# | 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 12 | Line 15 | |
15 | #include "mpiSimulation.hpp" | |
16 | #endif | |
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 |
24 | + | #define NPTim_ENS 4 |
25 | + | #define NPTfm_ENS 5 |
26 | + | |
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 27 | 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 62 | Line 92 | void SimSetup::receiveParse(void){ | |
92 | ||
93 | #endif // is_mpi | |
94 | ||
95 | < | void SimSetup::createSim( void ){ |
95 | > | void SimSetup::createSim(void){ |
96 | ||
97 | < | MakeStamps *the_stamps; |
68 | < | Globals* the_globals; |
69 | < | int i, j; |
70 | < | |
71 | < | // get the stamps and globals; |
72 | < | the_stamps = stamps; |
73 | < | the_globals = globals; |
74 | < | |
75 | < | // set the easy ones first |
76 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
77 | < | simnfo->dt = the_globals->getDt(); |
78 | < | simnfo->run_time = the_globals->getRunTime(); |
79 | < | |
80 | < | // get the ones we know are there, yet still may need some work. |
81 | < | n_components = the_globals->getNComponents(); |
82 | < | strcpy( force_field, the_globals->getForceField() ); |
83 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
84 | < | strcpy( simnfo->ensemble, ensemble ); |
85 | < | |
86 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
87 | < | simnfo->usePBC = the_globals->getPBC(); |
88 | < | |
89 | < | |
90 | < | |
91 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
92 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
93 | < | else{ |
94 | < | sprintf( painCave.errMsg, |
95 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
96 | < | force_field ); |
97 | < | painCave.isFatal = 1; |
98 | < | simError(); |
99 | < | } |
100 | < | |
101 | < | #ifdef IS_MPI |
102 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
103 | < | MPIcheckPoint(); |
104 | < | #endif // is_mpi |
105 | < | |
97 | > | int i, j, k, globalAtomIndex; |
98 | ||
99 | + | // gather all of the information from the Bass file |
100 | ||
101 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
109 | < | the_components = the_globals->getComponents(); |
110 | < | components_nmol = new int[n_components]; |
111 | < | comp_stamps = new MoleculeStamp*[n_components]; |
101 | > | gatherInfo(); |
102 | ||
103 | < | if( !the_globals->haveNMol() ){ |
114 | < | // we don't have the total number of molecules, so we assume it is |
115 | < | // given in each component |
103 | > | // creation of complex system objects |
104 | ||
105 | < | tot_nmol = 0; |
118 | < | for( i=0; i<n_components; i++ ){ |
105 | > | sysObjectsCreation(); |
106 | ||
107 | < | if( !the_components[i]->haveNMol() ){ |
121 | < | // we have a problem |
122 | < | sprintf( painCave.errMsg, |
123 | < | "SimSetup Error. No global NMol or component NMol" |
124 | < | " given. Cannot calculate the number of atoms.\n" ); |
125 | < | painCave.isFatal = 1; |
126 | < | simError(); |
127 | < | } |
107 | > | // check on the post processing info |
108 | ||
109 | < | tot_nmol += the_components[i]->getNMol(); |
130 | < | components_nmol[i] = the_components[i]->getNMol(); |
131 | < | } |
132 | < | } |
133 | < | else{ |
134 | < | sprintf( painCave.errMsg, |
135 | < | "SimSetup error.\n" |
136 | < | "\tSorry, the ability to specify total" |
137 | < | " nMols and then give molfractions in the components\n" |
138 | < | "\tis not currently supported." |
139 | < | " Please give nMol in the components.\n" ); |
140 | < | painCave.isFatal = 1; |
141 | < | simError(); |
142 | < | |
143 | < | |
144 | < | // tot_nmol = the_globals->getNMol(); |
145 | < | |
146 | < | // //we have the total number of molecules, now we check for molfractions |
147 | < | // for( i=0; i<n_components; i++ ){ |
148 | < | |
149 | < | // if( !the_components[i]->haveMolFraction() ){ |
150 | < | |
151 | < | // if( !the_components[i]->haveNMol() ){ |
152 | < | // //we have a problem |
153 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
154 | < | // << " nMol was given in component |
155 | < | |
156 | < | } |
109 | > | finalInfoCheck(); |
110 | ||
111 | < | #ifdef IS_MPI |
159 | < | strcpy( checkPointMsg, "Have the number of components" ); |
160 | < | MPIcheckPoint(); |
161 | < | #endif // is_mpi |
111 | > | // initialize the system coordinates |
112 | ||
113 | < | // make an array of molecule stamps that match the components used. |
164 | < | // also extract the used stamps out into a separate linked list |
113 | > | if( !isInfoArray ) initSystemCoords(); |
114 | ||
115 | < | simnfo->nComponents = n_components; |
167 | < | simnfo->componentsNmol = components_nmol; |
168 | < | simnfo->compStamps = comp_stamps; |
169 | < | simnfo->headStamp = new LinkedMolStamp(); |
170 | < | |
171 | < | char* id; |
172 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
173 | < | LinkedMolStamp* currentStamp = NULL; |
174 | < | for( i=0; i<n_components; i++ ){ |
175 | < | |
176 | < | id = the_components[i]->getType(); |
177 | < | comp_stamps[i] = NULL; |
178 | < | |
179 | < | // check to make sure the component isn't already in the list |
180 | < | |
181 | < | comp_stamps[i] = headStamp->match( id ); |
182 | < | if( comp_stamps[i] == NULL ){ |
183 | < | |
184 | < | // extract the component from the list; |
185 | < | |
186 | < | currentStamp = the_stamps->extractMolStamp( id ); |
187 | < | if( currentStamp == NULL ){ |
188 | < | sprintf( painCave.errMsg, |
189 | < | "SimSetup error: Component \"%s\" was not found in the " |
190 | < | "list of declared molecules\n", |
191 | < | id ); |
192 | < | painCave.isFatal = 1; |
193 | < | simError(); |
194 | < | } |
195 | < | |
196 | < | headStamp->add( currentStamp ); |
197 | < | comp_stamps[i] = headStamp->match( id ); |
198 | < | } |
199 | < | } |
200 | < | |
201 | < | #ifdef IS_MPI |
202 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
203 | < | MPIcheckPoint(); |
204 | < | #endif // is_mpi |
205 | < | |
206 | < | |
207 | < | |
208 | < | |
209 | < | // caclulate the number of atoms, bonds, bends and torsions |
210 | < | |
211 | < | tot_atoms = 0; |
212 | < | tot_bonds = 0; |
213 | < | tot_bends = 0; |
214 | < | tot_torsions = 0; |
215 | < | for( i=0; i<n_components; i++ ){ |
216 | < | |
217 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
218 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
219 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
220 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
221 | < | } |
222 | < | |
223 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
224 | < | |
225 | < | simnfo->n_atoms = tot_atoms; |
226 | < | simnfo->n_bonds = tot_bonds; |
227 | < | simnfo->n_bends = tot_bends; |
228 | < | simnfo->n_torsions = tot_torsions; |
229 | < | simnfo->n_SRI = tot_SRI; |
230 | < | simnfo->n_mol = tot_nmol; |
231 | < | |
232 | < | |
233 | < | #ifdef IS_MPI |
234 | < | |
235 | < | // divide the molecules among processors here. |
236 | < | |
237 | < | mpiSim = new mpiSimulation( simnfo ); |
238 | < | |
239 | < | |
240 | < | |
241 | < | globalIndex = mpiSim->divideLabor(); |
242 | < | |
243 | < | // set up the local variables |
244 | < | |
245 | < | int localMol, allMol; |
246 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
247 | < | |
248 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
249 | < | int* molCompType = mpiSim->getMolComponentType(); |
250 | < | |
251 | < | allMol = 0; |
252 | < | localMol = 0; |
253 | < | local_atoms = 0; |
254 | < | local_bonds = 0; |
255 | < | local_bends = 0; |
256 | < | local_torsions = 0; |
257 | < | for( i=0; i<n_components; i++ ){ |
258 | < | |
259 | < | for( j=0; j<components_nmol[i]; j++ ){ |
260 | < | |
261 | < | if( mol2proc[j] == worldRank ){ |
262 | < | |
263 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
264 | < | local_bonds += comp_stamps[i]->getNBonds(); |
265 | < | local_bends += comp_stamps[i]->getNBends(); |
266 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
267 | < | localMol++; |
268 | < | } |
269 | < | allMol++; |
270 | < | } |
271 | < | } |
272 | < | local_SRI = local_bonds + local_bends + local_torsions; |
273 | < | |
274 | < | |
275 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
276 | < | |
277 | < | if( local_atoms != simnfo->n_atoms ){ |
278 | < | sprintf( painCave.errMsg, |
279 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
280 | < | " localAtom (%d) are not equal.\n", |
281 | < | simnfo->n_atoms, |
282 | < | local_atoms ); |
283 | < | painCave.isFatal = 1; |
284 | < | simError(); |
285 | < | } |
286 | < | |
287 | < | simnfo->n_bonds = local_bonds; |
288 | < | simnfo->n_bends = local_bends; |
289 | < | simnfo->n_torsions = local_torsions; |
290 | < | simnfo->n_SRI = local_SRI; |
291 | < | simnfo->n_mol = localMol; |
292 | < | |
293 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
294 | < | MPIcheckPoint(); |
295 | < | |
296 | < | |
297 | < | #endif // is_mpi |
298 | < | |
299 | < | |
300 | < | // create the atom and short range interaction arrays |
301 | < | |
302 | < | Atom::createArrays(simnfo->n_atoms); |
303 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
304 | < | the_molecules = new Molecule[simnfo->n_mol]; |
305 | < | int molIndex; |
115 | > | // make the output filenames |
116 | ||
117 | < | // initialize the molecule's stampID's |
308 | < | |
309 | < | #ifdef IS_MPI |
310 | < | |
311 | < | |
312 | < | molIndex = 0; |
313 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
314 | < | |
315 | < | if(mol2proc[i] == worldRank ){ |
316 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
317 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
