# | Line 12 | Line 12 | |
---|---|---|
12 | #include "mpiSimulation.hpp" | |
13 | #endif | |
14 | ||
15 | + | // some defines for ensemble and Forcefield cases |
16 | + | |
17 | + | #define NVE_ENS 0 |
18 | + | #define NVT_ENS 1 |
19 | + | #define NPTi_ENS 2 |
20 | + | #define NPTf_ENS 3 |
21 | + | #define NPTim_ENS 4 |
22 | + | #define NPTfm_ENS 5 |
23 | + | |
24 | + | |
25 | + | #define FF_DUFF 0 |
26 | + | #define FF_LJ 1 |
27 | + | |
28 | + | |
29 | SimSetup::SimSetup(){ | |
30 | stamps = new MakeStamps(); | |
31 | globals = new Globals(); | |
# | Line 64 | Line 78 | void SimSetup::createSim( void ){ | |
78 | ||
79 | void SimSetup::createSim( void ){ | |
80 | ||
81 | < | MakeStamps *the_stamps; |
68 | < | Globals* the_globals; |
69 | < | ExtendedSystem* the_extendedsystem; |
70 | < | int i, j; |
71 | < | |
72 | < | // get the stamps and globals; |
73 | < | the_stamps = stamps; |
74 | < | the_globals = globals; |
75 | < | |
76 | < | // set the easy ones first |
77 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
78 | < | simnfo->dt = the_globals->getDt(); |
79 | < | simnfo->run_time = the_globals->getRunTime(); |
80 | < | |
81 | < | // get the ones we know are there, yet still may need some work. |
82 | < | n_components = the_globals->getNComponents(); |
83 | < | strcpy( force_field, the_globals->getForceField() ); |
84 | < | |
85 | < | // get the ensemble and set up an extended system if we need it: |
86 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
87 | < | if( !strcasecmp( ensemble, "NPT" ) ) { |
88 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
89 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 | < | if (the_globals->haveTargetPressure()) |
91 | < | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 | < | else { |
93 | < | sprintf( painCave.errMsg, |
94 | < | "SimSetup error: If you use the constant pressure\n" |
95 | < | " ensemble, you must set targetPressure.\n" |
96 | < | " This was found in the BASS file.\n"); |
97 | < | painCave.isFatal = 1; |
98 | < | simError(); |
99 | < | } |
100 | < | |
101 | < | if (the_globals->haveTauThermostat()) |
102 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 | < | else if (the_globals->haveQmass()) |
104 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
105 | < | else { |
106 | < | sprintf( painCave.errMsg, |
107 | < | "SimSetup error: If you use one of the constant temperature\n" |
108 | < | " ensembles, you must set either tauThermostat or qMass.\n" |
109 | < | " Neither of these was found in the BASS file.\n"); |
110 | < | painCave.isFatal = 1; |
111 | < | simError(); |
112 | < | } |
113 | < | |
114 | < | if (the_globals->haveTauBarostat()) |
115 | < | the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 | < | else { |
117 | < | sprintf( painCave.errMsg, |
118 | < | "SimSetup error: If you use the constant pressure\n" |
119 | < | " ensemble, you must set tauBarostat.\n" |
120 | < | " This was found in the BASS file.\n"); |
121 | < | painCave.isFatal = 1; |
122 | < | simError(); |
123 | < | } |
124 | < | |
125 | < | } else if ( !strcasecmp( ensemble, "NVT") ) { |
126 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
127 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
128 | < | |
129 | < | if (the_globals->haveTauThermostat()) |
130 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 | < | else if (the_globals->haveQmass()) |
132 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
133 | < | else { |
134 | < | sprintf( painCave.errMsg, |
135 | < | "SimSetup error: If you use one of the constant temperature\n" |
136 | < | " ensembles, you must set either tauThermostat or qMass.\n" |
137 | < | " Neither of these was found in the BASS file.\n"); |
138 | < | painCave.isFatal = 1; |
139 | < | simError(); |
140 | < | } |
141 | < | |
142 | < | } else if ( !strcasecmp( ensemble, "NVE") ) { |
143 | < | } else { |
144 | < | sprintf( painCave.errMsg, |
145 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 | < | "reverting to NVE for this simulation.\n", |
147 | < | ensemble ); |
148 | < | painCave.isFatal = 0; |
149 | < | simError(); |
150 | < | strcpy( ensemble, "NVE" ); |
151 | < | } |
152 | < | strcpy( simnfo->ensemble, ensemble ); |
153 | < | |
154 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
155 | < | simnfo->usePBC = the_globals->getPBC(); |
156 | < | |
157 | < | int usesDipoles = 0; |
158 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
159 | < | the_ff = new TraPPE_ExFF(); |
160 | < | usesDipoles = 1; |
161 | < | } |
162 | < | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
163 | < | else{ |
164 | < | sprintf( painCave.errMsg, |
165 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
166 | < | force_field ); |
167 | < | painCave.isFatal = 1; |
168 | < | simError(); |
169 | < | } |
170 | < | |
171 | < | #ifdef IS_MPI |
172 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
173 | < | MPIcheckPoint(); |
174 | < | #endif // is_mpi |
175 | < | |
81 | > | int i, j, k, globalAtomIndex; |
82 | ||
83 | + | // gather all of the information from the Bass file |
84 | + | |
85 | + | gatherInfo(); |
86 | ||
87 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
179 | < | the_components = the_globals->getComponents(); |
180 | < | components_nmol = new int[n_components]; |
181 | < | comp_stamps = new MoleculeStamp*[n_components]; |
87 | > | // creation of complex system objects |
88 | ||
89 | < | if( !the_globals->haveNMol() ){ |
184 | < | // we don't have the total number of molecules, so we assume it is |
185 | < | // given in each component |
89 | > | sysObjectsCreation(); |
90 | ||
91 | < | tot_nmol = 0; |
188 | < | for( i=0; i<n_components; i++ ){ |
189 | < | |
190 | < | if( !the_components[i]->haveNMol() ){ |
191 | < | // we have a problem |
192 | < | sprintf( painCave.errMsg, |
193 | < | "SimSetup Error. No global NMol or component NMol" |
194 | < | " given. Cannot calculate the number of atoms.\n" ); |
195 | < | painCave.isFatal = 1; |
196 | < | simError(); |
197 | < | } |
198 | < | |
199 | < | tot_nmol += the_components[i]->getNMol(); |
200 | < | components_nmol[i] = the_components[i]->getNMol(); |
201 | < | } |
202 | < | } |
203 | < | else{ |
204 | < | sprintf( painCave.errMsg, |
205 | < | "SimSetup error.\n" |
206 | < | "\tSorry, the ability to specify total" |
207 | < | " nMols and then give molfractions in the components\n" |
208 | < | "\tis not currently supported." |
209 | < | " Please give nMol in the components.\n" ); |
210 | < | painCave.isFatal = 1; |
211 | < | simError(); |
212 | < | |
213 | < | |
214 | < | // tot_nmol = the_globals->getNMol(); |
215 | < | |
216 | < | // //we have the total number of molecules, now we check for molfractions |
217 | < | // for( i=0; i<n_components; i++ ){ |
218 | < | |
219 | < | // if( !the_components[i]->haveMolFraction() ){ |
220 | < | |
221 | < | // if( !the_components[i]->haveNMol() ){ |
222 | < | // //we have a problem |
223 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
224 | < | // << " nMol was given in component |
225 | < | |
226 | < | } |
227 | < | |
228 | < | #ifdef IS_MPI |
229 | < | strcpy( checkPointMsg, "Have the number of components" ); |
230 | < | MPIcheckPoint(); |
231 | < | #endif // is_mpi |
232 | < | |
233 | < | // make an array of molecule stamps that match the components used. |
234 | < | // also extract the used stamps out into a separate linked list |
235 | < | |
236 | < | simnfo->nComponents = n_components; |
237 | < | simnfo->componentsNmol = components_nmol; |
238 | < | simnfo->compStamps = comp_stamps; |
239 | < | simnfo->headStamp = new LinkedMolStamp(); |
91 | > | // check on the post processing info |
92 | ||
93 | < | char* id; |
242 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
243 | < | LinkedMolStamp* currentStamp = NULL; |
244 | < | for( i=0; i<n_components; i++ ){ |
93 | > | finalInfoCheck(); |
94 | ||
95 | < | id = the_components[i]->getType(); |
247 | < | comp_stamps[i] = NULL; |
248 | < | |
249 | < | // check to make sure the component isn't already in the list |
95 | > | // initialize the system coordinates |
96 | ||
97 | < | comp_stamps[i] = headStamp->match( id ); |
252 | < | if( comp_stamps[i] == NULL ){ |
253 | < | |
254 | < | // extract the component from the list; |
255 | < | |
256 | < | currentStamp = the_stamps->extractMolStamp( id ); |
257 | < | if( currentStamp == NULL ){ |
258 | < | sprintf( painCave.errMsg, |
259 | < | "SimSetup error: Component \"%s\" was not found in the " |
260 | < | "list of declared molecules\n", |
261 | < | id ); |
262 | < | painCave.isFatal = 1; |
263 | < | simError(); |
264 | < | } |
265 | < | |
266 | < | headStamp->add( currentStamp ); |
267 | < | comp_stamps[i] = headStamp->match( id ); |
268 | < | } |
269 | < | } |
270 | < | |
271 | < | #ifdef IS_MPI |
272 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
273 | < | MPIcheckPoint(); |
274 | < | #endif // is_mpi |
97 | > | initSystemCoords(); |
98 | ||
99 | ||
100 | + | // make the output filenames |
101 | ||
102 | < | |
103 | < | // caclulate the number of atoms, bonds, bends and torsions |
104 | < | |
281 | < | tot_atoms = 0; |
282 | < | tot_bonds = 0; |
283 | < | tot_bends = 0; |
284 | < | tot_torsions = 0; |
285 | < | for( i=0; i<n_components; i++ ){ |
286 | < | |
287 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
288 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
289 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
290 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
291 | < | } |
292 | < | |
293 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
294 | < | |
295 | < | simnfo->n_atoms = tot_atoms; |
296 | < | simnfo->n_bonds = tot_bonds; |
297 | < | simnfo->n_bends = tot_bends; |
298 | < | simnfo->n_torsions = tot_torsions; |
299 | < | simnfo->n_SRI = tot_SRI; |
300 | < | simnfo->n_mol = tot_nmol; |
301 | < | |
102 | > | makeOutNames(); |
103 | > | |
104 | > | // make the integrator |
105 | ||
106 | < | #ifdef IS_MPI |
304 | < | |
305 | < | // divide the molecules among processors here. |
306 | < | |
307 | < | mpiSim = new mpiSimulation( simnfo ); |
308 | < | |
309 | < | |
310 | < | |
311 | < | globalIndex = mpiSim->divideLabor(); |
312 | < | |
313 | < | // set up the local variables |
314 | < | |
315 | < | int localMol, allMol; |
316 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
317 | < | |
318 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
319 | < | int* molCompType = mpiSim->getMolComponentType(); |
320 | < | |
321 | < | allMol = 0; |
322 | < | localMol = 0; |
323 | < | local_atoms = 0; |
324 | < | local_bonds = 0; |
325 | < | local_bends = 0; |
326 | < | local_torsions = 0; |
327 | < | for( i=0; i<n_components; i++ ){ |
328 | < | |
329 | < | for( j=0; j<components_nmol[i]; j++ ){ |
330 | < | |
331 | < | if( mol2proc[allMol] == worldRank ){ |
332 | < | |
333 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
334 | < | local_bonds += comp_stamps[i]->getNBonds(); |
335 | < | local_bends += comp_stamps[i]->getNBends(); |
336 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
337 | < | localMol++; |
338 | < | } |
339 | < | allMol++; |
340 | < | } |
341 | < | } |
342 | < | local_SRI = local_bonds + local_bends + local_torsions; |
343 | < | |
344 | < | |
345 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
346 | < | |
347 | < | if( local_atoms != simnfo->n_atoms ){ |
348 | < | sprintf( painCave.errMsg, |
349 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
350 | < | " localAtom (%d) are not equal.\n", |
351 | < | simnfo->n_atoms, |
352 | < | local_atoms ); |
353 | < | painCave.isFatal = 1; |
354 | < | simError(); |
355 | < | } |
356 | < | |
357 | < | simnfo->n_bonds = local_bonds; |
358 | < | simnfo->n_bends = local_bends; |
359 | < | simnfo->n_torsions = local_torsions; |
360 | < | simnfo->n_SRI = local_SRI; |
361 | < | simnfo->n_mol = localMol; |
362 | < | |
363 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
364 | < | MPIcheckPoint(); |
365 | < | |
366 | < | |
367 | < | #endif // is_mpi |
368 | < | |
369 | < | |
370 | < | // create the atom and short range interaction arrays |
371 | < | |
372 | < | Atom::createArrays(simnfo->n_atoms); |
373 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
374 | < | the_molecules = new Molecule[simnfo->n_mol]; |
375 | < | int molIndex; |
376 | < | |
377 | < | // initialize the molecule's stampID's |
378 | < | |
379 | < | #ifdef IS_MPI |
380 | < | |
381 | < | |
382 | < | molIndex = 0; |
383 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
384 | < | |
385 | < | if(mol2proc[i] == worldRank ){ |
386 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
387 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
388 | < | the_molecules[molIndex].setGlobalIndex( i ); |
389 | < | molIndex++; |
390 | < | } |
391 | < | } |
392 | < | |
393 | < | #else // is_mpi |
394 | < | |
395 | < | molIndex = 0; |
396 | < | for(i=0; i<n_components; i++){ |
397 | < | for(j=0; j<components_nmol[i]; j++ ){ |
398 | < | the_molecules[molIndex].setStampID( i ); |
399 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
400 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
401 | < | molIndex++; |
402 | < | } |
403 | < | } |
404 | < | |
405 | < | |
406 | < | #endif // is_mpi |
407 | < | |
408 | < | |
409 | < | if( simnfo->n_SRI ){ |
410 | < | |
411 | < | Exclude::createArray(simnfo->n_SRI); |
412 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
413 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
414 | < | simnfo->globalExcludes = new int; |
415 | < | simnfo->n_exclude = simnfo->n_SRI; |
416 | < | } |
417 | < | else{ |
418 | < | |
419 | < | Exclude::createArray( 1 ); |
420 | < | the_excludes = new Exclude*; |
421 | < | the_excludes[0] = new Exclude(0); |
422 | < | the_excludes[0]->setPair( 0,0 ); |
423 | < | simnfo->globalExcludes = new int; |
424 | < | simnfo->globalExcludes[0] = 0; |
425 | < | simnfo->n_exclude = 0; |
426 | < | } |
427 | < | |
428 | < | // set the arrays into the SimInfo object |
429 | < | |
430 | < | simnfo->atoms = the_atoms; |
431 | < | simnfo->molecules = the_molecules; |
432 | < | simnfo->nGlobalExcludes = 0; |
433 | < | simnfo->excludes = the_excludes; |
434 | < | |
435 | < | |
436 | < | // get some of the tricky things that may still be in the globals |
437 | < | |
438 | < | |
439 | < | if( the_globals->haveBox() ){ |
440 | < | simnfo->box_x = the_globals->getBox(); |
441 | < | simnfo->box_y = the_globals->getBox(); |
442 | < | simnfo->box_z = the_globals->getBox(); |
443 | < | } |
444 | < | else if( the_globals->haveDensity() ){ |
445 | < | |
446 | < | double vol; |
447 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
448 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
449 | < | simnfo->box_y = simnfo->box_x; |
450 | < | simnfo->box_z = simnfo->box_x; |
451 | < | } |
452 | < | else{ |
453 | < | if( !the_globals->haveBoxX() ){ |
454 | < | sprintf( painCave.errMsg, |
455 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
456 | < | painCave.isFatal = 1; |
457 | < | simError(); |
458 | < | } |
459 | < | simnfo->box_x = the_globals->getBoxX(); |
460 | < | |
461 | < | if( !the_globals->haveBoxY() ){ |
462 | < | sprintf( painCave.errMsg, |
463 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
464 | < | painCave.isFatal = 1; |
465 | < | simError(); |
466 | < | } |
467 | < | simnfo->box_y = the_globals->getBoxY(); |
468 | < | |
469 | < | if( !the_globals->haveBoxZ() ){ |
470 | < | sprintf( painCave.errMsg, |
471 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
472 | < | painCave.isFatal = 1; |
473 | < | simError(); |
474 | < | } |
475 | < | simnfo->box_z = the_globals->getBoxZ(); |
476 | < | } |
477 | < | |
478 | < | #ifdef IS_MPI |
479 | < | strcpy( checkPointMsg, "Box size set up" ); |
480 | < | MPIcheckPoint(); |
481 | < | #endif // is_mpi |
482 | < | |
483 | < | |
484 | < | // initialize the arrays |
485 | < | |
486 | < | the_ff->setSimInfo( simnfo ); |
487 | < | |
488 | < | makeMolecules(); |
489 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
490 | < | simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
491 | < | for(i=0; i<simnfo->n_atoms; i++){ |
492 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
493 | < | } |
494 | < | for(i=0; i< simnfo->n_mol; i++) { |
495 | < | the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
496 | < | } |
497 | < | |
498 | < | if (the_globals->getUseRF() ) { |
499 | < | simnfo->useReactionField = 1; |
500 | < | |
501 | < | if( !the_globals->haveECR() ){ |
502 | < | sprintf( painCave.errMsg, |
503 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
504 | < | "box length for the electrostaticCutoffRadius.\n" |
505 | < | "I hope you have a very fast processor!\n"); |
506 | < | painCave.isFatal = 0; |
507 | < | simError(); |
508 | < | double smallest; |
509 | < | smallest = simnfo->box_x; |
510 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
511 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
512 | < | simnfo->ecr = 0.5 * smallest; |
513 | < | } else { |
514 | < | simnfo->ecr = the_globals->getECR(); |
515 | < | } |
516 | < | |
517 | < | if( !the_globals->haveEST() ){ |
518 | < | sprintf( painCave.errMsg, |
519 | < | "SimSetup Warning: using default value of 0.05 * the " |
520 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
521 | < | ); |
522 | < | painCave.isFatal = 0; |
523 | < | simError(); |
524 | < | simnfo->est = 0.05 * simnfo->ecr; |
525 | < | } else { |
526 | < | simnfo->est = the_globals->getEST(); |
527 | < | } |
528 | < | |
529 | < | if(!the_globals->haveDielectric() ){ |
530 | < | sprintf( painCave.errMsg, |
531 | < | "SimSetup Error: You are trying to use Reaction Field without" |
532 | < | "setting a dielectric constant!\n" |
533 | < | ); |
534 | < | painCave.isFatal = 1; |
535 | < | simError(); |
536 | < | } |
537 | < | simnfo->dielectric = the_globals->getDielectric(); |
538 | < | } else { |
539 | < | if (usesDipoles) { |
540 | < | |
541 | < | if( !the_globals->haveECR() ){ |
542 | < | sprintf( painCave.errMsg, |
543 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
544 | < | "box length for the electrostaticCutoffRadius.\n" |
545 | < | "I hope you have a very fast processor!\n"); |
546 | < | painCave.isFatal = 0; |
547 | < | simError(); |
548 | < | double smallest; |
549 | < | smallest = simnfo->box_x; |
550 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
551 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
552 | < | simnfo->ecr = 0.5 * smallest; |
553 | < | } else { |
554 | < | simnfo->ecr = the_globals->getECR(); |
555 | < | } |
556 | < | |
557 | < | if( !the_globals->haveEST() ){ |
558 | < | sprintf( painCave.errMsg, |
559 | < | "SimSetup Warning: using default value of 5%% of the " |
560 | < | "electrostaticCutoffRadius for the " |
561 | < | "electrostaticSkinThickness\n" |
562 | < | ); |
563 | < | painCave.isFatal = 0; |
564 | < | simError(); |
565 | < | simnfo->est = 0.05 * simnfo->ecr; |
566 | < | } else { |
567 | < | simnfo->est = the_globals->getEST(); |
568 | < | } |
569 | < | } |
570 | < | } |
571 | < | |
572 | < | #ifdef IS_MPI |
573 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
574 | < | MPIcheckPoint(); |
575 | < | #endif // is_mpi |
576 | < | |
577 | < | if( the_globals->haveInitialConfig() ){ |
578 | < | |
579 | < | InitializeFromFile* fileInit; |
580 | < | #ifdef IS_MPI // is_mpi |
581 | < | if( worldRank == 0 ){ |
582 | < | #endif //is_mpi |
583 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
584 | < | #ifdef IS_MPI |
585 | < | }else fileInit = new InitializeFromFile( NULL ); |
586 | < | #endif |
587 | < | fileInit->read_xyz( simnfo ); // default velocities on |
588 | < | |
589 | < | delete fileInit; |
590 | < | } |
591 | < | else{ |
592 | < | |
593 | < | #ifdef IS_MPI |
594 | < | |
595 | < | // no init from bass |
596 | < | |
597 | < | sprintf( painCave.errMsg, |
598 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
599 | < | painCave.isFatal; |
600 | < | simError(); |
601 | < | |
602 | < | #else |
603 | < | |
604 | < | initFromBass(); |
605 | < | |
606 | < | |
607 | < | #endif |
608 | < | } |
609 | < | |
610 | < | #ifdef IS_MPI |
611 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
612 | < | MPIcheckPoint(); |
613 | < | #endif // is_mpi |
614 | < | |
615 | < | |
616 | < | |
617 | < | |
618 | < | |
619 | < | |
620 | < | |
621 | < | #ifdef IS_MPI |
622 | < | if( worldRank == 0 ){ |
623 | < | #endif // is_mpi |
624 | < | |
625 | < | if( the_globals->haveFinalConfig() ){ |
626 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
627 | < | } |
628 | < | else{ |
629 | < | strcpy( simnfo->finalName, inFileName ); |
630 | < | char* endTest; |
631 | < | int nameLength = strlen( simnfo->finalName ); |
632 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
633 | < | if( !strcmp( endTest, ".bass" ) ){ |
634 | < | strcpy( endTest, ".eor" ); |
635 | < | } |
636 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
637 | < | strcpy( endTest, ".eor" ); |
638 | < | } |
639 | < | else{ |
640 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
641 | < | if( !strcmp( endTest, ".bss" ) ){ |
642 | < | strcpy( endTest, ".eor" ); |
643 | < | } |
644 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
645 | < | strcpy( endTest, ".eor" ); |
646 | < | } |
647 | < | else{ |
648 | < | strcat( simnfo->finalName, ".eor" ); |
649 | < | } |
650 | < | } |
651 | < | } |
652 | < | |
653 | < | // make the sample and status out names |
654 | < | |
655 | < | strcpy( simnfo->sampleName, inFileName ); |
656 | < | char* endTest; |
657 | < | int nameLength = strlen( simnfo->sampleName ); |
658 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
659 | < | if( !strcmp( endTest, ".bass" ) ){ |
660 | < | strcpy( endTest, ".dump" ); |
661 | < | } |
662 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
663 | < | strcpy( endTest, ".dump" ); |
664 | < | } |
665 | < | else{ |
666 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
667 | < | if( !strcmp( endTest, ".bss" ) ){ |
668 | < | strcpy( endTest, ".dump" ); |
669 | < | } |
670 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
671 | < | strcpy( endTest, ".dump" ); |
672 | < | } |
673 | < | else{ |
674 | < | strcat( simnfo->sampleName, ".dump" ); |
675 | < | } |
676 | < | } |
677 | < | |
678 | < | strcpy( simnfo->statusName, inFileName ); |
679 | < | nameLength = strlen( simnfo->statusName ); |
680 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
681 | < | if( !strcmp( endTest, ".bass" ) ){ |
682 | < | strcpy( endTest, ".stat" ); |
683 | < | } |
684 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
685 | < | strcpy( endTest, ".stat" ); |
686 | < | } |
687 | < | else{ |
688 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
689 | < | if( !strcmp( endTest, ".bss" ) ){ |
690 | < | strcpy( endTest, ".stat" ); |
691 | < | } |
692 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
693 | < | strcpy( endTest, ".stat" ); |
694 | < | } |
695 | < | else{ |
696 | < | strcat( simnfo->statusName, ".stat" ); |
697 | < | } |
698 | < | } |
699 | < | |
700 | < | #ifdef IS_MPI |
701 | < | } |
702 | < | #endif // is_mpi |
703 | < | |
704 | < | // set the status, sample, and themal kick times |
106 | > | makeIntegrator(); |
107 | ||
706 | – | if( the_globals->haveSampleTime() ){ |
707 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
708 | – | simnfo->statusTime = simnfo->sampleTime; |
709 | – | simnfo->thermalTime = simnfo->sampleTime; |
710 | – | } |
711 | – | else{ |
712 | – | simnfo->sampleTime = the_globals->getRunTime(); |
713 | – | simnfo->statusTime = simnfo->sampleTime; |
714 | – | simnfo->thermalTime = simnfo->sampleTime; |
715 | – | } |
716 | – | |
717 | – | if( the_globals->haveStatusTime() ){ |
718 | – | simnfo->statusTime = the_globals->getStatusTime(); |
719 | – | } |
720 | – | |
721 | – | if( the_globals->haveThermalTime() ){ |
722 | – | simnfo->thermalTime = the_globals->getThermalTime(); |
723 | – | } |
724 | – | |
725 | – | // check for the temperature set flag |
726 | – | |
727 | – | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
728 | – | |
729 | – | |
730 | – | // // make the longe range forces and the integrator |
731 | – | |
732 | – | // new AllLong( simnfo ); |
733 | – | |
734 | – | |
735 | – | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
736 | – | new Symplectic(simnfo, the_ff, the_extendedsystem); |
737 | – | } |
738 | – | else if( !strcmp( force_field, "LJ" ) ){ |
739 | – | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
740 | – | } |
741 | – | else { |
742 | – | std::cerr << "I'm a bug.\n"; |
743 | – | fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
744 | – | } |
108 | #ifdef IS_MPI | |
109 | mpiSim->mpiRefresh(); | |
110 | #endif | |
111 | ||
112 | // initialize the Fortran | |
113 | ||
114 | + | initFortran(); |
115 | ||
752 | – | simnfo->refreshSim(); |
753 | – | |
754 | – | if( !strcmp( simnfo->mixingRule, "standard") ){ |
755 | – | the_ff->initForceField( LB_MIXING_RULE ); |
756 | – | } |
757 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
758 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
759 | – | } |
760 | – | else{ |
761 | – | sprintf( painCave.errMsg, |
762 | – | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
763 | – | simnfo->mixingRule ); |
764 | – | painCave.isFatal = 1; |
765 | – | simError(); |
766 | – | } |
116 | ||
117 | ||
769 | – | #ifdef IS_MPI |
770 | – | strcpy( checkPointMsg, |
771 | – | "Successfully intialized the mixingRule for Fortran." ); |
772 | – | MPIcheckPoint(); |
773 | – | #endif // is_mpi |
118 | } | |
119 | ||
120 | ||
121 | void SimSetup::makeMolecules( void ){ | |
122 | ||
123 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
124 | < | molInit info; |
124 | > | molInit molInfo; |
125 | DirectionalAtom* dAtom; | |
126 | LinkedAssign* extras; | |
127 | LinkedAssign* current_extra; | |
# | Line 802 | Line 146 | void SimSetup::makeMolecules( void ){ | |
146 | ||
147 | atomOffset = 0; | |
148 | excludeOffset = 0; | |
149 | < | for(i=0; i<simnfo->n_mol; i++){ |
149 | > | for(i=0; i<info->n_mol; i++){ |
150 | ||
151 | stampID = the_molecules[i].getStampID(); | |
152 | ||
153 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
154 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
155 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
156 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
157 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
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 | < | info.myAtoms = &the_atoms[atomOffset]; |
160 | < | info.myExcludes = &the_excludes[excludeOffset]; |
161 | < | info.myBonds = new Bond*[info.nBonds]; |
162 | < | info.myBends = new Bend*[info.nBends]; |
163 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
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[info.nBonds]; |
166 | < | theBends = new bend_set[info.nBends]; |
167 | < | theTorsions = new torsion_set[info.nTorsions]; |
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<info.nAtoms; j++){ |
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 | < | simnfo->n_oriented++; |
178 | < | info.myAtoms[j] = dAtom; |
177 | > | info->n_oriented++; |
178 | > | molInfo.myAtoms[j] = dAtom; |
179 | ||
180 | ux = currentAtom->getOrntX(); | |
181 | uy = currentAtom->getOrntY(); | |
# | Line 849 | Line 193 | void SimSetup::makeMolecules( void ){ | |
193 | dAtom->setSUz( uz ); | |
194 | } | |
195 | else{ | |
196 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
196 | > | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
197 | } | |
198 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
198 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
199 | ||
200 | #ifdef IS_MPI | |
201 | ||
202 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
202 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
203 | ||
204 | #endif // is_mpi | |
205 | } | |
206 | ||
207 | // make the bonds | |
208 | < | for(j=0; j<info.nBonds; j++){ |
208 | > | for(j=0; j<molInfo.nBonds; j++){ |
209 | ||
210 | currentBond = comp_stamps[stampID]->getBond( j ); | |
211 | theBonds[j].a = currentBond->getA() + atomOffset; | |
# | Line 888 | Line 232 | void SimSetup::makeMolecules( void ){ | |
232 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
233 | #endif //is_mpi | |
234 | } | |
235 | < | excludeOffset += info.nBonds; |
235 | > | excludeOffset += molInfo.nBonds; |
236 | ||
237 | //make the bends | |
238 | < | for(j=0; j<info.nBends; j++){ |
238 | > | for(j=0; j<molInfo.nBends; j++){ |
239 | ||
240 | currentBend = comp_stamps[stampID]->getBend( j ); | |
241 | theBends[j].a = currentBend->getA() + atomOffset; | |
# | Line 974 | Line 318 | void SimSetup::makeMolecules( void ){ | |
318 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
319 | #endif //is_mpi | |
320 | } | |
321 | < | excludeOffset += info.nBends; |
321 | > | excludeOffset += molInfo.nBends; |
322 | ||
323 | < | for(j=0; j<info.nTorsions; j++){ |
323 | > | for(j=0; j<molInfo.nTorsions; j++){ |
324 | ||
325 | currentTorsion = comp_stamps[stampID]->getTorsion( j ); | |
326 | theTorsions[j].a = currentTorsion->getA() + atomOffset; | |
# | Line 1004 | Line 348 | void SimSetup::makeMolecules( void ){ | |
348 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
349 | #endif //is_mpi | |
350 | } | |
351 | < | excludeOffset += info.nTorsions; |
351 | > | excludeOffset += molInfo.nTorsions; |
352 | ||
353 | ||
354 | // send the arrays off to the forceField for init. | |
355 | ||
356 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
357 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
358 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
359 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
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( info ); |
362 | > | the_molecules[i].initialize( molInfo ); |
363 | ||
364 | ||
365 | < | atomOffset += info.nAtoms; |
365 | > | atomOffset += molInfo.nAtoms; |
366 | delete[] theBonds; | |
367 | delete[] theBends; | |
368 | delete[] theTorsions; | |
# | Line 1054 | Line 398 | void SimSetup::initFromBass( void ){ | |
398 | have_extra =1; | |
399 | ||
400 | n_cells = (int)temp3 - 1; | |
401 | < | cellx = simnfo->box_x / temp3; |
402 | < | celly = simnfo->box_y / temp3; |
403 | < | cellz = simnfo->box_z / temp3; |
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 ); | |
# | Line 1071 | Line 415 | void SimSetup::initFromBass( void ){ | |
415 | } | |
416 | else{ | |
417 | n_cells = (int)temp3; | |
418 | < | cellx = simnfo->box_x / temp3; |
419 | < | celly = simnfo->box_y / temp3; |
420 | < | cellz = simnfo->box_z / 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; | |
# | Line 1153 | Line 497 | void SimSetup::initFromBass( void ){ | |
497 | } | |
498 | ||
499 | ||
500 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
501 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
502 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
503 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
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 | ||
# | Line 1217 | Line 561 | void SimSetup::makeElement( double x, double y, double | |
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 | + | stamps = stamps; |
574 | + | globals = globals; |
575 | + | |
576 | + | // set the easy ones first |
577 | + | info->target_temp = globals->getTargetTemp(); |
578 | + | info->dt = globals->getDt(); |
579 | + | info->run_time = globals->getRunTime(); |
580 | + | n_components = globals->getNComponents(); |
581 | + | |
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{ |
590 | + | sprintf( painCave.errMsg, |
591 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
592 | + | force_field ); |
593 | + | painCave.isFatal = 1; |
594 | + | simError(); |
595 | + | } |
596 | + | |
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") ) |
604 | + | ensembleCase = NPTi_ENS; |
605 | + | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
606 | + | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
607 | + | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
608 | + | else{ |
609 | + | sprintf( painCave.errMsg, |
610 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
611 | + | "reverting to NVE for this simulation.\n", |
612 | + | ensemble ); |
613 | + | painCave.isFatal = 0; |
614 | + | simError(); |
615 | + | strcpy( ensemble, "NVE" ); |
616 | + | ensembleCase = NVE_ENS; |
617 | + | } |
618 | + | strcpy( info->ensemble, ensemble ); |
619 | + | |
620 | + | // get the mixing rule |
621 | + | |
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 | + | |
628 | + | the_components = globals->getComponents(); |
629 | + | components_nmol = new int[n_components]; |
630 | + | |
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 | + | |
636 | + | tot_nmol = 0; |
637 | + | for( i=0; i<n_components; i++ ){ |
638 | + | |
639 | + | if( !the_components[i]->haveNMol() ){ |
640 | + | // we have a problem |
641 | + | sprintf( painCave.errMsg, |
642 | + | "SimSetup Error. No global NMol or component NMol" |
643 | + | " given. Cannot calculate the number of atoms.\n" ); |
644 | + | painCave.isFatal = 1; |
645 | + | simError(); |
646 | + | } |
647 | + | |
648 | + | tot_nmol += the_components[i]->getNMol(); |
649 | + | components_nmol[i] = the_components[i]->getNMol(); |
650 | + | } |
651 | + | } |
652 | + | else{ |
653 | + | sprintf( painCave.errMsg, |
654 | + | "SimSetup error.\n" |
655 | + | "\tSorry, the ability to specify total" |
656 | + | " nMols and then give molfractions in the components\n" |
657 | + | "\tis not currently supported." |
658 | + | " Please give nMol in the components.\n" ); |
659 | + | painCave.isFatal = 1; |
660 | + | simError(); |
661 | + | } |
662 | + | |
663 | + | // set the status, sample, and thermal kick times |
664 | + | |
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 | + | if( globals->haveStatusTime() ){ |
677 | + | info->statusTime = globals->getStatusTime(); |
678 | + | } |
679 | + | |
680 | + | if( globals->haveThermalTime() ){ |
681 | + | info->thermalTime = globals->getThermalTime(); |
682 | + | } |
683 | + | |
684 | + | // check for the temperature set flag |
685 | + | |
686 | + | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
687 | + | |
688 | + | // get some of the tricky things that may still be in the globals |
689 | + | |
690 | + | double boxVector[3]; |
691 | + | if( globals->haveBox() ){ |
692 | + | boxVector[0] = globals->getBox(); |
693 | + | boxVector[1] = globals->getBox(); |
694 | + | boxVector[2] = globals->getBox(); |
695 | + | |
696 | + | info->setBox( boxVector ); |
697 | + | } |
698 | + | else if( globals->haveDensity() ){ |
699 | + | |
700 | + | double vol; |
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 | + | info->setBox( boxVector ); |
707 | + | } |
708 | + | else{ |
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] = globals->getBoxX(); |
716 | + | |
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] = globals->getBoxY(); |
724 | + | |
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] = globals->getBoxZ(); |
732 | + | |
733 | + | info->setBox( boxVector ); |
734 | + | } |
735 | + | |
736 | + | |
737 | + | |
738 | + | #ifdef IS_MPI |
739 | + | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
740 | + | MPIcheckPoint(); |
741 | + | #endif // is_mpi |
742 | + | |
743 | + | } |
744 | + | |
745 | + | |
746 | + | void SimSetup::finalInfoCheck( void ){ |
747 | + | int index; |
748 | + | int usesDipoles; |
749 | + | |
750 | + | |
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 | + | #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 | + | double theEcr, theEst; |
766 | + | |
767 | + | if (globals->getUseRF() ) { |
768 | + | info->useReactionField = 1; |
769 | + | |
770 | + | if( !globals->haveECR() ){ |
771 | + | sprintf( painCave.errMsg, |
772 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
773 | + | "box length for the electrostaticCutoffRadius.\n" |
774 | + | "I hope you have a very fast processor!\n"); |
775 | + | painCave.isFatal = 0; |
776 | + | simError(); |
777 | + | double smallest; |
778 | + | smallest = info->boxL[0]; |
779 | + | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
780 | + | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
781 | + | theEcr = 0.5 * smallest; |
782 | + | } else { |
783 | + | theEcr = globals->getECR(); |
784 | + | } |
785 | + | |
786 | + | if( !globals->haveEST() ){ |
787 | + | sprintf( painCave.errMsg, |
788 | + | "SimSetup Warning: using default value of 0.05 * the " |
789 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
790 | + | ); |
791 | + | painCave.isFatal = 0; |
792 | + | simError(); |
793 | + | theEst = 0.05 * theEcr; |
794 | + | } else { |
795 | + | theEst= globals->getEST(); |
796 | + | } |
797 | + | |
798 | + | info->setEcr( theEcr, theEst ); |
799 | + | |
800 | + | if(!globals->haveDielectric() ){ |
801 | + | sprintf( painCave.errMsg, |
802 | + | "SimSetup Error: You are trying to use Reaction Field without" |
803 | + | "setting a dielectric constant!\n" |
804 | + | ); |
805 | + | painCave.isFatal = 1; |
806 | + | simError(); |
807 | + | } |
808 | + | info->dielectric = globals->getDielectric(); |
809 | + | } |
810 | + | else { |
811 | + | if (usesDipoles) { |
812 | + | |
813 | + | if( !globals->haveECR() ){ |
814 | + | sprintf( painCave.errMsg, |
815 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
816 | + | "box length for the electrostaticCutoffRadius.\n" |
817 | + | "I hope you have a very fast processor!\n"); |
818 | + | painCave.isFatal = 0; |
819 | + | simError(); |
820 | + | double smallest; |
821 | + | smallest = info->boxL[0]; |
822 | + | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
823 | + | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
824 | + | theEcr = 0.5 * smallest; |
825 | + | } else { |
826 | + | theEcr = globals->getECR(); |
827 | + | } |
828 | + | |
829 | + | if( !globals->haveEST() ){ |
830 | + | sprintf( painCave.errMsg, |
831 | + | "SimSetup Warning: using default value of 0.05 * the " |
832 | + | "electrostaticCutoffRadius for the " |
833 | + | "electrostaticSkinThickness\n" |
834 | + | ); |
835 | + | painCave.isFatal = 0; |
836 | + | simError(); |
837 | + | theEst = 0.05 * theEcr; |
838 | + | } else { |
839 | + | theEst= globals->getEST(); |
840 | + | } |
841 | + | |
842 | + | info->setEcr( theEcr, theEst ); |
843 | + | } |
844 | + | } |
845 | + | |
846 | + | #ifdef IS_MPI |
847 | + | strcpy( checkPointMsg, "post processing checks out" ); |
848 | + | MPIcheckPoint(); |
849 | + | #endif // is_mpi |
850 | + | |
851 | + | } |
852 | + | |
853 | + | void SimSetup::initSystemCoords( void ){ |
854 | + | |
855 | + | if( globals->haveInitialConfig() ){ |
856 | + | |
857 | + | InitializeFromFile* fileInit; |
858 | + | #ifdef IS_MPI // is_mpi |
859 | + | if( worldRank == 0 ){ |
860 | + | #endif //is_mpi |
861 | + | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
862 | + | #ifdef IS_MPI |
863 | + | }else fileInit = new InitializeFromFile( NULL ); |
864 | + | #endif |
865 | + | fileInit->readInit( info ); // default velocities on |
866 | + | |
867 | + | delete fileInit; |
868 | + | } |
869 | + | else{ |
870 | + | |
871 | + | #ifdef IS_MPI |
872 | + | |
873 | + | // no init from bass |
874 | + | |
875 | + | sprintf( painCave.errMsg, |
876 | + | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
877 | + | painCave.isFatal; |
878 | + | simError(); |
879 | + | |
880 | + | #else |
881 | + | |
882 | + | initFromBass(); |
883 | + | |
884 | + | |
885 | + | #endif |
886 | + | } |
887 | + | |
888 | + | #ifdef IS_MPI |
889 | + | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
890 | + | MPIcheckPoint(); |
891 | + | #endif // is_mpi |
892 | + | |
893 | + | } |
894 | + | |
895 | + | |
896 | + | void SimSetup::makeOutNames( void ){ |
897 | + | |
898 | + | #ifdef IS_MPI |
899 | + | if( worldRank == 0 ){ |
900 | + | #endif // is_mpi |
901 | + | |
902 | + | if( globals->haveFinalConfig() ){ |
903 | + | strcpy( info->finalName, globals->getFinalConfig() ); |
904 | + | } |
905 | + | else{ |
906 | + | strcpy( info->finalName, inFileName ); |
907 | + | char* endTest; |
908 | + | int nameLength = strlen( info->finalName ); |
909 | + | endTest = &(info->finalName[nameLength - 5]); |
910 | + | if( !strcmp( endTest, ".bass" ) ){ |
911 | + | strcpy( endTest, ".eor" ); |
912 | + | } |
913 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
914 | + | strcpy( endTest, ".eor" ); |
915 | + | } |
916 | + | else{ |
917 | + | endTest = &(info->finalName[nameLength - 4]); |
918 | + | if( !strcmp( endTest, ".bss" ) ){ |
919 | + | strcpy( endTest, ".eor" ); |
920 | + | } |
921 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
922 | + | strcpy( endTest, ".eor" ); |
923 | + | } |
924 | + | else{ |
925 | + | strcat( info->finalName, ".eor" ); |
926 | + | } |
927 | + | } |
928 | + | } |
929 | + | |
930 | + | // make the sample and status out names |
931 | + | |
932 | + | strcpy( info->sampleName, inFileName ); |
933 | + | char* endTest; |
934 | + | int nameLength = strlen( info->sampleName ); |
935 | + | endTest = &(info->sampleName[nameLength - 5]); |
936 | + | if( !strcmp( endTest, ".bass" ) ){ |
937 | + | strcpy( endTest, ".dump" ); |
938 | + | } |
939 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
940 | + | strcpy( endTest, ".dump" ); |
941 | + | } |
942 | + | else{ |
943 | + | endTest = &(info->sampleName[nameLength - 4]); |
944 | + | if( !strcmp( endTest, ".bss" ) ){ |
945 | + | strcpy( endTest, ".dump" ); |
946 | + | } |
947 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
948 | + | strcpy( endTest, ".dump" ); |
949 | + | } |
950 | + | else{ |
951 | + | strcat( info->sampleName, ".dump" ); |
952 | + | } |
953 | + | } |
954 | + | |
955 | + | strcpy( info->statusName, inFileName ); |
956 | + | nameLength = strlen( info->statusName ); |
957 | + | endTest = &(info->statusName[nameLength - 5]); |
958 | + | if( !strcmp( endTest, ".bass" ) ){ |
959 | + | strcpy( endTest, ".stat" ); |
960 | + | } |
961 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
962 | + | strcpy( endTest, ".stat" ); |
963 | + | } |
964 | + | else{ |
965 | + | endTest = &(info->statusName[nameLength - 4]); |
966 | + | if( !strcmp( endTest, ".bss" ) ){ |
967 | + | strcpy( endTest, ".stat" ); |
968 | + | } |
969 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
970 | + | strcpy( endTest, ".stat" ); |
971 | + | } |
972 | + | else{ |
973 | + | strcat( info->statusName, ".stat" ); |
974 | + | } |
975 | + | } |
976 | + | |
977 | + | #ifdef IS_MPI |
978 | + | } |
979 | + | #endif // is_mpi |
980 | + | |
981 | + | } |
982 | + | |
983 | + | |
984 | + | void SimSetup::sysObjectsCreation( void ){ |
985 | + | |
986 | + | int i; |
987 | + | |
988 | + | // create the forceField |
989 | + | |
990 | + | createFF(); |
991 | + | |
992 | + | // extract componentList |
993 | + | |
994 | + | compList(); |
995 | + | |
996 | + | // calc the number of atoms, bond, bends, and torsions |
997 | + | |
998 | + | calcSysValues(); |
999 | + | |
1000 | + | #ifdef IS_MPI |
1001 | + | // divide the molecules among the processors |
1002 | + | |
1003 | + | mpiMolDivide(); |
1004 | + | #endif //is_mpi |
1005 | + | |
1006 | + | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1007 | + | |
1008 | + | makeSysArrays(); |
1009 | + | |
1010 | + | // make and initialize the molecules (all but atomic coordinates) |
1011 | + | |
1012 | + | makeMolecules(); |
1013 | + | info->identArray = new int[info->n_atoms]; |
1014 | + | for(i=0; i<info->n_atoms; i++){ |
1015 | + | info->identArray[i] = the_atoms[i]->getIdent(); |
1016 | + | } |
1017 | + | |
1018 | + | |
1019 | + | |
1020 | + | } |
1021 | + | |
1022 | + | |
1023 | + | void SimSetup::createFF( void ){ |
1024 | + | |
1025 | + | switch( ffCase ){ |
1026 | + | |
1027 | + | case FF_DUFF: |
1028 | + | the_ff = new DUFF(); |
1029 | + | break; |
1030 | + | |
1031 | + | case FF_LJ: |
1032 | + | the_ff = new LJFF(); |
1033 | + | break; |
1034 | + | |
1035 | + | default: |
1036 | + | sprintf( painCave.errMsg, |
1037 | + | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1038 | + | painCave.isFatal = 1; |
1039 | + | simError(); |
1040 | + | } |
1041 | + | |
1042 | + | #ifdef IS_MPI |
1043 | + | strcpy( checkPointMsg, "ForceField creation successful" ); |
1044 | + | MPIcheckPoint(); |
1045 | + | #endif // is_mpi |
1046 | + | |
1047 | + | } |
1048 | + | |
1049 | + | |
1050 | + | void SimSetup::compList( void ){ |
1051 | + | |
1052 | + | int i; |
1053 | + | |
1054 | + | comp_stamps = new MoleculeStamp*[n_components]; |
1055 | + | |
1056 | + | // make an array of molecule stamps that match the components used. |
1057 | + | // also extract the used stamps out into a separate linked list |
1058 | + | |
1059 | + | info->nComponents = n_components; |
1060 | + | info->componentsNmol = components_nmol; |
1061 | + | info->compStamps = comp_stamps; |
1062 | + | info->headStamp = new LinkedMolStamp(); |
1063 | + | |
1064 | + | char* id; |
1065 | + | LinkedMolStamp* headStamp = info->headStamp; |
1066 | + | LinkedMolStamp* currentStamp = NULL; |
1067 | + | for( i=0; i<n_components; i++ ){ |
1068 | + | |
1069 | + | id = the_components[i]->getType(); |
1070 | + | comp_stamps[i] = NULL; |
1071 | + | |
1072 | + | // check to make sure the component isn't already in the list |
1073 | + | |
1074 | + | comp_stamps[i] = headStamp->match( id ); |
1075 | + | if( comp_stamps[i] == NULL ){ |
1076 | + | |
1077 | + | // extract the component from the list; |
1078 | + | |
1079 | + | currentStamp = stamps->extractMolStamp( id ); |
1080 | + | if( currentStamp == NULL ){ |
1081 | + | sprintf( painCave.errMsg, |
1082 | + | "SimSetup error: Component \"%s\" was not found in the " |
1083 | + | "list of declared molecules\n", |
1084 | + | id ); |
1085 | + | painCave.isFatal = 1; |
1086 | + | simError(); |
1087 | + | } |
1088 | + | |
1089 | + | headStamp->add( currentStamp ); |
1090 | + | comp_stamps[i] = headStamp->match( id ); |
1091 | + | } |
1092 | + | } |
1093 | + | |
1094 | + | #ifdef IS_MPI |
1095 | + | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1096 | + | MPIcheckPoint(); |
1097 | + | #endif // is_mpi |
1098 | + | |
1099 | + | |
1100 | + | } |
1101 | + | |
1102 | + | void SimSetup::calcSysValues( void ){ |
1103 | + | int i, j, k; |
1104 | + | |
1105 | + | |
1106 | + | tot_atoms = 0; |
1107 | + | tot_bonds = 0; |
1108 | + | tot_bends = 0; |
1109 | + | tot_torsions = 0; |
1110 | + | for( i=0; i<n_components; i++ ){ |
1111 | + | |
1112 | + | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1113 | + | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1114 | + | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1115 | + | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1116 | + | } |
1117 | + | |
1118 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1119 | + | |
1120 | + | info->n_atoms = tot_atoms; |
1121 | + | info->n_bonds = tot_bonds; |
1122 | + | info->n_bends = tot_bends; |
1123 | + | info->n_torsions = tot_torsions; |
1124 | + | info->n_SRI = tot_SRI; |
1125 | + | info->n_mol = tot_nmol; |
1126 | + | |
1127 | + | info->molMembershipArray = new int[tot_atoms]; |
1128 | + | } |
1129 | + | |
1130 | + | |
1131 | + | #ifdef IS_MPI |
1132 | + | |
1133 | + | void SimSetup::mpiMolDivide( void ){ |
1134 | + | |
1135 | + | int i, j, k; |
1136 | + | int localMol, allMol; |
1137 | + | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1138 | + | |
1139 | + | mpiSim = new mpiSimulation( info ); |
1140 | + | |
1141 | + | globalIndex = mpiSim->divideLabor(); |
1142 | + | |
1143 | + | // set up the local variables |
1144 | + | |
1145 | + | mol2proc = mpiSim->getMolToProcMap(); |
1146 | + | molCompType = mpiSim->getMolComponentType(); |
1147 | + | |
1148 | + | allMol = 0; |
1149 | + | localMol = 0; |
1150 | + | local_atoms = 0; |
1151 | + | local_bonds = 0; |
1152 | + | local_bends = 0; |
1153 | + | local_torsions = 0; |
1154 | + | globalAtomIndex = 0; |
1155 | + | |
1156 | + | |
1157 | + | for( i=0; i<n_components; i++ ){ |
1158 | + | |
1159 | + | for( j=0; j<components_nmol[i]; j++ ){ |
1160 | + | |
1161 | + | if( mol2proc[allMol] == worldRank ){ |
1162 | + | |
1163 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1164 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1165 | + | local_bends += comp_stamps[i]->getNBends(); |
1166 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1167 | + | localMol++; |
1168 | + | } |
1169 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1170 | + | info->molMembershipArray[globalAtomIndex] = allMol; |
1171 | + | globalAtomIndex++; |
1172 | + | } |
1173 | + | |
1174 | + | allMol++; |
1175 | + | } |
1176 | + | } |
1177 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1178 | + | |
1179 | + | info->n_atoms = mpiSim->getMyNlocal(); |
1180 | + | |
1181 | + | if( local_atoms != info->n_atoms ){ |
1182 | + | sprintf( painCave.errMsg, |
1183 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1184 | + | " localAtom (%d) are not equal.\n", |
1185 | + | info->n_atoms, |
1186 | + | local_atoms ); |
1187 | + | painCave.isFatal = 1; |
1188 | + | simError(); |
1189 | + | } |
1190 | + | |
1191 | + | info->n_bonds = local_bonds; |
1192 | + | info->n_bends = local_bends; |
1193 | + | info->n_torsions = local_torsions; |
1194 | + | info->n_SRI = local_SRI; |
1195 | + | info->n_mol = localMol; |
1196 | + | |
1197 | + | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1198 | + | MPIcheckPoint(); |
1199 | + | } |
1200 | + | |
1201 | + | #endif // is_mpi |
1202 | + | |
1203 | + | |
1204 | + | void SimSetup::makeSysArrays( void ){ |
1205 | + | int i, j, k; |
1206 | + | |
1207 | + | |
1208 | + | // create the atom and short range interaction arrays |
1209 | + | |
1210 | + | Atom::createArrays(info->n_atoms); |
1211 | + | the_atoms = new Atom*[info->n_atoms]; |
1212 | + | the_molecules = new Molecule[info->n_mol]; |
1213 | + | int molIndex; |
1214 | + | |
1215 | + | // initialize the molecule's stampID's |
1216 | + | |
1217 | + | #ifdef IS_MPI |
1218 | + | |
1219 | + | |
1220 | + | molIndex = 0; |
1221 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1222 | + | |
1223 | + | if(mol2proc[i] == worldRank ){ |
1224 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
1225 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1226 | + | the_molecules[molIndex].setGlobalIndex( i ); |
1227 | + | molIndex++; |
1228 | + | } |
1229 | + | } |
1230 | + | |
1231 | + | #else // is_mpi |
1232 | + | |
1233 | + | molIndex = 0; |
1234 | + | globalAtomIndex = 0; |
1235 | + | for(i=0; i<n_components; i++){ |
1236 | + | for(j=0; j<components_nmol[i]; j++ ){ |
1237 | + | the_molecules[molIndex].setStampID( i ); |
1238 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1239 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1240 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1241 | + | info->molMembershipArray[globalAtomIndex] = molIndex; |
1242 | + | globalAtomIndex++; |
1243 | + | } |
1244 | + | molIndex++; |
1245 | + | } |
1246 | + | } |
1247 | + | |
1248 | + | |
1249 | + | #endif // is_mpi |
1250 | + | |
1251 | + | |
1252 | + | if( info->n_SRI ){ |
1253 | + | |
1254 | + | Exclude::createArray(info->n_SRI); |
1255 | + | the_excludes = new Exclude*[info->n_SRI]; |
1256 | + | for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1257 | + | info->globalExcludes = new int; |
1258 | + | info->n_exclude = info->n_SRI; |
1259 | + | } |
1260 | + | else{ |
1261 | + | |
1262 | + | Exclude::createArray( 1 ); |
1263 | + | the_excludes = new Exclude*; |
1264 | + | the_excludes[0] = new Exclude(0); |
1265 | + | the_excludes[0]->setPair( 0,0 ); |
1266 | + | info->globalExcludes = new int; |
1267 | + | info->globalExcludes[0] = 0; |
1268 | + | info->n_exclude = 0; |
1269 | + | } |
1270 | + | |
1271 | + | // set the arrays into the SimInfo object |
1272 | + | |
1273 | + | info->atoms = the_atoms; |
1274 | + | info->molecules = the_molecules; |
1275 | + | info->nGlobalExcludes = 0; |
1276 | + | info->excludes = the_excludes; |
1277 | + | |
1278 | + | the_ff->setSimInfo( info ); |
1279 | + | |
1280 | + | } |
1281 | + | |
1282 | + | void SimSetup::makeIntegrator( void ){ |
1283 | + | |
1284 | + | NVT* myNVT = NULL; |
1285 | + | NPTi* myNPTi = NULL; |
1286 | + | NPTf* myNPTf = NULL; |
1287 | + | NPTim* myNPTim = NULL; |
1288 | + | NPTfm* myNPTfm = NULL; |
1289 | + | |
1290 | + | switch( ensembleCase ){ |
1291 | + | |
1292 | + | case NVE_ENS: |
1293 | + | new NVE( info, the_ff ); |
1294 | + | break; |
1295 | + | |
1296 | + | case NVT_ENS: |
1297 | + | myNVT = new NVT( info, the_ff ); |
1298 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1299 | + | |
1300 | + | if (globals->haveTauThermostat()) |
1301 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1302 | + | |
1303 | + | else { |
1304 | + | sprintf( painCave.errMsg, |
1305 | + | "SimSetup error: If you use the NVT\n" |
1306 | + | " ensemble, you must set tauThermostat.\n"); |
1307 | + | painCave.isFatal = 1; |
1308 | + | simError(); |
1309 | + | } |
1310 | + | break; |
1311 | + | |
1312 | + | case NPTi_ENS: |
1313 | + | myNPTi = new NPTi( info, the_ff ); |
1314 | + | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1315 | + | |
1316 | + | if (globals->haveTargetPressure()) |
1317 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1318 | + | else { |
1319 | + | sprintf( painCave.errMsg, |
1320 | + | "SimSetup error: If you use a constant pressure\n" |
1321 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1322 | + | painCave.isFatal = 1; |
1323 | + | simError(); |
1324 | + | } |
1325 | + | |
1326 | + | if( globals->haveTauThermostat() ) |
1327 | + | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1328 | + | else{ |
1329 | + | sprintf( painCave.errMsg, |
1330 | + | "SimSetup error: If you use an NPT\n" |
1331 | + | " ensemble, you must set tauThermostat.\n"); |
1332 | + | painCave.isFatal = 1; |
1333 | + | simError(); |
1334 | + | } |
1335 | + | |
1336 | + | if( globals->haveTauBarostat() ) |
1337 | + | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1338 | + | else{ |
1339 | + | sprintf( painCave.errMsg, |
1340 | + | "SimSetup error: If you use an NPT\n" |
1341 | + | " ensemble, you must set tauBarostat.\n"); |
1342 | + | painCave.isFatal = 1; |
1343 | + | simError(); |
1344 | + | } |
1345 | + | break; |
1346 | + | |
1347 | + | case NPTf_ENS: |
1348 | + | myNPTf = new NPTf( info, the_ff ); |
1349 | + | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1350 | + | |
1351 | + | if (globals->haveTargetPressure()) |
1352 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1353 | + | else { |
1354 | + | sprintf( painCave.errMsg, |
1355 | + | "SimSetup error: If you use a constant pressure\n" |
1356 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1357 | + | painCave.isFatal = 1; |
1358 | + | simError(); |
1359 | + | } |
1360 | + | |
1361 | + | if( globals->haveTauThermostat() ) |
1362 | + | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1363 | + | else{ |
1364 | + | sprintf( painCave.errMsg, |
1365 | + | "SimSetup error: If you use an NPT\n" |
1366 | + | " ensemble, you must set tauThermostat.\n"); |
1367 | + | painCave.isFatal = 1; |
1368 | + | simError(); |
1369 | + | } |
1370 | + | |
1371 | + | if( globals->haveTauBarostat() ) |
1372 | + | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1373 | + | else{ |
1374 | + | sprintf( painCave.errMsg, |
1375 | + | "SimSetup error: If you use an NPT\n" |
1376 | + | " ensemble, you must set tauBarostat.\n"); |
1377 | + | painCave.isFatal = 1; |
1378 | + | simError(); |
1379 | + | } |
1380 | + | break; |
1381 | + | |
1382 | + | case NPTim_ENS: |
1383 | + | myNPTim = new NPTim( info, the_ff ); |
1384 | + | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1385 | + | |
1386 | + | if (globals->haveTargetPressure()) |
1387 | + | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1388 | + | else { |
1389 | + | sprintf( painCave.errMsg, |
1390 | + | "SimSetup error: If you use a constant pressure\n" |
1391 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1392 | + | painCave.isFatal = 1; |
1393 | + | simError(); |
1394 | + | } |
1395 | + | |
1396 | + | if( globals->haveTauThermostat() ) |
1397 | + | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1398 | + | else{ |
1399 | + | sprintf( painCave.errMsg, |
1400 | + | "SimSetup error: If you use an NPT\n" |
1401 | + | " ensemble, you must set tauThermostat.\n"); |
1402 | + | painCave.isFatal = 1; |
1403 | + | simError(); |
1404 | + | } |
1405 | + | |
1406 | + | if( globals->haveTauBarostat() ) |
1407 | + | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1408 | + | else{ |
1409 | + | sprintf( painCave.errMsg, |
1410 | + | "SimSetup error: If you use an NPT\n" |
1411 | + | " ensemble, you must set tauBarostat.\n"); |
1412 | + | painCave.isFatal = 1; |
1413 | + | simError(); |
1414 | + | } |
1415 | + | break; |
1416 | + | |
1417 | + | case NPTfm_ENS: |
1418 | + | myNPTfm = new NPTfm( info, the_ff ); |
1419 | + | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1420 | + | |
1421 | + | if (globals->haveTargetPressure()) |
1422 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1423 | + | else { |
1424 | + | sprintf( painCave.errMsg, |
1425 | + | "SimSetup error: If you use a constant pressure\n" |
1426 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1427 | + | painCave.isFatal = 1; |
1428 | + | simError(); |
1429 | + | } |
1430 | + | |
1431 | + | if( globals->haveTauThermostat() ) |
1432 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1433 | + | else{ |
1434 | + | sprintf( painCave.errMsg, |
1435 | + | "SimSetup error: If you use an NPT\n" |
1436 | + | " ensemble, you must set tauThermostat.\n"); |
1437 | + | painCave.isFatal = 1; |
1438 | + | simError(); |
1439 | + | } |
1440 | + | |
1441 | + | if( globals->haveTauBarostat() ) |
1442 | + | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1443 | + | else{ |
1444 | + | sprintf( painCave.errMsg, |
1445 | + | "SimSetup error: If you use an NPT\n" |
1446 | + | " ensemble, you must set tauBarostat.\n"); |
1447 | + | painCave.isFatal = 1; |
1448 | + | simError(); |
1449 | + | } |
1450 | + | break; |
1451 | + | |
1452 | + | default: |
1453 | + | sprintf( painCave.errMsg, |
1454 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1455 | + | painCave.isFatal = 1; |
1456 | + | simError(); |
1457 | + | } |
1458 | + | |
1459 | + | } |
1460 | + | |
1461 | + | void SimSetup::initFortran( void ){ |
1462 | + | |
1463 | + | info->refreshSim(); |
1464 | + | |
1465 | + | if( !strcmp( info->mixingRule, "standard") ){ |
1466 | + | the_ff->initForceField( LB_MIXING_RULE ); |
1467 | + | } |
1468 | + | else if( !strcmp( info->mixingRule, "explicit") ){ |
1469 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1470 | + | } |
1471 | + | else{ |
1472 | + | sprintf( painCave.errMsg, |
1473 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1474 | + | info->mixingRule ); |
1475 | + | painCave.isFatal = 1; |
1476 | + | simError(); |
1477 | + | } |
1478 | + | |
1479 | + | |
1480 | + | #ifdef IS_MPI |
1481 | + | strcpy( checkPointMsg, |
1482 | + | "Successfully intialized the mixingRule for Fortran." ); |
1483 | + | MPIcheckPoint(); |
1484 | + | #endif // is_mpi |
1485 | + | |
1486 | + | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |