | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
185 | + | |
186 | + | u = sqrt( uSqr ); |
187 | + | ux = ux / u; |
188 | + | uy = uy / u; |
189 | + | uz = uz / u; |
190 | + | |
191 | + | dAtom->setSUx( ux ); |
192 | + | dAtom->setSUy( uy ); |
193 | + | dAtom->setSUz( uz ); |
194 | + | } |
195 | + | else{ |
196 | + | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
197 | + | } |
198 | + | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
199 | + | |
200 | + | #ifdef IS_MPI |
201 | + | |
202 | + | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
203 | + | |
204 | + | #endif // is_mpi |
205 | + | } |
206 | + | |
207 | + | // make the bonds |
208 | + | for(j=0; j<molInfo.nBonds; j++){ |
209 | + | |
210 | + | currentBond = comp_stamps[stampID]->getBond( j ); |
211 | + | theBonds[j].a = currentBond->getA() + atomOffset; |
212 | + | theBonds[j].b = currentBond->getB() + atomOffset; |
213 | + | |
214 | + | exI = theBonds[j].a; |
215 | + | exJ = theBonds[j].b; |
216 | + | |
217 | + | // exclude_I must always be the smaller of the pair |
218 | + | if( exI > exJ ){ |
219 | + | tempEx = exI; |
220 | + | exI = exJ; |
221 | + | exJ = tempEx; |
222 | + | } |
223 | + | #ifdef IS_MPI |
224 | + | tempEx = exI; |
225 | + | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
226 | + | tempEx = exJ; |
227 | + | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
228 | + | |
229 | + | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
230 | + | #else // isn't MPI |
231 | + | |
232 | + | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
233 | + | #endif //is_mpi |
234 | + | } |
235 | + | excludeOffset += molInfo.nBonds; |
236 | + | |
237 | + | //make the bends |
238 | + | for(j=0; j<molInfo.nBends; j++){ |
239 | + | |
240 | + | currentBend = comp_stamps[stampID]->getBend( j ); |
241 | + | theBends[j].a = currentBend->getA() + atomOffset; |
242 | + | theBends[j].b = currentBend->getB() + atomOffset; |
243 | + | theBends[j].c = currentBend->getC() + atomOffset; |
244 | + | |
245 | + | if( currentBend->haveExtras() ){ |
246 | + | |
247 | + | extras = currentBend->getExtras(); |
248 | + | current_extra = extras; |
249 | + | |
250 | + | while( current_extra != NULL ){ |
251 | + | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
252 | + | |
253 | + | switch( current_extra->getType() ){ |
254 | + | |
255 | + | case 0: |
256 | + | theBends[j].ghost = |
257 | + | current_extra->getInt() + atomOffset; |
258 | + | theBends[j].isGhost = 1; |
259 | + | break; |
260 | + | |
261 | + | case 1: |
262 | + | theBends[j].ghost = |
263 | + | (int)current_extra->getDouble() + atomOffset; |
264 | + | theBends[j].isGhost = 1; |
265 | + | break; |
266 | + | |
267 | + | default: |
268 | + | sprintf( painCave.errMsg, |
269 | + | "SimSetup Error: ghostVectorSource was neither a " |
270 | + | "double nor an int.\n" |
271 | + | "-->Bend[%d] in %s\n", |
272 | + | j, comp_stamps[stampID]->getID() ); |
273 | + | painCave.isFatal = 1; |
274 | + | simError(); |
275 | + | } |
276 | + | } |
277 | + | |
278 | + | else{ |
279 | + | |
280 | + | sprintf( painCave.errMsg, |
281 | + | "SimSetup Error: unhandled bend assignment:\n" |
282 | + | " -->%s in Bend[%d] in %s\n", |
283 | + | current_extra->getlhs(), |
284 | + | j, comp_stamps[stampID]->getID() ); |
285 | + | painCave.isFatal = 1; |
286 | + | simError(); |
287 | + | } |
288 | + | |
289 | + | current_extra = current_extra->getNext(); |
290 | + | } |
291 | + | } |
292 | + | |
293 | + | if( !theBends[j].isGhost ){ |
294 | + | |
295 | + | exI = theBends[j].a; |
296 | + | exJ = theBends[j].c; |
297 | + | } |
298 | + | else{ |
299 | + | |
300 | + | exI = theBends[j].a; |
301 | + | exJ = theBends[j].b; |
302 | + | } |
303 | + | |
304 | + | // exclude_I must always be the smaller of the pair |
305 | + | if( exI > exJ ){ |
306 | + | tempEx = exI; |
307 | + | exI = exJ; |
308 | + | exJ = tempEx; |
309 | + | } |
310 | + | #ifdef IS_MPI |
311 | + | tempEx = exI; |
312 | + | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
313 | + | tempEx = exJ; |
314 | + | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
315 | + | |
316 | + | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
317 | + | #else // isn't MPI |
318 | + | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
319 | + | #endif //is_mpi |
320 | + | } |
321 | + | excludeOffset += molInfo.nBends; |
322 | + | |
323 | + | for(j=0; j<molInfo.nTorsions; j++){ |
324 | + | |
325 | + | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
326 | + | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
327 | + | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
328 | + | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
329 | + | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
330 | + | |
331 | + | exI = theTorsions[j].a; |
332 | + | exJ = theTorsions[j].d; |
333 | + | |
334 | + | // exclude_I must always be the smaller of the pair |
335 | + | if( exI > exJ ){ |
336 | + | tempEx = exI; |
337 | + | exI = exJ; |
338 | + | exJ = tempEx; |
339 | + | } |
340 | + | #ifdef IS_MPI |
341 | + | tempEx = exI; |
342 | + | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
343 | + | tempEx = exJ; |
344 | + | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
345 | + | |
346 | + | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
347 | + | #else // isn't MPI |
348 | + | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 | + | #endif //is_mpi |
350 | + | } |
351 | + | excludeOffset += molInfo.nTorsions; |
352 | + | |
353 | + | |
354 | + | // send the arrays off to the forceField for init. |
355 | + | |
356 | + | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
357 | + | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
358 | + | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
359 | + | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
360 | + | |
361 | + | |
362 | + | the_molecules[i].initialize( molInfo ); |
363 | + | |
364 | + | |
365 | + | atomOffset += molInfo.nAtoms; |
366 | + | delete[] theBonds; |
367 | + | delete[] theBends; |
368 | + | delete[] theTorsions; |
369 | + | } |
370 | + | |
371 | + | #ifdef IS_MPI |
372 | + | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
373 | + | MPIcheckPoint(); |
374 | + | #endif // is_mpi |
375 | + | |
376 | + | // clean up the forcefield |
377 | + | the_ff->calcRcut(); |
378 | + | the_ff->cleanMe(); |
379 | + | |
380 | + | } |
381 | + | |
382 | + | void SimSetup::initFromBass( void ){ |
383 | + | |
384 | + | int i, j, k; |
385 | + | int n_cells; |
386 | + | double cellx, celly, cellz; |
387 | + | double temp1, temp2, temp3; |
388 | + | int n_per_extra; |
389 | + | int n_extra; |
390 | + | int have_extra, done; |
391 | + | |
392 | + | temp1 = (double)tot_nmol / 4.0; |
393 | + | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
394 | + | temp3 = ceil( temp2 ); |
395 | + | |
396 | + | have_extra =0; |
397 | + | if( temp2 < temp3 ){ // we have a non-complete lattice |
398 | + | have_extra =1; |
399 | + | |
400 | + | n_cells = (int)temp3 - 1; |
401 | + | cellx = info->boxL[0] / temp3; |
402 | + | celly = info->boxL[1] / temp3; |
403 | + | cellz = info->boxL[2] / temp3; |
404 | + | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
405 | + | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
406 | + | n_per_extra = (int)ceil( temp1 ); |
407 | + | |
408 | + | if( n_per_extra > 4){ |
409 | + | sprintf( painCave.errMsg, |
410 | + | "SimSetup error. There has been an error in constructing" |
411 | + | " the non-complete lattice.\n" ); |
412 | + | painCave.isFatal = 1; |
413 | + | simError(); |
414 | + | } |
415 | + | } |
416 | + | else{ |
417 | + | n_cells = (int)temp3; |
418 | + | cellx = info->boxL[0] / temp3; |
419 | + | celly = info->boxL[1] / temp3; |
420 | + | cellz = info->boxL[2] / temp3; |
421 | + | } |
422 | + | |
423 | + | current_mol = 0; |
424 | + | current_comp_mol = 0; |
425 | + | current_comp = 0; |
426 | + | current_atom_ndx = 0; |
427 | + | |
428 | + | for( i=0; i < n_cells ; i++ ){ |
429 | + | for( j=0; j < n_cells; j++ ){ |
430 | + | for( k=0; k < n_cells; k++ ){ |
431 | + | |
432 | + | makeElement( i * cellx, |
433 | + | j * celly, |
434 | + | k * cellz ); |
435 | + | |
436 | + | makeElement( i * cellx + 0.5 * cellx, |
437 | + | j * celly + 0.5 * celly, |
438 | + | k * cellz ); |
439 | + | |
440 | + | makeElement( i * cellx, |
441 | + | j * celly + 0.5 * celly, |
442 | + | k * cellz + 0.5 * cellz ); |
443 | + | |
444 | + | makeElement( i * cellx + 0.5 * cellx, |
445 | + | j * celly, |
446 | + | k * cellz + 0.5 * cellz ); |
447 | + | } |
448 | + | } |
449 | + | } |
450 | + | |
451 | + | if( have_extra ){ |
452 | + | done = 0; |
453 | + | |
454 | + | int start_ndx; |
455 | + | for( i=0; i < (n_cells+1) && !done; i++ ){ |
456 | + | for( j=0; j < (n_cells+1) && !done; j++ ){ |
457 | + | |
458 | + | if( i < n_cells ){ |
459 | + | |
460 | + | if( j < n_cells ){ |
461 | + | start_ndx = n_cells; |
462 | + | } |
463 | + | else start_ndx = 0; |
464 | + | } |
465 | + | else start_ndx = 0; |
466 | + | |