318 | < | molIndex++; |
319 | < | } |
320 | < | } |
321 | < | |
322 | < | #else // is_mpi |
323 | < | |
324 | < | molIndex = 0; |
325 | < | for(i=0; i<n_components; i++){ |
326 | < | for(j=0; j<components_nmol[i]; j++ ){ |
327 | < | the_molecules[molIndex].setStampID( i ); |
328 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
329 | < | molIndex++; |
330 | < | } |
331 | < | } |
332 | < | |
333 | < | |
334 | < | #endif // is_mpi |
335 | < | |
336 | < | |
337 | < | if( simnfo->n_SRI ){ |
338 | < | |
339 | < | Exclude::createArray(simnfo->n_SRI); |
340 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
341 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
342 | < | simnfo->globalExcludes = new int; |
343 | < | simnfo->n_exclude = simnfo->n_SRI; |
344 | < | } |
345 | < | else{ |
346 | < | |
347 | < | Exclude::createArray( 1 ); |
348 | < | the_excludes = new Exclude*; |
349 | < | the_excludes[0] = new Exclude(0); |
350 | < | the_excludes[0]->setPair( 0,0 ); |
351 | < | simnfo->globalExcludes = new int; |
352 | < | simnfo->globalExcludes[0] = 0; |
353 | < | simnfo->n_exclude = 0; |
354 | < | } |
355 | < | |
356 | < | // set the arrays into the SimInfo object |
357 | < | |
358 | < | simnfo->atoms = the_atoms; |
359 | < | simnfo->molecules = the_molecules; |
360 | < | simnfo->nGlobalExcludes = 0; |
361 | < | simnfo->excludes = the_excludes; |
362 | < | |
363 | < | |
364 | < | // get some of the tricky things that may still be in the globals |
365 | < | |
366 | < | |
367 | < | if( the_globals->haveBox() ){ |
368 | < | simnfo->box_x = the_globals->getBox(); |
369 | < | simnfo->box_y = the_globals->getBox(); |
370 | < | simnfo->box_z = the_globals->getBox(); |
371 | < | } |
372 | < | else if( the_globals->haveDensity() ){ |
373 | < | |
374 | < | double vol; |
375 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
376 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
377 | < | simnfo->box_y = simnfo->box_x; |
378 | < | simnfo->box_z = simnfo->box_x; |
379 | < | } |
380 | < | else{ |
381 | < | if( !the_globals->haveBoxX() ){ |
382 | < | sprintf( painCave.errMsg, |
383 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
384 | < | painCave.isFatal = 1; |
385 | < | simError(); |
386 | < | } |
387 | < | simnfo->box_x = the_globals->getBoxX(); |
388 | < | |
389 | < | if( !the_globals->haveBoxY() ){ |
390 | < | sprintf( painCave.errMsg, |
391 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
392 | < | painCave.isFatal = 1; |
393 | < | simError(); |
394 | < | } |
395 | < | simnfo->box_y = the_globals->getBoxY(); |
396 | < | |
397 | < | if( !the_globals->haveBoxZ() ){ |
398 | < | sprintf( painCave.errMsg, |
399 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
400 | < | painCave.isFatal = 1; |
401 | < | simError(); |
402 | < | } |
403 | < | simnfo->box_z = the_globals->getBoxZ(); |
404 | < | } |
405 | < | |
406 | < | #ifdef IS_MPI |
407 | < | strcpy( checkPointMsg, "Box size set up" ); |
408 | < | MPIcheckPoint(); |
409 | < | #endif // is_mpi |
410 | < | |
411 | < | |
412 | < | // initialize the arrays |
413 | < | |
414 | < | the_ff->setSimInfo( simnfo ); |
415 | < | |
416 | < | makeMolecules(); |
417 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
418 | < | for(i=0; i<simnfo->n_atoms; i++){ |
419 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
420 | < | } |
421 | < | |
422 | < | if (the_globals->getUseRF() ) { |
423 | < | simnfo->useReactionField = 1; |
424 | < | |
425 | < | if( !the_globals->haveECR() ){ |
426 | < | sprintf( painCave.errMsg, |
427 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
428 | < | "box length for the electrostaticCutoffRadius.\n" |
429 | < | "I hope you have a very fast processor!\n"); |
430 | < | painCave.isFatal = 0; |
431 | < | simError(); |
432 | < | double smallest; |
433 | < | smallest = simnfo->box_x; |
434 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
435 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
436 | < | simnfo->ecr = 0.5 * smallest; |
437 | < | } else { |
438 | < | simnfo->ecr = the_globals->getECR(); |
439 | < | } |
440 | < | |
441 | < | if( !the_globals->haveEST() ){ |
442 | < | sprintf( painCave.errMsg, |
443 | < | "SimSetup Warning: using default value of 0.05 * the " |
444 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
445 | < | ); |
446 | < | painCave.isFatal = 0; |
447 | < | simError(); |
448 | < | simnfo->est = 0.05 * simnfo->ecr; |
449 | < | } else { |
450 | < | simnfo->est = the_globals->getEST(); |
451 | < | } |
452 | < | |
453 | < | if(!the_globals->haveDielectric() ){ |
454 | < | sprintf( painCave.errMsg, |
455 | < | "SimSetup Error: You are trying to use Reaction Field without" |
456 | < | "setting a dielectric constant!\n" |
457 | < | ); |
458 | < | painCave.isFatal = 1; |
459 | < | simError(); |
460 | < | } |
461 | < | simnfo->dielectric = the_globals->getDielectric(); |
462 | < | } else { |
463 | < | if (simnfo->n_dipoles) { |
464 | < | |
465 | < | if( !the_globals->haveECR() ){ |
466 | < | sprintf( painCave.errMsg, |
467 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
468 | < | "box length for the electrostaticCutoffRadius.\n" |
469 | < | "I hope you have a very fast processor!\n"); |
470 | < | painCave.isFatal = 0; |
471 | < | simError(); |
472 | < | double smallest; |
473 | < | smallest = simnfo->box_x; |
474 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
475 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
476 | < | simnfo->ecr = 0.5 * smallest; |
477 | < | } else { |
478 | < | simnfo->ecr = the_globals->getECR(); |
479 | < | } |
480 | < | |
481 | < | if( !the_globals->haveEST() ){ |
482 | < | sprintf( painCave.errMsg, |
483 | < | "SimSetup Warning: using default value of 5% of the" |
484 | < | "electrostaticCutoffRadius for the " |
485 | < | "electrostaticSkinThickness\n" |
486 | < | ); |
487 | < | painCave.isFatal = 0; |
488 | < | simError(); |
489 | < | simnfo->est = 0.05 * simnfo->ecr; |
490 | < | } else { |
491 | < | simnfo->est = the_globals->getEST(); |
492 | < | } |
493 | < | } |
494 | < | } |
495 | < | |
496 | < | #ifdef IS_MPI |
497 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
498 | < | MPIcheckPoint(); |
499 | < | #endif // is_mpi |
500 | < | |
501 | < | if( the_globals->haveInitialConfig() ){ |
502 | < | |
503 | < | InitializeFromFile* fileInit; |
504 | < | #ifdef IS_MPI // is_mpi |
505 | < | if( worldRank == 0 ){ |
506 | < | #endif //is_mpi |
507 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
508 | < | #ifdef IS_MPI |
509 | < | }else fileInit = new InitializeFromFile( NULL ); |
510 | < | #endif |
511 | < | fileInit->read_xyz( simnfo ); // default velocities on |
512 | < | |
513 | < | delete fileInit; |
514 | < | } |
515 | < | else{ |
516 | < | |
517 | < | #ifdef IS_MPI |
518 | < | |
519 | < | // no init from bass |
520 | < | |
521 | < | sprintf( painCave.errMsg, |
522 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
523 | < | painCave.isFatal; |
524 | < | simError(); |
525 | < | |
526 | < | #else |
527 | < | |
528 | < | initFromBass(); |
529 | < | |
530 | < | |
531 | < | #endif |
532 | < | } |
533 | < | |
534 | < | #ifdef IS_MPI |
535 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
536 | < | MPIcheckPoint(); |
537 | < | #endif // is_mpi |
538 | < | |
539 | < | |
117 | > | makeOutNames(); |
118 | ||
119 | < | |
119 | > | // make the integrator |
120 | ||
121 | < | |
544 | < | |
545 | < | #ifdef IS_MPI |
546 | < | if( worldRank == 0 ){ |
547 | < | #endif // is_mpi |
548 | < | |
549 | < | if( the_globals->haveFinalConfig() ){ |
550 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
551 | < | } |
552 | < | else{ |
553 | < | strcpy( simnfo->finalName, inFileName ); |
554 | < | char* endTest; |
555 | < | int nameLength = strlen( simnfo->finalName ); |
556 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
557 | < | if( !strcmp( endTest, ".bass" ) ){ |
558 | < | strcpy( endTest, ".eor" ); |
559 | < | } |
560 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
561 | < | strcpy( endTest, ".eor" ); |
562 | < | } |
563 | < | else{ |
564 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
565 | < | if( !strcmp( endTest, ".bss" ) ){ |
566 | < | strcpy( endTest, ".eor" ); |
567 | < | } |
568 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
569 | < | strcpy( endTest, ".eor" ); |
570 | < | } |
571 | < | else{ |
572 | < | strcat( simnfo->finalName, ".eor" ); |
573 | < | } |
574 | < | } |
575 | < | } |
576 | < | |
577 | < | // make the sample and status out names |
578 | < | |
579 | < | strcpy( simnfo->sampleName, inFileName ); |
580 | < | char* endTest; |
581 | < | int nameLength = strlen( simnfo->sampleName ); |
582 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
583 | < | if( !strcmp( endTest, ".bass" ) ){ |
584 | < | strcpy( endTest, ".dump" ); |
585 | < | } |
586 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
587 | < | strcpy( endTest, ".dump" ); |
588 | < | } |
589 | < | else{ |
590 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
591 | < | if( !strcmp( endTest, ".bss" ) ){ |
592 | < | strcpy( endTest, ".dump" ); |
593 | < | } |
594 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
595 | < | strcpy( endTest, ".dump" ); |
596 | < | } |
597 | < | else{ |
598 | < | strcat( simnfo->sampleName, ".dump" ); |
599 | < | } |
600 | < | } |
601 | < | |
602 | < | strcpy( simnfo->statusName, inFileName ); |
603 | < | nameLength = strlen( simnfo->statusName ); |
604 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
605 | < | if( !strcmp( endTest, ".bass" ) ){ |
606 | < | strcpy( endTest, ".stat" ); |
607 | < | } |
608 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
609 | < | strcpy( endTest, ".stat" ); |
610 | < | } |
611 | < | else{ |
612 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
613 | < | if( !strcmp( endTest, ".bss" ) ){ |
614 | < | strcpy( endTest, ".stat" ); |
615 | < | } |
616 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
617 | < | strcpy( endTest, ".stat" ); |
618 | < | } |
619 | < | else{ |
620 | < | strcat( simnfo->statusName, ".stat" ); |
621 | < | } |
622 | < | } |
623 | < | |
624 | < | #ifdef IS_MPI |
625 | < | } |
626 | < | #endif // is_mpi |
121 | > | makeIntegrator(); |
122 | ||
628 | – | // set the status, sample, and themal kick times |
629 | – | |
630 | – | if( the_globals->haveSampleTime() ){ |
631 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
632 | – | simnfo->statusTime = simnfo->sampleTime; |
633 | – | simnfo->thermalTime = simnfo->sampleTime; |
634 | – | } |
635 | – | else{ |
636 | – | simnfo->sampleTime = the_globals->getRunTime(); |
637 | – | simnfo->statusTime = simnfo->sampleTime; |
638 | – | simnfo->thermalTime = simnfo->sampleTime; |
639 | – | } |
640 | – | |
641 | – | if( the_globals->haveStatusTime() ){ |
642 | – | simnfo->statusTime = the_globals->getStatusTime(); |
643 | – | } |
644 | – | |
645 | – | if( the_globals->haveThermalTime() ){ |
646 | – | simnfo->thermalTime = the_globals->getThermalTime(); |
647 | – | } |
648 | – | |
649 | – | // check for the temperature set flag |
650 | – | |
651 | – | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
652 | – | |
653 | – | |
654 | – | // // make the longe range forces and the integrator |
655 | – | |
656 | – | // new AllLong( simnfo ); |
657 | – | |
658 | – | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
659 | – | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
660 | – | |
123 | #ifdef IS_MPI | |
124 | mpiSim->mpiRefresh(); | |
125 | #endif | |
126 | ||
127 | // initialize the Fortran | |
128 | ||
129 | + | initFortran(); |
130 | ||
668 | – | simnfo->refreshSim(); |
669 | – | |
670 | – | if( !strcmp( simnfo->mixingRule, "standard") ){ |
671 | – | the_ff->initForceField( LB_MIXING_RULE ); |
672 | – | } |
673 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
674 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
675 | – | } |
676 | – | else{ |
677 | – | sprintf( painCave.errMsg, |
678 | – | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
679 | – | simnfo->mixingRule ); |
680 | – | painCave.isFatal = 1; |
681 | – | simError(); |
682 | – | } |
131 | ||
132 | ||
685 | – | #ifdef IS_MPI |
686 | – | strcpy( checkPointMsg, |
687 | – | "Successfully intialized the mixingRule for Fortran." ); |
688 | – | MPIcheckPoint(); |
689 | – | #endif // is_mpi |
133 | } | |
134 | ||
135 | ||
136 | void SimSetup::makeMolecules( void ){ | |
137 | ||
138 | + | int k,l; |
139 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
140 | < | molInit info; |
140 | > | molInit molInfo; |
141 | DirectionalAtom* dAtom; | |
142 | LinkedAssign* extras; | |
143 | LinkedAssign* current_extra; | |
# | Line 716 | Line 160 | void SimSetup::makeMolecules( void ){ | |
160 | ||
161 | double ux, uy, uz, u, uSqr; | |
162 | ||
163 | < | atomOffset = 0; |
720 | < | excludeOffset = 0; |
721 | < | for(i=0; i<simnfo->n_mol; i++){ |
163 | > | for(k=0; k<nInfo; k++){ |
164 | ||
165 | < | stampID = the_molecules[i].getStampID(); |
165 | > | the_ff->setSimInfo( &(info[k]) ); |
166 | ||
167 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
168 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
169 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
170 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
171 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
167 | > | atomOffset = 0; |
168 | > | excludeOffset = 0; |
169 | > | for(i=0; i<info[k].n_mol; i++){ |
170 | > | |
171 | > | stampID = info[k].molecules[i].getStampID(); |
172 | ||
173 | < | info.myAtoms = &the_atoms[atomOffset]; |
174 | < | info.myExcludes = &the_excludes[excludeOffset]; |
175 | < | info.myBonds = new Bond*[info.nBonds]; |
176 | < | info.myBends = new Bend*[info.nBends]; |
177 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
173 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
174 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
175 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
176 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
177 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
178 | > | |
179 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
180 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
181 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
182 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
183 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
184 | ||
185 | < | theBonds = new bond_pair[info.nBonds]; |
186 | < | theBends = new bend_set[info.nBends]; |
187 | < | theTorsions = new torsion_set[info.nTorsions]; |
185 | > | theBonds = new bond_pair[molInfo.nBonds]; |
186 | > | theBends = new bend_set[molInfo.nBends]; |
187 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
188 | ||
189 | < | // make the Atoms |
189 | > | // make the Atoms |
190 | ||
191 | < | for(j=0; j<info.nAtoms; j++){ |
744 | < | |
745 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
746 | < | if( currentAtom->haveOrientation() ){ |
191 | > | for(j=0; j<molInfo.nAtoms; j++){ |
192 | ||
193 | < | dAtom = new DirectionalAtom(j + atomOffset); |
194 | < | simnfo->n_oriented++; |
195 | < | info.myAtoms[j] = dAtom; |
196 | < | |
197 | < | ux = currentAtom->getOrntX(); |
198 | < | uy = currentAtom->getOrntY(); |
199 | < | uz = currentAtom->getOrntZ(); |
200 | < | |
201 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
202 | < | |
203 | < | u = sqrt( uSqr ); |
204 | < | ux = ux / u; |
205 | < | uy = uy / u; |
206 | < | uz = uz / u; |
207 | < | |
208 | < | dAtom->setSUx( ux ); |
209 | < | dAtom->setSUy( uy ); |
210 | < | dAtom->setSUz( uz ); |
211 | < | } |
212 | < | else{ |
213 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
214 | < | } |
215 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
193 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
194 | > | if( currentAtom->haveOrientation() ){ |
195 | > | |
196 | > | dAtom = new DirectionalAtom( (j + atomOffset), |
197 | > | info[k].getConfiguration() ); |
198 | > | info[k].n_oriented++; |
199 | > | molInfo.myAtoms[j] = dAtom; |
200 | > | |
201 | > | ux = currentAtom->getOrntX(); |
202 | > | uy = currentAtom->getOrntY(); |
203 | > | uz = currentAtom->getOrntZ(); |
204 | > | |
205 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
206 | > | |
207 | > | u = sqrt( uSqr ); |
208 | > | ux = ux / u; |
209 | > | uy = uy / u; |
210 | > | uz = uz / u; |
211 | > | |
212 | > | dAtom->setSUx( ux ); |
213 | > | dAtom->setSUy( uy ); |
214 | > | dAtom->setSUz( uz ); |
215 | > | } |
216 | > | else{ |
217 | > | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
218 | > | info[k].getConfiguration() ); |
219 | > | } |
220 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
221 | ||
222 | #ifdef IS_MPI | |
223 | ||
224 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
224 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
225 | ||
226 | #endif // is_mpi | |
227 | < | } |
227 | > | } |
228 | ||
229 | // make the bonds | |
230 | < | for(j=0; j<info.nBonds; j++){ |
230 | > | for(j=0; j<molInfo.nBonds; j++){ |
231 | ||
232 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
233 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
234 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
235 | < | |
236 | < | exI = theBonds[j].a; |
237 | < | exJ = theBonds[j].b; |
238 | < | |
239 | < | // exclude_I must always be the smaller of the pair |
240 | < | if( exI > exJ ){ |
241 | < | tempEx = exI; |
242 | < | exI = exJ; |
243 | < | exJ = tempEx; |
244 | < | } |
232 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
233 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
234 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
235 | > | |
236 | > | exI = theBonds[j].a; |
237 | > | exJ = theBonds[j].b; |
238 | > | |
239 | > | // exclude_I must always be the smaller of the pair |
240 | > | if( exI > exJ ){ |
241 | > | tempEx = exI; |
242 | > | exI = exJ; |
243 | > | exJ = tempEx; |
244 | > | } |
245 | #ifdef IS_MPI | |
246 | < | tempEx = exI; |
247 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
248 | < | tempEx = exJ; |
249 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
250 | < | |
251 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
246 | > | tempEx = exI; |
247 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
248 | > | tempEx = exJ; |
249 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
250 | > | |
251 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
252 | #else // isn't MPI | |
253 | < | |
254 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
253 | > | |
254 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
255 | #endif //is_mpi | |
256 | < | } |
257 | < | excludeOffset += info.nBonds; |
808 | < | |
809 | < | //make the bends |
810 | < | for(j=0; j<info.nBends; j++){ |
256 | > | } |
257 | > | excludeOffset += molInfo.nBonds; |
258 | ||
259 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
260 | < | theBends[j].a = currentBend->getA() + atomOffset; |
261 | < | theBends[j].b = currentBend->getB() + atomOffset; |
262 | < | theBends[j].c = currentBend->getC() + atomOffset; |
259 | > | //make the bends |
260 | > | for(j=0; j<molInfo.nBends; j++){ |
261 | > | |
262 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
263 | > | theBends[j].a = currentBend->getA() + atomOffset; |
264 | > | theBends[j].b = currentBend->getB() + atomOffset; |
265 | > | theBends[j].c = currentBend->getC() + atomOffset; |
266 | > | |
267 | > | if( currentBend->haveExtras() ){ |
268 | ||
269 | < | if( currentBend->haveExtras() ){ |
270 | < | |
271 | < | extras = currentBend->getExtras(); |
272 | < | current_extra = extras; |
273 | < | |
274 | < | while( current_extra != NULL ){ |
275 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
269 | > | extras = currentBend->getExtras(); |
270 | > | current_extra = extras; |
271 | > | |
272 | > | while( current_extra != NULL ){ |
273 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
274 | > | |
275 | > | switch( current_extra->getType() ){ |
276 | ||
277 | < | switch( current_extra->getType() ){ |
277 | > | case 0: |
278 | > | theBends[j].ghost = |
279 | > | current_extra->getInt() + atomOffset; |
280 | > | theBends[j].isGhost = 1; |
281 | > | break; |
282 | > | |
283 | > | case 1: |
284 | > | theBends[j].ghost = |
285 | > | (int)current_extra->getDouble() + atomOffset; |
286 | > | theBends[j].isGhost = 1; |
287 | > | break; |
288 | > | |
289 | > | default: |
290 | > | sprintf( painCave.errMsg, |
291 | > | "SimSetup Error: ghostVectorSource was neither a " |
292 | > | "double nor an int.\n" |
293 | > | "-->Bend[%d] in %s\n", |
294 | > | j, comp_stamps[stampID]->getID() ); |
295 | > | painCave.isFatal = 1; |
296 | > | simError(); |
297 | > | } |
298 | > | } |
299 | > | |
300 | > | else{ |
301 | ||
827 | – | case 0: |
828 | – | theBends[j].ghost = |
829 | – | current_extra->getInt() + atomOffset; |
830 | – | theBends[j].isGhost = 1; |
831 | – | break; |
832 | – | |
833 | – | case 1: |
834 | – | theBends[j].ghost = |
835 | – | (int)current_extra->getDouble() + atomOffset; |
836 | – | theBends[j].isGhost = 1; |
837 | – | break; |
838 | – | |
839 | – | default: |
302 | sprintf( painCave.errMsg, | |
303 | < | "SimSetup Error: ghostVectorSource was neither a " |
304 | < | "double nor an int.\n" |
305 | < | "-->Bend[%d] in %s\n", |
303 | > | "SimSetup Error: unhandled bend assignment:\n" |
304 | > | " -->%s in Bend[%d] in %s\n", |
305 | > | current_extra->getlhs(), |
306 | j, comp_stamps[stampID]->getID() ); | |
307 | painCave.isFatal = 1; | |
308 | simError(); | |
309 | } | |
848 | – | } |
849 | – | |
850 | – | else{ |
310 | ||
311 | < | sprintf( painCave.errMsg, |
853 | < | "SimSetup Error: unhandled bend assignment:\n" |
854 | < | " -->%s in Bend[%d] in %s\n", |
855 | < | current_extra->getlhs(), |
856 | < | j, comp_stamps[stampID]->getID() ); |
857 | < | painCave.isFatal = 1; |
858 | < | simError(); |
311 | > | current_extra = current_extra->getNext(); |
312 | } | |
313 | + | } |
314 | + | |
315 | + | if( !theBends[j].isGhost ){ |
316 | ||
317 | < | current_extra = current_extra->getNext(); |
317 | > | exI = theBends[j].a; |
318 | > | exJ = theBends[j].c; |
319 | } | |
320 | < | } |
320 | > | else{ |
321 | ||
322 | < | if( !theBends[j].isGhost ){ |
323 | < | |
324 | < | exI = theBends[j].a; |
868 | < | exJ = theBends[j].c; |
869 | < | } |
870 | < | else{ |
322 | > | exI = theBends[j].a; |
323 | > | exJ = theBends[j].b; |
324 | > | } |
325 | ||
326 | < | exI = theBends[j].a; |
327 | < | exJ = theBends[j].b; |
328 | < | } |
329 | < | |
330 | < | // exclude_I must always be the smaller of the pair |
331 | < | if( exI > exJ ){ |
326 | > | // exclude_I must always be the smaller of the pair |
327 | > | if( exI > exJ ){ |
328 | > | tempEx = exI; |
329 | > | exI = exJ; |
330 | > | exJ = tempEx; |
331 | > | } |
332 | > | #ifdef IS_MPI |
333 | tempEx = exI; | |
334 | < | exI = exJ; |
335 | < | exJ = tempEx; |
334 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
335 | > | tempEx = exJ; |
336 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
337 | > | |
338 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
339 | > | #else // isn't MPI |
340 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
341 | > | #endif //is_mpi |
342 | } | |
343 | < | #ifdef IS_MPI |
883 | < | tempEx = exI; |
884 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
885 | < | tempEx = exJ; |
886 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
343 | > | excludeOffset += molInfo.nBends; |
344 | ||
345 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
345 | > | for(j=0; j<molInfo.nTorsions; j++){ |
346 | > | |
347 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
348 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
349 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
350 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
351 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
352 | > | |
353 | > | exI = theTorsions[j].a; |
354 | > | exJ = theTorsions[j].d; |
355 | > | |
356 | > | // exclude_I must always be the smaller of the pair |
357 | > | if( exI > exJ ){ |
358 | > | tempEx = exI; |
359 | > | exI = exJ; |
360 | > | exJ = tempEx; |
361 | > | } |
362 | > | #ifdef IS_MPI |
363 | > | tempEx = exI; |
364 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
365 | > | tempEx = exJ; |
366 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
367 | > | |
368 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
369 | #else // isn't MPI | |
370 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
370 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
371 | #endif //is_mpi | |
372 | < | } |
373 | < | excludeOffset += info.nBends; |
894 | < | |
895 | < | for(j=0; j<info.nTorsions; j++){ |
372 | > | } |
373 | > | excludeOffset += molInfo.nTorsions; |
374 | ||
897 | – | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
898 | – | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
899 | – | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
900 | – | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
901 | – | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
375 | ||
376 | < | exI = theTorsions[j].a; |
377 | < | exJ = theTorsions[j].d; |
376 | > | // send the arrays off to the forceField for init. |
377 | > | |
378 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
379 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
380 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
381 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
382 | > | |
383 | > | |
384 | > | info[k].molecules[i].initialize( molInfo ); |
385 | ||
906 | – | // exclude_I must always be the smaller of the pair |
907 | – | if( exI > exJ ){ |
908 | – | tempEx = exI; |
909 | – | exI = exJ; |
910 | – | exJ = tempEx; |
911 | – | } |
912 | – | #ifdef IS_MPI |
913 | – | tempEx = exI; |
914 | – | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
915 | – | tempEx = exJ; |
916 | – | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
386 | ||
387 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
388 | < | #else // isn't MPI |
389 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
390 | < | #endif //is_mpi |
387 | > | atomOffset += molInfo.nAtoms; |
388 | > | delete[] theBonds; |
389 | > | delete[] theBends; |
390 | > | delete[] theTorsions; |
391 | } | |
923 | – | excludeOffset += info.nTorsions; |
924 | – | |
925 | – | |
926 | – | // send the arrays off to the forceField for init. |
927 | – | |
928 | – | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
929 | – | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
930 | – | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
931 | – | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
932 | – | |
933 | – | |
934 | – | the_molecules[i].initialize( info ); |
935 | – | |
936 | – | |
937 | – | atomOffset += info.nAtoms; |
938 | – | delete[] theBonds; |
939 | – | delete[] theBends; |
940 | – | delete[] theTorsions; |
392 | } | |
393 | < | |
393 | > | |
394 | #ifdef IS_MPI | |
395 | sprintf( checkPointMsg, "all molecules initialized succesfully" ); | |
396 | MPIcheckPoint(); | |
397 | #endif // is_mpi | |
398 | < | |
398 | > | |
399 | // clean up the forcefield | |
400 | + | |
401 | the_ff->calcRcut(); | |
402 | the_ff->cleanMe(); | |
403 | < | |
403 | > | |
404 | } | |
405 | ||
406 | void SimSetup::initFromBass( void ){ | |
# | Line 961 | Line 413 | void SimSetup::initFromBass( void ){ | |
413 | int n_extra; | |
414 | int have_extra, done; | |
415 | ||
416 | < | temp1 = (double)tot_nmol / 4.0; |
417 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
418 | < | temp3 = ceil( temp2 ); |
416 | > | double vel[3]; |
417 | > | vel[0] = 0.0; |
418 | > | vel[1] = 0.0; |
419 | > | vel[2] = 0.0; |
420 | ||
421 | + | temp1 = (double)tot_nmol / 4.0; |
422 | + | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
423 | + | temp3 = ceil( temp2 ); |
424 | + | |
425 | have_extra =0; | |
426 | if( temp2 < temp3 ){ // we have a non-complete lattice | |
427 | have_extra =1; | |
428 | ||
429 | n_cells = (int)temp3 - 1; | |
430 | < | cellx = simnfo->box_x / temp3; |
431 | < | celly = simnfo->box_y / temp3; |
432 | < | cellz = simnfo->box_z / temp3; |
430 | > | cellx = info[0].boxL[0] / temp3; |
431 | > | celly = info[0].boxL[1] / temp3; |
432 | > | cellz = info[0].boxL[2] / temp3; |
433 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
434 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
435 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 987 | Line 444 | void SimSetup::initFromBass( void ){ | |
444 | } | |
445 | else{ | |
446 | n_cells = (int)temp3; | |
447 | < | cellx = simnfo->box_x / temp3; |
448 | < | celly = simnfo->box_y / temp3; |
449 | < | cellz = simnfo->box_z / temp3; |
447 | > | cellx = info[0].boxL[0] / temp3; |
448 | > | celly = info[0].boxL[1] / temp3; |
449 | > | cellz = info[0].boxL[2] / temp3; |
450 | } | |
451 | ||
452 | current_mol = 0; | |
# | Line 1068 | Line 525 | void SimSetup::initFromBass( void ){ | |
525 | } | |
526 | } | |
527 | ||
528 | < | |
529 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1073 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1074 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1075 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
528 | > | for( i=0; i<info[0].n_atoms; i++ ){ |
529 | > | info[0].atoms[i]->setVel( vel ); |
530 | } | |
531 | } | |
532 | ||
# | Line 1082 | Line 536 | void SimSetup::makeElement( double x, double y, double | |
536 | AtomStamp* current_atom; | |
537 | DirectionalAtom* dAtom; | |
538 | double rotMat[3][3]; | |
539 | + | double pos[3]; |
540 | ||
541 | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ | |
542 | ||
# | Line 1097 | Line 552 | void SimSetup::makeElement( double x, double y, double | |
552 | painCave.isFatal = 1; | |
553 | simError(); | |
554 | } | |
555 | + | |
556 | + | pos[0] = x + current_atom->getPosX(); |
557 | + | pos[1] = y + current_atom->getPosY(); |
558 | + | pos[2] = z + current_atom->getPosZ(); |
559 | + | |
560 | + | info[0].atoms[current_atom_ndx]->setPos( pos ); |
561 | ||
562 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1102 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1103 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
562 | > | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
563 | ||
564 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
564 | > | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
565 | ||
1107 | – | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1108 | – | |
566 | rotMat[0][0] = 1.0; | |
567 | rotMat[0][1] = 0.0; | |
568 | rotMat[0][2] = 0.0; | |
# | Line 1131 | Line 588 | void SimSetup::makeElement( double x, double y, double | |
588 | ||
589 | current_comp_mol = 0; | |
590 | current_comp++; | |
591 | + | } |
592 | + | } |
593 | + | |
594 | + | |
595 | + | void SimSetup::gatherInfo( void ){ |
596 | + | int i,j,k; |
597 | + | |
598 | + | ensembleCase = -1; |
599 | + | ffCase = -1; |
600 | + | |
601 | + | // set the easy ones first |
602 | + | |
603 | + | for( i=0; i<nInfo; i++){ |
604 | + | info[i].target_temp = globals->getTargetTemp(); |
605 | + | info[i].dt = globals->getDt(); |
606 | + | info[i].run_time = globals->getRunTime(); |
607 | + | } |
608 | + | n_components = globals->getNComponents(); |
609 | + | |
610 | + | |
611 | + | // get the forceField |
612 | + | |
613 | + | strcpy( force_field, globals->getForceField() ); |
614 | + | |
615 | + | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
616 | + | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
617 | + | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
618 | + | else{ |
619 | + | sprintf( painCave.errMsg, |
620 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
621 | + | force_field ); |
622 | + | painCave.isFatal = 1; |
623 | + | simError(); |
624 | + | } |
625 | + | |
626 | + | // get the ensemble |
627 | + | |
628 | + | strcpy( ensemble, globals->getEnsemble() ); |
629 | + | |
630 | + | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
631 | + | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
632 | + | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
633 | + | ensembleCase = NPTi_ENS; |
634 | + | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
635 | + | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
636 | + | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
637 | + | else{ |
638 | + | sprintf( painCave.errMsg, |
639 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
640 | + | "reverting to NVE for this simulation.\n", |
641 | + | ensemble ); |
642 | + | painCave.isFatal = 0; |
643 | + | simError(); |
644 | + | strcpy( ensemble, "NVE" ); |
645 | + | ensembleCase = NVE_ENS; |
646 | + | } |
647 | + | |
648 | + | for(i=0; i<nInfo; i++){ |
649 | + | |
650 | + | strcpy( info[i].ensemble, ensemble ); |
651 | + | |
652 | + | // get the mixing rule |
653 | + | |
654 | + | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
655 | + | info[i].usePBC = globals->getPBC(); |
656 | + | } |
657 | + | |
658 | + | // get the components and calculate the tot_nMol and indvidual n_mol |
659 | + | |
660 | + | the_components = globals->getComponents(); |
661 | + | components_nmol = new int[n_components]; |
662 | + | |
663 | + | |
664 | + | if( !globals->haveNMol() ){ |
665 | + | // we don't have the total number of molecules, so we assume it is |
666 | + | // given in each component |
667 | + | |
668 | + | tot_nmol = 0; |
669 | + | for( i=0; i<n_components; i++ ){ |
670 | + | |
671 | + | if( !the_components[i]->haveNMol() ){ |
672 | + | // we have a problem |
673 | + | sprintf( painCave.errMsg, |
674 | + | "SimSetup Error. No global NMol or component NMol" |
675 | + | " given. Cannot calculate the number of atoms.\n" ); |
676 | + | painCave.isFatal = 1; |
677 | + | simError(); |
678 | + | } |
679 | + | |
680 | + | tot_nmol += the_components[i]->getNMol(); |
681 | + | components_nmol[i] = the_components[i]->getNMol(); |
682 | + | } |
683 | + | } |
684 | + | else{ |
685 | + | sprintf( painCave.errMsg, |
686 | + | "SimSetup error.\n" |
687 | + | "\tSorry, the ability to specify total" |
688 | + | " nMols and then give molfractions in the components\n" |
689 | + | "\tis not currently supported." |
690 | + | " Please give nMol in the components.\n" ); |
691 | + | painCave.isFatal = 1; |
692 | + | simError(); |
693 | + | } |
694 | + | |
695 | + | // set the status, sample, and thermal kick times |
696 | + | |
697 | + | for(i=0; i<nInfo; i++){ |
698 | + | |
699 | + | if( globals->haveSampleTime() ){ |
700 | + | info[i].sampleTime = globals->getSampleTime(); |
701 | + | info[i].statusTime = info[i].sampleTime; |
702 | + | info[i].thermalTime = info[i].sampleTime; |
703 | + | } |
704 | + | else{ |
705 | + | info[i].sampleTime = globals->getRunTime(); |
706 | + | info[i].statusTime = info[i].sampleTime; |
707 | + | info[i].thermalTime = info[i].sampleTime; |
708 | + | } |
709 | + | |
710 | + | if( globals->haveStatusTime() ){ |
711 | + | info[i].statusTime = globals->getStatusTime(); |
712 | + | } |
713 | + | |
714 | + | if( globals->haveThermalTime() ){ |
715 | + | info[i].thermalTime = globals->getThermalTime(); |
716 | + | } |
717 | + | |
718 | + | // check for the temperature set flag |
719 | + | |
720 | + | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
721 | + | |
722 | + | // get some of the tricky things that may still be in the globals |
723 | + | |
724 | + | double boxVector[3]; |
725 | + | if( globals->haveBox() ){ |
726 | + | boxVector[0] = globals->getBox(); |
727 | + | boxVector[1] = globals->getBox(); |
728 | + | boxVector[2] = globals->getBox(); |
729 | + | |
730 | + | info[i].setBox( boxVector ); |
731 | + | } |
732 | + | else if( globals->haveDensity() ){ |
733 | + | |
734 | + | double vol; |
735 | + | vol = (double)tot_nmol / globals->getDensity(); |
736 | + | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
737 | + | boxVector[1] = boxVector[0]; |
738 | + | boxVector[2] = boxVector[0]; |
739 | + | |
740 | + | info[i].setBox( boxVector ); |
741 | + | } |
742 | + | else{ |
743 | + | if( !globals->haveBoxX() ){ |
744 | + | sprintf( painCave.errMsg, |
745 | + | "SimSetup error, no periodic BoxX size given.\n" ); |
746 | + | painCave.isFatal = 1; |
747 | + | simError(); |
748 | + | } |
749 | + | boxVector[0] = globals->getBoxX(); |
750 | + | |
751 | + | if( !globals->haveBoxY() ){ |
752 | + | sprintf( painCave.errMsg, |
753 | + | "SimSetup error, no periodic BoxY size given.\n" ); |
754 | + | painCave.isFatal = 1; |
755 | + | simError(); |
756 | + | } |
757 | + | boxVector[1] = globals->getBoxY(); |
758 | + | |
759 | + | if( !globals->haveBoxZ() ){ |
760 | + | sprintf( painCave.errMsg, |
761 | + | "SimSetup error, no periodic BoxZ size given.\n" ); |
762 | + | painCave.isFatal = 1; |
763 | + | simError(); |
764 | + | } |
765 | + | boxVector[2] = globals->getBoxZ(); |
766 | + | |
767 | + | info[i].setBox( boxVector ); |
768 | + | } |
769 | + | |
770 | + | } |
771 | + | |
772 | + | #ifdef IS_MPI |
773 | + | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
774 | + | MPIcheckPoint(); |
775 | + | #endif // is_mpi |
776 | + | |
777 | + | } |
778 | + | |
779 | + | |
780 | + | void SimSetup::finalInfoCheck( void ){ |
781 | + | int index; |
782 | + | int usesDipoles; |
783 | + | int i; |
784 | + | |
785 | + | for(i=0; i<nInfo; i++){ |
786 | + | // check electrostatic parameters |
787 | + | |
788 | + | index = 0; |
789 | + | usesDipoles = 0; |
790 | + | while( (index < info[i].n_atoms) && !usesDipoles ){ |
791 | + | usesDipoles = (info[i].atoms[index])->hasDipole(); |
792 | + | index++; |
793 | + | } |
794 | + | |
795 | + | #ifdef IS_MPI |
796 | + | int myUse = usesDipoles; |
797 | + | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
798 | + | #endif //is_mpi |
799 | + | |
800 | + | double theEcr, theEst; |
801 | + | |
802 | + | if (globals->getUseRF() ) { |
803 | + | info[i].useReactionField = 1; |
804 | + | |
805 | + | if( !globals->haveECR() ){ |
806 | + | sprintf( painCave.errMsg, |
807 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
808 | + | "box length for the electrostaticCutoffRadius.\n" |
809 | + | "I hope you have a very fast processor!\n"); |
810 | + | painCave.isFatal = 0; |
811 | + | simError(); |
812 | + | double smallest; |
813 | + | smallest = info[i].boxL[0]; |
814 | + | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
815 | + | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
816 | + | theEcr = 0.5 * smallest; |
817 | + | } else { |
818 | + | theEcr = globals->getECR(); |
819 | + | } |
820 | + | |
821 | + | if( !globals->haveEST() ){ |
822 | + | sprintf( painCave.errMsg, |
823 | + | "SimSetup Warning: using default value of 0.05 * the " |
824 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 | + | ); |
826 | + | painCave.isFatal = 0; |
827 | + | simError(); |
828 | + | theEst = 0.05 * theEcr; |
829 | + | } else { |
830 | + | theEst= globals->getEST(); |
831 | + | } |
832 | + | |
833 | + | info[i].setEcr( theEcr, theEst ); |
834 | + | |
835 | + | if(!globals->haveDielectric() ){ |
836 | + | sprintf( painCave.errMsg, |
837 | + | "SimSetup Error: You are trying to use Reaction Field without" |
838 | + | "setting a dielectric constant!\n" |
839 | + | ); |
840 | + | painCave.isFatal = 1; |
841 | + | simError(); |
842 | + | } |
843 | + | info[i].dielectric = globals->getDielectric(); |
844 | + | } |
845 | + | else { |
846 | + | if (usesDipoles) { |
847 | + | |
848 | + | if( !globals->haveECR() ){ |
849 | + | sprintf( painCave.errMsg, |
850 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
851 | + | "box length for the electrostaticCutoffRadius.\n" |
852 | + | "I hope you have a very fast processor!\n"); |
853 | + | painCave.isFatal = 0; |
854 | + | simError(); |
855 | + | double smallest; |
856 | + | smallest = info[i].boxL[0]; |
857 | + | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
858 | + | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
859 | + | theEcr = 0.5 * smallest; |
860 | + | } else { |
861 | + | theEcr = globals->getECR(); |
862 | + | } |
863 | + | |
864 | + | if( !globals->haveEST() ){ |
865 | + | sprintf( painCave.errMsg, |
866 | + | "SimSetup Warning: using default value of 0.05 * the " |
867 | + | "electrostaticCutoffRadius for the " |
868 | + | "electrostaticSkinThickness\n" |
869 | + | ); |
870 | + | painCave.isFatal = 0; |
871 | + | simError(); |
872 | + | theEst = 0.05 * theEcr; |
873 | + | } else { |
874 | + | theEst= globals->getEST(); |
875 | + | } |
876 | + | |
877 | + | info[i].setEcr( theEcr, theEst ); |
878 | + | } |
879 | + | } |
880 | } | |
881 | + | |
882 | + | #ifdef IS_MPI |
883 | + | strcpy( checkPointMsg, "post processing checks out" ); |
884 | + | MPIcheckPoint(); |
885 | + | #endif // is_mpi |
886 | + | |
887 | } | |
888 | + | |
889 | + | void SimSetup::initSystemCoords( void ){ |
890 | + | int i; |
891 | + | |
892 | + | char* inName; |
893 | + | |
894 | + | |
895 | + | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
896 | + | |
897 | + | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
898 | + | |
899 | + | if( globals->haveInitialConfig() ){ |
900 | + | |
901 | + | InitializeFromFile* fileInit; |
902 | + | #ifdef IS_MPI // is_mpi |
903 | + | if( worldRank == 0 ){ |
904 | + | #endif //is_mpi |
905 | + | inName = globals->getInitialConfig(); |
906 | + | fileInit = new InitializeFromFile( inName ); |
907 | + | #ifdef IS_MPI |
908 | + | }else fileInit = new InitializeFromFile( NULL ); |
909 | + | #endif |
910 | + | fileInit->readInit( info ); // default velocities on |
911 | + | |
912 | + | delete fileInit; |
913 | + | } |
914 | + | else{ |
915 | + | |
916 | + | #ifdef IS_MPI |
917 | + | |
918 | + | // no init from bass |
919 | + | |
920 | + | sprintf( painCave.errMsg, |
921 | + | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
922 | + | painCave.isFatal; |
923 | + | simError(); |
924 | + | |
925 | + | #else |
926 | + | |
927 | + | initFromBass(); |
928 | + | |
929 | + | |
930 | + | #endif |
931 | + | } |
932 | + | |
933 | + | #ifdef IS_MPI |
934 | + | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
935 | + | MPIcheckPoint(); |
936 | + | #endif // is_mpi |
937 | + | |
938 | + | } |
939 | + | |
940 | + | |
941 | + | void SimSetup::makeOutNames( void ){ |
942 | + | |
943 | + | int k; |
944 | + | |
945 | + | |
946 | + | for(k=0; k<nInfo; k++){ |
947 | + | |
948 | + | #ifdef IS_MPI |
949 | + | if( worldRank == 0 ){ |
950 | + | #endif // is_mpi |
951 | + | |
952 | + | if( globals->haveFinalConfig() ){ |
953 | + | strcpy( info[k].finalName, globals->getFinalConfig() ); |
954 | + | } |
955 | + | else{ |
956 | + | strcpy( info[k].finalName, inFileName ); |
957 | + | char* endTest; |
958 | + | int nameLength = strlen( info[k].finalName ); |
959 | + | endTest = &(info[k].finalName[nameLength - 5]); |
960 | + | if( !strcmp( endTest, ".bass" ) ){ |
961 | + | strcpy( endTest, ".eor" ); |
962 | + | } |
963 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
964 | + | strcpy( endTest, ".eor" ); |
965 | + | } |
966 | + | else{ |
967 | + | endTest = &(info[k].finalName[nameLength - 4]); |
968 | + | if( !strcmp( endTest, ".bss" ) ){ |
969 | + | strcpy( endTest, ".eor" ); |
970 | + | } |
971 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
972 | + | strcpy( endTest, ".eor" ); |
973 | + | } |
974 | + | else{ |
975 | + | strcat( info[k].finalName, ".eor" ); |
976 | + | } |
977 | + | } |
978 | + | } |
979 | + | |
980 | + | // make the sample and status out names |
981 | + | |
982 | + | strcpy( info[k].sampleName, inFileName ); |
983 | + | char* endTest; |
984 | + | int nameLength = strlen( info[k].sampleName ); |
985 | + | endTest = &(info[k].sampleName[nameLength - 5]); |
986 | + | if( !strcmp( endTest, ".bass" ) ){ |
987 | + | strcpy( endTest, ".dump" ); |
988 | + | } |
989 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
990 | + | strcpy( endTest, ".dump" ); |
991 | + | } |
992 | + | else{ |
993 | + | endTest = &(info[k].sampleName[nameLength - 4]); |
994 | + | if( !strcmp( endTest, ".bss" ) ){ |
995 | + | strcpy( endTest, ".dump" ); |
996 | + | } |
997 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
998 | + | strcpy( endTest, ".dump" ); |
999 | + | } |
1000 | + | else{ |
1001 | + | strcat( info[k].sampleName, ".dump" ); |
1002 | + | } |
1003 | + | } |
1004 | + | |
1005 | + | strcpy( info[k].statusName, inFileName ); |
1006 | + | nameLength = strlen( info[k].statusName ); |
1007 | + | endTest = &(info[k].statusName[nameLength - 5]); |
1008 | + | if( !strcmp( endTest, ".bass" ) ){ |
1009 | + | strcpy( endTest, ".stat" ); |
1010 | + | } |
1011 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
1012 | + | strcpy( endTest, ".stat" ); |
1013 | + | } |
1014 | + | else{ |
1015 | + | endTest = &(info[k].statusName[nameLength - 4]); |
1016 | + | if( !strcmp( endTest, ".bss" ) ){ |
1017 | + | strcpy( endTest, ".stat" ); |
1018 | + | } |
1019 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
1020 | + | strcpy( endTest, ".stat" ); |
1021 | + | } |
1022 | + | else{ |
1023 | + | strcat( info[k].statusName, ".stat" ); |
1024 | + | } |
1025 | + | } |
1026 | + | |
1027 | + | #ifdef IS_MPI |
1028 | + | } |
1029 | + | #endif // is_mpi |
1030 | + | } |
1031 | + | } |
1032 | + | |
1033 | + | |
1034 | + | void SimSetup::sysObjectsCreation( void ){ |
1035 | + | |
1036 | + | int i,k; |
1037 | + | |
1038 | + | // create the forceField |
1039 | + | |
1040 | + | createFF(); |
1041 | + | |
1042 | + | // extract componentList |
1043 | + | |
1044 | + | compList(); |
1045 | + | |
1046 | + | // calc the number of atoms, bond, bends, and torsions |
1047 | + | |
1048 | + | calcSysValues(); |
1049 | + | |
1050 | + | #ifdef IS_MPI |
1051 | + | // divide the molecules among the processors |
1052 | + | |
1053 | + | mpiMolDivide(); |
1054 | + | #endif //is_mpi |
1055 | + | |
1056 | + | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1057 | + | |
1058 | + | makeSysArrays(); |
1059 | + | |
1060 | + | // make and initialize the molecules (all but atomic coordinates) |
1061 | + | |
1062 | + | makeMolecules(); |
1063 | + | |
1064 | + | for(k=0; k<nInfo; k++){ |
1065 | + | info[k].identArray = new int[info[k].n_atoms]; |
1066 | + | for(i=0; i<info[k].n_atoms; i++){ |
1067 | + | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1068 | + | } |
1069 | + | } |
1070 | + | } |
1071 | + | |
1072 | + | |
1073 | + | void SimSetup::createFF( void ){ |
1074 | + | |
1075 | + | switch( ffCase ){ |
1076 | + | |
1077 | + | case FF_DUFF: |
1078 | + | the_ff = new DUFF(); |
1079 | + | break; |
1080 | + | |
1081 | + | case FF_LJ: |
1082 | + | the_ff = new LJFF(); |
1083 | + | break; |
1084 | + | |
1085 | + | case FF_EAM: |
1086 | + | the_ff = new EAM_FF(); |
1087 | + | break; |
1088 | + | |
1089 | + | default: |
1090 | + | sprintf( painCave.errMsg, |
1091 | + | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1092 | + | painCave.isFatal = 1; |
1093 | + | simError(); |
1094 | + | } |
1095 | + | |
1096 | + | #ifdef IS_MPI |
1097 | + | strcpy( checkPointMsg, "ForceField creation successful" ); |
1098 | + | MPIcheckPoint(); |
1099 | + | #endif // is_mpi |
1100 | + | |
1101 | + | } |
1102 | + | |
1103 | + | |
1104 | + | void SimSetup::compList( void ){ |
1105 | + | |
1106 | + | int i; |
1107 | + | char* id; |
1108 | + | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1109 | + | LinkedMolStamp* currentStamp = NULL; |
1110 | + | comp_stamps = new MoleculeStamp*[n_components]; |
1111 | + | |
1112 | + | // make an array of molecule stamps that match the components used. |
1113 | + | // also extract the used stamps out into a separate linked list |
1114 | + | |
1115 | + | for(i=0; i<nInfo; i++){ |
1116 | + | info[i].nComponents = n_components; |
1117 | + | info[i].componentsNmol = components_nmol; |
1118 | + | info[i].compStamps = comp_stamps; |
1119 | + | info[i].headStamp = headStamp; |
1120 | + | } |
1121 | + | |
1122 | + | |
1123 | + | for( i=0; i<n_components; i++ ){ |
1124 | + | |
1125 | + | id = the_components[i]->getType(); |
1126 | + | comp_stamps[i] = NULL; |
1127 | + | |
1128 | + | // check to make sure the component isn't already in the list |
1129 | + | |
1130 | + | comp_stamps[i] = headStamp->match( id ); |
1131 | + | if( comp_stamps[i] == NULL ){ |
1132 | + | |
1133 | + | // extract the component from the list; |
1134 | + | |
1135 | + | currentStamp = stamps->extractMolStamp( id ); |
1136 | + | if( currentStamp == NULL ){ |
1137 | + | sprintf( painCave.errMsg, |
1138 | + | "SimSetup error: Component \"%s\" was not found in the " |
1139 | + | "list of declared molecules\n", |
1140 | + | id ); |
1141 | + | painCave.isFatal = 1; |
1142 | + | simError(); |
1143 | + | } |
1144 | + | |
1145 | + | headStamp->add( currentStamp ); |
1146 | + | comp_stamps[i] = headStamp->match( id ); |
1147 | + | } |
1148 | + | } |
1149 | + | |
1150 | + | #ifdef IS_MPI |
1151 | + | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1152 | + | MPIcheckPoint(); |
1153 | + | #endif // is_mpi |
1154 | + | |
1155 | + | |
1156 | + | } |
1157 | + | |
1158 | + | void SimSetup::calcSysValues( void ){ |
1159 | + | int i, j, k; |
1160 | + | |
1161 | + | int *molMembershipArray; |
1162 | + | |
1163 | + | tot_atoms = 0; |
1164 | + | tot_bonds = 0; |
1165 | + | tot_bends = 0; |
1166 | + | tot_torsions = 0; |
1167 | + | for( i=0; i<n_components; i++ ){ |
1168 | + | |
1169 | + | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1170 | + | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1171 | + | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1172 | + | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1173 | + | } |
1174 | + | |
1175 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1176 | + | molMembershipArray = new int[tot_atoms]; |
1177 | + | |
1178 | + | for(i=0; i<nInfo; i++){ |
1179 | + | info[i].n_atoms = tot_atoms; |
1180 | + | info[i].n_bonds = tot_bonds; |
1181 | + | info[i].n_bends = tot_bends; |
1182 | + | info[i].n_torsions = tot_torsions; |
1183 | + | info[i].n_SRI = tot_SRI; |
1184 | + | info[i].n_mol = tot_nmol; |
1185 | + | |
1186 | + | info[i].molMembershipArray = molMembershipArray; |
1187 | + | } |
1188 | + | } |
1189 | + | |
1190 | + | #ifdef IS_MPI |
1191 | + | |
1192 | + | void SimSetup::mpiMolDivide( void ){ |
1193 | + | |
1194 | + | int i, j, k; |
1195 | + | int localMol, allMol; |
1196 | + | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1197 | + | |
1198 | + | mpiSim = new mpiSimulation( info ); |
1199 | + | |
1200 | + | globalIndex = mpiSim->divideLabor(); |
1201 | + | |
1202 | + | // set up the local variables |
1203 | + | |
1204 | + | mol2proc = mpiSim->getMolToProcMap(); |
1205 | + | molCompType = mpiSim->getMolComponentType(); |
1206 | + | |
1207 | + | allMol = 0; |
1208 | + | localMol = 0; |
1209 | + | local_atoms = 0; |
1210 | + | local_bonds = 0; |
1211 | + | local_bends = 0; |
1212 | + | local_torsions = 0; |
1213 | + | globalAtomIndex = 0; |
1214 | + | |
1215 | + | |
1216 | + | for( i=0; i<n_components; i++ ){ |
1217 | + | |
1218 | + | for( j=0; j<components_nmol[i]; j++ ){ |
1219 | + | |
1220 | + | if( mol2proc[allMol] == worldRank ){ |
1221 | + | |
1222 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1223 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1224 | + | local_bends += comp_stamps[i]->getNBends(); |
1225 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1226 | + | localMol++; |
1227 | + | } |
1228 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1229 | + | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1230 | + | globalAtomIndex++; |
1231 | + | } |
1232 | + | |
1233 | + | allMol++; |
1234 | + | } |
1235 | + | } |
1236 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1237 | + | |
1238 | + | info[0].n_atoms = mpiSim->getMyNlocal(); |
1239 | + | |
1240 | + | if( local_atoms != info[0].n_atoms ){ |
1241 | + | sprintf( painCave.errMsg, |
1242 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1243 | + | " localAtom (%d) are not equal.\n", |
1244 | + | info[0].n_atoms, |
1245 | + | local_atoms ); |
1246 | + | painCave.isFatal = 1; |
1247 | + | simError(); |
1248 | + | } |
1249 | + | |
1250 | + | info[0].n_bonds = local_bonds; |
1251 | + | info[0].n_bends = local_bends; |
1252 | + | info[0].n_torsions = local_torsions; |
1253 | + | info[0].n_SRI = local_SRI; |
1254 | + | info[0].n_mol = localMol; |
1255 | + | |
1256 | + | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1257 | + | MPIcheckPoint(); |
1258 | + | } |
1259 | + | |
1260 | + | #endif // is_mpi |
1261 | + | |
1262 | + | |
1263 | + | void SimSetup::makeSysArrays( void ){ |
1264 | + | int i, j, k, l; |
1265 | + | |
1266 | + | Atom** the_atoms; |
1267 | + | Molecule* the_molecules; |
1268 | + | Exclude** the_excludes; |
1269 | + | |
1270 | + | |
1271 | + | for(l=0; l<nInfo; l++){ |
1272 | + | |
1273 | + | // create the atom and short range interaction arrays |
1274 | + | |
1275 | + | the_atoms = new Atom*[info[l].n_atoms]; |
1276 | + | the_molecules = new Molecule[info[l].n_mol]; |
1277 | + | int molIndex; |
1278 | + | |
1279 | + | // initialize the molecule's stampID's |
1280 | + | |
1281 | + | #ifdef IS_MPI |
1282 | + | |
1283 | + | |
1284 | + | molIndex = 0; |
1285 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1286 | + | |
1287 | + | if(mol2proc[i] == worldRank ){ |
1288 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
1289 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1290 | + | the_molecules[molIndex].setGlobalIndex( i ); |
1291 | + | molIndex++; |
1292 | + | } |
1293 | + | } |
1294 | + | |
1295 | + | #else // is_mpi |
1296 | + | |
1297 | + | molIndex = 0; |
1298 | + | globalAtomIndex = 0; |
1299 | + | for(i=0; i<n_components; i++){ |
1300 | + | for(j=0; j<components_nmol[i]; j++ ){ |
1301 | + | the_molecules[molIndex].setStampID( i ); |
1302 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1303 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1304 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1305 | + | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1306 | + | globalAtomIndex++; |
1307 | + | } |
1308 | + | molIndex++; |
1309 | + | } |
1310 | + | } |
1311 | + | |
1312 | + | |
1313 | + | #endif // is_mpi |
1314 | + | |
1315 | + | |
1316 | + | if( info[l].n_SRI ){ |
1317 | + | |
1318 | + | Exclude::createArray(info[l].n_SRI); |
1319 | + | the_excludes = new Exclude*[info[l].n_SRI]; |
1320 | + | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1321 | + | the_excludes[ex] = new Exclude(ex); |
1322 | + | } |
1323 | + | info[l].globalExcludes = new int; |
1324 | + | info[l].n_exclude = info[l].n_SRI; |
1325 | + | } |
1326 | + | else{ |
1327 | + | |
1328 | + | Exclude::createArray( 1 ); |
1329 | + | the_excludes = new Exclude*; |
1330 | + | the_excludes[0] = new Exclude(0); |
1331 | + | the_excludes[0]->setPair( 0,0 ); |
1332 | + | info[l].globalExcludes = new int; |
1333 | + | info[l].globalExcludes[0] = 0; |
1334 | + | info[l].n_exclude = 0; |
1335 | + | } |
1336 | + | |
1337 | + | // set the arrays into the SimInfo object |
1338 | + | |
1339 | + | info[l].atoms = the_atoms; |
1340 | + | info[l].molecules = the_molecules; |
1341 | + | info[l].nGlobalExcludes = 0; |
1342 | + | info[l].excludes = the_excludes; |
1343 | + | |
1344 | + | the_ff->setSimInfo( info ); |
1345 | + | |
1346 | + | } |
1347 | + | } |
1348 | + | |
1349 | + | void SimSetup::makeIntegrator( void ){ |
1350 | + | |
1351 | + | int k; |
1352 | + | |
1353 | + | NVT<RealIntegrator>* myNVT = NULL; |
1354 | + | NPTi<RealIntegrator>* myNPTi = NULL; |
1355 | + | NPTf<RealIntegrator>* myNPTf = NULL; |
1356 | + | NPTim<RealIntegrator>* myNPTim = NULL; |
1357 | + | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1358 | + | |
1359 | + | for(k=0; k<nInfo; k++){ |
1360 | + | |
1361 | + | switch( ensembleCase ){ |
1362 | + | |
1363 | + | case NVE_ENS: |
1364 | + | if (globals->haveZconstraints()){ |
1365 | + | setupZConstraint(info[k]); |
1366 | + | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1367 | + | } |
1368 | + | |
1369 | + | else |
1370 | + | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1371 | + | break; |
1372 | + | |
1373 | + | case NVT_ENS: |
1374 | + | if (globals->haveZconstraints()){ |
1375 | + | setupZConstraint(info[k]); |
1376 | + | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1377 | + | } |
1378 | + | else |
1379 | + | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1380 | + | |
1381 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1382 | + | |
1383 | + | if (globals->haveTauThermostat()) |
1384 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1385 | + | |
1386 | + | else { |
1387 | + | sprintf( painCave.errMsg, |
1388 | + | "SimSetup error: If you use the NVT\n" |
1389 | + | " ensemble, you must set tauThermostat.\n"); |
1390 | + | painCave.isFatal = 1; |
1391 | + | simError(); |
1392 | + | } |
1393 | + | break; |
1394 | + | |
1395 | + | case NPTi_ENS: |
1396 | + | if (globals->haveZconstraints()){ |
1397 | + | setupZConstraint(info[k]); |
1398 | + | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1399 | + | } |
1400 | + | else |
1401 | + | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1402 | + | |
1403 | + | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1404 | + | |
1405 | + | if (globals->haveTargetPressure()) |
1406 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1407 | + | else { |
1408 | + | sprintf( painCave.errMsg, |
1409 | + | "SimSetup error: If you use a constant pressure\n" |
1410 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1411 | + | painCave.isFatal = 1; |
1412 | + | simError(); |
1413 | + | } |
1414 | + | |
1415 | + | if( globals->haveTauThermostat() ) |
1416 | + | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1417 | + | else{ |
1418 | + | sprintf( painCave.errMsg, |
1419 | + | "SimSetup error: If you use an NPT\n" |
1420 | + | " ensemble, you must set tauThermostat.\n"); |
1421 | + | painCave.isFatal = 1; |
1422 | + | simError(); |
1423 | + | } |
1424 | + | |
1425 | + | if( globals->haveTauBarostat() ) |
1426 | + | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1427 | + | else{ |
1428 | + | sprintf( painCave.errMsg, |
1429 | + | "SimSetup error: If you use an NPT\n" |
1430 | + | " ensemble, you must set tauBarostat.\n"); |
1431 | + | painCave.isFatal = 1; |
1432 | + | simError(); |
1433 | + | } |
1434 | + | break; |
1435 | + | |
1436 | + | case NPTf_ENS: |
1437 | + | if (globals->haveZconstraints()){ |
1438 | + | setupZConstraint(info[k]); |
1439 | + | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1440 | + | } |
1441 | + | else |
1442 | + | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1443 | + | |
1444 | + | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1445 | + | |
1446 | + | if (globals->haveTargetPressure()) |
1447 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1448 | + | else { |
1449 | + | sprintf( painCave.errMsg, |
1450 | + | "SimSetup error: If you use a constant pressure\n" |
1451 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1452 | + | painCave.isFatal = 1; |
1453 | + | simError(); |
1454 | + | } |
1455 | + | |
1456 | + | if( globals->haveTauThermostat() ) |
1457 | + | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1458 | + | else{ |
1459 | + | sprintf( painCave.errMsg, |
1460 | + | "SimSetup error: If you use an NPT\n" |
1461 | + | " ensemble, you must set tauThermostat.\n"); |
1462 | + | painCave.isFatal = 1; |
1463 | + | simError(); |
1464 | + | } |
1465 | + | |
1466 | + | if( globals->haveTauBarostat() ) |
1467 | + | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1468 | + | else{ |
1469 | + | sprintf( painCave.errMsg, |
1470 | + | "SimSetup error: If you use an NPT\n" |
1471 | + | " ensemble, you must set tauBarostat.\n"); |
1472 | + | painCave.isFatal = 1; |
1473 | + | simError(); |
1474 | + | } |
1475 | + | break; |
1476 | + | |
1477 | + | case NPTim_ENS: |
1478 | + | if (globals->haveZconstraints()){ |
1479 | + | setupZConstraint(info[k]); |
1480 | + | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1481 | + | } |
1482 | + | else |
1483 | + | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1484 | + | |
1485 | + | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1486 | + | |
1487 | + | if (globals->haveTargetPressure()) |
1488 | + | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1489 | + | else { |
1490 | + | sprintf( painCave.errMsg, |
1491 | + | "SimSetup error: If you use a constant pressure\n" |
1492 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1493 | + | painCave.isFatal = 1; |
1494 | + | simError(); |
1495 | + | } |
1496 | + | |
1497 | + | if( globals->haveTauThermostat() ) |
1498 | + | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1499 | + | else{ |
1500 | + | sprintf( painCave.errMsg, |
1501 | + | "SimSetup error: If you use an NPT\n" |
1502 | + | " ensemble, you must set tauThermostat.\n"); |
1503 | + | painCave.isFatal = 1; |
1504 | + | simError(); |
1505 | + | } |
1506 | + | |
1507 | + | if( globals->haveTauBarostat() ) |
1508 | + | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1509 | + | else{ |
1510 | + | sprintf( painCave.errMsg, |
1511 | + | "SimSetup error: If you use an NPT\n" |
1512 | + | " ensemble, you must set tauBarostat.\n"); |
1513 | + | painCave.isFatal = 1; |
1514 | + | simError(); |
1515 | + | } |
1516 | + | break; |
1517 | + | |
1518 | + | case NPTfm_ENS: |
1519 | + | if (globals->haveZconstraints()){ |
1520 | + | setupZConstraint(info[k]); |
1521 | + | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1522 | + | } |
1523 | + | else |
1524 | + | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1525 | + | |
1526 | + | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1527 | + | |
1528 | + | if (globals->haveTargetPressure()) |
1529 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1530 | + | else { |
1531 | + | sprintf( painCave.errMsg, |
1532 | + | "SimSetup error: If you use a constant pressure\n" |
1533 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1534 | + | painCave.isFatal = 1; |
1535 | + | simError(); |
1536 | + | } |
1537 | + | |
1538 | + | if( globals->haveTauThermostat() ) |
1539 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1540 | + | else{ |
1541 | + | sprintf( painCave.errMsg, |
1542 | + | "SimSetup error: If you use an NPT\n" |
1543 | + | " ensemble, you must set tauThermostat.\n"); |
1544 | + | painCave.isFatal = 1; |
1545 | + | simError(); |
1546 | + | } |
1547 | + | |
1548 | + | if( globals->haveTauBarostat() ) |
1549 | + | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1550 | + | else{ |
1551 | + | sprintf( painCave.errMsg, |
1552 | + | "SimSetup error: If you use an NPT\n" |
1553 | + | " ensemble, you must set tauBarostat.\n"); |
1554 | + | painCave.isFatal = 1; |
1555 | + | simError(); |
1556 | + | } |
1557 | + | break; |
1558 | + | |
1559 | + | default: |
1560 | + | sprintf( painCave.errMsg, |
1561 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1562 | + | painCave.isFatal = 1; |
1563 | + | simError(); |
1564 | + | } |
1565 | + | } |
1566 | + | } |
1567 | + | |
1568 | + | void SimSetup::initFortran( void ){ |
1569 | + | |
1570 | + | info[0].refreshSim(); |
1571 | + | |
1572 | + | if( !strcmp( info[0].mixingRule, "standard") ){ |
1573 | + | the_ff->initForceField( LB_MIXING_RULE ); |
1574 | + | } |
1575 | + | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1576 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1577 | + | } |
1578 | + | else{ |
1579 | + | sprintf( painCave.errMsg, |
1580 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1581 | + | info[0].mixingRule ); |
1582 | + | painCave.isFatal = 1; |
1583 | + | simError(); |
1584 | + | } |
1585 | + | |
1586 | + | |
1587 | + | #ifdef IS_MPI |
1588 | + | strcpy( checkPointMsg, |
1589 | + | "Successfully intialized the mixingRule for Fortran." ); |
1590 | + | MPIcheckPoint(); |
1591 | + | #endif // is_mpi |
1592 | + | |
1593 | + | } |
1594 | + | |
1595 | + | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1596 | + | { |
1597 | + | int nZConstraints; |
1598 | + | ZconStamp** zconStamp; |
1599 | + | |
1600 | + | if(globals->haveZconstraintTime()){ |
1601 | + | |
1602 | + | //add sample time of z-constraint into SimInfo's property list |
1603 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1604 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
1605 | + | zconsTimeProp->setData(globals->getZconsTime()); |
1606 | + | theInfo.addProperty(zconsTimeProp); |
1607 | + | } |
1608 | + | else{ |
1609 | + | sprintf( painCave.errMsg, |
1610 | + | "ZConstraint error: If you use an ZConstraint\n" |
1611 | + | " , you must set sample time.\n"); |
1612 | + | painCave.isFatal = 1; |
1613 | + | simError(); |
1614 | + | } |
1615 | + | |
1616 | + | // |
1617 | + | nZConstraints = globals->getNzConstraints(); |
1618 | + | zconStamp = globals->getZconStamp(); |
1619 | + | ZConsParaItem tempParaItem; |
1620 | + | |
1621 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1622 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1623 | + | |
1624 | + | for(int i = 0; i < nZConstraints; i++){ |
1625 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1626 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1627 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1628 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1629 | + | |
1630 | + | zconsParaData->addItem(tempParaItem); |
1631 | + | } |
1632 | + | |
1633 | + | //sort the parameters by index of molecules |
1634 | + | zconsParaData->sortByIndex(); |
1635 | + | |
1636 | + | //push data into siminfo, therefore, we can retrieve later |
1637 | + | theInfo.addProperty(zconsParaData); |
1638 | + | |
1639 | + | //push zconsTol into siminfo, if user does not specify |
1640 | + | //value for zconsTol, a default value will be used |
1641 | + | DoubleData* zconsTol = new DoubleData(); |
1642 | + | zconsTol->setID(ZCONSTOL_ID); |
1643 | + | if(globals->haveZconsTol()){ |
1644 | + | zconsTol->setData(globals->getZconsTol()); |
1645 | + | } |
1646 | + | else{ |
1647 | + | double defaultZConsTol = 1E-6; |
1648 | + | sprintf( painCave.errMsg, |
1649 | + | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1650 | + | " , default value %f is used.\n", defaultZConsTol); |
1651 | + | painCave.isFatal = 0; |
1652 | + | simError(); |
1653 | + | |
1654 | + | zconsTol->setData(defaultZConsTol); |
1655 | + | } |
1656 | + | theInfo.addProperty(zconsTol); |
1657 | + | |
1658 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1659 | + | //Be careful, do not use inFileName, since it is a pointer which |
1660 | + | //point to a string at master node, and slave nodes do not contain that string |
1661 | + | |
1662 | + | string zconsOutput(theInfo.finalName); |
1663 | + | |
1664 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1665 | + | |
1666 | + | StringData* zconsFilename = new StringData(); |
1667 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
1668 | + | zconsFilename->setData(zconsOutput); |
1669 | + | |
1670 | + | theInfo.addProperty(zconsFilename); |
1671 | + | } |
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