# | Line 1 | Line 1 | |
---|---|---|
1 | + | #include <algorithm> |
2 | #include <cstdlib> | |
3 | #include <iostream> | |
4 | #include <cmath> | |
5 | + | #include <string> |
6 | ||
7 | #include "SimSetup.hpp" | |
8 | #include "parse_me.h" | |
# | Line 12 | Line 14 | |
14 | #include "mpiSimulation.hpp" | |
15 | #endif | |
16 | ||
17 | + | // some defines for ensemble and Forcefield cases |
18 | + | |
19 | + | #define NVE_ENS 0 |
20 | + | #define NVT_ENS 1 |
21 | + | #define NPTi_ENS 2 |
22 | + | #define NPTf_ENS 3 |
23 | + | #define NPTim_ENS 4 |
24 | + | #define NPTfm_ENS 5 |
25 | + | #define NVEZCONS_ENS 6 |
26 | + | #define NVTZCONS_ENS 7 |
27 | + | #define NPTiZCONS_ENS 8 |
28 | + | #define NPTfZCONS_ENS 9 |
29 | + | #define NPTimZCONS_ENS 10 |
30 | + | #define NPTfmZCONS_ENS 11 |
31 | + | |
32 | + | #define FF_DUFF 0 |
33 | + | #define FF_LJ 1 |
34 | + | #define FF_EAM 2 |
35 | + | |
36 | + | using namespace std; |
37 | + | |
38 | SimSetup::SimSetup(){ | |
39 | + | |
40 | + | isInfoArray = 0; |
41 | + | nInfo = 1; |
42 | + | |
43 | stamps = new MakeStamps(); | |
44 | globals = new Globals(); | |
45 | ||
46 | + | |
47 | #ifdef IS_MPI | |
48 | strcpy( checkPointMsg, "SimSetup creation successful" ); | |
49 | MPIcheckPoint(); | |
# | Line 27 | Line 55 | SimSetup::~SimSetup(){ | |
55 | delete globals; | |
56 | } | |
57 | ||
58 | + | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
59 | + | info = the_info; |
60 | + | nInfo = theNinfo; |
61 | + | isInfoArray = 1; |
62 | + | } |
63 | + | |
64 | + | |
65 | void SimSetup::parseFile( char* fileName ){ | |
66 | ||
67 | #ifdef IS_MPI | |
# | Line 64 | Line 99 | void SimSetup::createSim( void ){ | |
99 | ||
100 | void SimSetup::createSim( void ){ | |
101 | ||
102 | < | 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 | < | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
91 | < | } else if ( !strcasecmp( ensemble, "NVT") ) { |
92 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
93 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
94 | < | } else if ( !strcasecmp( ensemble, "NVE") ) { |
95 | < | } else { |
96 | < | sprintf( painCave.errMsg, |
97 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
98 | < | "reverting to NVE for this simulation.\n", |
99 | < | ensemble ); |
100 | < | painCave.isFatal = 0; |
101 | < | simError(); |
102 | < | strcpy( ensemble, "NVE" ); |
103 | < | } |
104 | < | strcpy( simnfo->ensemble, ensemble ); |
105 | < | |
106 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
107 | < | simnfo->usePBC = the_globals->getPBC(); |
108 | < | |
109 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
110 | < | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
111 | < | else{ |
112 | < | sprintf( painCave.errMsg, |
113 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
114 | < | force_field ); |
115 | < | painCave.isFatal = 1; |
116 | < | simError(); |
117 | < | } |
118 | < | |
119 | < | #ifdef IS_MPI |
120 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
121 | < | MPIcheckPoint(); |
122 | < | #endif // is_mpi |
123 | < | |
102 | > | int i, j, k, globalAtomIndex; |
103 | ||
104 | < | |
126 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
127 | < | the_components = the_globals->getComponents(); |
128 | < | components_nmol = new int[n_components]; |
129 | < | comp_stamps = new MoleculeStamp*[n_components]; |
130 | < | |
131 | < | if( !the_globals->haveNMol() ){ |
132 | < | // we don't have the total number of molecules, so we assume it is |
133 | < | // given in each component |
134 | < | |
135 | < | tot_nmol = 0; |
136 | < | for( i=0; i<n_components; i++ ){ |
137 | < | |
138 | < | if( !the_components[i]->haveNMol() ){ |
139 | < | // we have a problem |
140 | < | sprintf( painCave.errMsg, |
141 | < | "SimSetup Error. No global NMol or component NMol" |
142 | < | " given. Cannot calculate the number of atoms.\n" ); |
143 | < | painCave.isFatal = 1; |
144 | < | simError(); |
145 | < | } |
146 | < | |
147 | < | tot_nmol += the_components[i]->getNMol(); |
148 | < | components_nmol[i] = the_components[i]->getNMol(); |
149 | < | } |
150 | < | } |
151 | < | else{ |
152 | < | sprintf( painCave.errMsg, |
153 | < | "SimSetup error.\n" |
154 | < | "\tSorry, the ability to specify total" |
155 | < | " nMols and then give molfractions in the components\n" |
156 | < | "\tis not currently supported." |
157 | < | " Please give nMol in the components.\n" ); |
158 | < | painCave.isFatal = 1; |
159 | < | simError(); |
160 | < | |
161 | < | |
162 | < | // tot_nmol = the_globals->getNMol(); |
163 | < | |
164 | < | // //we have the total number of molecules, now we check for molfractions |
165 | < | // for( i=0; i<n_components; i++ ){ |
166 | < | |
167 | < | // if( !the_components[i]->haveMolFraction() ){ |
168 | < | |
169 | < | // if( !the_components[i]->haveNMol() ){ |
170 | < | // //we have a problem |
171 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
172 | < | // << " nMol was given in component |
173 | < | |
174 | < | } |
175 | < | |
176 | < | #ifdef IS_MPI |
177 | < | strcpy( checkPointMsg, "Have the number of components" ); |
178 | < | MPIcheckPoint(); |
179 | < | #endif // is_mpi |
180 | < | |
181 | < | // make an array of molecule stamps that match the components used. |
182 | < | // also extract the used stamps out into a separate linked list |
183 | < | |
184 | < | simnfo->nComponents = n_components; |
185 | < | simnfo->componentsNmol = components_nmol; |
186 | < | simnfo->compStamps = comp_stamps; |
187 | < | simnfo->headStamp = new LinkedMolStamp(); |
104 | > | // gather all of the information from the Bass file |
105 | ||
106 | < | char* id; |
190 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
191 | < | LinkedMolStamp* currentStamp = NULL; |
192 | < | for( i=0; i<n_components; i++ ){ |
106 | > | gatherInfo(); |
107 | ||
108 | < | id = the_components[i]->getType(); |
195 | < | comp_stamps[i] = NULL; |
196 | < | |
197 | < | // check to make sure the component isn't already in the list |
108 | > | // creation of complex system objects |
109 | ||
110 | < | comp_stamps[i] = headStamp->match( id ); |
200 | < | if( comp_stamps[i] == NULL ){ |
201 | < | |
202 | < | // extract the component from the list; |
203 | < | |
204 | < | currentStamp = the_stamps->extractMolStamp( id ); |
205 | < | if( currentStamp == NULL ){ |
206 | < | sprintf( painCave.errMsg, |
207 | < | "SimSetup error: Component \"%s\" was not found in the " |
208 | < | "list of declared molecules\n", |
209 | < | id ); |
210 | < | painCave.isFatal = 1; |
211 | < | simError(); |
212 | < | } |
213 | < | |
214 | < | headStamp->add( currentStamp ); |
215 | < | comp_stamps[i] = headStamp->match( id ); |
216 | < | } |
217 | < | } |
110 | > | sysObjectsCreation(); |
111 | ||
112 | < | #ifdef IS_MPI |
220 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
221 | < | MPIcheckPoint(); |
222 | < | #endif // is_mpi |
112 | > | // check on the post processing info |
113 | ||
114 | + | finalInfoCheck(); |
115 | ||
116 | + | // initialize the system coordinates |
117 | ||
118 | < | |
227 | < | // caclulate the number of atoms, bonds, bends and torsions |
228 | < | |
229 | < | tot_atoms = 0; |
230 | < | tot_bonds = 0; |
231 | < | tot_bends = 0; |
232 | < | tot_torsions = 0; |
233 | < | for( i=0; i<n_components; i++ ){ |
234 | < | |
235 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
236 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
237 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
238 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
239 | < | } |
240 | < | |
241 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
242 | < | |
243 | < | simnfo->n_atoms = tot_atoms; |
244 | < | simnfo->n_bonds = tot_bonds; |
245 | < | simnfo->n_bends = tot_bends; |
246 | < | simnfo->n_torsions = tot_torsions; |
247 | < | simnfo->n_SRI = tot_SRI; |
248 | < | simnfo->n_mol = tot_nmol; |
249 | < | |
118 | > | initSystemCoords(); |
119 | ||
251 | – | #ifdef IS_MPI |
120 | ||
121 | < | // divide the molecules among processors here. |
254 | < | |
255 | < | mpiSim = new mpiSimulation( simnfo ); |
256 | < | |
257 | < | |
258 | < | |
259 | < | globalIndex = mpiSim->divideLabor(); |
260 | < | |
261 | < | // set up the local variables |
262 | < | |
263 | < | int localMol, allMol; |
264 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
265 | < | |
266 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
267 | < | int* molCompType = mpiSim->getMolComponentType(); |
268 | < | |
269 | < | allMol = 0; |
270 | < | localMol = 0; |
271 | < | local_atoms = 0; |
272 | < | local_bonds = 0; |
273 | < | local_bends = 0; |
274 | < | local_torsions = 0; |
275 | < | for( i=0; i<n_components; i++ ){ |
276 | < | |
277 | < | for( j=0; j<components_nmol[i]; j++ ){ |
278 | < | |
279 | < | if( mol2proc[j] == worldRank ){ |
280 | < | |
281 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