467 | + | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
468 | + | |
469 | + | makeElement( i * cellx, |
470 | + | j * celly, |
471 | + | k * cellz ); |
472 | + | done = ( current_mol >= tot_nmol ); |
473 | + | |
474 | + | if( !done && n_per_extra > 1 ){ |
475 | + | makeElement( i * cellx + 0.5 * cellx, |
476 | + | j * celly + 0.5 * celly, |
477 | + | k * cellz ); |
478 | + | done = ( current_mol >= tot_nmol ); |
479 | + | } |
480 | + | |
481 | + | if( !done && n_per_extra > 2){ |
482 | + | makeElement( i * cellx, |
483 | + | j * celly + 0.5 * celly, |
484 | + | k * cellz + 0.5 * cellz ); |
485 | + | done = ( current_mol >= tot_nmol ); |
486 | + | } |
487 | + | |
488 | + | if( !done && n_per_extra > 3){ |
489 | + | makeElement( i * cellx + 0.5 * cellx, |
490 | + | j * celly, |
491 | + | k * cellz + 0.5 * cellz ); |
492 | + | done = ( current_mol >= tot_nmol ); |
493 | + | } |
494 | + | } |
495 | + | } |
496 | + | } |
497 | + | } |
498 | + | |
499 | + | |
500 | + | for( i=0; i<info->n_atoms; i++ ){ |
501 | + | info->atoms[i]->set_vx( 0.0 ); |
502 | + | info->atoms[i]->set_vy( 0.0 ); |
503 | + | info->atoms[i]->set_vz( 0.0 ); |
504 | + | } |
505 | + | } |
506 | + | |
507 | + | void SimSetup::makeElement( double x, double y, double z ){ |
508 | + | |
509 | + | int k; |
510 | + | AtomStamp* current_atom; |
511 | + | DirectionalAtom* dAtom; |
512 | + | double rotMat[3][3]; |
513 | + | |
514 | + | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
515 | + | |
516 | + | current_atom = comp_stamps[current_comp]->getAtom( k ); |
517 | + | if( !current_atom->havePosition() ){ |
518 | + | sprintf( painCave.errMsg, |
519 | + | "SimSetup:initFromBass error.\n" |
520 | + | "\tComponent %s, atom %s does not have a position specified.\n" |
521 | + | "\tThe initialization routine is unable to give a start" |
522 | + | " position.\n", |
523 | + | comp_stamps[current_comp]->getID(), |
524 | + | current_atom->getType() ); |
525 | + | painCave.isFatal = 1; |
526 | + | simError(); |
527 | + | } |
528 | + | |
529 | + | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
530 | + | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
531 | + | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
532 | + | |
533 | + | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
534 | + | |
535 | + | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
536 | + | |
537 | + | rotMat[0][0] = 1.0; |
538 | + | rotMat[0][1] = 0.0; |
539 | + | rotMat[0][2] = 0.0; |
540 | + | |
541 | + | rotMat[1][0] = 0.0; |
542 | + | rotMat[1][1] = 1.0; |
543 | + | rotMat[1][2] = 0.0; |
544 | + | |
545 | + | rotMat[2][0] = 0.0; |
546 | + | rotMat[2][1] = 0.0; |
547 | + | rotMat[2][2] = 1.0; |
548 | + | |
549 | + | dAtom->setA( rotMat ); |
550 | + | } |
551 | + | |
552 | + | current_atom_ndx++; |
553 | + | } |
554 | + | |
555 | + | current_mol++; |
556 | + | current_comp_mol++; |
557 | + | |
558 | + | if( current_comp_mol >= components_nmol[current_comp] ){ |
559 | + | |
560 | + | current_comp_mol = 0; |
561 | + | current_comp++; |
562 | + | } |
563 | + | } |
564 | + | |
565 | + | |
566 | + | void SimSetup::gatherInfo( void ){ |
567 | + | int i,j,k; |
568 | + | |
569 | ensembleCase = -1; | |
570 | ffCase = -1; | |
571 | ||
572 | // get the stamps and globals; | |
573 | < | the_stamps = stamps; |
574 | < | the_globals = globals; |
573 | > | stamps = stamps; |
574 | > | globals = globals; |
575 | ||
576 | // set the easy ones first | |
577 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
578 | < | simnfo->dt = the_globals->getDt(); |
579 | < | simnfo->run_time = the_globals->getRunTime(); |
577 | > | info->target_temp = globals->getTargetTemp(); |
578 | > | info->dt = globals->getDt(); |
579 | > | info->run_time = globals->getRunTime(); |
580 | > | n_components = globals->getNComponents(); |
581 | ||
100 | – | // get the ones we know are there, yet still may need some work. |
101 | – | n_components = the_globals->getNComponents(); |
102 | – | strcpy( force_field, the_globals->getForceField() ); |
582 | ||
583 | + | // get the forceField |
584 | + | |
585 | + | strcpy( force_field, globals->getForceField() ); |
586 | + | |
587 | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; | |
588 | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; | |
589 | else{ | |
# | Line 111 | Line 594 | void SimSetup::createSim( void ){ | |
594 | simError(); | |
595 | } | |
596 | ||
597 | < | // get the ensemble: |
115 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
597 | > | // get the ensemble |
598 | ||
599 | + | strcpy( ensemble, globals->getEnsemble() ); |
600 | + | |
601 | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; | |
602 | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; | |
603 | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) | |
# | Line 131 | Line 615 | void SimSetup::createSim( void ){ | |
615 | strcpy( ensemble, "NVE" ); | |
616 | ensembleCase = NVE_ENS; | |
617 | } | |
618 | < | strcpy( simnfo->ensemble, ensemble ); |
618 | > | strcpy( info->ensemble, ensemble ); |
619 | ||
620 | + | // get the mixing rule |
621 | ||
622 | < | // if( !strcasecmp( ensemble, "NPT" ) ) { |
623 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
624 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
625 | < | // if (the_globals->haveTargetPressure()) |
141 | < | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
142 | < | // else { |
143 | < | // sprintf( painCave.errMsg, |
144 | < | // "SimSetup error: If you use the constant pressure\n" |
145 | < | // " ensemble, you must set targetPressure.\n" |
146 | < | // " This was found in the BASS file.\n"); |
147 | < | // painCave.isFatal = 1; |
148 | < | // simError(); |
149 | < | // } |
150 | < | |
151 | < | // if (the_globals->haveTauThermostat()) |
152 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
153 | < | // else if (the_globals->haveQmass()) |
154 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
155 | < | // else { |
156 | < | // sprintf( painCave.errMsg, |
157 | < | // "SimSetup error: If you use one of the constant temperature\n" |
158 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
159 | < | // " Neither of these was found in the BASS file.\n"); |
160 | < | // painCave.isFatal = 1; |
161 | < | // simError(); |
162 | < | // } |
163 | < | |
164 | < | // if (the_globals->haveTauBarostat()) |
165 | < | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
166 | < | // else { |
167 | < | // sprintf( painCave.errMsg, |
168 | < | // "SimSetup error: If you use the constant pressure\n" |
169 | < | // " ensemble, you must set tauBarostat.\n" |
170 | < | // " This was found in the BASS file.\n"); |
171 | < | // painCave.isFatal = 1; |
172 | < | // simError(); |
173 | < | // } |
174 | < | |
175 | < | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
176 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
177 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
178 | < | |
179 | < | // if (the_globals->haveTauThermostat()) |
180 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
181 | < | // else if (the_globals->haveQmass()) |
182 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
183 | < | // else { |
184 | < | // sprintf( painCave.errMsg, |
185 | < | // "SimSetup error: If you use one of the constant temperature\n" |
186 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
187 | < | // " Neither of these was found in the BASS file.\n"); |
188 | < | // painCave.isFatal = 1; |
189 | < | // simError(); |
190 | < | // } |
191 | < | |
192 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
193 | < | simnfo->usePBC = the_globals->getPBC(); |
194 | < | |
195 | < | int usesDipoles = 0; |
196 | < | switch( ffCase ){ |
197 | < | |
198 | < | case FF_DUFF: |
199 | < | the_ff = new DUFF(); |
200 | < | usesDipoles = 1; |
201 | < | break; |
202 | < | |
203 | < | case FF_LJ: |
204 | < | the_ff = new LJFF(); |
205 | < | break; |
206 | < | |
207 | < | default: |
208 | < | sprintf( painCave.errMsg, |
209 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
210 | < | painCave.isFatal = 1; |
211 | < | simError(); |
212 | < | } |
213 | < | |
214 | < | #ifdef IS_MPI |
215 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
216 | < | MPIcheckPoint(); |
217 | < | #endif // is_mpi |
218 | < | |
622 | > | strcpy( info->mixingRule, globals->getMixingRule() ); |
623 | > | info->usePBC = globals->getPBC(); |
624 | > | |
625 | > | |
626 | // get the components and calculate the tot_nMol and indvidual n_mol | |
627 | < | the_components = the_globals->getComponents(); |
627 | > | |
628 | > | the_components = globals->getComponents(); |
629 | components_nmol = new int[n_components]; | |
222 | – | comp_stamps = new MoleculeStamp*[n_components]; |
630 | ||
631 | < | if( !the_globals->haveNMol() ){ |
631 | > | |
632 | > | if( !globals->haveNMol() ){ |
633 | // we don't have the total number of molecules, so we assume it is | |
634 | // given in each component | |
635 | ||
# | Line 250 | Line 658 | void SimSetup::createSim( void ){ | |
658 | " Please give nMol in the components.\n" ); | |