282 | < | local_bonds += comp_stamps[i]->getNBonds(); |
283 | < | local_bends += comp_stamps[i]->getNBends(); |
284 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
285 | < | localMol++; |
286 | < | } |
287 | < | allMol++; |
288 | < | } |
289 | < | } |
290 | < | local_SRI = local_bonds + local_bends + local_torsions; |
291 | < | |
121 | > | // make the output filenames |
122 | ||
123 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
123 | > | makeOutNames(); |
124 | > | |
125 | > | // make the integrator |
126 | ||
127 | < | if( local_atoms != simnfo->n_atoms ){ |
296 | < | sprintf( painCave.errMsg, |
297 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
298 | < | " localAtom (%d) are not equal.\n", |
299 | < | simnfo->n_atoms, |
300 | < | local_atoms ); |
301 | < | painCave.isFatal = 1; |
302 | < | simError(); |
303 | < | } |
304 | < | |
305 | < | simnfo->n_bonds = local_bonds; |
306 | < | simnfo->n_bends = local_bends; |
307 | < | simnfo->n_torsions = local_torsions; |
308 | < | simnfo->n_SRI = local_SRI; |
309 | < | simnfo->n_mol = localMol; |
310 | < | |
311 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
312 | < | MPIcheckPoint(); |
313 | < | |
314 | < | |
315 | < | #endif // is_mpi |
316 | < | |
317 | < | |
318 | < | // create the atom and short range interaction arrays |
319 | < | |
320 | < | Atom::createArrays(simnfo->n_atoms); |
321 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
322 | < | the_molecules = new Molecule[simnfo->n_mol]; |
323 | < | int molIndex; |
324 | < | |
325 | < | // initialize the molecule's stampID's |
326 | < | |
327 | < | #ifdef IS_MPI |
328 | < | |
329 | < | |
330 | < | molIndex = 0; |
331 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
332 | < | |
333 | < | if(mol2proc[i] == worldRank ){ |
334 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
335 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
336 | < | molIndex++; |
337 | < | } |
338 | < | } |
339 | < | |
340 | < | #else // is_mpi |
341 | < | |
342 | < | molIndex = 0; |
343 | < | for(i=0; i<n_components; i++){ |
344 | < | for(j=0; j<components_nmol[i]; j++ ){ |
345 | < | the_molecules[molIndex].setStampID( i ); |
346 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
347 | < | molIndex++; |
348 | < | } |
349 | < | } |
350 | < | |
351 | < | |
352 | < | #endif // is_mpi |
353 | < | |
354 | < | |
355 | < | if( simnfo->n_SRI ){ |
356 | < | |
357 | < | Exclude::createArray(simnfo->n_SRI); |
358 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
359 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
360 | < | simnfo->globalExcludes = new int; |
361 | < | simnfo->n_exclude = simnfo->n_SRI; |
362 | < | } |
363 | < | else{ |
364 | < | |
365 | < | Exclude::createArray( 1 ); |
366 | < | the_excludes = new Exclude*; |
367 | < | the_excludes[0] = new Exclude(0); |
368 | < | the_excludes[0]->setPair( 0,0 ); |
369 | < | simnfo->globalExcludes = new int; |
370 | < | simnfo->globalExcludes[0] = 0; |
371 | < | simnfo->n_exclude = 0; |
372 | < | } |
373 | < | |
374 | < | // set the arrays into the SimInfo object |
375 | < | |
376 | < | simnfo->atoms = the_atoms; |
377 | < | simnfo->molecules = the_molecules; |
378 | < | simnfo->nGlobalExcludes = 0; |
379 | < | simnfo->excludes = the_excludes; |
380 | < | |
381 | < | |
382 | < | // get some of the tricky things that may still be in the globals |
383 | < | |
384 | < | |
385 | < | if( the_globals->haveBox() ){ |
386 | < | simnfo->box_x = the_globals->getBox(); |
387 | < | simnfo->box_y = the_globals->getBox(); |
388 | < | simnfo->box_z = the_globals->getBox(); |
389 | < | } |
390 | < | else if( the_globals->haveDensity() ){ |
391 | < | |
392 | < | double vol; |
393 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
394 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
395 | < | simnfo->box_y = simnfo->box_x; |
396 | < | simnfo->box_z = simnfo->box_x; |
397 | < | } |
398 | < | else{ |
399 | < | if( !the_globals->haveBoxX() ){ |
400 | < | sprintf( painCave.errMsg, |
401 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
402 | < | painCave.isFatal = 1; |
403 | < | simError(); |
404 | < | } |
405 | < | simnfo->box_x = the_globals->getBoxX(); |
406 | < | |
407 | < | if( !the_globals->haveBoxY() ){ |
408 | < | sprintf( painCave.errMsg, |
409 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
410 | < | painCave.isFatal = 1; |
411 | < | simError(); |
412 | < | } |
413 | < | simnfo->box_y = the_globals->getBoxY(); |
414 | < | |
415 | < | if( !the_globals->haveBoxZ() ){ |
416 | < | sprintf( painCave.errMsg, |
417 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
418 | < | painCave.isFatal = 1; |
419 | < | simError(); |
420 | < | } |
421 | < | simnfo->box_z = the_globals->getBoxZ(); |
422 | < | } |
423 | < | |
424 | < | #ifdef IS_MPI |
425 | < | strcpy( checkPointMsg, "Box size set up" ); |
426 | < | MPIcheckPoint(); |
427 | < | #endif // is_mpi |
428 | < | |
429 | < | |
430 | < | // initialize the arrays |
431 | < | |
432 | < | the_ff->setSimInfo( simnfo ); |
433 | < | |
434 | < | makeMolecules(); |
435 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
436 | < | for(i=0; i<simnfo->n_atoms; i++){ |
437 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
438 | < | } |
439 | < | |
440 | < | if (the_globals->getUseRF() ) { |
441 | < | simnfo->useReactionField = 1; |
442 | < | |
443 | < | if( !the_globals->haveECR() ){ |
444 | < | sprintf( painCave.errMsg, |
445 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
446 | < | "box length for the electrostaticCutoffRadius.\n" |
447 | < | "I hope you have a very fast processor!\n"); |
448 | < | painCave.isFatal = 0; |
449 | < | simError(); |
450 | < | double smallest; |
451 | < | smallest = simnfo->box_x; |
452 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
453 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
454 | < | simnfo->ecr = 0.5 * smallest; |
455 | < | } else { |
456 | < | simnfo->ecr = the_globals->getECR(); |
457 | < | } |
458 | < | |
459 | < | if( !the_globals->haveEST() ){ |
460 | < | sprintf( painCave.errMsg, |
461 | < | "SimSetup Warning: using default value of 0.05 * the " |
462 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
463 | < | ); |
464 | < | painCave.isFatal = 0; |
465 | < | simError(); |
466 | < | simnfo->est = 0.05 * simnfo->ecr; |
467 | < | } else { |
468 | < | simnfo->est = the_globals->getEST(); |
469 | < | } |
470 | < | |
471 | < | if(!the_globals->haveDielectric() ){ |
472 | < | sprintf( painCave.errMsg, |
473 | < | "SimSetup Error: You are trying to use Reaction Field without" |
474 | < | "setting a dielectric constant!\n" |
475 | < | ); |
476 | < | painCave.isFatal = 1; |
477 | < | simError(); |
478 | < | } |
479 | < | simnfo->dielectric = the_globals->getDielectric(); |
480 | < | } else { |
481 | < | if (simnfo->n_dipoles) { |
482 | < | |
483 | < | if( !the_globals->haveECR() ){ |
484 | < | sprintf( painCave.errMsg, |
485 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
486 | < | "box length for the electrostaticCutoffRadius.\n" |
487 | < | "I hope you have a very fast processor!\n"); |
488 | < | painCave.isFatal = 0; |
489 | < | simError(); |
490 | < | double smallest; |
491 | < | smallest = simnfo->box_x; |
492 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
493 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
494 | < | simnfo->ecr = 0.5 * smallest; |
495 | < | } else { |
496 | < | simnfo->ecr = the_globals->getECR(); |
497 | < | } |
498 | < | |
499 | < | if( !the_globals->haveEST() ){ |
500 | < | sprintf( painCave.errMsg, |
501 | < | "SimSetup Warning: using default value of 5% of the" |
502 | < | "electrostaticCutoffRadius for the " |
503 | < | "electrostaticSkinThickness\n" |
504 | < | ); |
505 | < | painCave.isFatal = 0; |
506 | < | simError(); |
507 | < | simnfo->est = 0.05 * simnfo->ecr; |
508 | < | } else { |
509 | < | simnfo->est = the_globals->getEST(); |
510 | < | } |
511 | < | } |
512 | < | } |
513 | < | |
514 | < | #ifdef IS_MPI |
515 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
516 | < | MPIcheckPoint(); |
517 | < | #endif // is_mpi |
518 | < | |
519 | < | if( the_globals->haveInitialConfig() ){ |
520 | < | |
521 | < | InitializeFromFile* fileInit; |
522 | < | #ifdef IS_MPI // is_mpi |
523 | < | if( worldRank == 0 ){ |
524 | < | #endif //is_mpi |
525 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
526 | < | #ifdef IS_MPI |
527 | < | }else fileInit = new InitializeFromFile( NULL ); |
528 | < | #endif |
529 | < | fileInit->read_xyz( simnfo ); // default velocities on |
530 | < | |
531 | < | delete fileInit; |
532 | < | } |
533 | < | else{ |
534 | < | |
535 | < | #ifdef IS_MPI |
536 | < | |
537 | < | // no init from bass |
127 | > | makeIntegrator(); |
128 | ||
539 | – | sprintf( painCave.errMsg, |
540 | – | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
541 | – | painCave.isFatal; |
542 | – | simError(); |
543 | – | |
544 | – | #else |
545 | – | |
546 | – | initFromBass(); |
547 | – | |
548 | – | |
549 | – | #endif |
550 | – | } |
551 | – | |
129 | #ifdef IS_MPI | |
553 | – | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
554 | – | MPIcheckPoint(); |
555 | – | #endif // is_mpi |
556 | – | |
557 | – | |
558 | – | |
559 | – | |
560 | – | |
561 | – | |
562 | – | |
563 | – | #ifdef IS_MPI |
564 | – | if( worldRank == 0 ){ |
565 | – | #endif // is_mpi |
566 | – | |
567 | – | if( the_globals->haveFinalConfig() ){ |
568 | – | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
569 | – | } |
570 | – | else{ |
571 | – | strcpy( simnfo->finalName, inFileName ); |
572 | – | char* endTest; |
573 | – | int nameLength = strlen( simnfo->finalName ); |
574 | – | endTest = &(simnfo->finalName[nameLength - 5]); |
575 | – | if( !strcmp( endTest, ".bass" ) ){ |
576 | – | strcpy( endTest, ".eor" ); |
577 | – | } |
578 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
579 | – | strcpy( endTest, ".eor" ); |
580 | – | } |
581 | – | else{ |
582 | – | endTest = &(simnfo->finalName[nameLength - 4]); |
583 | – | if( !strcmp( endTest, ".bss" ) ){ |
584 | – | strcpy( endTest, ".eor" ); |
585 | – | } |
586 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
587 | – | strcpy( endTest, ".eor" ); |
588 | – | } |
589 | – | else{ |
590 | – | strcat( simnfo->finalName, ".eor" ); |
591 | – | } |
592 | – | } |
593 | – | } |
594 | – | |
595 | – | // make the sample and status out names |
596 | – | |
597 | – | strcpy( simnfo->sampleName, inFileName ); |
598 | – | char* endTest; |
599 | – | int nameLength = strlen( simnfo->sampleName ); |
600 | – | endTest = &(simnfo->sampleName[nameLength - 5]); |
601 | – | if( !strcmp( endTest, ".bass" ) ){ |
602 | – | strcpy( endTest, ".dump" ); |
603 | – | } |
604 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
605 | – | strcpy( endTest, ".dump" ); |
606 | – | } |
607 | – | else{ |
608 | – | endTest = &(simnfo->sampleName[nameLength - 4]); |
609 | – | if( !strcmp( endTest, ".bss" ) ){ |
610 | – | strcpy( endTest, ".dump" ); |
611 | – | } |
612 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
613 | – | strcpy( endTest, ".dump" ); |
614 | – | } |
615 | – | else{ |
616 | – | strcat( simnfo->sampleName, ".dump" ); |
617 | – | } |
618 | – | } |
619 | – | |
620 | – | strcpy( simnfo->statusName, inFileName ); |
621 | – | nameLength = strlen( simnfo->statusName ); |
622 | – | endTest = &(simnfo->statusName[nameLength - 5]); |
623 | – | if( !strcmp( endTest, ".bass" ) ){ |
624 | – | strcpy( endTest, ".stat" ); |
625 | – | } |
626 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
627 | – | strcpy( endTest, ".stat" ); |
628 | – | } |
629 | – | else{ |
630 | – | endTest = &(simnfo->statusName[nameLength - 4]); |
631 | – | if( !strcmp( endTest, ".bss" ) ){ |
632 | – | strcpy( endTest, ".stat" ); |
633 | – | } |
634 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
635 | – | strcpy( endTest, ".stat" ); |
636 | – | } |
637 | – | else{ |
638 | – | strcat( simnfo->statusName, ".stat" ); |
639 | – | } |
640 | – | } |
641 | – | |
642 | – | #ifdef IS_MPI |
643 | – | } |
644 | – | #endif // is_mpi |
645 | – | |
646 | – | // set the status, sample, and themal kick times |
647 | – | |
648 | – | if( the_globals->haveSampleTime() ){ |
649 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
650 | – | simnfo->statusTime = simnfo->sampleTime; |
651 | – | simnfo->thermalTime = simnfo->sampleTime; |
652 | – | } |
653 | – | else{ |
654 | – | simnfo->sampleTime = the_globals->getRunTime(); |
655 | – | simnfo->statusTime = simnfo->sampleTime; |
656 | – | simnfo->thermalTime = simnfo->sampleTime; |
657 | – | } |
658 | – | |
659 | – | if( the_globals->haveStatusTime() ){ |
660 | – | simnfo->statusTime = the_globals->getStatusTime(); |
661 | – | } |
662 | – | |
663 | – | if( the_globals->haveThermalTime() ){ |
664 | – | simnfo->thermalTime = the_globals->getThermalTime(); |
665 | – | } |
666 | – | |
667 | – | // check for the temperature set flag |
668 | – | |
669 | – | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
670 | – | |
671 | – | |
672 | – | // // make the longe range forces and the integrator |
673 | – | |
674 | – | // new AllLong( simnfo ); |
675 | – | |
676 | – | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo, |
677 | – | the_ff, |
678 | – | the_extendedsystem); |
679 | – | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, |
680 | – | the_ff, |
681 | – | the_extendedsystem ); |
682 | – | |
683 | – | #ifdef IS_MPI |
130 | mpiSim->mpiRefresh(); | |
131 | #endif | |
132 | ||
133 | // initialize the Fortran | |
134 | ||
135 | + | initFortran(); |
136 | ||
690 | – | simnfo->refreshSim(); |
691 | – | |
692 | – | if( !strcmp( simnfo->mixingRule, "standard") ){ |
693 | – | the_ff->initForceField( LB_MIXING_RULE ); |
694 | – | } |
695 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
696 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
697 | – | } |
698 | – | else{ |
699 | – | sprintf( painCave.errMsg, |
700 | – | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
701 | – | simnfo->mixingRule ); |
702 | – | painCave.isFatal = 1; |
703 | – | simError(); |
704 | – | } |
137 | ||
138 | ||
707 | – | #ifdef IS_MPI |
708 | – | strcpy( checkPointMsg, |
709 | – | "Successfully intialized the mixingRule for Fortran." ); |
710 | – | MPIcheckPoint(); |
711 | – | #endif // is_mpi |
139 | } | |
140 | ||
141 | ||
142 | void SimSetup::makeMolecules( void ){ | |
143 | ||
144 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
145 | < | molInit info; |
145 | > | molInit molInfo; |
146 | DirectionalAtom* dAtom; | |
147 | LinkedAssign* extras; | |
148 | LinkedAssign* current_extra; | |
# | Line 740 | Line 167 | void SimSetup::makeMolecules( void ){ | |
167 | ||
168 | atomOffset = 0; | |
169 | excludeOffset = 0; | |
170 | < | for(i=0; i<simnfo->n_mol; i++){ |
170 | > | for(i=0; i<info->n_mol; i++){ |
171 | ||
172 | stampID = the_molecules[i].getStampID(); | |
173 | ||
174 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
175 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
176 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
177 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
174 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
175 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
176 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
177 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
179 | ||
180 | < | info.myAtoms = &the_atoms[atomOffset]; |
181 | < | info.myExcludes = &the_excludes[excludeOffset]; |
182 | < | info.myBonds = new Bond*[info.nBonds]; |
183 | < | info.myBends = new Bend*[info.nBends]; |
184 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
180 | > | molInfo.myAtoms = &the_atoms[atomOffset]; |
181 | > | molInfo.myExcludes = &the_excludes[excludeOffset]; |
182 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
183 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
184 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
185 | ||
186 | < | theBonds = new bond_pair[info.nBonds]; |
187 | < | theBends = new bend_set[info.nBends]; |
188 | < | theTorsions = new torsion_set[info.nTorsions]; |
186 | > | theBonds = new bond_pair[molInfo.nBonds]; |
187 | > | theBends = new bend_set[molInfo.nBends]; |
188 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
189 | ||
190 | // make the Atoms | |
191 | ||
192 | < | for(j=0; j<info.nAtoms; j++){ |
192 | > | for(j=0; j<molInfo.nAtoms; j++){ |
193 | ||
194 | currentAtom = comp_stamps[stampID]->getAtom( j ); | |
195 | if( currentAtom->haveOrientation() ){ | |
196 | ||
197 | dAtom = new DirectionalAtom(j + atomOffset); | |
198 | < | simnfo->n_oriented++; |
199 | < | info.myAtoms[j] = dAtom; |
198 | > | info->n_oriented++; |
199 | > | molInfo.myAtoms[j] = dAtom; |
200 | ||
201 | ux = currentAtom->getOrntX(); | |
202 | uy = currentAtom->getOrntY(); | |
# | Line 787 | Line 214 | void SimSetup::makeMolecules( void ){ | |
214 | dAtom->setSUz( uz ); | |
215 | } | |
216 | else{ | |
217 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
217 | > | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
218 | } | |
219 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
219 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
220 | ||
221 | #ifdef IS_MPI | |
222 | ||
223 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
223 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
224 | ||
225 | #endif // is_mpi | |
226 | } | |
227 | ||
228 | // make the bonds | |
229 | < | for(j=0; j<info.nBonds; j++){ |
229 | > | for(j=0; j<molInfo.nBonds; j++){ |
230 | ||
231 | currentBond = comp_stamps[stampID]->getBond( j ); | |
232 | theBonds[j].a = currentBond->getA() + atomOffset; | |
# | Line 826 | Line 253 | void SimSetup::makeMolecules( void ){ | |
253 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
254 | #endif //is_mpi | |
255 | } | |
256 | < | excludeOffset += info.nBonds; |
256 | > | excludeOffset += molInfo.nBonds; |
257 | ||
258 | //make the bends | |
259 | < | for(j=0; j<info.nBends; j++){ |
259 | > | for(j=0; j<molInfo.nBends; j++){ |
260 | ||
261 | currentBend = comp_stamps[stampID]->getBend( j ); | |
262 | theBends[j].a = currentBend->getA() + atomOffset; | |
# | Line 912 | Line 339 | void SimSetup::makeMolecules( void ){ | |
339 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
340 | #endif //is_mpi | |
341 | } | |
342 | < | excludeOffset += info.nBends; |
342 | > | excludeOffset += molInfo.nBends; |
343 | ||
344 | < | for(j=0; j<info.nTorsions; j++){ |
344 | > | for(j=0; j<molInfo.nTorsions; j++){ |
345 | ||
346 | currentTorsion = comp_stamps[stampID]->getTorsion( j ); | |
347 | theTorsions[j].a = currentTorsion->getA() + atomOffset; | |
# | Line 942 | Line 369 | void SimSetup::makeMolecules( void ){ | |
369 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
370 | #endif //is_mpi | |
371 | } | |
372 | < | excludeOffset += info.nTorsions; |
372 | > | excludeOffset += molInfo.nTorsions; |
373 | ||
374 | ||
375 | // send the arrays off to the forceField for init. | |
376 | ||
377 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
378 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
379 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
380 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
377 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
378 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
379 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
380 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
381 | ||
382 | ||
383 | < | the_molecules[i].initialize( info ); |
383 | > | the_molecules[i].initialize( molInfo ); |
384 | ||
385 | ||
386 | < | atomOffset += info.nAtoms; |
386 | > | atomOffset += molInfo.nAtoms; |
387 | delete[] theBonds; | |
388 | delete[] theBends; | |
389 | delete[] theTorsions; | |
# | Line 992 | Line 419 | void SimSetup::initFromBass( void ){ | |
419 | have_extra =1; | |
420 | ||
421 | n_cells = (int)temp3 - 1; | |
422 | < | cellx = simnfo->box_x / temp3; |
423 | < | celly = simnfo->box_y / temp3; |
424 | < | cellz = simnfo->box_z / temp3; |
422 | > | cellx = info->boxL[0] / temp3; |
423 | > | celly = info->boxL[1] / temp3; |
424 | > | cellz = info->boxL[2] / temp3; |
425 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
426 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
427 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 1009 | Line 436 | void SimSetup::initFromBass( void ){ | |
436 | } | |
437 | else{ | |
438 | n_cells = (int)temp3; | |
439 | < | cellx = simnfo->box_x / temp3; |
440 | < | celly = simnfo->box_y / temp3; |
441 | < | cellz = simnfo->box_z / temp3; |
439 | > | cellx = info->boxL[0] / temp3; |
440 | > | celly = info->boxL[1] / temp3; |
441 | > | cellz = info->boxL[2] / temp3; |
442 | } | |
443 | ||
444 | current_mol = 0; | |
# | Line 1091 | Line 518 | void SimSetup::initFromBass( void ){ | |
518 | } | |
519 | ||
520 | ||
521 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
522 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
523 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
524 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
521 | > | for( i=0; i<info->n_atoms; i++ ){ |
522 | > | info->atoms[i]->set_vx( 0.0 ); |
523 | > | info->atoms[i]->set_vy( 0.0 ); |
524 | > | info->atoms[i]->set_vz( 0.0 ); |
525 | } | |
526 | } | |
527 | ||
# | Line 1155 | Line 582 | void SimSetup::makeElement( double x, double y, double | |
582 | current_comp++; | |
583 | } | |
584 | } | |
585 | + | |
586 | + | |
587 | + | void SimSetup::gatherInfo( void ){ |
588 | + | int i,j,k; |
589 | + | |
590 | + | ensembleCase = -1; |
591 | + | ffCase = -1; |
592 | + | |
593 | + | // get the stamps and globals; |
594 | + | stamps = stamps; |
595 | + | globals = globals; |
596 | + | |
597 | + | // set the easy ones first |
598 | + | info->target_temp = globals->getTargetTemp(); |
599 | + | info->dt = globals->getDt(); |
600 | + | info->run_time = globals->getRunTime(); |
601 | + | n_components = globals->getNComponents(); |
602 | + | |
603 | + | |
604 | + | // get the forceField |
605 | + | |
606 | + | strcpy( force_field, globals->getForceField() ); |
607 | + | |
608 | + | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
609 | + | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
610 | + | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
611 | + | else{ |
612 | + | sprintf( painCave.errMsg, |
613 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
614 | + | force_field ); |
615 | + | painCave.isFatal = 1; |
616 | + | simError(); |
617 | + | } |
618 | + | |
619 | + | // get the ensemble |
620 | + | |
621 | + | strcpy( ensemble, globals->getEnsemble() ); |
622 | + | |
623 | + | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
624 | + | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
625 | + | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
626 | + | ensembleCase = NPTi_ENS; |
627 | + | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
628 | + | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
629 | + | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
630 | + | |
631 | + | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
632 | + | else if( !strcasecmp( ensemble, "NVTZCONS")) ensembleCase = NVTZCONS_ENS; |
633 | + | else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT")) |
634 | + | ensembleCase = NPTiZCONS_ENS; |
635 | + | else if( !strcasecmp( ensemble, "NPTfCONS")) ensembleCase = NPTfZCONS_ENS; |
636 | + | else if( !strcasecmp( ensemble, "NPTimZCONS")) ensembleCase = NPTimZCONS_ENS; |
637 | + | else if( !strcasecmp( ensemble, "NPTfmCONS")) ensembleCase = NPTfmZCONS_ENS; |
638 | + | |
639 | + | else{ |
640 | + | sprintf( painCave.errMsg, |
641 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
642 | + | "reverting to NVE for this simulation.\n", |
643 | + | ensemble ); |
644 | + | painCave.isFatal = 0; |
645 | + | simError(); |
646 | + | strcpy( ensemble, "NVE" ); |
647 | + | ensembleCase = NVE_ENS; |
648 | + | } |
649 | + | strcpy( info->ensemble, ensemble ); |
650 | + | |
651 | + | // get the mixing rule |
652 | + | |
653 | + | strcpy( info->mixingRule, globals->getMixingRule() ); |
654 | + | info->usePBC = globals->getPBC(); |
655 | + | |
656 | + | |
657 | + | // get the components and calculate the tot_nMol and indvidual n_mol |
658 | + | |
659 | + | the_components = globals->getComponents(); |
660 | + | components_nmol = new int[n_components]; |
661 | + | |
662 | + | |
663 | + | if( !globals->haveNMol() ){ |
664 | + | // we don't have the total number of molecules, so we assume it is |
665 | + | // given in each component |
666 | + | |
667 | + | tot_nmol = 0; |
668 | + | for( i=0; i<n_components; i++ ){ |
669 | + | |
670 | + | if( !the_components[i]->haveNMol() ){ |
671 | + | // we have a problem |
672 | + | sprintf( painCave.errMsg, |
673 | + | "SimSetup Error. No global NMol or component NMol" |
674 | + | " given. Cannot calculate the number of atoms.\n" ); |
675 | + | painCave.isFatal = 1; |
676 | + | simError(); |
677 | + | } |
678 | + | |
679 | + | tot_nmol += the_components[i]->getNMol(); |
680 | + | components_nmol[i] = the_components[i]->getNMol(); |
681 | + | } |
682 | + | } |
683 | + | else{ |
684 | + | sprintf( painCave.errMsg, |
685 | + | "SimSetup error.\n" |
686 | + | "\tSorry, the ability to specify total" |
687 | + | " nMols and then give molfractions in the components\n" |
688 | + | "\tis not currently supported." |
689 | + | " Please give nMol in the components.\n" ); |
690 | + | painCave.isFatal = 1; |
691 | + | simError(); |
692 | + | } |
693 | + | |
694 | + | // set the status, sample, and thermal kick times |
695 | + | |
696 | + | if( globals->haveSampleTime() ){ |
697 | + | info->sampleTime = globals->getSampleTime(); |
698 | + | info->statusTime = info->sampleTime; |
699 | + | info->thermalTime = info->sampleTime; |
700 | + | } |
701 | + | else{ |
702 | + | info->sampleTime = globals->getRunTime(); |
703 | + | info->statusTime = info->sampleTime; |
704 | + | info->thermalTime = info->sampleTime; |
705 | + | } |
706 | + | |
707 | + | if( globals->haveStatusTime() ){ |
708 | + | info->statusTime = globals->getStatusTime(); |
709 | + | } |
710 | + | |
711 | + | if( globals->haveThermalTime() ){ |
712 | + | info->thermalTime = globals->getThermalTime(); |
713 | + | } |
714 | + | |
715 | + | // check for the temperature set flag |
716 | + | |
717 | + | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
718 | + | |
719 | + | // get some of the tricky things that may still be in the globals |
720 | + | |
721 | + | double boxVector[3]; |
722 | + | if( globals->haveBox() ){ |
723 | + | boxVector[0] = globals->getBox(); |
724 | + | boxVector[1] = globals->getBox(); |
725 | + | boxVector[2] = globals->getBox(); |
726 | + | |
727 | + | info->setBox( boxVector ); |
728 | + | } |
729 | + | else if( globals->haveDensity() ){ |
730 | + | |
731 | + | double vol; |
732 | + | vol = (double)tot_nmol / globals->getDensity(); |
733 | + | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
734 | + | boxVector[1] = boxVector[0]; |
735 | + | boxVector[2] = boxVector[0]; |
736 | + | |
737 | + | info->setBox( boxVector ); |
738 | + | } |
739 | + | else{ |
740 | + | if( !globals->haveBoxX() ){ |
741 | + | sprintf( painCave.errMsg, |
742 | + | "SimSetup error, no periodic BoxX size given.\n" ); |
743 | + | painCave.isFatal = 1; |
744 | + | simError(); |
745 | + | } |
746 | + | boxVector[0] = globals->getBoxX(); |
747 | + | |
748 | + | if( !globals->haveBoxY() ){ |
749 | + | sprintf( painCave.errMsg, |
750 | + | "SimSetup error, no periodic BoxY size given.\n" ); |
751 | + | painCave.isFatal = 1; |
752 | + | simError(); |
753 | + | } |
754 | + | boxVector[1] = globals->getBoxY(); |
755 | + | |
756 | + | if( !globals->haveBoxZ() ){ |
757 | + | sprintf( painCave.errMsg, |
758 | + | "SimSetup error, no periodic BoxZ size given.\n" ); |
759 | + | painCave.isFatal = 1; |
760 | + | simError(); |
761 | + | } |
762 | + | boxVector[2] = globals->getBoxZ(); |
763 | + | |
764 | + | info->setBox( boxVector ); |
765 | + | } |
766 | + | |
767 | + | |
768 | + | |
769 | + | #ifdef IS_MPI |
770 | + | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
771 | + | MPIcheckPoint(); |
772 | + | #endif // is_mpi |
773 | + | |
774 | + | } |
775 | + | |
776 | + | |
777 | + | void SimSetup::finalInfoCheck( void ){ |
778 | + | int index; |
779 | + | int usesDipoles; |
780 | + | |
781 | + | |
782 | + | // check electrostatic parameters |
783 | + | |
784 | + | index = 0; |
785 | + | usesDipoles = 0; |
786 | + | while( (index < info->n_atoms) && !usesDipoles ){ |
787 | + | usesDipoles = ((info->atoms)[index])->hasDipole(); |
788 | + | index++; |
789 | + | } |
790 | + | |
791 | + | #ifdef IS_MPI |
792 | + | int myUse = usesDipoles; |
793 | + | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
794 | + | #endif //is_mpi |
795 | + | |
796 | + | double theEcr, theEst; |
797 | + | |
798 | + | if (globals->getUseRF() ) { |
799 | + | info->useReactionField = 1; |
800 | + | |
801 | + | if( !globals->haveECR() ){ |
802 | + | sprintf( painCave.errMsg, |
803 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
804 | + | "box length for the electrostaticCutoffRadius.\n" |
805 | + | "I hope you have a very fast processor!\n"); |
806 | + | painCave.isFatal = 0; |
807 | + | simError(); |
808 | + | double smallest; |
809 | + | smallest = info->boxL[0]; |
810 | + | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
811 | + | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
812 | + | theEcr = 0.5 * smallest; |
813 | + | } else { |
814 | + | theEcr = globals->getECR(); |
815 | + | } |
816 | + | |
817 | + | if( !globals->haveEST() ){ |
818 | + | sprintf( painCave.errMsg, |
819 | + | "SimSetup Warning: using default value of 0.05 * the " |
820 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
821 | + | ); |
822 | + | painCave.isFatal = 0; |
823 | + | simError(); |
824 | + | theEst = 0.05 * theEcr; |
825 | + | } else { |
826 | + | theEst= globals->getEST(); |
827 | + | } |
828 | + | |
829 | + | info->setEcr( theEcr, theEst ); |
830 | + | |
831 | + | if(!globals->haveDielectric() ){ |
832 | + | sprintf( painCave.errMsg, |
833 | + | "SimSetup Error: You are trying to use Reaction Field without" |
834 | + | "setting a dielectric constant!\n" |
835 | + | ); |
836 | + | painCave.isFatal = 1; |
837 | + | simError(); |
838 | + | } |
839 | + | info->dielectric = globals->getDielectric(); |
840 | + | } |
841 | + | else { |
842 | + | if (usesDipoles) { |
843 | + | |
844 | + | if( !globals->haveECR() ){ |
845 | + | sprintf( painCave.errMsg, |
846 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
847 | + | "box length for the electrostaticCutoffRadius.\n" |
848 | + | "I hope you have a very fast processor!\n"); |
849 | + | painCave.isFatal = 0; |
850 | + | simError(); |
851 | + | double smallest; |
852 | + | smallest = info->boxL[0]; |
853 | + | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
854 | + | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
855 | + | theEcr = 0.5 * smallest; |
856 | + | } else { |
857 | + | theEcr = globals->getECR(); |
858 | + | } |
859 | + | |
860 | + | if( !globals->haveEST() ){ |
861 | + | sprintf( painCave.errMsg, |
862 | + | "SimSetup Warning: using default value of 0.05 * the " |
863 | + | "electrostaticCutoffRadius for the " |
864 | + | "electrostaticSkinThickness\n" |
865 | + | ); |
866 | + | painCave.isFatal = 0; |
867 | + | simError(); |
868 | + | theEst = 0.05 * theEcr; |
869 | + | } else { |
870 | + | theEst= globals->getEST(); |
871 | + | } |
872 | + | |
873 | + | info->setEcr( theEcr, theEst ); |
874 | + | } |
875 | + | } |
876 | + | |
877 | + | #ifdef IS_MPI |
878 | + | strcpy( checkPointMsg, "post processing checks out" ); |
879 | + | MPIcheckPoint(); |
880 | + | #endif // is_mpi |
881 | + | |
882 | + | } |
883 | + | |
884 | + | void SimSetup::initSystemCoords( void ){ |
885 | + | |
886 | + | if( globals->haveInitialConfig() ){ |
887 | + | |
888 | + | InitializeFromFile* fileInit; |
889 | + | #ifdef IS_MPI // is_mpi |
890 | + | if( worldRank == 0 ){ |
891 | + | #endif //is_mpi |
892 | + | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
893 | + | #ifdef IS_MPI |
894 | + | }else fileInit = new InitializeFromFile( NULL ); |
895 | + | #endif |
896 | + | fileInit->readInit( info ); // default velocities on |
897 | + | |
898 | + | delete fileInit; |
899 | + | } |
900 | + | else{ |
901 | + | |
902 | + | #ifdef IS_MPI |
903 | + | |
904 | + | // no init from bass |
905 | + | |
906 | + | sprintf( painCave.errMsg, |
907 | + | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
908 | + | painCave.isFatal; |
909 | + | simError(); |
910 | + | |
911 | + | #else |
912 | + | |
913 | + | initFromBass(); |
914 | + | |
915 | + | |
916 | + | #endif |
917 | + | } |
918 | + | |
919 | + | #ifdef IS_MPI |
920 | + | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
921 | + | MPIcheckPoint(); |
922 | + | #endif // is_mpi |
923 | + | |
924 | + | } |
925 | + | |
926 | + | |
927 | + | void SimSetup::makeOutNames( void ){ |
928 | + | |
929 | + | #ifdef IS_MPI |
930 | + | if( worldRank == 0 ){ |
931 | + | #endif // is_mpi |
932 | + | |
933 | + | if( globals->haveFinalConfig() ){ |
934 | + | strcpy( info->finalName, globals->getFinalConfig() ); |
935 | + | } |
936 | + | else{ |
937 | + | strcpy( info->finalName, inFileName ); |
938 | + | char* endTest; |
939 | + | int nameLength = strlen( info->finalName ); |
940 | + | endTest = &(info->finalName[nameLength - 5]); |
941 | + | if( !strcmp( endTest, ".bass" ) ){ |
942 | + | strcpy( endTest, ".eor" ); |
943 | + | } |
944 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
945 | + | strcpy( endTest, ".eor" ); |
946 | + | } |
947 | + | else{ |
948 | + | endTest = &(info->finalName[nameLength - 4]); |
949 | + | if( !strcmp( endTest, ".bss" ) ){ |
950 | + | strcpy( endTest, ".eor" ); |
951 | + | } |
952 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
953 | + | strcpy( endTest, ".eor" ); |
954 | + | } |
955 | + | else{ |
956 | + | strcat( info->finalName, ".eor" ); |
957 | + | } |
958 | + | } |
959 | + | } |
960 | + | |
961 | + | // make the sample and status out names |
962 | + | |
963 | + | strcpy( info->sampleName, inFileName ); |
964 | + | char* endTest; |
965 | + | int nameLength = strlen( info->sampleName ); |
966 | + | endTest = &(info->sampleName[nameLength - 5]); |
967 | + | if( !strcmp( endTest, ".bass" ) ){ |
968 | + | strcpy( endTest, ".dump" ); |
969 | + | } |
970 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
971 | + | strcpy( endTest, ".dump" ); |
972 | + | } |
973 | + | else{ |
974 | + | endTest = &(info->sampleName[nameLength - 4]); |
975 | + | if( !strcmp( endTest, ".bss" ) ){ |
976 | + | strcpy( endTest, ".dump" ); |
977 | + | } |
978 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
979 | + | strcpy( endTest, ".dump" ); |
980 | + | } |
981 | + | else{ |
982 | + | strcat( info->sampleName, ".dump" ); |
983 | + | } |
984 | + | } |
985 | + | |
986 | + | strcpy( info->statusName, inFileName ); |
987 | + | nameLength = strlen( info->statusName ); |
988 | + | endTest = &(info->statusName[nameLength - 5]); |
989 | + | if( !strcmp( endTest, ".bass" ) ){ |
990 | + | strcpy( endTest, ".stat" ); |
991 | + | } |
992 | + | else if( !strcmp( endTest, ".BASS" ) ){ |
993 | + | strcpy( endTest, ".stat" ); |
994 | + | } |
995 | + | else{ |
996 | + | endTest = &(info->statusName[nameLength - 4]); |
997 | + | if( !strcmp( endTest, ".bss" ) ){ |
998 | + | strcpy( endTest, ".stat" ); |
999 | + | } |
1000 | + | else if( !strcmp( endTest, ".mdl" ) ){ |
1001 | + | strcpy( endTest, ".stat" ); |
1002 | + | } |
1003 | + | else{ |
1004 | + | strcat( info->statusName, ".stat" ); |
1005 | + | } |
1006 | + | } |
1007 | + | |
1008 | + | #ifdef IS_MPI |
1009 | + | } |
1010 | + | #endif // is_mpi |
1011 | + | |
1012 | + | } |
1013 | + | |
1014 | + | |
1015 | + | void SimSetup::sysObjectsCreation( void ){ |
1016 | + | |
1017 | + | int i; |
1018 | + | |
1019 | + | // create the forceField |
1020 | + | |
1021 | + | createFF(); |
1022 | + | |
1023 | + | // extract componentList |
1024 | + | |
1025 | + | compList(); |
1026 | + | |
1027 | + | // calc the number of atoms, bond, bends, and torsions |
1028 | + | |
1029 | + | calcSysValues(); |
1030 | + | |
1031 | + | #ifdef IS_MPI |
1032 | + | // divide the molecules among the processors |
1033 | + | |
1034 | + | mpiMolDivide(); |
1035 | + | #endif //is_mpi |
1036 | + | |
1037 | + | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1038 | + | |
1039 | + | makeSysArrays(); |
1040 | + | |
1041 | + | // make and initialize the molecules (all but atomic coordinates) |
1042 | + | |
1043 | + | makeMolecules(); |
1044 | + | info->identArray = new int[info->n_atoms]; |
1045 | + | for(i=0; i<info->n_atoms; i++){ |
1046 | + | info->identArray[i] = the_atoms[i]->getIdent(); |
1047 | + | } |
1048 | + | |
1049 | + | |
1050 | + | |
1051 | + | } |
1052 | + | |
1053 | + | |
1054 | + | void SimSetup::createFF( void ){ |
1055 | + | |
1056 | + | switch( ffCase ){ |
1057 | + | |
1058 | + | case FF_DUFF: |
1059 | + | the_ff = new DUFF(); |
1060 | + | break; |
1061 | + | |
1062 | + | case FF_LJ: |
1063 | + | the_ff = new LJFF(); |
1064 | + | break; |
1065 | + | |
1066 | + | case FF_EAM: |
1067 | + | the_ff = new EAM_FF(); |
1068 | + | break; |
1069 | + | |
1070 | + | default: |
1071 | + | sprintf( painCave.errMsg, |
1072 | + | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1073 | + | painCave.isFatal = 1; |
1074 | + | simError(); |
1075 | + | } |
1076 | + | |
1077 | + | #ifdef IS_MPI |
1078 | + | strcpy( checkPointMsg, "ForceField creation successful" ); |
1079 | + | MPIcheckPoint(); |
1080 | + | #endif // is_mpi |
1081 | + | |
1082 | + | } |
1083 | + | |
1084 | + | |
1085 | + | void SimSetup::compList( void ){ |
1086 | + | |
1087 | + | int i; |
1088 | + | |
1089 | + | comp_stamps = new MoleculeStamp*[n_components]; |
1090 | + | |
1091 | + | // make an array of molecule stamps that match the components used. |
1092 | + | // also extract the used stamps out into a separate linked list |
1093 | + | |
1094 | + | info->nComponents = n_components; |
1095 | + | info->componentsNmol = components_nmol; |
1096 | + | info->compStamps = comp_stamps; |
1097 | + | info->headStamp = new LinkedMolStamp(); |
1098 | + | |
1099 | + | char* id; |
1100 | + | LinkedMolStamp* headStamp = info->headStamp; |
1101 | + | LinkedMolStamp* currentStamp = NULL; |
1102 | + | for( i=0; i<n_components; i++ ){ |
1103 | + | |
1104 | + | id = the_components[i]->getType(); |
1105 | + | comp_stamps[i] = NULL; |
1106 | + | |
1107 | + | // check to make sure the component isn't already in the list |
1108 | + | |
1109 | + | comp_stamps[i] = headStamp->match( id ); |
1110 | + | if( comp_stamps[i] == NULL ){ |
1111 | + | |
1112 | + | // extract the component from the list; |
1113 | + | |
1114 | + | currentStamp = stamps->extractMolStamp( id ); |
1115 | + | if( currentStamp == NULL ){ |
1116 | + | sprintf( painCave.errMsg, |
1117 | + | "SimSetup error: Component \"%s\" was not found in the " |
1118 | + | "list of declared molecules\n", |
1119 | + | id ); |
1120 | + | painCave.isFatal = 1; |
1121 | + | simError(); |
1122 | + | } |
1123 | + | |
1124 | + | headStamp->add( currentStamp ); |
1125 | + | comp_stamps[i] = headStamp->match( id ); |
1126 | + | } |
1127 | + | } |
1128 | + | |
1129 | + | #ifdef IS_MPI |
1130 | + | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1131 | + | MPIcheckPoint(); |
1132 | + | #endif // is_mpi |
1133 | + | |
1134 | + | |
1135 | + | } |
1136 | + | |
1137 | + | void SimSetup::calcSysValues( void ){ |
1138 | + | int i, j, k; |
1139 | + | |
1140 | + | |
1141 | + | tot_atoms = 0; |
1142 | + | tot_bonds = 0; |
1143 | + | tot_bends = 0; |
1144 | + | tot_torsions = 0; |
1145 | + | for( i=0; i<n_components; i++ ){ |
1146 | + | |
1147 | + | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1148 | + | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1149 | + | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1150 | + | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1151 | + | } |
1152 | + | |
1153 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1154 | + | |
1155 | + | info->n_atoms = tot_atoms; |
1156 | + | info->n_bonds = tot_bonds; |
1157 | + | info->n_bends = tot_bends; |
1158 | + | info->n_torsions = tot_torsions; |
1159 | + | info->n_SRI = tot_SRI; |
1160 | + | info->n_mol = tot_nmol; |
1161 | + | |
1162 | + | info->molMembershipArray = new int[tot_atoms]; |
1163 | + | } |
1164 | + | |
1165 | + | |
1166 | + | #ifdef IS_MPI |
1167 | + | |
1168 | + | void SimSetup::mpiMolDivide( void ){ |
1169 | + | |
1170 | + | int i, j, k; |
1171 | + | int localMol, allMol; |
1172 | + | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1173 | + | |
1174 | + | mpiSim = new mpiSimulation( info ); |
1175 | + | |
1176 | + | globalIndex = mpiSim->divideLabor(); |
1177 | + | |
1178 | + | // set up the local variables |
1179 | + | |
1180 | + | mol2proc = mpiSim->getMolToProcMap(); |
1181 | + | molCompType = mpiSim->getMolComponentType(); |
1182 | + | |
1183 | + | allMol = 0; |
1184 | + | localMol = 0; |
1185 | + | local_atoms = 0; |
1186 | + | local_bonds = 0; |
1187 | + | local_bends = 0; |
1188 | + | local_torsions = 0; |
1189 | + | globalAtomIndex = 0; |
1190 | + | |
1191 | + | |
1192 | + | for( i=0; i<n_components; i++ ){ |
1193 | + | |
1194 | + | for( j=0; j<components_nmol[i]; j++ ){ |
1195 | + | |
1196 | + | if( mol2proc[allMol] == worldRank ){ |
1197 | + | |
1198 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1199 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1200 | + | local_bends += comp_stamps[i]->getNBends(); |
1201 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1202 | + | localMol++; |
1203 | + | } |
1204 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1205 | + | info->molMembershipArray[globalAtomIndex] = allMol; |
1206 | + | globalAtomIndex++; |
1207 | + | } |
1208 | + | |
1209 | + | allMol++; |
1210 | + | } |
1211 | + | } |
1212 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1213 | + | |
1214 | + | info->n_atoms = mpiSim->getMyNlocal(); |
1215 | + | |
1216 | + | if( local_atoms != info->n_atoms ){ |
1217 | + | sprintf( painCave.errMsg, |
1218 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1219 | + | " localAtom (%d) are not equal.\n", |
1220 | + | info->n_atoms, |
1221 | + | local_atoms ); |
1222 | + | painCave.isFatal = 1; |
1223 | + | simError(); |
1224 | + | } |
1225 | + | |
1226 | + | info->n_bonds = local_bonds; |
1227 | + | info->n_bends = local_bends; |
1228 | + | info->n_torsions = local_torsions; |
1229 | + | info->n_SRI = local_SRI; |
1230 | + | info->n_mol = localMol; |
1231 | + | |
1232 | + | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1233 | + | MPIcheckPoint(); |
1234 | + | } |
1235 | + | |
1236 | + | #endif // is_mpi |
1237 | + | |
1238 | + | |
1239 | + | void SimSetup::makeSysArrays( void ){ |
1240 | + | int i, j, k; |
1241 | + | |
1242 | + | |
1243 | + | // create the atom and short range interaction arrays |
1244 | + | |
1245 | + | Atom::createArrays(info->n_atoms); |
1246 | + | the_atoms = new Atom*[info->n_atoms]; |
1247 | + | the_molecules = new Molecule[info->n_mol]; |
1248 | + | int molIndex; |
1249 | + | |
1250 | + | // initialize the molecule's stampID's |
1251 | + | |
1252 | + | #ifdef IS_MPI |
1253 | + | |
1254 | + | |
1255 | + | molIndex = 0; |
1256 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1257 | + | |
1258 | + | if(mol2proc[i] == worldRank ){ |
1259 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
1260 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1261 | + | the_molecules[molIndex].setGlobalIndex( i ); |
1262 | + | molIndex++; |
1263 | + | } |
1264 | + | } |
1265 | + | |
1266 | + | #else // is_mpi |
1267 | + | |
1268 | + | molIndex = 0; |
1269 | + | globalAtomIndex = 0; |
1270 | + | for(i=0; i<n_components; i++){ |
1271 | + | for(j=0; j<components_nmol[i]; j++ ){ |
1272 | + | the_molecules[molIndex].setStampID( i ); |
1273 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
1274 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1275 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1276 | + | info->molMembershipArray[globalAtomIndex] = molIndex; |
1277 | + | globalAtomIndex++; |
1278 | + | } |
1279 | + | molIndex++; |
1280 | + | } |
1281 | + | } |
1282 | + | |
1283 | + | |
1284 | + | #endif // is_mpi |
1285 | + | |
1286 | + | |
1287 | + | if( info->n_SRI ){ |
1288 | + | |
1289 | + | Exclude::createArray(info->n_SRI); |
1290 | + | the_excludes = new Exclude*[info->n_SRI]; |
1291 | + | for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1292 | + | info->globalExcludes = new int; |
1293 | + | info->n_exclude = info->n_SRI; |
1294 | + | } |
1295 | + | else{ |
1296 | + | |
1297 | + | Exclude::createArray( 1 ); |
1298 | + | the_excludes = new Exclude*; |
1299 | + | the_excludes[0] = new Exclude(0); |
1300 | + | the_excludes[0]->setPair( 0,0 ); |
1301 | + | info->globalExcludes = new int; |
1302 | + | info->globalExcludes[0] = 0; |
1303 | + | info->n_exclude = 0; |
1304 | + | } |
1305 | + | |
1306 | + | // set the arrays into the SimInfo object |
1307 | + | |
1308 | + | info->atoms = the_atoms; |
1309 | + | info->molecules = the_molecules; |
1310 | + | info->nGlobalExcludes = 0; |
1311 | + | info->excludes = the_excludes; |
1312 | + | |
1313 | + | the_ff->setSimInfo( info ); |
1314 | + | |
1315 | + | } |
1316 | + | |
1317 | + | void SimSetup::makeIntegrator( void ){ |
1318 | + | |
1319 | + | NVT<RealIntegrator>* myNVT = NULL; |
1320 | + | NPTi<RealIntegrator>* myNPTi = NULL; |
1321 | + | NPTf<RealIntegrator>* myNPTf = NULL; |
1322 | + | NPTim<RealIntegrator>* myNPTim = NULL; |
1323 | + | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1324 | + | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1325 | + | ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL; |
1326 | + | ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL; |
1327 | + | ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL; |
1328 | + | ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL; |
1329 | + | ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL; |
1330 | + | |
1331 | + | cerr << "setting integrator" <<endl; |
1332 | + | |
1333 | + | switch( ensembleCase ){ |
1334 | + | |
1335 | + | case NVE_ENS: |
1336 | + | new NVE<RealIntegrator>( info, the_ff ); |
1337 | + | break; |
1338 | + | |
1339 | + | case NVT_ENS: |
1340 | + | myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1341 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1342 | + | |
1343 | + | if (globals->haveTauThermostat()) |
1344 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1345 | + | |
1346 | + | else { |
1347 | + | sprintf( painCave.errMsg, |
1348 | + | "SimSetup error: If you use the NVT\n" |
1349 | + | " ensemble, you must set tauThermostat.\n"); |
1350 | + | painCave.isFatal = 1; |
1351 | + | simError(); |
1352 | + | } |
1353 | + | break; |
1354 | + | |
1355 | + | case NPTi_ENS: |
1356 | + | myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1357 | + | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1358 | + | |
1359 | + | if (globals->haveTargetPressure()) |
1360 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1361 | + | else { |
1362 | + | sprintf( painCave.errMsg, |
1363 | + | "SimSetup error: If you use a constant pressure\n" |
1364 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1365 | + | painCave.isFatal = 1; |
1366 | + | simError(); |
1367 | + | } |
1368 | + | |
1369 | + | if( globals->haveTauThermostat() ) |
1370 | + | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1371 | + | else{ |
1372 | + | sprintf( painCave.errMsg, |
1373 | + | "SimSetup error: If you use an NPT\n" |
1374 | + | " ensemble, you must set tauThermostat.\n"); |
1375 | + | painCave.isFatal = 1; |
1376 | + | simError(); |
1377 | + | } |
1378 | + | |
1379 | + | if( globals->haveTauBarostat() ) |
1380 | + | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1381 | + | else{ |
1382 | + | sprintf( painCave.errMsg, |
1383 | + | "SimSetup error: If you use an NPT\n" |
1384 | + | " ensemble, you must set tauBarostat.\n"); |
1385 | + | painCave.isFatal = 1; |
1386 | + | simError(); |
1387 | + | } |
1388 | + | break; |
1389 | + | |
1390 | + | case NPTf_ENS: |
1391 | + | myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1392 | + | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1393 | + | |
1394 | + | if (globals->haveTargetPressure()) |
1395 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1396 | + | else { |
1397 | + | sprintf( painCave.errMsg, |
1398 | + | "SimSetup error: If you use a constant pressure\n" |
1399 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1400 | + | painCave.isFatal = 1; |
1401 | + | simError(); |
1402 | + | } |
1403 | + | |
1404 | + | if( globals->haveTauThermostat() ) |
1405 | + | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1406 | + | else{ |
1407 | + | sprintf( painCave.errMsg, |
1408 | + | "SimSetup error: If you use an NPT\n" |
1409 | + | " ensemble, you must set tauThermostat.\n"); |
1410 | + | painCave.isFatal = 1; |
1411 | + | simError(); |
1412 | + | } |
1413 | + | |
1414 | + | if( globals->haveTauBarostat() ) |
1415 | + | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1416 | + | else{ |
1417 | + | sprintf( painCave.errMsg, |
1418 | + | "SimSetup error: If you use an NPT\n" |
1419 | + | " ensemble, you must set tauBarostat.\n"); |
1420 | + | painCave.isFatal = 1; |
1421 | + | simError(); |
1422 | + | } |
1423 | + | break; |
1424 | + | |
1425 | + | case NPTim_ENS: |
1426 | + | myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1427 | + | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1428 | + | |
1429 | + | if (globals->haveTargetPressure()) |
1430 | + | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1431 | + | else { |
1432 | + | sprintf( painCave.errMsg, |
1433 | + | "SimSetup error: If you use a constant pressure\n" |
1434 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1435 | + | painCave.isFatal = 1; |
1436 | + | simError(); |
1437 | + | } |
1438 | + | |
1439 | + | if( globals->haveTauThermostat() ) |
1440 | + | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1441 | + | else{ |
1442 | + | sprintf( painCave.errMsg, |
1443 | + | "SimSetup error: If you use an NPT\n" |
1444 | + | " ensemble, you must set tauThermostat.\n"); |
1445 | + | painCave.isFatal = 1; |
1446 | + | simError(); |
1447 | + | } |
1448 | + | |
1449 | + | if( globals->haveTauBarostat() ) |
1450 | + | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1451 | + | else{ |
1452 | + | sprintf( painCave.errMsg, |
1453 | + | "SimSetup error: If you use an NPT\n" |
1454 | + | " ensemble, you must set tauBarostat.\n"); |
1455 | + | painCave.isFatal = 1; |
1456 | + | simError(); |
1457 | + | } |
1458 | + | break; |
1459 | + | |
1460 | + | case NPTfm_ENS: |
1461 | + | myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1462 | + | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1463 | + | |
1464 | + | if (globals->haveTargetPressure()) |
1465 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1466 | + | else { |
1467 | + | sprintf( painCave.errMsg, |
1468 | + | "SimSetup error: If you use a constant pressure\n" |
1469 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1470 | + | painCave.isFatal = 1; |
1471 | + | simError(); |
1472 | + | } |
1473 | + | |
1474 | + | if( globals->haveTauThermostat() ) |
1475 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1476 | + | else{ |
1477 | + | sprintf( painCave.errMsg, |
1478 | + | "SimSetup error: If you use an NPT\n" |
1479 | + | " ensemble, you must set tauThermostat.\n"); |
1480 | + | painCave.isFatal = 1; |
1481 | + | simError(); |
1482 | + | } |
1483 | + | |
1484 | + | if( globals->haveTauBarostat() ) |
1485 | + | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1486 | + | else{ |
1487 | + | sprintf( painCave.errMsg, |
1488 | + | "SimSetup error: If you use an NPT\n" |
1489 | + | " ensemble, you must set tauBarostat.\n"); |
1490 | + | painCave.isFatal = 1; |
1491 | + | simError(); |
1492 | + | } |
1493 | + | break; |
1494 | + | |
1495 | + | case NVEZCONS_ENS: |
1496 | + | |
1497 | + | |
1498 | + | //setup index of z-constraint molecules, z-constraint sampel time |
1499 | + | //and z-constraint force output name. These parameter should be known |
1500 | + | //before constructing the z-constraint integrator |
1501 | + | setupZConstraint(); |
1502 | + | |
1503 | + | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1504 | + | |
1505 | + | break; |
1506 | + | |
1507 | + | |
1508 | + | case NVTZCONS_ENS: |
1509 | + | |
1510 | + | setupZConstraint(); |
1511 | + | |
1512 | + | myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff ); |
1513 | + | myNVTZCons->setTargetTemp(globals->getTargetTemp()); |
1514 | + | |
1515 | + | if (globals->haveTauThermostat()) |
1516 | + | myNVTZCons->setTauThermostat(globals->getTauThermostat()); |
1517 | + | |
1518 | + | else { |
1519 | + | sprintf( painCave.errMsg, |
1520 | + | "SimSetup error: If you use the NVT\n" |
1521 | + | " ensemble, you must set tauThermostat.\n"); |
1522 | + | painCave.isFatal = 1; |
1523 | + | simError(); |
1524 | + | } |
1525 | + | break; |
1526 | + | |
1527 | + | case NPTiZCONS_ENS: |
1528 | + | |
1529 | + | setupZConstraint(); |
1530 | + | |
1531 | + | myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff ); |
1532 | + | myNPTiZCons->setTargetTemp( globals->getTargetTemp() ); |
1533 | + | |
1534 | + | if (globals->haveTargetPressure()) |
1535 | + | myNPTiZCons->setTargetPressure(globals->getTargetPressure()); |
1536 | + | else { |
1537 | + | sprintf( painCave.errMsg, |
1538 | + | "SimSetup error: If you use a constant pressure\n" |
1539 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1540 | + | painCave.isFatal = 1; |
1541 | + | simError(); |
1542 | + | } |
1543 | + | |
1544 | + | if( globals->haveTauThermostat() ) |
1545 | + | myNPTiZCons->setTauThermostat( globals->getTauThermostat() ); |
1546 | + | else{ |
1547 | + | sprintf( painCave.errMsg, |
1548 | + | "SimSetup error: If you use an NPT\n" |
1549 | + | " ensemble, you must set tauThermostat.\n"); |
1550 | + | painCave.isFatal = 1; |
1551 | + | simError(); |
1552 | + | } |
1553 | + | |
1554 | + | if( globals->haveTauBarostat() ) |
1555 | + | myNPTiZCons->setTauBarostat( globals->getTauBarostat() ); |
1556 | + | else{ |
1557 | + | sprintf( painCave.errMsg, |
1558 | + | "SimSetup error: If you use an NPT\n" |
1559 | + | " ensemble, you must set tauBarostat.\n"); |
1560 | + | painCave.isFatal = 1; |
1561 | + | simError(); |
1562 | + | } |
1563 | + | |
1564 | + | break; |
1565 | + | |
1566 | + | case NPTfZCONS_ENS: |
1567 | + | |
1568 | + | setupZConstraint(); |
1569 | + | |
1570 | + | myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff ); |
1571 | + | myNPTfZCons->setTargetTemp( globals->getTargetTemp()); |
1572 | + | |
1573 | + | if (globals->haveTargetPressure()) |
1574 | + | myNPTfZCons->setTargetPressure(globals->getTargetPressure()); |
1575 | + | else { |
1576 | + | sprintf( painCave.errMsg, |
1577 | + | "SimSetup error: If you use a constant pressure\n" |
1578 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1579 | + | painCave.isFatal = 1; |
1580 | + | simError(); |
1581 | + | } |
1582 | + | |
1583 | + | if( globals->haveTauThermostat() ) |
1584 | + | myNPTfZCons->setTauThermostat( globals->getTauThermostat() ); |
1585 | + | else{ |
1586 | + | sprintf( painCave.errMsg, |
1587 | + | "SimSetup error: If you use an NPT\n" |
1588 | + | " ensemble, you must set tauThermostat.\n"); |
1589 | + | painCave.isFatal = 1; |
1590 | + | simError(); |
1591 | + | } |
1592 | + | |
1593 | + | if( globals->haveTauBarostat() ) |
1594 | + | myNPTfZCons->setTauBarostat( globals->getTauBarostat() ); |
1595 | + | else{ |
1596 | + | sprintf( painCave.errMsg, |
1597 | + | "SimSetup error: If you use an NPT\n" |
1598 | + | " ensemble, you must set tauBarostat.\n"); |
1599 | + | painCave.isFatal = 1; |
1600 | + | simError(); |
1601 | + | } |
1602 | + | |
1603 | + | break; |
1604 | + | |
1605 | + | case NPTimZCONS_ENS: |
1606 | + | |
1607 | + | setupZConstraint(); |
1608 | + | |
1609 | + | myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff ); |
1610 | + | myNPTimZCons->setTargetTemp( globals->getTargetTemp()); |
1611 | + | |
1612 | + | if (globals->haveTargetPressure()) |
1613 | + | myNPTimZCons->setTargetPressure(globals->getTargetPressure()); |
1614 | + | else { |
1615 | + | sprintf( painCave.errMsg, |
1616 | + | "SimSetup error: If you use a constant pressure\n" |
1617 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1618 | + | painCave.isFatal = 1; |
1619 | + | simError(); |
1620 | + | } |
1621 | + | |
1622 | + | if( globals->haveTauThermostat() ) |
1623 | + | myNPTimZCons->setTauThermostat( globals->getTauThermostat() ); |
1624 | + | else{ |
1625 | + | sprintf( painCave.errMsg, |
1626 | + | "SimSetup error: If you use an NPT\n" |
1627 | + | " ensemble, you must set tauThermostat.\n"); |
1628 | + | painCave.isFatal = 1; |
1629 | + | simError(); |
1630 | + | } |
1631 | + | |
1632 | + | if( globals->haveTauBarostat() ) |
1633 | + | myNPTimZCons->setTauBarostat( globals->getTauBarostat() ); |
1634 | + | else{ |
1635 | + | sprintf( painCave.errMsg, |
1636 | + | "SimSetup error: If you use an NPT\n" |
1637 | + | " ensemble, you must set tauBarostat.\n"); |
1638 | + | painCave.isFatal = 1; |
1639 | + | simError(); |
1640 | + | } |
1641 | + | |
1642 | + | break; |
1643 | + | |
1644 | + | case NPTfmZCONS_ENS: |
1645 | + | |
1646 | + | setupZConstraint(); |
1647 | + | |
1648 | + | myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff ); |
1649 | + | myNPTfmZCons->setTargetTemp( globals->getTargetTemp()); |
1650 | + | |
1651 | + | if (globals->haveTargetPressure()) |
1652 | + | myNPTfmZCons->setTargetPressure(globals->getTargetPressure()); |
1653 | + | else { |
1654 | + | sprintf( painCave.errMsg, |
1655 | + | "SimSetup error: If you use a constant pressure\n" |
1656 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1657 | + | painCave.isFatal = 1; |
1658 | + | simError(); |
1659 | + | } |
1660 | + | |
1661 | + | if( globals->haveTauThermostat() ) |
1662 | + | myNPTfmZCons->setTauThermostat( globals->getTauThermostat() ); |
1663 | + | else{ |
1664 | + | sprintf( painCave.errMsg, |
1665 | + | "SimSetup error: If you use an NPT\n" |
1666 | + | " ensemble, you must set tauThermostat.\n"); |
1667 | + | painCave.isFatal = 1; |
1668 | + | simError(); |
1669 | + | } |
1670 | + | |
1671 | + | if( globals->haveTauBarostat() ) |
1672 | + | myNPTfmZCons->setTauBarostat( globals->getTauBarostat() ); |
1673 | + | else{ |
1674 | + | sprintf( painCave.errMsg, |
1675 | + | "SimSetup error: If you use an NPT\n" |
1676 | + | " ensemble, you must set tauBarostat.\n"); |
1677 | + | painCave.isFatal = 1; |
1678 | + | simError(); |
1679 | + | } |
1680 | + | break; |
1681 | + | |
1682 | + | |
1683 | + | |
1684 | + | default: |
1685 | + | sprintf( painCave.errMsg, |
1686 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1687 | + | painCave.isFatal = 1; |
1688 | + | simError(); |
1689 | + | } |
1690 | + | |
1691 | + | } |
1692 | + | |
1693 | + | void SimSetup::initFortran( void ){ |
1694 | + | |
1695 | + | info->refreshSim(); |
1696 | + | |
1697 | + | if( !strcmp( info->mixingRule, "standard") ){ |
1698 | + | the_ff->initForceField( LB_MIXING_RULE ); |
1699 | + | } |
1700 | + | else if( !strcmp( info->mixingRule, "explicit") ){ |
1701 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1702 | + | } |
1703 | + | else{ |
1704 | + | sprintf( painCave.errMsg, |
1705 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1706 | + | info->mixingRule ); |
1707 | + | painCave.isFatal = 1; |
1708 | + | simError(); |
1709 | + | } |
1710 | + | |
1711 | + | |
1712 | + | #ifdef IS_MPI |
1713 | + | strcpy( checkPointMsg, |
1714 | + | "Successfully intialized the mixingRule for Fortran." ); |
1715 | + | MPIcheckPoint(); |
1716 | + | #endif // is_mpi |
1717 | + | |
1718 | + | } |
1719 | + | |
1720 | + | void SimSetup::setupZConstraint() |
1721 | + | { |
1722 | + | if(globals->haveZConsTime()){ |
1723 | + | |
1724 | + | //add sample time of z-constraint into SimInfo's property list |
1725 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1726 | + | zconsTimeProp->setID("zconstime"); |
1727 | + | zconsTimeProp->setData(globals->getZConsTime()); |
1728 | + | info->addProperty(zconsTimeProp); |
1729 | + | } |
1730 | + | else{ |
1731 | + | sprintf( painCave.errMsg, |
1732 | + | "ZConstraint error: If you use an ZConstraint\n" |
1733 | + | " , you must set sample time.\n"); |
1734 | + | painCave.isFatal = 1; |
1735 | + | simError(); |
1736 | + | } |
1737 | + | |
1738 | + | if(globals->haveIndexOfAllZConsMols()){ |
1739 | + | |
1740 | + | //add index of z-constraint molecules into SimInfo's property list |
1741 | + | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1742 | + | |
1743 | + | //sort the index |
1744 | + | sort(tempIndex.begin(), tempIndex.end()); |
1745 | + | |
1746 | + | IndexData* zconsIndex = new IndexData(); |
1747 | + | zconsIndex->setID("zconsindex"); |
1748 | + | zconsIndex->setIndexData(tempIndex); |
1749 | + | info->addProperty(zconsIndex); |
1750 | + | } |
1751 | + | else{ |
1752 | + | sprintf( painCave.errMsg, |
1753 | + | "SimSetup error: If you use an ZConstraint\n" |
1754 | + | " , you must set index of z-constraint molecules.\n"); |
1755 | + | painCave.isFatal = 1; |
1756 | + | simError(); |
1757 | + | |
1758 | + | } |
1759 | + | |
1760 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1761 | + | //Be careful, do not use inFileName, since it is a pointer which |
1762 | + | //point to a string at master node, and slave nodes do not contain that string |
1763 | + | |
1764 | + | string zconsOutput(info->finalName); |
1765 | + | |
1766 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1767 | + | |
1768 | + | StringData* zconsFilename = new StringData(); |
1769 | + | zconsFilename->setID("zconsfilename"); |
1770 | + | zconsFilename->setData(zconsOutput); |
1771 | + | |
1772 | + | info->addProperty(zconsFilename); |
1773 | + | |
1774 | + | } |
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