659 | painCave.isFatal = 1; | |
660 | simError(); | |
253 | – | |
254 | – | |
255 | – | // tot_nmol = the_globals->getNMol(); |
256 | – | |
257 | – | // //we have the total number of molecules, now we check for molfractions |
258 | – | // for( i=0; i<n_components; i++ ){ |
259 | – | |
260 | – | // if( !the_components[i]->haveMolFraction() ){ |
261 | – | |
262 | – | // if( !the_components[i]->haveNMol() ){ |
263 | – | // //we have a problem |
264 | – | // std::cerr << "SimSetup error. Neither molFraction nor " |
265 | – | // << " nMol was given in component |
266 | – | |
661 | } | |
662 | ||
663 | < | #ifdef IS_MPI |
270 | < | strcpy( checkPointMsg, "Have the number of components" ); |
271 | < | MPIcheckPoint(); |
272 | < | #endif // is_mpi |
273 | < | |
274 | < | // make an array of molecule stamps that match the components used. |
275 | < | // also extract the used stamps out into a separate linked list |
276 | < | |
277 | < | simnfo->nComponents = n_components; |
278 | < | simnfo->componentsNmol = components_nmol; |
279 | < | simnfo->compStamps = comp_stamps; |
280 | < | simnfo->headStamp = new LinkedMolStamp(); |
663 | > | // set the status, sample, and thermal kick times |
664 | ||
665 | < | char* id; |
666 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
667 | < | LinkedMolStamp* currentStamp = NULL; |
668 | < | for( i=0; i<n_components; i++ ){ |
286 | < | |
287 | < | id = the_components[i]->getType(); |
288 | < | comp_stamps[i] = NULL; |
289 | < | |
290 | < | // check to make sure the component isn't already in the list |
291 | < | |
292 | < | comp_stamps[i] = headStamp->match( id ); |
293 | < | if( comp_stamps[i] == NULL ){ |
294 | < | |
295 | < | // extract the component from the list; |
296 | < | |
297 | < | currentStamp = the_stamps->extractMolStamp( id ); |
298 | < | if( currentStamp == NULL ){ |
299 | < | sprintf( painCave.errMsg, |
300 | < | "SimSetup error: Component \"%s\" was not found in the " |
301 | < | "list of declared molecules\n", |
302 | < | id ); |
303 | < | painCave.isFatal = 1; |
304 | < | simError(); |
305 | < | } |
306 | < | |
307 | < | headStamp->add( currentStamp ); |
308 | < | comp_stamps[i] = headStamp->match( id ); |
309 | < | } |
665 | > | if( globals->haveSampleTime() ){ |
666 | > | info->sampleTime = globals->getSampleTime(); |
667 | > | info->statusTime = info->sampleTime; |
668 | > | info->thermalTime = info->sampleTime; |
669 | } | |
670 | + | else{ |
671 | + | info->sampleTime = globals->getRunTime(); |
672 | + | info->statusTime = info->sampleTime; |
673 | + | info->thermalTime = info->sampleTime; |
674 | + | } |
675 | ||
676 | < | #ifdef IS_MPI |
677 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
314 | < | MPIcheckPoint(); |
315 | < | #endif // is_mpi |
316 | < | |
317 | < | |
318 | < | |
319 | < | |
320 | < | // caclulate the number of atoms, bonds, bends and torsions |
321 | < | |
322 | < | tot_atoms = 0; |
323 | < | tot_bonds = 0; |
324 | < | tot_bends = 0; |
325 | < | tot_torsions = 0; |
326 | < | for( i=0; i<n_components; i++ ){ |
327 | < | |
328 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
329 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
330 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
331 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
676 | > | if( globals->haveStatusTime() ){ |
677 | > | info->statusTime = globals->getStatusTime(); |
678 | } | |
679 | ||
680 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
681 | < | |
682 | < | simnfo->n_atoms = tot_atoms; |
337 | < | simnfo->n_bonds = tot_bonds; |
338 | < | simnfo->n_bends = tot_bends; |
339 | < | simnfo->n_torsions = tot_torsions; |
340 | < | simnfo->n_SRI = tot_SRI; |
341 | < | simnfo->n_mol = tot_nmol; |
342 | < | |
343 | < | simnfo->molMembershipArray = new int[tot_atoms]; |
344 | < | |
345 | < | #ifdef IS_MPI |
346 | < | |
347 | < | // divide the molecules among processors here. |
348 | < | |
349 | < | mpiSim = new mpiSimulation( simnfo ); |
350 | < | |
351 | < | globalIndex = mpiSim->divideLabor(); |
352 | < | |
353 | < | // set up the local variables |
354 | < | |
355 | < | int localMol, allMol; |
356 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
357 | < | |
358 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
359 | < | int* molCompType = mpiSim->getMolComponentType(); |
360 | < | |
361 | < | allMol = 0; |
362 | < | localMol = 0; |
363 | < | local_atoms = 0; |
364 | < | local_bonds = 0; |
365 | < | local_bends = 0; |
366 | < | local_torsions = 0; |
367 | < | globalAtomIndex = 0; |
680 | > | if( globals->haveThermalTime() ){ |
681 | > | info->thermalTime = globals->getThermalTime(); |
682 | > | } |
683 | ||
684 | + | // check for the temperature set flag |
685 | ||
686 | < | for( i=0; i<n_components; i++ ){ |
686 | > | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
687 | ||
372 | – | for( j=0; j<components_nmol[i]; j++ ){ |
373 | – | |
374 | – | if( mol2proc[allMol] == worldRank ){ |
375 | – | |
376 | – | local_atoms += comp_stamps[i]->getNAtoms(); |
377 | – | local_bonds += comp_stamps[i]->getNBonds(); |
378 | – | local_bends += comp_stamps[i]->getNBends(); |
379 | – | local_torsions += comp_stamps[i]->getNTorsions(); |
380 | – | localMol++; |
381 | – | } |
382 | – | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
383 | – | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
384 | – | globalAtomIndex++; |
385 | – | } |
386 | – | |
387 | – | allMol++; |
388 | – | } |
389 | – | } |
390 | – | local_SRI = local_bonds + local_bends + local_torsions; |
391 | – | |
392 | – | simnfo->n_atoms = mpiSim->getMyNlocal(); |
393 | – | |
394 | – | if( local_atoms != simnfo->n_atoms ){ |
395 | – | sprintf( painCave.errMsg, |
396 | – | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
397 | – | " localAtom (%d) are not equal.\n", |
398 | – | simnfo->n_atoms, |
399 | – | local_atoms ); |
400 | – | painCave.isFatal = 1; |
401 | – | simError(); |
402 | – | } |
403 | – | |
404 | – | simnfo->n_bonds = local_bonds; |
405 | – | simnfo->n_bends = local_bends; |
406 | – | simnfo->n_torsions = local_torsions; |
407 | – | simnfo->n_SRI = local_SRI; |
408 | – | simnfo->n_mol = localMol; |
409 | – | |
410 | – | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
411 | – | MPIcheckPoint(); |
412 | – | |
413 | – | |
414 | – | #endif // is_mpi |
415 | – | |
416 | – | |
417 | – | // create the atom and short range interaction arrays |
418 | – | |
419 | – | Atom::createArrays(simnfo->n_atoms); |
420 | – | the_atoms = new Atom*[simnfo->n_atoms]; |
421 | – | the_molecules = new Molecule[simnfo->n_mol]; |
422 | – | int molIndex; |
423 | – | |
424 | – | // initialize the molecule's stampID's |
425 | – | |
426 | – | #ifdef IS_MPI |
427 | – | |
428 | – | |
429 | – | molIndex = 0; |
430 | – | for(i=0; i<mpiSim->getTotNmol(); i++){ |
431 | – | |
432 | – | if(mol2proc[i] == worldRank ){ |
433 | – | the_molecules[molIndex].setStampID( molCompType[i] ); |
434 | – | the_molecules[molIndex].setMyIndex( molIndex ); |
435 | – | the_molecules[molIndex].setGlobalIndex( i ); |
436 | – | molIndex++; |
437 | – | } |
438 | – | } |
439 | – | |
440 | – | #else // is_mpi |
441 | – | |
442 | – | molIndex = 0; |
443 | – | globalAtomIndex = 0; |
444 | – | for(i=0; i<n_components; i++){ |
445 | – | for(j=0; j<components_nmol[i]; j++ ){ |
446 | – | the_molecules[molIndex].setStampID( i ); |
447 | – | the_molecules[molIndex].setMyIndex( molIndex ); |
448 | – | the_molecules[molIndex].setGlobalIndex( molIndex ); |
449 | – | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
450 | – | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
451 | – | globalAtomIndex++; |
452 | – | } |
453 | – | molIndex++; |
454 | – | } |
455 | – | } |
456 | – | |
457 | – | |
458 | – | #endif // is_mpi |
459 | – | |
460 | – | |
461 | – | if( simnfo->n_SRI ){ |
462 | – | |
463 | – | Exclude::createArray(simnfo->n_SRI); |
464 | – | the_excludes = new Exclude*[simnfo->n_SRI]; |
465 | – | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
466 | – | simnfo->globalExcludes = new int; |
467 | – | simnfo->n_exclude = simnfo->n_SRI; |
468 | – | } |
469 | – | else{ |
470 | – | |
471 | – | Exclude::createArray( 1 ); |
472 | – | the_excludes = new Exclude*; |
473 | – | the_excludes[0] = new Exclude(0); |
474 | – | the_excludes[0]->setPair( 0,0 ); |
475 | – | simnfo->globalExcludes = new int; |
476 | – | simnfo->globalExcludes[0] = 0; |
477 | – | simnfo->n_exclude = 0; |
478 | – | } |
479 | – | |
480 | – | // set the arrays into the SimInfo object |
481 | – | |
482 | – | simnfo->atoms = the_atoms; |
483 | – | simnfo->molecules = the_molecules; |
484 | – | simnfo->nGlobalExcludes = 0; |
485 | – | simnfo->excludes = the_excludes; |
486 | – | |
487 | – | |
688 | // get some of the tricky things that may still be in the globals | |
689 | ||
690 | double boxVector[3]; | |
691 | < | if( the_globals->haveBox() ){ |
692 | < | boxVector[0] = the_globals->getBox(); |
693 | < | boxVector[1] = the_globals->getBox(); |
694 | < | boxVector[2] = the_globals->getBox(); |
691 | > | if( globals->haveBox() ){ |
692 | > | boxVector[0] = globals->getBox(); |
693 | > | boxVector[1] = globals->getBox(); |
694 | > | boxVector[2] = globals->getBox(); |
695 | ||
696 | < | simnfo->setBox( boxVector ); |
696 | > | info->setBox( boxVector ); |
697 | } | |
698 | < | else if( the_globals->haveDensity() ){ |
698 | > | else if( globals->haveDensity() ){ |
699 | ||
700 | double vol; | |
701 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
701 | > | vol = (double)tot_nmol / globals->getDensity(); |
702 | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); | |
703 | boxVector[1] = boxVector[0]; | |
704 | boxVector[2] = boxVector[0]; | |
705 | ||
706 | < | simnfo->setBox( boxVector ); |
706 | > | info->setBox( boxVector ); |
707 | } | |
708 | else{ | |
709 | < | if( !the_globals->haveBoxX() ){ |
709 | > | if( !globals->haveBoxX() ){ |
710 | sprintf( painCave.errMsg, | |
711 | "SimSetup error, no periodic BoxX size given.\n" ); | |
712 | painCave.isFatal = 1; | |
713 | simError(); | |
714 | } | |
715 | < | boxVector[0] = the_globals->getBoxX(); |
715 | > | boxVector[0] = globals->getBoxX(); |
716 | ||
717 | < | if( !the_globals->haveBoxY() ){ |
717 | > | if( !globals->haveBoxY() ){ |
718 | sprintf( painCave.errMsg, | |
719 | "SimSetup error, no periodic BoxY size given.\n" ); | |
720 | painCave.isFatal = 1; | |
721 | simError(); | |
722 | } | |
723 | < | boxVector[1] = the_globals->getBoxY(); |
723 | > | boxVector[1] = globals->getBoxY(); |
724 | ||
725 | < | if( !the_globals->haveBoxZ() ){ |
725 | > | if( !globals->haveBoxZ() ){ |
726 | sprintf( painCave.errMsg, | |
727 | "SimSetup error, no periodic BoxZ size given.\n" ); | |
728 | painCave.isFatal = 1; | |
729 | simError(); | |
730 | } | |
731 | < | boxVector[2] = the_globals->getBoxZ(); |
731 | > | boxVector[2] = globals->getBoxZ(); |
732 | ||
733 | < | simnfo->setBox( boxVector ); |
733 | > | info->setBox( boxVector ); |
734 | } | |
735 | ||
736 | + | |
737 | + | |
738 | #ifdef IS_MPI | |
739 | < | strcpy( checkPointMsg, "Box size set up" ); |
739 | > | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
740 | MPIcheckPoint(); | |
741 | #endif // is_mpi | |
742 | ||
743 | + | } |
744 | ||
542 | – | // initialize the arrays |
745 | ||
746 | < | the_ff->setSimInfo( simnfo ); |
746 | > | void SimSetup::finalInfoCheck( void ){ |
747 | > | int index; |
748 | > | int usesDipoles; |
749 | > | |
750 | ||
751 | < | makeMolecules(); |
752 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
753 | < | for(i=0; i<simnfo->n_atoms; i++){ |
754 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
751 | > | // check electrostatic parameters |
752 | > | |
753 | > | index = 0; |
754 | > | usesDipoles = 0; |
755 | > | while( (index < info->n_atoms) && !usesDipoles ){ |
756 | > | usesDipoles = ((info->atoms)[index])->hasDipole(); |
757 | > | index++; |
758 | } | |
759 | ||
760 | < | if (the_globals->getUseRF() ) { |
761 | < | simnfo->useReactionField = 1; |
762 | < | |
763 | < | if( !the_globals->haveECR() ){ |
760 | > | #ifdef IS_MPI |
761 | > | int myUse = usesDipoles; |
762 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
763 | > | #endif //is_mpi |
764 | > | |
765 | > | |
766 | > | if (globals->getUseRF() ) { |
767 | > | info->useReactionField = 1; |
768 | > | |
769 | > | if( !globals->haveECR() ){ |
770 | sprintf( painCave.errMsg, | |
771 | "SimSetup Warning: using default value of 1/2 the smallest " | |
772 | "box length for the electrostaticCutoffRadius.\n" | |
# | Line 560 | Line 774 | void SimSetup::createSim( void ){ | |
774 | painCave.isFatal = 0; | |
775 | simError(); | |
776 | double smallest; | |
777 | < | smallest = simnfo->boxLx; |
778 | < | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
779 | < | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
780 | < | simnfo->ecr = 0.5 * smallest; |
777 | > | smallest = info->boxL[0]; |
778 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
779 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
780 | > | info->ecr = 0.5 * smallest; |
781 | } else { | |
782 | < | simnfo->ecr = the_globals->getECR(); |
782 | > | info->ecr = globals->getECR(); |
783 | } | |
784 | ||
785 | < | if( !the_globals->haveEST() ){ |
785 | > | if( !globals->haveEST() ){ |
786 | sprintf( painCave.errMsg, | |
787 | "SimSetup Warning: using default value of 0.05 * the " | |
788 | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" | |
789 | ); | |
790 | painCave.isFatal = 0; | |
791 | simError(); | |
792 | < | simnfo->est = 0.05 * simnfo->ecr; |
792 | > | info->est = 0.05 * info->ecr; |
793 | } else { | |
794 | < | simnfo->est = the_globals->getEST(); |
794 | > | info->est = globals->getEST(); |
795 | } | |
796 | ||
797 | < | if(!the_globals->haveDielectric() ){ |
797 | > | if(!globals->haveDielectric() ){ |
798 | sprintf( painCave.errMsg, | |
799 | "SimSetup Error: You are trying to use Reaction Field without" | |
800 | "setting a dielectric constant!\n" | |
# | Line 588 | Line 802 | void SimSetup::createSim( void ){ | |
802 | painCave.isFatal = 1; | |
803 | simError(); | |
804 | } | |
805 | < | simnfo->dielectric = the_globals->getDielectric(); |
806 | < | } else { |
805 | > | info->dielectric = globals->getDielectric(); |
806 | > | } |
807 | > | else { |
808 | if (usesDipoles) { | |
809 | ||
810 | < | if( !the_globals->haveECR() ){ |
810 | > | if( !globals->haveECR() ){ |
811 | sprintf( painCave.errMsg, | |
812 | "SimSetup Warning: using default value of 1/2 the smallest " | |
813 | "box length for the electrostaticCutoffRadius.\n" | |
# | Line 600 | Line 815 | void SimSetup::createSim( void ){ | |
815 | painCave.isFatal = 0; | |
816 | simError(); | |
817 | double smallest; | |
818 | < | smallest = simnfo->boxLx; |
819 | < | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
820 | < | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
821 | < | simnfo->ecr = 0.5 * smallest; |
818 | > | smallest = info->boxL[0]; |
819 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
820 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
821 | > | info->ecr = 0.5 * smallest; |
822 | } else { | |
823 | < | simnfo->ecr = the_globals->getECR(); |
823 | > | info->ecr = globals->getECR(); |
824 | } | |
825 | ||
826 | < | if( !the_globals->haveEST() ){ |
826 | > | if( !globals->haveEST() ){ |
827 | sprintf( painCave.errMsg, | |
828 | "SimSetup Warning: using default value of 5%% of the " | |
829 | "electrostaticCutoffRadius for the " | |
# | Line 616 | Line 831 | void SimSetup::createSim( void ){ | |
831 | ); | |
832 | painCave.isFatal = 0; | |
833 | simError(); | |
834 | < | simnfo->est = 0.05 * simnfo->ecr; |
834 | > | info->est = 0.05 * info->ecr; |
835 | } else { | |
836 | < | simnfo->est = the_globals->getEST(); |
836 | > | info->est = globals->getEST(); |
837 | } | |
838 | } | |
839 | } | |
840 | ||
841 | #ifdef IS_MPI | |
842 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
842 | > | strcpy( checkPointMsg, "post processing checks out" ); |
843 | MPIcheckPoint(); | |
844 | #endif // is_mpi | |
845 | ||
846 | < | if( the_globals->haveInitialConfig() ){ |
846 | > | } |
847 | > | |
848 | > | void SimSetup::initSystemCoords( void ){ |
849 | > | |
850 | > | if( globals->haveInitialConfig() ){ |
851 | ||
852 | InitializeFromFile* fileInit; | |
853 | #ifdef IS_MPI // is_mpi | |
854 | if( worldRank == 0 ){ | |
855 | #endif //is_mpi | |
856 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
856 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
857 | #ifdef IS_MPI | |
858 | }else fileInit = new InitializeFromFile( NULL ); | |
859 | #endif | |
860 | < | fileInit->read_xyz( simnfo ); // default velocities on |
860 | > | fileInit->read_xyz( info ); // default velocities on |
861 | ||
862 | delete fileInit; | |
863 | } | |
# | Line 666 | Line 885 | void SimSetup::createSim( void ){ | |
885 | MPIcheckPoint(); | |
886 | #endif // is_mpi | |
887 | ||
888 | + | } |
889 | ||
670 | – | |
671 | – | |
672 | – | |
890 | ||
891 | < | |
891 | > | void SimSetup::makeOutNames( void ){ |
892 | > | |
893 | #ifdef IS_MPI | |
894 | if( worldRank == 0 ){ | |
895 | #endif // is_mpi | |
896 | ||
897 | < | if( the_globals->haveFinalConfig() ){ |
898 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
897 | > | if( globals->haveFinalConfig() ){ |
898 | > | strcpy( info->finalName, globals->getFinalConfig() ); |
899 | } | |
900 | else{ | |
901 | < | strcpy( simnfo->finalName, inFileName ); |
901 | > | strcpy( info->finalName, inFileName ); |
902 | char* endTest; | |
903 | < | int nameLength = strlen( simnfo->finalName ); |
904 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
903 | > | int nameLength = strlen( info->finalName ); |
904 | > | endTest = &(info->finalName[nameLength - 5]); |
905 | if( !strcmp( endTest, ".bass" ) ){ | |
906 | strcpy( endTest, ".eor" ); | |
907 | } | |
# | Line 691 | Line 909 | void SimSetup::createSim( void ){ | |
909 | strcpy( endTest, ".eor" ); | |
910 | } | |
911 | else{ | |
912 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
912 | > | endTest = &(info->finalName[nameLength - 4]); |
913 | if( !strcmp( endTest, ".bss" ) ){ | |
914 | strcpy( endTest, ".eor" ); | |
915 | } | |
# | Line 699 | Line 917 | void SimSetup::createSim( void ){ | |
917 | strcpy( endTest, ".eor" ); | |
918 | } | |
919 | else{ | |
920 | < | strcat( simnfo->finalName, ".eor" ); |
920 | > | strcat( info->finalName, ".eor" ); |
921 | } | |
922 | } | |
923 | } | |
924 | ||
925 | // make the sample and status out names | |
926 | ||
927 | < | strcpy( simnfo->sampleName, inFileName ); |
927 | > | strcpy( info->sampleName, inFileName ); |
928 | char* endTest; | |
929 | < | int nameLength = strlen( simnfo->sampleName ); |
930 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
929 | > | int nameLength = strlen( info->sampleName ); |
930 | > | endTest = &(info->sampleName[nameLength - 5]); |
931 | if( !strcmp( endTest, ".bass" ) ){ | |
932 | strcpy( endTest, ".dump" ); | |
933 | } | |
# | Line 717 | Line 935 | void SimSetup::createSim( void ){ | |
935 | strcpy( endTest, ".dump" ); | |
936 | } | |
937 | else{ | |
938 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
938 | > | endTest = &(info->sampleName[nameLength - 4]); |
939 | if( !strcmp( endTest, ".bss" ) ){ | |
940 | strcpy( endTest, ".dump" ); | |
941 | } | |
# | Line 725 | Line 943 | void SimSetup::createSim( void ){ | |
943 | strcpy( endTest, ".dump" ); | |
944 | } | |
945 | else{ | |
946 | < | strcat( simnfo->sampleName, ".dump" ); |
946 | > | strcat( info->sampleName, ".dump" ); |
947 | } | |
948 | } | |
949 | ||
950 | < | strcpy( simnfo->statusName, inFileName ); |
951 | < | nameLength = strlen( simnfo->statusName ); |
952 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
950 | > | strcpy( info->statusName, inFileName ); |
951 | > | nameLength = strlen( info->statusName ); |
952 | > | endTest = &(info->statusName[nameLength - 5]); |
953 | if( !strcmp( endTest, ".bass" ) ){ | |
954 | strcpy( endTest, ".stat" ); | |
955 | } | |
# | Line 739 | Line 957 | void SimSetup::createSim( void ){ | |
957 | strcpy( endTest, ".stat" ); | |
958 | } | |
959 | else{ | |
960 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
960 | > | endTest = &(info->statusName[nameLength - 4]); |
961 | if( !strcmp( endTest, ".bss" ) ){ | |
962 | strcpy( endTest, ".stat" ); | |
963 | } | |
# | Line 747 | Line 965 | void SimSetup::createSim( void ){ | |
965 | strcpy( endTest, ".stat" ); | |
966 | } | |
967 | else{ | |
968 | < | strcat( simnfo->statusName, ".stat" ); |
968 | > | strcat( info->statusName, ".stat" ); |
969 | } | |
970 | } | |
971 | ||
972 | #ifdef IS_MPI | |
973 | } | |
974 | #endif // is_mpi | |
975 | + | |
976 | + | } |
977 | + | |
978 | + | |
979 | + | void SimSetup::sysObjectsCreation( void ){ |
980 | + | |
981 | + | int i; |
982 | + | |
983 | + | // create the forceField |
984 | + | |
985 | + | createFF(); |
986 | + | |
987 | + | // extract componentList |
988 | + | |
989 | + | compList(); |
990 | + | |
991 | + | // calc the number of atoms, bond, bends, and torsions |
992 | + | |
993 | + | calcSysValues(); |
994 | + | |
995 | + | #ifdef IS_MPI |
996 | + | // divide the molecules among the processors |
997 | ||
998 | < | // set the status, sample, and themal kick times |
998 | > | mpiMolDivide(); |
999 | > | #endif //is_mpi |
1000 | ||
1001 | < | if( the_globals->haveSampleTime() ){ |
1002 | < | simnfo->sampleTime = the_globals->getSampleTime(); |
1003 | < | simnfo->statusTime = simnfo->sampleTime; |
1004 | < | simnfo->thermalTime = simnfo->sampleTime; |
1001 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1002 | > | |
1003 | > | makeSysArrays(); |
1004 | > | |
1005 | > | // make and initialize the molecules (all but atomic coordinates) |
1006 | > | |
1007 | > | makeMolecules(); |
1008 | > | info->identArray = new int[info->n_atoms]; |
1009 | > | for(i=0; i<info->n_atoms; i++){ |
1010 | > | info->identArray[i] = the_atoms[i]->getIdent(); |
1011 | } | |
1012 | < | else{ |
1013 | < | simnfo->sampleTime = the_globals->getRunTime(); |
1014 | < | simnfo->statusTime = simnfo->sampleTime; |
1015 | < | simnfo->thermalTime = simnfo->sampleTime; |
1012 | > | |
1013 | > | |
1014 | > | |
1015 | > | } |
1016 | > | |
1017 | > | |
1018 | > | void SimSetup::createFF( void ){ |
1019 | > | |
1020 | > | switch( ffCase ){ |
1021 | > | |
1022 | > | case FF_DUFF: |
1023 | > | the_ff = new DUFF(); |
1024 | > | break; |
1025 | > | |
1026 | > | case FF_LJ: |
1027 | > | the_ff = new LJFF(); |
1028 | > | break; |
1029 | > | |
1030 | > | default: |
1031 | > | sprintf( painCave.errMsg, |
1032 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1033 | > | painCave.isFatal = 1; |
1034 | > | simError(); |
1035 | } | |
1036 | ||
1037 | < | if( the_globals->haveStatusTime() ){ |
1038 | < | simnfo->statusTime = the_globals->getStatusTime(); |
1037 | > | #ifdef IS_MPI |
1038 | > | strcpy( checkPointMsg, "ForceField creation successful" ); |
1039 | > | MPIcheckPoint(); |
1040 | > | #endif // is_mpi |
1041 | > | |
1042 | > | } |
1043 | > | |
1044 | > | |
1045 | > | void SimSetup::compList( void ){ |
1046 | > | |
1047 | > | int i; |
1048 | > | |
1049 | > | comp_stamps = new MoleculeStamp*[n_components]; |
1050 | > | |
1051 | > | // make an array of molecule stamps that match the components used. |
1052 | > | // also extract the used stamps out into a separate linked list |
1053 | > | |
1054 | > | info->nComponents = n_components; |
1055 | > | info->componentsNmol = components_nmol; |
1056 | > | info->compStamps = comp_stamps; |
1057 | > | info->headStamp = new LinkedMolStamp(); |
1058 | > | |
1059 | > | char* id; |
1060 | > | LinkedMolStamp* headStamp = info->headStamp; |
1061 | > | LinkedMolStamp* currentStamp = NULL; |
1062 | > | for( i=0; i<n_components; i++ ){ |
1063 | > | |
1064 | > | id = the_components[i]->getType(); |
1065 | > | comp_stamps[i] = NULL; |
1066 | > | |
1067 | > | // check to make sure the component isn't already in the list |
1068 | > | |
1069 | > | comp_stamps[i] = headStamp->match( id ); |
1070 | > | if( comp_stamps[i] == NULL ){ |
1071 | > | |
1072 | > | // extract the component from the list; |
1073 | > | |
1074 | > | currentStamp = stamps->extractMolStamp( id ); |
1075 | > | if( currentStamp == NULL ){ |
1076 | > | sprintf( painCave.errMsg, |
1077 | > | "SimSetup error: Component \"%s\" was not found in the " |
1078 | > | "list of declared molecules\n", |
1079 | > | id ); |
1080 | > | painCave.isFatal = 1; |
1081 | > | simError(); |
1082 | > | } |
1083 | > | |
1084 | > | headStamp->add( currentStamp ); |
1085 | > | comp_stamps[i] = headStamp->match( id ); |
1086 | > | } |
1087 | } | |
1088 | ||
1089 | < | if( the_globals->haveThermalTime() ){ |
1090 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
1089 | > | #ifdef IS_MPI |
1090 | > | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1091 | > | MPIcheckPoint(); |
1092 | > | #endif // is_mpi |
1093 | > | |
1094 | > | |
1095 | > | } |
1096 | > | |
1097 | > | void SimSetup::calcSysValues( void ){ |
1098 | > | int i, j, k; |
1099 | > | |
1100 | > | |
1101 | > | tot_atoms = 0; |
1102 | > | tot_bonds = 0; |
1103 | > | tot_bends = 0; |
1104 | > | tot_torsions = 0; |
1105 | > | for( i=0; i<n_components; i++ ){ |
1106 | > | |
1107 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1108 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1109 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1110 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1111 | } | |
1112 | ||
1113 | < | // check for the temperature set flag |
1113 | > | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1114 | ||
1115 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
1115 | > | info->n_atoms = tot_atoms; |
1116 | > | info->n_bonds = tot_bonds; |
1117 | > | info->n_bends = tot_bends; |
1118 | > | info->n_torsions = tot_torsions; |
1119 | > | info->n_SRI = tot_SRI; |
1120 | > | info->n_mol = tot_nmol; |
1121 | > | |
1122 | > | info->molMembershipArray = new int[tot_atoms]; |
1123 | > | } |
1124 | ||
1125 | ||
1126 | < | // make the integrator |
1126 | > | #ifdef IS_MPI |
1127 | > | |
1128 | > | void SimSetup::mpiMolDivide( void ){ |
1129 | ||
1130 | + | int i, j, k; |
1131 | + | int localMol, allMol; |
1132 | + | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1133 | + | |
1134 | + | mpiSim = new mpiSimulation( info ); |
1135 | ||
1136 | + | globalIndex = mpiSim->divideLabor(); |
1137 | + | |
1138 | + | // set up the local variables |
1139 | + | |
1140 | + | mol2proc = mpiSim->getMolToProcMap(); |
1141 | + | molCompType = mpiSim->getMolComponentType(); |
1142 | + | |
1143 | + | allMol = 0; |
1144 | + | localMol = 0; |
1145 | + | local_atoms = 0; |
1146 | + | local_bonds = 0; |
1147 | + | local_bends = 0; |
1148 | + | local_torsions = 0; |
1149 | + | globalAtomIndex = 0; |
1150 | + | |
1151 | + | |
1152 | + | for( i=0; i<n_components; i++ ){ |
1153 | + | |
1154 | + | for( j=0; j<components_nmol[i]; j++ ){ |
1155 | + | |
1156 | + | if( mol2proc[allMol] == worldRank ){ |
1157 | + | |
1158 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1159 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1160 | + | local_bends += comp_stamps[i]->getNBends(); |
1161 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1162 | + | localMol++; |
1163 | + | } |
1164 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1165 | + | info->molMembershipArray[globalAtomIndex] = allMol; |
1166 | + | globalAtomIndex++; |
1167 | + | } |
1168 | + | |
1169 | + | allMol++; |
1170 | + | } |
1171 | + | } |
1172 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1173 | + | |
1174 | + | info->n_atoms = mpiSim->getMyNlocal(); |
1175 | + | |
1176 | + | if( local_atoms != info->n_atoms ){ |
1177 | + | sprintf( painCave.errMsg, |
1178 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1179 | + | " localAtom (%d) are not equal.\n", |
1180 | + | info->n_atoms, |
1181 | + | local_atoms ); |
1182 | + | painCave.isFatal = 1; |
1183 | + | simError(); |
1184 | + | } |
1185 | + | |
1186 | + | info->n_bonds = local_bonds; |
1187 | + | info->n_bends = local_bends; |
1188 | + | info->n_torsions = local_torsions; |
1189 | + | info->n_SRI = local_SRI; |
1190 | + | info->n_mol = localMol; |
1191 | + | |
1192 | + | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1193 | + | MPIcheckPoint(); |
1194 | + | } |
1195 | + | |
1196 | + | #endif // is_mpi |
1197 | + | |
1198 | + | |
1199 | + | void SimSetup::makeSysArrays( void ){ |
1200 | + | int i, j, k; |
1201 | + | |
1202 | + | |
1203 | + | // create the atom and short range interaction arrays |
1204 | + | |
1205 | + | Atom::createArrays(info->n_atoms); |
1206 | + | the_atoms = new Atom*[info->n_atoms]; |
1207 | + | the_molecules = new Molecule[info->n_mol]; |
1208 | + | int molIndex; |
1209 | + | |
1210 | + | // initialize the molecule's stampID's |
1211 | + | |
1212 | + | #ifdef IS_MPI |
1213 | + | |
1214 | + | |
1215 | + | molIndex = 0; |
1216 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1217 | + | |
1218 | + | if(mol2proc[i] == worldRank ){ |
1219 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
1220 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1221 | + | the_molecules[molIndex].setGlobalIndex( i ); |
1222 | + | molIndex++; |
1223 | + | } |
1224 | + | } |
1225 | + | |
1226 | + | #else // is_mpi |
1227 | + | |
1228 | + | molIndex = 0; |
1229 | + | globalAtomIndex = 0; |
1230 | + | for(i=0; i<n_components; i++){ |
1231 | + | for(j=0; j<components_nmol[i]; j++ ){ |
1232 | + | the_molecules[molIndex].setStampID( i ); |
1233 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1234 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1235 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1236 | + | info->molMembershipArray[globalAtomIndex] = molIndex; |
1237 | + | globalAtomIndex++; |
1238 | + | } |
1239 | + | molIndex++; |
1240 | + | } |
1241 | + | } |
1242 | + | |
1243 | + | |
1244 | + | #endif // is_mpi |
1245 | + | |
1246 | + | |
1247 | + | if( info->n_SRI ){ |
1248 | + | |
1249 | + | Exclude::createArray(info->n_SRI); |
1250 | + | the_excludes = new Exclude*[info->n_SRI]; |
1251 | + | for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1252 | + | info->globalExcludes = new int; |
1253 | + | info->n_exclude = info->n_SRI; |
1254 | + | } |
1255 | + | else{ |
1256 | + | |
1257 | + | Exclude::createArray( 1 ); |
1258 | + | the_excludes = new Exclude*; |
1259 | + | the_excludes[0] = new Exclude(0); |
1260 | + | the_excludes[0]->setPair( 0,0 ); |
1261 | + | info->globalExcludes = new int; |
1262 | + | info->globalExcludes[0] = 0; |
1263 | + | info->n_exclude = 0; |
1264 | + | } |
1265 | + | |
1266 | + | // set the arrays into the SimInfo object |
1267 | + | |
1268 | + | info->atoms = the_atoms; |
1269 | + | info->molecules = the_molecules; |
1270 | + | info->nGlobalExcludes = 0; |
1271 | + | info->excludes = the_excludes; |
1272 | + | |
1273 | + | the_ff->setSimInfo( info ); |
1274 | + | |
1275 | + | } |
1276 | + | |
1277 | + | void SimSetup::makeIntegrator( void ){ |
1278 | + | |
1279 | NVT* myNVT = NULL; | |
1280 | NPTi* myNPTi = NULL; | |
1281 | NPTf* myNPTf = NULL; | |
# | Line 793 | Line 1285 | void SimSetup::createSim( void ){ | |
1285 | switch( ensembleCase ){ | |
1286 | ||
1287 | case NVE_ENS: | |
1288 | < | new NVE( simnfo, the_ff ); |
1288 | > | new NVE( info, the_ff ); |
1289 | break; | |
1290 | ||
1291 | case NVT_ENS: | |
1292 | < | myNVT = new NVT( simnfo, the_ff ); |
1293 | < | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
1292 | > | myNVT = new NVT( info, the_ff ); |
1293 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1294 | ||
1295 | < | if (the_globals->haveTauThermostat()) |
1296 | < | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
1295 | > | if (globals->haveTauThermostat()) |
1296 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1297 | ||
1298 | else { | |
1299 | sprintf( painCave.errMsg, | |
# | Line 813 | Line 1305 | void SimSetup::createSim( void ){ | |
1305 | break; | |
1306 | ||
1307 | case NPTi_ENS: | |
1308 | < | myNPTi = new NPTi( simnfo, the_ff ); |
1309 | < | myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
1308 | > | myNPTi = new NPTi( info, the_ff ); |
1309 | > | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1310 | ||
1311 | < | if (the_globals->haveTargetPressure()) |
1312 | < | myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
1311 | > | if (globals->haveTargetPressure()) |
1312 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1313 | else { | |
1314 | sprintf( painCave.errMsg, | |
1315 | "SimSetup error: If you use a constant pressure\n" | |
# | Line 826 | Line 1318 | void SimSetup::createSim( void ){ | |
1318 | simError(); | |
1319 | } | |
1320 | ||
1321 | < | if( the_globals->haveTauThermostat() ) |
1322 | < | myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
1321 | > | if( globals->haveTauThermostat() ) |
1322 | > | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1323 | else{ | |
1324 | sprintf( painCave.errMsg, | |
1325 | "SimSetup error: If you use an NPT\n" | |
# | Line 836 | Line 1328 | void SimSetup::createSim( void ){ | |
1328 | simError(); | |
1329 | } | |
1330 | ||
1331 | < | if( the_globals->haveTauBarostat() ) |
1332 | < | myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
1331 | > | if( globals->haveTauBarostat() ) |
1332 | > | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1333 | else{ | |
1334 | sprintf( painCave.errMsg, | |
1335 | "SimSetup error: If you use an NPT\n" | |
# | Line 848 | Line 1340 | void SimSetup::createSim( void ){ | |
1340 | break; | |
1341 | ||
1342 | case NPTf_ENS: | |
1343 | < | myNPTf = new NPTf( simnfo, the_ff ); |
1344 | < | myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
1343 | > | myNPTf = new NPTf( info, the_ff ); |
1344 | > | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1345 | ||
1346 | < | if (the_globals->haveTargetPressure()) |
1347 | < | myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
1346 | > | if (globals->haveTargetPressure()) |
1347 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1348 | else { | |
1349 | sprintf( painCave.errMsg, | |
1350 | "SimSetup error: If you use a constant pressure\n" | |
# | Line 861 | Line 1353 | void SimSetup::createSim( void ){ | |
1353 | simError(); | |
1354 | } | |
1355 | ||
1356 | < | if( the_globals->haveTauThermostat() ) |
1357 | < | myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
1356 | > | if( globals->haveTauThermostat() ) |
1357 | > | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1358 | else{ | |
1359 | sprintf( painCave.errMsg, | |
1360 | "SimSetup error: If you use an NPT\n" | |
# | Line 871 | Line 1363 | void SimSetup::createSim( void ){ | |
1363 | simError(); | |
1364 | } | |
1365 | ||
1366 | < | if( the_globals->haveTauBarostat() ) |
1367 | < | myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
1366 | > | if( globals->haveTauBarostat() ) |
1367 | > | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1368 | else{ | |
1369 | sprintf( painCave.errMsg, | |
1370 | "SimSetup error: If you use an NPT\n" | |
# | Line 883 | Line 1375 | void SimSetup::createSim( void ){ | |
1375 | break; | |
1376 | ||
1377 | case NPTim_ENS: | |
1378 | < | myNPTim = new NPTim( simnfo, the_ff ); |
1379 | < | myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
1378 | > | myNPTim = new NPTim( info, the_ff ); |
1379 | > | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1380 | ||
1381 | < | if (the_globals->haveTargetPressure()) |
1382 | < | myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
1381 | > | if (globals->haveTargetPressure()) |
1382 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1383 | else { | |
1384 | sprintf( painCave.errMsg, | |
1385 | "SimSetup error: If you use a constant pressure\n" | |
# | Line 896 | Line 1388 | void SimSetup::createSim( void ){ | |
1388 | simError(); | |
1389 | } | |
1390 | ||
1391 | < | if( the_globals->haveTauThermostat() ) |
1392 | < | myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
1391 | > | if( globals->haveTauThermostat() ) |
1392 | > | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1393 | else{ | |
1394 | sprintf( painCave.errMsg, | |
1395 | "SimSetup error: If you use an NPT\n" | |
# | Line 906 | Line 1398 | void SimSetup::createSim( void ){ | |
1398 | simError(); | |
1399 | } | |
1400 | ||
1401 | < | if( the_globals->haveTauBarostat() ) |
1402 | < | myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
1401 | > | if( globals->haveTauBarostat() ) |
1402 | > | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1403 | else{ | |
1404 | sprintf( painCave.errMsg, | |
1405 | "SimSetup error: If you use an NPT\n" | |
# | Line 918 | Line 1410 | void SimSetup::createSim( void ){ | |
1410 | break; | |
1411 | ||
1412 | case NPTfm_ENS: | |
1413 | < | myNPTfm = new NPTfm( simnfo, the_ff ); |
1414 | < | myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
1413 | > | myNPTfm = new NPTfm( info, the_ff ); |
1414 | > | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1415 | ||
1416 | < | if (the_globals->haveTargetPressure()) |
1417 | < | myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
1416 | > | if (globals->haveTargetPressure()) |
1417 | > | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1418 | else { | |
1419 | sprintf( painCave.errMsg, | |
1420 | "SimSetup error: If you use a constant pressure\n" | |
# | Line 931 | Line 1423 | void SimSetup::createSim( void ){ | |
1423 | simError(); | |
1424 | } | |
1425 | ||
1426 | < | if( the_globals->haveTauThermostat() ) |
1427 | < | myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
1426 | > | if( globals->haveTauThermostat() ) |
1427 | > | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1428 | else{ | |
1429 | sprintf( painCave.errMsg, | |
1430 | "SimSetup error: If you use an NPT\n" | |
# | Line 941 | Line 1433 | void SimSetup::createSim( void ){ | |
1433 | simError(); | |
1434 | } | |
1435 | ||
1436 | < | if( the_globals->haveTauBarostat() ) |
1437 | < | myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
1436 | > | if( globals->haveTauBarostat() ) |
1437 | > | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1438 | else{ | |
1439 | sprintf( painCave.errMsg, | |
1440 | "SimSetup error: If you use an NPT\n" | |
# | Line 959 | Line 1451 | void SimSetup::createSim( void ){ | |
1451 | simError(); | |
1452 | } | |
1453 | ||
1454 | + | } |
1455 | ||
1456 | < | #ifdef IS_MPI |
964 | < | mpiSim->mpiRefresh(); |
965 | < | #endif |
1456 | > | void SimSetup::initFortran( void ){ |
1457 | ||
1458 | < | // initialize the Fortran |
968 | < | |
969 | < | |
970 | < | simnfo->refreshSim(); |
1458 | > | info->refreshSim(); |
1459 | ||
1460 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
1460 | > | if( !strcmp( info->mixingRule, "standard") ){ |
1461 | the_ff->initForceField( LB_MIXING_RULE ); | |
1462 | } | |
1463 | < | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
1463 | > | else if( !strcmp( info->mixingRule, "explicit") ){ |
1464 | the_ff->initForceField( EXPLICIT_MIXING_RULE ); | |
1465 | } | |
1466 | else{ | |
1467 | sprintf( painCave.errMsg, | |
1468 | "SimSetup Error: unknown mixing rule -> \"%s\"\n", | |
1469 | < | simnfo->mixingRule ); |
1469 | > | info->mixingRule ); |
1470 | painCave.isFatal = 1; | |
1471 | simError(); | |
1472 | } | |
# | Line 989 | Line 1477 | void SimSetup::createSim( void ){ | |
1477 | "Successfully intialized the mixingRule for Fortran." ); | |
1478 | MPIcheckPoint(); | |
1479 | #endif // is_mpi | |
992 | – | } |
1480 | ||
994 | – | |
995 | – | void SimSetup::makeMolecules( void ){ |
996 | – | |
997 | – | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
998 | – | molInit info; |
999 | – | DirectionalAtom* dAtom; |
1000 | – | LinkedAssign* extras; |
1001 | – | LinkedAssign* current_extra; |
1002 | – | AtomStamp* currentAtom; |
1003 | – | BondStamp* currentBond; |
1004 | – | BendStamp* currentBend; |
1005 | – | TorsionStamp* currentTorsion; |
1006 | – | |
1007 | – | bond_pair* theBonds; |
1008 | – | bend_set* theBends; |
1009 | – | torsion_set* theTorsions; |
1010 | – | |
1011 | – | |
1012 | – | //init the forceField paramters |
1013 | – | |
1014 | – | the_ff->readParams(); |
1015 | – | |
1016 | – | |
1017 | – | // init the atoms |
1018 | – | |
1019 | – | double ux, uy, uz, u, uSqr; |
1020 | – | |
1021 | – | atomOffset = 0; |
1022 | – | excludeOffset = 0; |
1023 | – | for(i=0; i<simnfo->n_mol; i++){ |
1024 | – | |
1025 | – | stampID = the_molecules[i].getStampID(); |
1026 | – | |
1027 | – | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
1028 | – | info.nBonds = comp_stamps[stampID]->getNBonds(); |
1029 | – | info.nBends = comp_stamps[stampID]->getNBends(); |
1030 | – | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
1031 | – | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
1032 | – | |
1033 | – | info.myAtoms = &the_atoms[atomOffset]; |
1034 | – | info.myExcludes = &the_excludes[excludeOffset]; |
1035 | – | info.myBonds = new Bond*[info.nBonds]; |
1036 | – | info.myBends = new Bend*[info.nBends]; |
1037 | – | info.myTorsions = new Torsion*[info.nTorsions]; |
1038 | – | |
1039 | – | theBonds = new bond_pair[info.nBonds]; |
1040 | – | theBends = new bend_set[info.nBends]; |
1041 | – | theTorsions = new torsion_set[info.nTorsions]; |
1042 | – | |
1043 | – | // make the Atoms |
1044 | – | |
1045 | – | for(j=0; j<info.nAtoms; j++){ |
1046 | – | |
1047 | – | currentAtom = comp_stamps[stampID]->getAtom( j ); |
1048 | – | if( currentAtom->haveOrientation() ){ |
1049 | – | |
1050 | – | dAtom = new DirectionalAtom(j + atomOffset); |
1051 | – | simnfo->n_oriented++; |
1052 | – | info.myAtoms[j] = dAtom; |
1053 | – | |
1054 | – | ux = currentAtom->getOrntX(); |
1055 | – | uy = currentAtom->getOrntY(); |
1056 | – | uz = currentAtom->getOrntZ(); |
1057 | – | |
1058 | – | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
1059 | – | |
1060 | – | u = sqrt( uSqr ); |
1061 | – | ux = ux / u; |
1062 | – | uy = uy / u; |
1063 | – | uz = uz / u; |
1064 | – | |
1065 | – | dAtom->setSUx( ux ); |
1066 | – | dAtom->setSUy( uy ); |
1067 | – | dAtom->setSUz( uz ); |
1068 | – | } |
1069 | – | else{ |
1070 | – | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
1071 | – | } |
1072 | – | info.myAtoms[j]->setType( currentAtom->getType() ); |
1073 | – | |
1074 | – | #ifdef IS_MPI |
1075 | – | |
1076 | – | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1077 | – | |
1078 | – | #endif // is_mpi |
1079 | – | } |
1080 | – | |
1081 | – | // make the bonds |
1082 | – | for(j=0; j<info.nBonds; j++){ |
1083 | – | |
1084 | – | currentBond = comp_stamps[stampID]->getBond( j ); |
1085 | – | theBonds[j].a = currentBond->getA() + atomOffset; |
1086 | – | theBonds[j].b = currentBond->getB() + atomOffset; |
1087 | – | |
1088 | – | exI = theBonds[j].a; |
1089 | – | exJ = theBonds[j].b; |
1090 | – | |
1091 | – | // exclude_I must always be the smaller of the pair |
1092 | – | if( exI > exJ ){ |
1093 | – | tempEx = exI; |
1094 | – | exI = exJ; |
1095 | – | exJ = tempEx; |
1096 | – | } |
1097 | – | #ifdef IS_MPI |
1098 | – | tempEx = exI; |
1099 | – | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1100 | – | tempEx = exJ; |
1101 | – | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1102 | – | |
1103 | – | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1104 | – | #else // isn't MPI |
1105 | – | |
1106 | – | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1107 | – | #endif //is_mpi |
1108 | – | } |
1109 | – | excludeOffset += info.nBonds; |
1110 | – | |
1111 | – | //make the bends |
1112 | – | for(j=0; j<info.nBends; j++){ |
1113 | – | |
1114 | – | currentBend = comp_stamps[stampID]->getBend( j ); |
1115 | – | theBends[j].a = currentBend->getA() + atomOffset; |
1116 | – | theBends[j].b = currentBend->getB() + atomOffset; |
1117 | – | theBends[j].c = currentBend->getC() + atomOffset; |
1118 | – | |
1119 | – | if( currentBend->haveExtras() ){ |
1120 | – | |
1121 | – | extras = currentBend->getExtras(); |
1122 | – | current_extra = extras; |
1123 | – | |
1124 | – | while( current_extra != NULL ){ |
1125 | – | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1126 | – | |
1127 | – | switch( current_extra->getType() ){ |
1128 | – | |
1129 | – | case 0: |
1130 | – | theBends[j].ghost = |
1131 | – | current_extra->getInt() + atomOffset; |
1132 | – | theBends[j].isGhost = 1; |
1133 | – | break; |
1134 | – | |
1135 | – | case 1: |
1136 | – | theBends[j].ghost = |
1137 | – | (int)current_extra->getDouble() + atomOffset; |
1138 | – | theBends[j].isGhost = 1; |
1139 | – | break; |
1140 | – | |
1141 | – | default: |
1142 | – | sprintf( painCave.errMsg, |
1143 | – | "SimSetup Error: ghostVectorSource was neither a " |
1144 | – | "double nor an int.\n" |
1145 | – | "-->Bend[%d] in %s\n", |
1146 | – | j, comp_stamps[stampID]->getID() ); |
1147 | – | painCave.isFatal = 1; |
1148 | – | simError(); |
1149 | – | } |
1150 | – | } |
1151 | – | |
1152 | – | else{ |
1153 | – | |
1154 | – | sprintf( painCave.errMsg, |
1155 | – | "SimSetup Error: unhandled bend assignment:\n" |
1156 | – | " -->%s in Bend[%d] in %s\n", |
1157 | – | current_extra->getlhs(), |
1158 | – | j, comp_stamps[stampID]->getID() ); |
1159 | – | painCave.isFatal = 1; |
1160 | – | simError(); |
1161 | – | } |
1162 | – | |
1163 | – | current_extra = current_extra->getNext(); |
1164 | – | } |
1165 | – | } |
1166 | – | |
1167 | – | if( !theBends[j].isGhost ){ |
1168 | – | |
1169 | – | exI = theBends[j].a; |
1170 | – | exJ = theBends[j].c; |
1171 | – | } |
1172 | – | else{ |
1173 | – | |
1174 | – | exI = theBends[j].a; |
1175 | – | exJ = theBends[j].b; |
1176 | – | } |
1177 | – | |
1178 | – | // exclude_I must always be the smaller of the pair |
1179 | – | if( exI > exJ ){ |
1180 | – | tempEx = exI; |
1181 | – | exI = exJ; |
1182 | – | exJ = tempEx; |
1183 | – | } |
1184 | – | #ifdef IS_MPI |
1185 | – | tempEx = exI; |
1186 | – | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1187 | – | tempEx = exJ; |
1188 | – | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1189 | – | |
1190 | – | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1191 | – | #else // isn't MPI |
1192 | – | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1193 | – | #endif //is_mpi |
1194 | – | } |
1195 | – | excludeOffset += info.nBends; |
1196 | – | |
1197 | – | for(j=0; j<info.nTorsions; j++){ |
1198 | – | |
1199 | – | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1200 | – | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1201 | – | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1202 | – | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1203 | – | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1204 | – | |
1205 | – | exI = theTorsions[j].a; |
1206 | – | exJ = theTorsions[j].d; |
1207 | – | |
1208 | – | // exclude_I must always be the smaller of the pair |
1209 | – | if( exI > exJ ){ |
1210 | – | tempEx = exI; |
1211 | – | exI = exJ; |
1212 | – | exJ = tempEx; |
1213 | – | } |
1214 | – | #ifdef IS_MPI |
1215 | – | tempEx = exI; |
1216 | – | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1217 | – | tempEx = exJ; |
1218 | – | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1219 | – | |
1220 | – | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1221 | – | #else // isn't MPI |
1222 | – | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1223 | – | #endif //is_mpi |
1224 | – | } |
1225 | – | excludeOffset += info.nTorsions; |
1226 | – | |
1227 | – | |
1228 | – | // send the arrays off to the forceField for init. |
1229 | – | |
1230 | – | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1231 | – | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1232 | – | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1233 | – | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1234 | – | |
1235 | – | |
1236 | – | the_molecules[i].initialize( info ); |
1237 | – | |
1238 | – | |
1239 | – | atomOffset += info.nAtoms; |
1240 | – | delete[] theBonds; |
1241 | – | delete[] theBends; |
1242 | – | delete[] theTorsions; |
1243 | – | } |
1244 | – | |
1245 | – | #ifdef IS_MPI |
1246 | – | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1247 | – | MPIcheckPoint(); |
1248 | – | #endif // is_mpi |
1249 | – | |
1250 | – | // clean up the forcefield |
1251 | – | the_ff->calcRcut(); |
1252 | – | the_ff->cleanMe(); |
1253 | – | |
1481 | } | |
1255 | – | |
1256 | – | void SimSetup::initFromBass( void ){ |
1257 | – | |
1258 | – | int i, j, k; |
1259 | – | int n_cells; |
1260 | – | double cellx, celly, cellz; |
1261 | – | double temp1, temp2, temp3; |
1262 | – | int n_per_extra; |
1263 | – | int n_extra; |
1264 | – | int have_extra, done; |
1265 | – | |
1266 | – | temp1 = (double)tot_nmol / 4.0; |
1267 | – | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1268 | – | temp3 = ceil( temp2 ); |
1269 | – | |
1270 | – | have_extra =0; |
1271 | – | if( temp2 < temp3 ){ // we have a non-complete lattice |
1272 | – | have_extra =1; |
1273 | – | |
1274 | – | n_cells = (int)temp3 - 1; |
1275 | – | cellx = simnfo->boxLx / temp3; |
1276 | – | celly = simnfo->boxLy / temp3; |
1277 | – | cellz = simnfo->boxLz / temp3; |
1278 | – | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1279 | – | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1280 | – | n_per_extra = (int)ceil( temp1 ); |
1281 | – | |
1282 | – | if( n_per_extra > 4){ |
1283 | – | sprintf( painCave.errMsg, |
1284 | – | "SimSetup error. There has been an error in constructing" |
1285 | – | " the non-complete lattice.\n" ); |
1286 | – | painCave.isFatal = 1; |
1287 | – | simError(); |
1288 | – | } |
1289 | – | } |
1290 | – | else{ |
1291 | – | n_cells = (int)temp3; |
1292 | – | cellx = simnfo->boxLx / temp3; |
1293 | – | celly = simnfo->boxLy / temp3; |
1294 | – | cellz = simnfo->boxLz / temp3; |
1295 | – | } |
1296 | – | |
1297 | – | current_mol = 0; |
1298 | – | current_comp_mol = 0; |
1299 | – | current_comp = 0; |
1300 | – | current_atom_ndx = 0; |
1301 | – | |
1302 | – | for( i=0; i < n_cells ; i++ ){ |
1303 | – | for( j=0; j < n_cells; j++ ){ |
1304 | – | for( k=0; k < n_cells; k++ ){ |
1305 | – | |
1306 | – | makeElement( i * cellx, |
1307 | – | j * celly, |
1308 | – | k * cellz ); |
1309 | – | |
1310 | – | makeElement( i * cellx + 0.5 * cellx, |
1311 | – | j * celly + 0.5 * celly, |
1312 | – | k * cellz ); |
1313 | – | |
1314 | – | makeElement( i * cellx, |
1315 | – | j * celly + 0.5 * celly, |
1316 | – | k * cellz + 0.5 * cellz ); |
1317 | – | |
1318 | – | makeElement( i * cellx + 0.5 * cellx, |
1319 | – | j * celly, |
1320 | – | k * cellz + 0.5 * cellz ); |
1321 | – | } |
1322 | – | } |
1323 | – | } |
1324 | – | |
1325 | – | if( have_extra ){ |
1326 | – | done = 0; |
1327 | – | |
1328 | – | int start_ndx; |
1329 | – | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1330 | – | for( j=0; j < (n_cells+1) && !done; j++ ){ |
1331 | – | |
1332 | – | if( i < n_cells ){ |
1333 | – | |
1334 | – | if( j < n_cells ){ |
1335 | – | start_ndx = n_cells; |
1336 | – | } |
1337 | – | else start_ndx = 0; |
1338 | – | } |
1339 | – | else start_ndx = 0; |
1340 | – | |
1341 | – | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1342 | – | |
1343 | – | makeElement( i * cellx, |
1344 | – | j * celly, |
1345 | – | k * cellz ); |
1346 | – | done = ( current_mol >= tot_nmol ); |
1347 | – | |
1348 | – | if( !done && n_per_extra > 1 ){ |
1349 | – | makeElement( i * cellx + 0.5 * cellx, |
1350 | – | j * celly + 0.5 * celly, |
1351 | – | k * cellz ); |
1352 | – | done = ( current_mol >= tot_nmol ); |
1353 | – | } |
1354 | – | |
1355 | – | if( !done && n_per_extra > 2){ |
1356 | – | makeElement( i * cellx, |
1357 | – | j * celly + 0.5 * celly, |
1358 | – | k * cellz + 0.5 * cellz ); |
1359 | – | done = ( current_mol >= tot_nmol ); |
1360 | – | } |
1361 | – | |
1362 | – | if( !done && n_per_extra > 3){ |
1363 | – | makeElement( i * cellx + 0.5 * cellx, |
1364 | – | j * celly, |
1365 | – | k * cellz + 0.5 * cellz ); |
1366 | – | done = ( current_mol >= tot_nmol ); |
1367 | – | } |
1368 | – | } |
1369 | – | } |
1370 | – | } |
1371 | – | } |
1372 | – | |
1373 | – | |
1374 | – | for( i=0; i<simnfo->n_atoms; i++ ){ |
1375 | – | simnfo->atoms[i]->set_vx( 0.0 ); |
1376 | – | simnfo->atoms[i]->set_vy( 0.0 ); |
1377 | – | simnfo->atoms[i]->set_vz( 0.0 ); |
1378 | – | } |
1379 | – | } |
1380 | – | |
1381 | – | void SimSetup::makeElement( double x, double y, double z ){ |
1382 | – | |
1383 | – | int k; |
1384 | – | AtomStamp* current_atom; |
1385 | – | DirectionalAtom* dAtom; |
1386 | – | double rotMat[3][3]; |
1387 | – | |
1388 | – | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1389 | – | |
1390 | – | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1391 | – | if( !current_atom->havePosition() ){ |
1392 | – | sprintf( painCave.errMsg, |
1393 | – | "SimSetup:initFromBass error.\n" |
1394 | – | "\tComponent %s, atom %s does not have a position specified.\n" |
1395 | – | "\tThe initialization routine is unable to give a start" |
1396 | – | " position.\n", |
1397 | – | comp_stamps[current_comp]->getID(), |
1398 | – | current_atom->getType() ); |
1399 | – | painCave.isFatal = 1; |
1400 | – | simError(); |
1401 | – | } |
1402 | – | |
1403 | – | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1404 | – | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1405 | – | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1406 | – | |
1407 | – | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1408 | – | |
1409 | – | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1410 | – | |
1411 | – | rotMat[0][0] = 1.0; |
1412 | – | rotMat[0][1] = 0.0; |
1413 | – | rotMat[0][2] = 0.0; |
1414 | – | |
1415 | – | rotMat[1][0] = 0.0; |
1416 | – | rotMat[1][1] = 1.0; |
1417 | – | rotMat[1][2] = 0.0; |
1418 | – | |
1419 | – | rotMat[2][0] = 0.0; |
1420 | – | rotMat[2][1] = 0.0; |
1421 | – | rotMat[2][2] = 1.0; |
1422 | – | |
1423 | – | dAtom->setA( rotMat ); |
1424 | – | } |
1425 | – | |
1426 | – | current_atom_ndx++; |
1427 | – | } |
1428 | – | |
1429 | – | current_mol++; |
1430 | – | current_comp_mol++; |
1431 | – | |
1432 | – | if( current_comp_mol >= components_nmol[current_comp] ){ |
1433 | – | |
1434 | – | current_comp_mol = 0; |
1435 | – | current_comp++; |
1436 | – | } |
1437 | – | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |