# | 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 | + | |
27 | + | |
28 | + | #define FF_DUFF 0 |
29 | + | #define FF_LJ 1 |
30 | + | #define FF_EAM 2 |
31 | + | |
32 | + | using namespace std; |
33 | + | |
34 | SimSetup::SimSetup(){ | |
35 | + | |
36 | + | isInfoArray = 0; |
37 | + | nInfo = 1; |
38 | + | |
39 | stamps = new MakeStamps(); | |
40 | globals = new Globals(); | |
41 | ||
42 | + | |
43 | #ifdef IS_MPI | |
44 | strcpy( checkPointMsg, "SimSetup creation successful" ); | |
45 | MPIcheckPoint(); | |
# | Line 27 | Line 51 | SimSetup::~SimSetup(){ | |
51 | delete globals; | |
52 | } | |
53 | ||
54 | + | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
55 | + | info = the_info; |
56 | + | nInfo = theNinfo; |
57 | + | isInfoArray = 1; |
58 | + | } |
59 | + | |
60 | + | |
61 | void SimSetup::parseFile( char* fileName ){ | |
62 | ||
63 | #ifdef IS_MPI | |
# | Line 64 | Line 95 | void SimSetup::createSim( void ){ | |
95 | ||
96 | void SimSetup::createSim( void ){ | |
97 | ||
98 | < | MakeStamps *the_stamps; |
68 | < | Globals* the_globals; |
69 | < | int i, j; |
70 | < | |
71 | < | // get the stamps and globals; |
72 | < | the_stamps = stamps; |
73 | < | the_globals = globals; |
74 | < | |
75 | < | // set the easy ones first |
76 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
77 | < | simnfo->dt = the_globals->getDt(); |
78 | < | simnfo->run_time = the_globals->getRunTime(); |
79 | < | |
80 | < | // get the ones we know are there, yet still may need some work. |
81 | < | n_components = the_globals->getNComponents(); |
82 | < | strcpy( force_field, the_globals->getForceField() ); |
83 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
84 | < | strcpy( simnfo->ensemble, ensemble ); |
85 | < | |
86 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
87 | < | simnfo->usePBC = the_globals->getPBC(); |
88 | < | |
89 | < | |
90 | < | |
91 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
92 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
93 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
94 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
95 | < | else{ |
96 | < | sprintf( painCave.errMsg, |
97 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
98 | < | force_field ); |
99 | < | painCave.isFatal = 1; |
100 | < | simError(); |
101 | < | } |
102 | < | |
103 | < | #ifdef IS_MPI |
104 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
105 | < | MPIcheckPoint(); |
106 | < | #endif // is_mpi |
107 | < | |
98 | > | int i, j, k, globalAtomIndex; |
99 | ||
100 | < | |
110 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
111 | < | the_components = the_globals->getComponents(); |
112 | < | components_nmol = new int[n_components]; |
113 | < | comp_stamps = new MoleculeStamp*[n_components]; |
114 | < | |
115 | < | if( !the_globals->haveNMol() ){ |
116 | < | // we don't have the total number of molecules, so we assume it is |
117 | < | // given in each component |
118 | < | |
119 | < | tot_nmol = 0; |
120 | < | for( i=0; i<n_components; i++ ){ |
121 | < | |
122 | < | if( !the_components[i]->haveNMol() ){ |
123 | < | // we have a problem |
124 | < | sprintf( painCave.errMsg, |
125 | < | "SimSetup Error. No global NMol or component NMol" |
126 | < | " given. Cannot calculate the number of atoms.\n" ); |
127 | < | painCave.isFatal = 1; |
128 | < | simError(); |
129 | < | } |
130 | < | |
131 | < | tot_nmol += the_components[i]->getNMol(); |
132 | < | components_nmol[i] = the_components[i]->getNMol(); |
133 | < | } |
134 | < | } |
135 | < | else{ |
136 | < | sprintf( painCave.errMsg, |
137 | < | "SimSetup error.\n" |
138 | < | "\tSorry, the ability to specify total" |
139 | < | " nMols and then give molfractions in the components\n" |
140 | < | "\tis not currently supported." |
141 | < | " Please give nMol in the components.\n" ); |
142 | < | painCave.isFatal = 1; |
143 | < | simError(); |
144 | < | |
145 | < | |
146 | < | // tot_nmol = the_globals->getNMol(); |
147 | < | |
148 | < | // //we have the total number of molecules, now we check for molfractions |
149 | < | // for( i=0; i<n_components; i++ ){ |
150 | < | |
151 | < | // if( !the_components[i]->haveMolFraction() ){ |
152 | < | |
153 | < | // if( !the_components[i]->haveNMol() ){ |
154 | < | // //we have a problem |
155 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
156 | < | // << " nMol was given in component |
157 | < | |
158 | < | } |
159 | < | |
160 | < | #ifdef IS_MPI |
161 | < | strcpy( checkPointMsg, "Have the number of components" ); |
162 | < | MPIcheckPoint(); |
163 | < | #endif // is_mpi |
164 | < | |
165 | < | // make an array of molecule stamps that match the components used. |
166 | < | // also extract the used stamps out into a separate linked list |
167 | < | |
168 | < | simnfo->nComponents = n_components; |
169 | < | simnfo->componentsNmol = components_nmol; |
170 | < | simnfo->compStamps = comp_stamps; |
171 | < | simnfo->headStamp = new LinkedMolStamp(); |
100 | > | // gather all of the information from the Bass file |
101 | ||
102 | < | char* id; |
174 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
175 | < | LinkedMolStamp* currentStamp = NULL; |
176 | < | for( i=0; i<n_components; i++ ){ |
102 | > | gatherInfo(); |
103 | ||
104 | < | id = the_components[i]->getType(); |
179 | < | comp_stamps[i] = NULL; |
180 | < | |
181 | < | // check to make sure the component isn't already in the list |
104 | > | // creation of complex system objects |
105 | ||
106 | < | comp_stamps[i] = headStamp->match( id ); |
184 | < | if( comp_stamps[i] == NULL ){ |
185 | < | |
186 | < | // extract the component from the list; |
187 | < | |
188 | < | currentStamp = the_stamps->extractMolStamp( id ); |
189 | < | if( currentStamp == NULL ){ |
190 | < | sprintf( painCave.errMsg, |
191 | < | "SimSetup error: Component \"%s\" was not found in the " |
192 | < | "list of declared molecules\n", |
193 | < | id ); |
194 | < | painCave.isFatal = 1; |
195 | < | simError(); |
196 | < | } |
197 | < | |
198 | < | headStamp->add( currentStamp ); |
199 | < | comp_stamps[i] = headStamp->match( id ); |
200 | < | } |
201 | < | } |
106 | > | sysObjectsCreation(); |
107 | ||
108 | < | #ifdef IS_MPI |
204 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
205 | < | MPIcheckPoint(); |
206 | < | #endif // is_mpi |
108 | > | // check on the post processing info |
109 | ||
110 | + | finalInfoCheck(); |
111 | ||
112 | + | // initialize the system coordinates |
113 | ||
114 | < | |
211 | < | // caclulate the number of atoms, bonds, bends and torsions |
212 | < | |
213 | < | tot_atoms = 0; |
214 | < | tot_bonds = 0; |
215 | < | tot_bends = 0; |
216 | < | tot_torsions = 0; |
217 | < | for( i=0; i<n_components; i++ ){ |
218 | < | |
219 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
220 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
221 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
222 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
223 | < | } |
224 | < | |
225 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
226 | < | |
227 | < | simnfo->n_atoms = tot_atoms; |
228 | < | simnfo->n_bonds = tot_bonds; |
229 | < | simnfo->n_bends = tot_bends; |
230 | < | simnfo->n_torsions = tot_torsions; |
231 | < | simnfo->n_SRI = tot_SRI; |
232 | < | simnfo->n_mol = tot_nmol; |
233 | < | |
114 | > | initSystemCoords(); |
115 | ||
235 | – | #ifdef IS_MPI |
116 | ||
117 | < | // divide the molecules among processors here. |
238 | < | |
239 | < | mpiSim = new mpiSimulation( simnfo ); |
240 | < | |
241 | < | |
117 | > | // make the output filenames |
118 | ||
119 | < | globalIndex = mpiSim->divideLabor(); |
120 | < | |
121 | < | |
246 | < | |
247 | < | // set up the local variables |
119 | > | makeOutNames(); |
120 | > | |
121 | > | // make the integrator |
122 | ||
123 | < | int localMol, allMol; |
250 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
123 | > | makeIntegrator(); |
124 | ||
252 | – | allMol = 0; |
253 | – | localMol = 0; |
254 | – | local_atoms = 0; |
255 | – | local_bonds = 0; |
256 | – | local_bends = 0; |
257 | – | local_torsions = 0; |
258 | – | for( i=0; i<n_components; i++ ){ |
259 | – | |
260 | – | for( j=0; j<components_nmol[i]; j++ ){ |
261 | – | |
262 | – | if( mpiSim->getMyMolStart() <= allMol && |
263 | – | allMol <= mpiSim->getMyMolEnd() ){ |
264 | – | |
265 | – | local_atoms += comp_stamps[i]->getNAtoms(); |
266 | – | local_bonds += comp_stamps[i]->getNBonds(); |
267 | – | local_bends += comp_stamps[i]->getNBends(); |
268 | – | local_torsions += comp_stamps[i]->getNTorsions(); |
269 | – | localMol++; |
270 | – | } |
271 | – | allMol++; |
272 | – | } |
273 | – | } |
274 | – | local_SRI = local_bonds + local_bends + local_torsions; |
275 | – | |
276 | – | |
277 | – | simnfo->n_atoms = mpiSim->getMyNlocal(); |
278 | – | |
279 | – | if( local_atoms != simnfo->n_atoms ){ |
280 | – | sprintf( painCave.errMsg, |
281 | – | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
282 | – | " localAtom (%d) are note equal.\n", |
283 | – | simnfo->n_atoms, |
284 | – | local_atoms ); |
285 | – | painCave.isFatal = 1; |
286 | – | simError(); |
287 | – | } |
288 | – | |
289 | – | simnfo->n_bonds = local_bonds; |
290 | – | simnfo->n_bends = local_bends; |
291 | – | simnfo->n_torsions = local_torsions; |
292 | – | simnfo->n_SRI = local_SRI; |
293 | – | simnfo->n_mol = localMol; |
294 | – | |
295 | – | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
296 | – | MPIcheckPoint(); |
297 | – | |
298 | – | |
299 | – | #endif // is_mpi |
300 | – | |
301 | – | |
302 | – | // create the atom and short range interaction arrays |
303 | – | |
304 | – | Atom::createArrays(simnfo->n_atoms); |
305 | – | the_atoms = new Atom*[simnfo->n_atoms]; |
306 | – | the_molecules = new Molecule[simnfo->n_mol]; |
307 | – | |
308 | – | |
309 | – | if( simnfo->n_SRI ){ |
310 | – | Exclude::createArray(simnfo->n_SRI); |
311 | – | the_excludes = new Exclude*[simnfo->n_SRI]; |
312 | – | simnfo->globalExcludes = new int; |
313 | – | simnfo->n_exclude = tot_SRI; |
314 | – | } |
315 | – | else{ |
316 | – | |
317 | – | Exclude::createArray( 1 ); |
318 | – | the_excludes = new Exclude*; |
319 | – | the_excludes[0] = new Exclude(0); |
320 | – | the_excludes[0]->setPair( 0,0 ); |
321 | – | simnfo->globalExcludes = new int; |
322 | – | simnfo->globalExcludes[0] = 0; |
323 | – | simnfo->n_exclude = 0; |
324 | – | } |
325 | – | |
326 | – | // set the arrays into the SimInfo object |
327 | – | |
328 | – | simnfo->atoms = the_atoms; |
329 | – | simnfo->sr_interactions = the_sris; |
330 | – | simnfo->nGlobalExcludes = 0; |
331 | – | simnfo->excludes = the_excludes; |
332 | – | |
333 | – | |
334 | – | // get some of the tricky things that may still be in the globals |
335 | – | |
336 | – | |
337 | – | if( the_globals->haveBox() ){ |
338 | – | simnfo->box_x = the_globals->getBox(); |
339 | – | simnfo->box_y = the_globals->getBox(); |
340 | – | simnfo->box_z = the_globals->getBox(); |
341 | – | } |
342 | – | else if( the_globals->haveDensity() ){ |
343 | – | |
344 | – | double vol; |
345 | – | vol = (double)tot_nmol / the_globals->getDensity(); |
346 | – | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
347 | – | simnfo->box_y = simnfo->box_x; |
348 | – | simnfo->box_z = simnfo->box_x; |
349 | – | } |
350 | – | else{ |
351 | – | if( !the_globals->haveBoxX() ){ |
352 | – | sprintf( painCave.errMsg, |
353 | – | "SimSetup error, no periodic BoxX size given.\n" ); |
354 | – | painCave.isFatal = 1; |
355 | – | simError(); |
356 | – | } |
357 | – | simnfo->box_x = the_globals->getBoxX(); |
358 | – | |
359 | – | if( !the_globals->haveBoxY() ){ |
360 | – | sprintf( painCave.errMsg, |
361 | – | "SimSetup error, no periodic BoxY size given.\n" ); |
362 | – | painCave.isFatal = 1; |
363 | – | simError(); |
364 | – | } |
365 | – | simnfo->box_y = the_globals->getBoxY(); |
366 | – | |
367 | – | if( !the_globals->haveBoxZ() ){ |
368 | – | sprintf( painCave.errMsg, |
369 | – | "SimSetup error, no periodic BoxZ size given.\n" ); |
370 | – | painCave.isFatal = 1; |
371 | – | simError(); |
372 | – | } |
373 | – | simnfo->box_z = the_globals->getBoxZ(); |
374 | – | } |
375 | – | |
125 | #ifdef IS_MPI | |
126 | < | strcpy( checkPointMsg, "Box size set up" ); |
378 | < | MPIcheckPoint(); |
379 | < | #endif // is_mpi |
380 | < | |
381 | < | |
382 | < | // initialize the arrays |
383 | < | |
384 | < | the_ff->setSimInfo( simnfo ); |
385 | < | |
386 | < | makeAtoms(); |
387 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
388 | < | for(i=0; i<simnfo->n_atoms; i++){ |
389 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
390 | < | } |
391 | < | |
392 | < | if( tot_bonds ){ |
393 | < | makeBonds(); |
394 | < | } |
395 | < | |
396 | < | if( tot_bends ){ |
397 | < | makeBends(); |
398 | < | } |
399 | < | |
400 | < | if( tot_torsions ){ |
401 | < | makeTorsions(); |
402 | < | } |
403 | < | |
404 | < | |
405 | < | if (the_globals->getUseRF() ) { |
406 | < | simnfo->useReactionField = 1; |
407 | < | |
408 | < | if( !the_globals->haveECR() ){ |
409 | < | sprintf( painCave.errMsg, |
410 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
411 | < | "box length for the electrostaticCutoffRadius.\n" |
412 | < | "I hope you have a very fast processor!\n"); |
413 | < | painCave.isFatal = 0; |
414 | < | simError(); |
415 | < | double smallest; |
416 | < | smallest = simnfo->box_x; |
417 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
418 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
419 | < | simnfo->ecr = 0.5 * smallest; |
420 | < | } else { |
421 | < | simnfo->ecr = the_globals->getECR(); |
422 | < | } |
423 | < | |
424 | < | if( !the_globals->haveEST() ){ |
425 | < | sprintf( painCave.errMsg, |
426 | < | "SimSetup Warning: using default value of 0.05 * the " |
427 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
428 | < | ); |
429 | < | painCave.isFatal = 0; |
430 | < | simError(); |
431 | < | simnfo->est = 0.05 * simnfo->ecr; |
432 | < | } else { |
433 | < | simnfo->est = the_globals->getEST(); |
434 | < | } |
435 | < | |
436 | < | if(!the_globals->haveDielectric() ){ |
437 | < | sprintf( painCave.errMsg, |
438 | < | "SimSetup Error: You are trying to use Reaction Field without" |
439 | < | "setting a dielectric constant!\n" |
440 | < | ); |
441 | < | painCave.isFatal = 1; |
442 | < | simError(); |
443 | < | } |
444 | < | simnfo->dielectric = the_globals->getDielectric(); |
445 | < | } else { |
446 | < | if (simnfo->n_dipoles) { |
447 | < | |
448 | < | if( !the_globals->haveECR() ){ |
449 | < | sprintf( painCave.errMsg, |
450 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
451 | < | "box length for the electrostaticCutoffRadius.\n" |
452 | < | "I hope you have a very fast processor!\n"); |
453 | < | painCave.isFatal = 0; |
454 | < | simError(); |
455 | < | double smallest; |
456 | < | smallest = simnfo->box_x; |
457 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
458 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
459 | < | simnfo->ecr = 0.5 * smallest; |
460 | < | } else { |
461 | < | simnfo->ecr = the_globals->getECR(); |
462 | < | } |
463 | < | |
464 | < | if( !the_globals->haveEST() ){ |
465 | < | sprintf( painCave.errMsg, |
466 | < | "SimSetup Warning: using default value of 5% of the" |
467 | < | "electrostaticCutoffRadius for the " |
468 | < | "electrostaticSkinThickness\n" |
469 | < | ); |
470 | < | painCave.isFatal = 0; |
471 | < | simError(); |
472 | < | simnfo->est = 0.05 * simnfo->ecr; |
473 | < | } else { |
474 | < | simnfo->est = the_globals->getEST(); |
475 | < | } |
476 | < | } |
477 | < | } |
478 | < | |
479 | < | #ifdef IS_MPI |
480 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
481 | < | MPIcheckPoint(); |
482 | < | #endif // is_mpi |
483 | < | |
484 | < | if( the_globals->haveInitialConfig() ){ |
485 | < | |
486 | < | InitializeFromFile* fileInit; |
487 | < | #ifdef IS_MPI // is_mpi |
488 | < | if( worldRank == 0 ){ |
489 | < | #endif //is_mpi |
490 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
491 | < | #ifdef IS_MPI |
492 | < | }else fileInit = new InitializeFromFile( NULL ); |
126 | > | mpiSim->mpiRefresh(); |
127 | #endif | |
494 | – | fileInit->read_xyz( simnfo ); // default velocities on |
128 | ||
129 | < | delete fileInit; |
497 | < | } |
498 | < | else{ |
129 | > | // initialize the Fortran |
130 | ||
131 | < | #ifdef IS_MPI |
501 | < | |
502 | < | // no init from bass |
503 | < | |
504 | < | sprintf( painCave.errMsg, |
505 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
506 | < | painCave.isFatal; |
507 | < | simError(); |
508 | < | |
509 | < | #else |
510 | < | |
511 | < | initFromBass(); |
512 | < | |
513 | < | |
514 | < | #endif |
515 | < | } |
516 | < | |
517 | < | #ifdef IS_MPI |
518 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
519 | < | MPIcheckPoint(); |
520 | < | #endif // is_mpi |
521 | < | |
522 | < | |
523 | < | |
524 | < | |
525 | < | |
526 | < | |
527 | < | |
528 | < | #ifdef IS_MPI |
529 | < | if( worldRank == 0 ){ |
530 | < | #endif // is_mpi |
531 | < | |
532 | < | if( the_globals->haveFinalConfig() ){ |
533 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
534 | < | } |
535 | < | else{ |
536 | < | strcpy( simnfo->finalName, inFileName ); |
537 | < | char* endTest; |
538 | < | int nameLength = strlen( simnfo->finalName ); |
539 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
540 | < | if( !strcmp( endTest, ".bass" ) ){ |
541 | < | strcpy( endTest, ".eor" ); |
542 | < | } |
543 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
544 | < | strcpy( endTest, ".eor" ); |
545 | < | } |
546 | < | else{ |
547 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
548 | < | if( !strcmp( endTest, ".bss" ) ){ |
549 | < | strcpy( endTest, ".eor" ); |
550 | < | } |
551 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
552 | < | strcpy( endTest, ".eor" ); |
553 | < | } |
554 | < | else{ |
555 | < | strcat( simnfo->finalName, ".eor" ); |
556 | < | } |
557 | < | } |
558 | < | } |
559 | < | |
560 | < | // make the sample and status out names |
561 | < | |
562 | < | strcpy( simnfo->sampleName, inFileName ); |
563 | < | char* endTest; |
564 | < | int nameLength = strlen( simnfo->sampleName ); |
565 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
566 | < | if( !strcmp( endTest, ".bass" ) ){ |
567 | < | strcpy( endTest, ".dump" ); |
568 | < | } |
569 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
570 | < | strcpy( endTest, ".dump" ); |
571 | < | } |
572 | < | else{ |
573 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
574 | < | if( !strcmp( endTest, ".bss" ) ){ |
575 | < | strcpy( endTest, ".dump" ); |
576 | < | } |
577 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
578 | < | strcpy( endTest, ".dump" ); |
579 | < | } |
580 | < | else{ |
581 | < | strcat( simnfo->sampleName, ".dump" ); |
582 | < | } |
583 | < | } |
584 | < | |
585 | < | strcpy( simnfo->statusName, inFileName ); |
586 | < | nameLength = strlen( simnfo->statusName ); |
587 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
588 | < | if( !strcmp( endTest, ".bass" ) ){ |
589 | < | strcpy( endTest, ".stat" ); |
590 | < | } |
591 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
592 | < | strcpy( endTest, ".stat" ); |
593 | < | } |
594 | < | else{ |
595 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
596 | < | if( !strcmp( endTest, ".bss" ) ){ |
597 | < | strcpy( endTest, ".stat" ); |
598 | < | } |
599 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
600 | < | strcpy( endTest, ".stat" ); |
601 | < | } |
602 | < | else{ |
603 | < | strcat( simnfo->statusName, ".stat" ); |
604 | < | } |
605 | < | } |
606 | < | |
607 | < | #ifdef IS_MPI |
608 | < | } |
609 | < | #endif // is_mpi |
610 | < | |
611 | < | // set the status, sample, and themal kick times |
612 | < | |
613 | < | if( the_globals->haveSampleTime() ){ |
614 | < | simnfo->sampleTime = the_globals->getSampleTime(); |
615 | < | simnfo->statusTime = simnfo->sampleTime; |
616 | < | simnfo->thermalTime = simnfo->sampleTime; |
617 | < | } |
618 | < | else{ |
619 | < | simnfo->sampleTime = the_globals->getRunTime(); |
620 | < | simnfo->statusTime = simnfo->sampleTime; |
621 | < | simnfo->thermalTime = simnfo->sampleTime; |
622 | < | } |
131 | > | initFortran(); |
132 | ||
624 | – | if( the_globals->haveStatusTime() ){ |
625 | – | simnfo->statusTime = the_globals->getStatusTime(); |
626 | – | } |
133 | ||
628 | – | if( the_globals->haveThermalTime() ){ |
629 | – | simnfo->thermalTime = the_globals->getThermalTime(); |
630 | – | } |
134 | ||
632 | – | // check for the temperature set flag |
633 | – | |
634 | – | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
635 | – | |
636 | – | |
637 | – | // // make the longe range forces and the integrator |
638 | – | |
639 | – | // new AllLong( simnfo ); |
640 | – | |
641 | – | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 | – | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
643 | – | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
644 | – | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
645 | – | |
646 | – | |
647 | – | |
648 | – | // initialize the Fortran |
649 | – | |
650 | – | simnfo->refreshSim(); |
651 | – | |
652 | – | if( !strcmp( simnfo->mixingRule, "standard") ){ |
653 | – | the_ff->initForceField( LB_MIXING_RULE ); |
654 | – | } |
655 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
656 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
657 | – | } |
658 | – | else{ |
659 | – | sprintf( painCave.errMsg, |
660 | – | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
661 | – | simnfo->mixingRule ); |
662 | – | painCave.isFatal = 1; |
663 | – | simError(); |
664 | – | } |
665 | – | |
666 | – | |
667 | – | #ifdef IS_MPI |
668 | – | strcpy( checkPointMsg, |
669 | – | "Successfully intialized the mixingRule for Fortran." ); |
670 | – | MPIcheckPoint(); |
671 | – | #endif // is_mpi |
135 | } | |
136 | ||
137 | ||
138 | void SimSetup::makeMolecules( void ){ | |
139 | ||
140 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
141 | < | molInit info; |
141 | > | molInit molInfo; |
142 | DirectionalAtom* dAtom; | |
143 | LinkedAssign* extras; | |
144 | LinkedAssign* current_extra; | |
# | Line 683 | Line 146 | void SimSetup::makeMolecules( void ){ | |
146 | BondStamp* currentBond; | |
147 | BendStamp* currentBend; | |
148 | TorsionStamp* currentTorsion; | |
149 | + | |
150 | + | bond_pair* theBonds; |
151 | + | bend_set* theBends; |
152 | + | torsion_set* theTorsions; |
153 | + | |
154 | ||
155 | //init the forceField paramters | |
156 | ||
157 | the_ff->readParams(); | |
158 | ||
159 | ||
160 | < | // init the molecules |
160 | > | // init the atoms |
161 | ||
162 | + | double ux, uy, uz, u, uSqr; |
163 | + | |
164 | atomOffset = 0; | |
165 | excludeOffset = 0; | |
166 | < | for(i=0; i<simnfo->n_mol; i++){ |
166 | > | for(i=0; i<info->n_mol; i++){ |
167 | ||
168 | stampID = the_molecules[i].getStampID(); | |
169 | ||
170 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
171 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
172 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
173 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
174 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
170 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
171 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
172 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
173 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
174 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
175 | ||
176 | < | info.myAtoms = &the_atoms[atomOffset]; |
177 | < | info.myExcludes = &the_excludes[excludeOffset]; |
178 | < | info.myBonds = new Bond*[info.nBonds]; |
179 | < | info.myBends = new Bend*[info.nBends]; |
180 | < | info.myTorsions = new Torsions*[info.nTorsions]; |
176 | > | molInfo.myAtoms = &the_atoms[atomOffset]; |
177 | > | molInfo.myExcludes = &the_excludes[excludeOffset]; |
178 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
179 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
180 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
181 | ||
182 | < | theBonds = new bond_pair[info.nBonds]; |
183 | < | theBends = new bend_set[info.nBends]; |
184 | < | theTorsions = new torsion_set[info.nTorsions]; |
182 | > | theBonds = new bond_pair[molInfo.nBonds]; |
183 | > | theBends = new bend_set[molInfo.nBends]; |
184 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
185 | ||
186 | // make the Atoms | |
187 | ||
188 | < | for(j=0; j<info.nAtoms; j++){ |
188 | > | for(j=0; j<molInfo.nAtoms; j++){ |
189 | ||
190 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
190 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
191 | if( currentAtom->haveOrientation() ){ | |
192 | ||
193 | dAtom = new DirectionalAtom(j + atomOffset); | |
194 | < | simnfo->n_oriented++; |
195 | < | info.myAtoms[j] = dAtom; |
194 | > | info->n_oriented++; |
195 | > | molInfo.myAtoms[j] = dAtom; |
196 | ||
197 | ux = currentAtom->getOrntX(); | |
198 | uy = currentAtom->getOrntY(); | |
# | Line 740 | Line 210 | void SimSetup::makeMolecules( void ){ | |
210 | dAtom->setSUz( uz ); | |
211 | } | |
212 | else{ | |
213 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
213 | > | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
214 | } | |
215 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
215 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
216 | ||
217 | #ifdef IS_MPI | |
218 | ||
219 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
219 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
220 | ||
221 | #endif // is_mpi | |
222 | } | |
223 | ||
224 | // make the bonds | |
225 | < | for(j=0; j<info.nBonds; j++){ |
225 | > | for(j=0; j<molInfo.nBonds; j++){ |
226 | ||
227 | currentBond = comp_stamps[stampID]->getBond( j ); | |
228 | theBonds[j].a = currentBond->getA() + atomOffset; | |
229 | theBonds[j].b = currentBond->getB() + atomOffset; | |
230 | ||
231 | < | exI = theBonds[i].a; |
232 | < | exJ = theBonds[i].b; |
231 | > | exI = theBonds[j].a; |
232 | > | exJ = theBonds[j].b; |
233 | ||
234 | // exclude_I must always be the smaller of the pair | |
235 | if( exI > exJ ){ | |
# | Line 775 | Line 245 | void SimSetup::makeMolecules( void ){ | |
245 | ||
246 | the_excludes[j+excludeOffset]->setPair( exI, exJ ); | |
247 | #else // isn't MPI | |
248 | + | |
249 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
250 | #endif //is_mpi | |
251 | } | |
252 | < | excludeOffset += info.nBonds; |
252 | > | excludeOffset += molInfo.nBonds; |
253 | ||
254 | //make the bends | |
255 | < | for(j=0; j<info.nBends; j++){ |
255 | > | for(j=0; j<molInfo.nBends; j++){ |
256 | ||
257 | currentBend = comp_stamps[stampID]->getBend( j ); | |
258 | theBends[j].a = currentBend->getA() + atomOffset; | |
# | Line 790 | Line 261 | void SimSetup::makeMolecules( void ){ | |
261 | ||
262 | if( currentBend->haveExtras() ){ | |
263 | ||
264 | < | extras = current_bend->getExtras(); |
264 | > | extras = currentBend->getExtras(); |
265 | current_extra = extras; | |
266 | ||
267 | while( current_extra != NULL ){ | |
# | Line 812 | Line 283 | void SimSetup::makeMolecules( void ){ | |
283 | ||
284 | default: | |
285 | sprintf( painCave.errMsg, | |
286 | < | "SimSetup Error: ghostVectorSource was neiter a " |
286 | > | "SimSetup Error: ghostVectorSource was neither a " |
287 | "double nor an int.\n" | |
288 | "-->Bend[%d] in %s\n", | |
289 | j, comp_stamps[stampID]->getID() ); | |
# | Line 864 | Line 335 | void SimSetup::makeMolecules( void ){ | |
335 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
336 | #endif //is_mpi | |
337 | } | |
338 | < | excludeOffset += info.nBends; |
338 | > | excludeOffset += molInfo.nBends; |
339 | ||
340 | < | for(j=0; j<info.nTorsions; j++){ |
340 | > | for(j=0; j<molInfo.nTorsions; j++){ |
341 | ||
342 | currentTorsion = comp_stamps[stampID]->getTorsion( j ); | |
343 | theTorsions[j].a = currentTorsion->getA() + atomOffset; | |
# | Line 894 | Line 365 | void SimSetup::makeMolecules( void ){ | |
365 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
366 | #endif //is_mpi | |
367 | } | |
368 | < | excludeOffset += info.nTorsions; |
368 | > | excludeOffset += molInfo.nTorsions; |
369 | ||
370 | ||
371 | // send the arrays off to the forceField for init. | |
372 | ||
373 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
374 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
375 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
376 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
373 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
374 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
375 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
376 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
377 | ||
378 | ||
379 | < | the_molecules[i].initialize( info ); |
380 | < | atomOffset += info.nAtoms; |
379 | > | the_molecules[i].initialize( molInfo ); |
380 | > | |
381 | > | |
382 | > | atomOffset += molInfo.nAtoms; |
383 | > | delete[] theBonds; |
384 | > | delete[] theBends; |
385 | > | delete[] theTorsions; |
386 | } | |
387 | ||
388 | < | // clean up the forcefield |
388 | > | #ifdef IS_MPI |
389 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
390 | > | MPIcheckPoint(); |
391 | > | #endif // is_mpi |
392 | ||
393 | + | // clean up the forcefield |
394 | + | the_ff->calcRcut(); |
395 | the_ff->cleanMe(); | |
396 | + | |
397 | } | |
398 | ||
399 | + | void SimSetup::initFromBass( void ){ |
400 | ||
401 | + | int i, j, k; |
402 | + | int n_cells; |
403 | + | double cellx, celly, cellz; |
404 | + | double temp1, temp2, temp3; |
405 | + | int n_per_extra; |
406 | + | int n_extra; |
407 | + | int have_extra, done; |
408 | ||
409 | < | void SimSetup::makeAtoms( void ){ |
409 | > | temp1 = (double)tot_nmol / 4.0; |
410 | > | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
411 | > | temp3 = ceil( temp2 ); |
412 | ||
413 | < | int i, j, k, index; |
414 | < | double ux, uy, uz, uSqr, u; |
415 | < | AtomStamp* current_atom; |
413 | > | have_extra =0; |
414 | > | if( temp2 < temp3 ){ // we have a non-complete lattice |
415 | > | have_extra =1; |
416 | ||
417 | < | DirectionalAtom* dAtom; |
418 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
417 | > | n_cells = (int)temp3 - 1; |
418 | > | cellx = info->boxL[0] / temp3; |
419 | > | celly = info->boxL[1] / temp3; |
420 | > | cellz = info->boxL[2] / temp3; |
421 | > | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
422 | > | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
423 | > | n_per_extra = (int)ceil( temp1 ); |
424 | ||
425 | < | lMolIndex = 0; |
426 | < | molIndex = 0; |
427 | < | index = 0; |
428 | < | for( i=0; i<n_components; i++ ){ |
429 | < | |
430 | < | for( j=0; j<components_nmol[i]; j++ ){ |
934 | < | |
935 | < | #ifdef IS_MPI |
936 | < | if( mpiSim->getMyMolStart() <= molIndex && |
937 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
938 | < | #endif // is_mpi |
939 | < | |
940 | < | molStart = index; |
941 | < | nMemb = comp_stamps[i]->getNAtoms(); |
942 | < | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
943 | < | |
944 | < | current_atom = comp_stamps[i]->getAtom( k ); |
945 | < | if( current_atom->haveOrientation() ){ |
946 | < | |
947 | < | dAtom = new DirectionalAtom(index); |
948 | < | simnfo->n_oriented++; |
949 | < | the_atoms[index] = dAtom; |
950 | < | |
951 | < | ux = current_atom->getOrntX(); |
952 | < | uy = current_atom->getOrntY(); |
953 | < | uz = current_atom->getOrntZ(); |
954 | < | |
955 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
956 | < | |
957 | < | u = sqrt( uSqr ); |
958 | < | ux = ux / u; |
959 | < | uy = uy / u; |
960 | < | uz = uz / u; |
961 | < | |
962 | < | dAtom->setSUx( ux ); |
963 | < | dAtom->setSUy( uy ); |
964 | < | dAtom->setSUz( uz ); |
965 | < | } |
966 | < | else{ |
967 | < | the_atoms[index] = new GeneralAtom(index); |
968 | < | } |
969 | < | the_atoms[index]->setType( current_atom->getType() ); |
970 | < | the_atoms[index]->setIndex( index ); |
971 | < | |
972 | < | // increment the index and repeat; |
973 | < | index++; |
974 | < | } |
975 | < | |
976 | < | molEnd = index -1; |
977 | < | the_molecules[lMolIndex].setNMembers( nMemb ); |
978 | < | the_molecules[lMolIndex].setStartAtom( molStart ); |
979 | < | the_molecules[lMolIndex].setEndAtom( molEnd ); |
980 | < | the_molecules[lMolIndex].setStampID( i ); |
981 | < | lMolIndex++; |
982 | < | |
983 | < | #ifdef IS_MPI |
984 | < | } |
985 | < | #endif //is_mpi |
986 | < | |
987 | < | molIndex++; |
425 | > | if( n_per_extra > 4){ |
426 | > | sprintf( painCave.errMsg, |
427 | > | "SimSetup error. There has been an error in constructing" |
428 | > | " the non-complete lattice.\n" ); |
429 | > | painCave.isFatal = 1; |
430 | > | simError(); |
431 | } | |
432 | } | |
433 | + | else{ |
434 | + | n_cells = (int)temp3; |
435 | + | cellx = info->boxL[0] / temp3; |
436 | + | celly = info->boxL[1] / temp3; |
437 | + | cellz = info->boxL[2] / temp3; |
438 | + | } |
439 | ||
440 | < | #ifdef IS_MPI |
441 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
442 | < | |
443 | < | delete[] globalIndex; |
440 | > | current_mol = 0; |
441 | > | current_comp_mol = 0; |
442 | > | current_comp = 0; |
443 | > | current_atom_ndx = 0; |
444 | ||
445 | < | mpiSim->mpiRefresh(); |
446 | < | #endif //IS_MPI |
447 | < | |
999 | < | the_ff->initializeAtoms(); |
1000 | < | } |
445 | > | for( i=0; i < n_cells ; i++ ){ |
446 | > | for( j=0; j < n_cells; j++ ){ |
447 | > | for( k=0; k < n_cells; k++ ){ |
448 | ||
449 | < | void SimSetup::makeBonds( void ){ |
449 | > | makeElement( i * cellx, |
450 | > | j * celly, |
451 | > | k * cellz ); |
452 | ||
453 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
454 | < | bond_pair* the_bonds; |
455 | < | BondStamp* current_bond; |
453 | > | makeElement( i * cellx + 0.5 * cellx, |
454 | > | j * celly + 0.5 * celly, |
455 | > | k * cellz ); |
456 | ||
457 | < | the_bonds = new bond_pair[tot_bonds]; |
458 | < | index = 0; |
459 | < | offset = 0; |
1011 | < | molIndex = 0; |
457 | > | makeElement( i * cellx, |
458 | > | j * celly + 0.5 * celly, |
459 | > | k * cellz + 0.5 * cellz ); |
460 | ||
461 | < | for( i=0; i<n_components; i++ ){ |
461 | > | makeElement( i * cellx + 0.5 * cellx, |
462 | > | j * celly, |
463 | > | k * cellz + 0.5 * cellz ); |
464 | > | } |
465 | > | } |
466 | > | } |
467 | ||
468 | < | for( j=0; j<components_nmol[i]; j++ ){ |
468 | > | if( have_extra ){ |
469 | > | done = 0; |
470 | ||
471 | < | #ifdef IS_MPI |
472 | < | if( mpiSim->getMyMolStart() <= molIndex && |
473 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1020 | < | #endif // is_mpi |
1021 | < | |
1022 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
1023 | < | |
1024 | < | current_bond = comp_stamps[i]->getBond( k ); |
1025 | < | the_bonds[index].a = current_bond->getA() + offset; |
1026 | < | the_bonds[index].b = current_bond->getB() + offset; |
471 | > | int start_ndx; |
472 | > | for( i=0; i < (n_cells+1) && !done; i++ ){ |
473 | > | for( j=0; j < (n_cells+1) && !done; j++ ){ |
474 | ||
475 | < | exI = the_bonds[index].a; |
1029 | < | exJ = the_bonds[index].b; |
475 | > | if( i < n_cells ){ |
476 | ||
477 | < | // exclude_I must always be the smaller of the pair |
478 | < | if( exI > exJ ){ |
1033 | < | tempEx = exI; |
1034 | < | exI = exJ; |
1035 | < | exJ = tempEx; |
477 | > | if( j < n_cells ){ |
478 | > | start_ndx = n_cells; |
479 | } | |
480 | + | else start_ndx = 0; |
481 | + | } |
482 | + | else start_ndx = 0; |
483 | ||
484 | < | |
1039 | < | #ifdef IS_MPI |
484 | > | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
485 | ||
486 | < | the_excludes[index*2] = |
487 | < | the_atoms[exI]->getGlobalIndex() + 1; |
488 | < | the_excludes[index*2 + 1] = |
489 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
486 | > | makeElement( i * cellx, |
487 | > | j * celly, |
488 | > | k * cellz ); |
489 | > | done = ( current_mol >= tot_nmol ); |
490 | ||
491 | < | #else // isn't MPI |
492 | < | |
493 | < | the_excludes[index*2] = exI + 1; |
494 | < | the_excludes[index*2 + 1] = exJ + 1; |
495 | < | // fortran index from 1 (hence the +1 in the indexing) |
496 | < | #endif //is_mpi |
497 | < | |
498 | < | // increment the index and repeat; |
499 | < | index++; |
491 | > | if( !done && n_per_extra > 1 ){ |
492 | > | makeElement( i * cellx + 0.5 * cellx, |
493 | > | j * celly + 0.5 * celly, |
494 | > | k * cellz ); |
495 | > | done = ( current_mol >= tot_nmol ); |
496 | > | } |
497 | > | |
498 | > | if( !done && n_per_extra > 2){ |
499 | > | makeElement( i * cellx, |
500 | > | j * celly + 0.5 * celly, |
501 | > | k * cellz + 0.5 * cellz ); |
502 | > | done = ( current_mol >= tot_nmol ); |
503 | > | } |
504 | > | |
505 | > | if( !done && n_per_extra > 3){ |
506 | > | makeElement( i * cellx + 0.5 * cellx, |
507 | > | j * celly, |
508 | > | k * cellz + 0.5 * cellz ); |
509 | > | done = ( current_mol >= tot_nmol ); |
510 | > | } |
511 | } | |
1056 | – | offset += comp_stamps[i]->getNAtoms(); |
1057 | – | |
1058 | – | #ifdef IS_MPI |
512 | } | |
513 | < | #endif //is_mpi |
1061 | < | |
1062 | < | molIndex++; |
1063 | < | } |
513 | > | } |
514 | } | |
515 | ||
516 | < | the_ff->initializeBonds( the_bonds ); |
516 | > | |
517 | > | for( i=0; i<info->n_atoms; i++ ){ |
518 | > | info->atoms[i]->set_vx( 0.0 ); |
519 | > | info->atoms[i]->set_vy( 0.0 ); |
520 | > | info->atoms[i]->set_vz( 0.0 ); |
521 | > | } |
522 | } | |
523 | ||
524 | < | void SimSetup::makeBends( void ){ |
524 | > | void SimSetup::makeElement( double x, double y, double z ){ |
525 | ||
526 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
527 | < | bend_set* the_bends; |
528 | < | BendStamp* current_bend; |
529 | < | LinkedAssign* extras; |
1075 | < | LinkedAssign* current_extra; |
1076 | < | |
526 | > | int k; |
527 | > | AtomStamp* current_atom; |
528 | > | DirectionalAtom* dAtom; |
529 | > | double rotMat[3][3]; |
530 | ||
531 | < | the_bends = new bend_set[tot_bends]; |
1079 | < | index = 0; |
1080 | < | offset = 0; |
1081 | < | molIndex = 0; |
1082 | < | for( i=0; i<n_components; i++ ){ |
531 | > | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
532 | ||
533 | < | for( j=0; j<components_nmol[i]; j++ ){ |
533 | > | current_atom = comp_stamps[current_comp]->getAtom( k ); |
534 | > | if( !current_atom->havePosition() ){ |
535 | > | sprintf( painCave.errMsg, |
536 | > | "SimSetup:initFromBass error.\n" |
537 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
538 | > | "\tThe initialization routine is unable to give a start" |
539 | > | " position.\n", |
540 | > | comp_stamps[current_comp]->getID(), |
541 | > | current_atom->getType() ); |
542 | > | painCave.isFatal = 1; |
543 | > | simError(); |
544 | > | } |
545 | ||
546 | < | #ifdef IS_MPI |
547 | < | if( mpiSim->getMyMolStart() <= molIndex && |
548 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1089 | < | #endif // is_mpi |
546 | > | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
547 | > | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
548 | > | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
549 | ||
550 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
551 | < | |
552 | < | current_bend = comp_stamps[i]->getBend( k ); |
553 | < | the_bends[index].a = current_bend->getA() + offset; |
554 | < | the_bends[index].b = current_bend->getB() + offset; |
555 | < | the_bends[index].c = current_bend->getC() + offset; |
556 | < | |
557 | < | if( current_bend->haveExtras() ){ |
558 | < | |
559 | < | extras = current_bend->getExtras(); |
560 | < | current_extra = extras; |
561 | < | |
562 | < | while( current_extra != NULL ){ |
563 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
564 | < | |
565 | < | switch( current_extra->getType() ){ |
566 | < | |
567 | < | case 0: |
568 | < | the_bends[index].ghost = |
569 | < | current_extra->getInt() + offset; |
570 | < | the_bends[index].isGhost = 1; |
571 | < | break; |
572 | < | |
573 | < | case 1: |
574 | < | the_bends[index].ghost = |
575 | < | (int)current_extra->getDouble() + offset; |
576 | < | the_bends[index].isGhost = 1; |
577 | < | break; |
578 | < | |
579 | < | default: |
580 | < | sprintf( painCave.errMsg, |
581 | < | "SimSetup Error: ghostVectorSource was neiter a " |
582 | < | "double nor an int.\n" |
583 | < | "-->Bend[%d] in %s\n", |
584 | < | k, comp_stamps[i]->getID() ); |
585 | < | painCave.isFatal = 1; |
586 | < | simError(); |
587 | < | } |
588 | < | } |
589 | < | |
590 | < | else{ |
591 | < | |
1133 | < | sprintf( painCave.errMsg, |
1134 | < | "SimSetup Error: unhandled bend assignment:\n" |
1135 | < | " -->%s in Bend[%d] in %s\n", |
1136 | < | current_extra->getlhs(), |
1137 | < | k, comp_stamps[i]->getID() ); |
1138 | < | painCave.isFatal = 1; |
1139 | < | simError(); |
1140 | < | } |
1141 | < | |
1142 | < | current_extra = current_extra->getNext(); |
1143 | < | } |
1144 | < | } |
1145 | < | |
1146 | < | if( !the_bends[index].isGhost ){ |
1147 | < | |
1148 | < | exI = the_bends[index].a; |
1149 | < | exJ = the_bends[index].c; |
1150 | < | } |
1151 | < | else{ |
1152 | < | |
1153 | < | exI = the_bends[index].a; |
1154 | < | exJ = the_bends[index].b; |
1155 | < | } |
1156 | < | |
1157 | < | // exclude_I must always be the smaller of the pair |
1158 | < | if( exI > exJ ){ |
1159 | < | tempEx = exI; |
1160 | < | exI = exJ; |
1161 | < | exJ = tempEx; |
1162 | < | } |
550 | > | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
551 | > | |
552 | > | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
553 | > | |
554 | > | rotMat[0][0] = 1.0; |
555 | > | rotMat[0][1] = 0.0; |
556 | > | rotMat[0][2] = 0.0; |
557 | > | |
558 | > | rotMat[1][0] = 0.0; |
559 | > | rotMat[1][1] = 1.0; |
560 | > | rotMat[1][2] = 0.0; |
561 | > | |
562 | > | rotMat[2][0] = 0.0; |
563 | > | rotMat[2][1] = 0.0; |
564 | > | rotMat[2][2] = 1.0; |
565 | > | |
566 | > | dAtom->setA( rotMat ); |
567 | > | } |
568 | > | |
569 | > | current_atom_ndx++; |
570 | > | } |
571 | > | |
572 | > | current_mol++; |
573 | > | current_comp_mol++; |
574 | > | |
575 | > | if( current_comp_mol >= components_nmol[current_comp] ){ |
576 | > | |
577 | > | current_comp_mol = 0; |
578 | > | current_comp++; |
579 | > | } |
580 | > | } |
581 | > | |
582 | > | |
583 | > | void SimSetup::gatherInfo( void ){ |
584 | > | int i,j,k; |
585 | > | |
586 | > | ensembleCase = -1; |
587 | > | ffCase = -1; |
588 | > | |
589 | > | // get the stamps and globals; |
590 | > | stamps = stamps; |
591 | > | globals = globals; |
592 | ||
593 | + | // set the easy ones first |
594 | + | info->target_temp = globals->getTargetTemp(); |
595 | + | info->dt = globals->getDt(); |
596 | + | info->run_time = globals->getRunTime(); |
597 | + | n_components = globals->getNComponents(); |
598 | ||
1165 | – | #ifdef IS_MPI |
599 | ||
600 | < | the_excludes[(index + tot_bonds)*2] = |
1168 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1169 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
1170 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1171 | < | |
1172 | < | #else // isn't MPI |
1173 | < | |
1174 | < | the_excludes[(index + tot_bonds)*2] = exI + 1; |
1175 | < | the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1176 | < | // fortran index from 1 (hence the +1 in the indexing) |
1177 | < | #endif //is_mpi |
1178 | < | |
1179 | < | |
1180 | < | // increment the index and repeat; |
1181 | < | index++; |
1182 | < | } |
1183 | < | offset += comp_stamps[i]->getNAtoms(); |
1184 | < | |
1185 | < | #ifdef IS_MPI |
1186 | < | } |
1187 | < | #endif //is_mpi |
600 | > | // get the forceField |
601 | ||
602 | < | molIndex++; |
603 | < | } |
602 | > | strcpy( force_field, globals->getForceField() ); |
603 | > | |
604 | > | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
605 | > | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
606 | > | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
607 | > | else{ |
608 | > | sprintf( painCave.errMsg, |
609 | > | "SimSetup Error. Unrecognized force field -> %s\n", |
610 | > | force_field ); |
611 | > | painCave.isFatal = 1; |
612 | > | simError(); |
613 | } | |
614 | ||
615 | < | #ifdef IS_MPI |
1194 | < | sprintf( checkPointMsg, |
1195 | < | "Successfully created the bends list.\n" ); |
1196 | < | MPIcheckPoint(); |
1197 | < | #endif // is_mpi |
1198 | < | |
615 | > | // get the ensemble |
616 | ||
617 | < | the_ff->initializeBends( the_bends ); |
1201 | < | } |
617 | > | strcpy( ensemble, globals->getEnsemble() ); |
618 | ||
619 | < | void SimSetup::makeTorsions( void ){ |
619 | > | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
620 | > | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
621 | > | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
622 | > | ensembleCase = NPTi_ENS; |
623 | > | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
624 | > | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
625 | > | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
626 | > | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
627 | > | else{ |
628 | > | sprintf( painCave.errMsg, |
629 | > | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
630 | > | "reverting to NVE for this simulation.\n", |
631 | > | ensemble ); |
632 | > | painCave.isFatal = 0; |
633 | > | simError(); |
634 | > | strcpy( ensemble, "NVE" ); |
635 | > | ensembleCase = NVE_ENS; |
636 | > | } |
637 | > | strcpy( info->ensemble, ensemble ); |
638 | ||
639 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1206 | < | torsion_set* the_torsions; |
1207 | < | TorsionStamp* current_torsion; |
639 | > | // get the mixing rule |
640 | ||
641 | < | the_torsions = new torsion_set[tot_torsions]; |
642 | < | index = 0; |
1211 | < | offset = 0; |
1212 | < | molIndex = 0; |
1213 | < | for( i=0; i<n_components; i++ ){ |
1214 | < | |
1215 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1216 | < | |
1217 | < | #ifdef IS_MPI |
1218 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1219 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1220 | < | #endif // is_mpi |
1221 | < | |
1222 | < | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1223 | < | |
1224 | < | current_torsion = comp_stamps[i]->getTorsion( k ); |
1225 | < | the_torsions[index].a = current_torsion->getA() + offset; |
1226 | < | the_torsions[index].b = current_torsion->getB() + offset; |
1227 | < | the_torsions[index].c = current_torsion->getC() + offset; |
1228 | < | the_torsions[index].d = current_torsion->getD() + offset; |
1229 | < | |
1230 | < | exI = the_torsions[index].a; |
1231 | < | exJ = the_torsions[index].d; |
1232 | < | |
641 | > | strcpy( info->mixingRule, globals->getMixingRule() ); |
642 | > | info->usePBC = globals->getPBC(); |
643 | ||
644 | < | // exclude_I must always be the smaller of the pair |
645 | < | if( exI > exJ ){ |
646 | < | tempEx = exI; |
647 | < | exI = exJ; |
648 | < | exJ = tempEx; |
1239 | < | } |
644 | > | |
645 | > | // get the components and calculate the tot_nMol and indvidual n_mol |
646 | > | |
647 | > | the_components = globals->getComponents(); |
648 | > | components_nmol = new int[n_components]; |
649 | ||
650 | ||
651 | < | #ifdef IS_MPI |
652 | < | |
653 | < | the_excludes[(index + tot_bonds + tot_bends)*2] = |
1245 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1246 | < | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1247 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1248 | < | |
1249 | < | #else // isn't MPI |
1250 | < | |
1251 | < | the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1252 | < | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1253 | < | // fortran indexes from 1 (hence the +1 in the indexing) |
1254 | < | #endif //is_mpi |
1255 | < | |
651 | > | if( !globals->haveNMol() ){ |
652 | > | // we don't have the total number of molecules, so we assume it is |
653 | > | // given in each component |
654 | ||
655 | < | // increment the index and repeat; |
656 | < | index++; |
1259 | < | } |
1260 | < | offset += comp_stamps[i]->getNAtoms(); |
655 | > | tot_nmol = 0; |
656 | > | for( i=0; i<n_components; i++ ){ |
657 | ||
658 | < | #ifdef IS_MPI |
658 | > | if( !the_components[i]->haveNMol() ){ |
659 | > | // we have a problem |
660 | > | sprintf( painCave.errMsg, |
661 | > | "SimSetup Error. No global NMol or component NMol" |
662 | > | " given. Cannot calculate the number of atoms.\n" ); |
663 | > | painCave.isFatal = 1; |
664 | > | simError(); |
665 | } | |
1264 | – | #endif //is_mpi |
666 | ||
667 | < | molIndex++; |
667 | > | tot_nmol += the_components[i]->getNMol(); |
668 | > | components_nmol[i] = the_components[i]->getNMol(); |
669 | } | |
670 | } | |
671 | + | else{ |
672 | + | sprintf( painCave.errMsg, |
673 | + | "SimSetup error.\n" |
674 | + | "\tSorry, the ability to specify total" |
675 | + | " nMols and then give molfractions in the components\n" |
676 | + | "\tis not currently supported." |
677 | + | " Please give nMol in the components.\n" ); |
678 | + | painCave.isFatal = 1; |
679 | + | simError(); |
680 | + | } |
681 | ||
682 | < | the_ff->initializeTorsions( the_torsions ); |
683 | < | } |
682 | > | // set the status, sample, and thermal kick times |
683 | > | |
684 | > | if( globals->haveSampleTime() ){ |
685 | > | info->sampleTime = globals->getSampleTime(); |
686 | > | info->statusTime = info->sampleTime; |
687 | > | info->thermalTime = info->sampleTime; |
688 | > | } |
689 | > | else{ |
690 | > | info->sampleTime = globals->getRunTime(); |
691 | > | info->statusTime = info->sampleTime; |
692 | > | info->thermalTime = info->sampleTime; |
693 | > | } |
694 | ||
695 | < | void SimSetup::initFromBass( void ){ |
695 | > | if( globals->haveStatusTime() ){ |
696 | > | info->statusTime = globals->getStatusTime(); |
697 | > | } |
698 | ||
699 | < | int i, j, k; |
700 | < | int n_cells; |
701 | < | double cellx, celly, cellz; |
1278 | < | double temp1, temp2, temp3; |
1279 | < | int n_per_extra; |
1280 | < | int n_extra; |
1281 | < | int have_extra, done; |
699 | > | if( globals->haveThermalTime() ){ |
700 | > | info->thermalTime = globals->getThermalTime(); |
701 | > | } |
702 | ||
703 | < | temp1 = (double)tot_nmol / 4.0; |
1284 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1285 | < | temp3 = ceil( temp2 ); |
703 | > | // check for the temperature set flag |
704 | ||
705 | < | have_extra =0; |
1288 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
1289 | < | have_extra =1; |
705 | > | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
706 | ||
707 | < | n_cells = (int)temp3 - 1; |
1292 | < | cellx = simnfo->box_x / temp3; |
1293 | < | celly = simnfo->box_y / temp3; |
1294 | < | cellz = simnfo->box_z / temp3; |
1295 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1296 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1297 | < | n_per_extra = (int)ceil( temp1 ); |
707 | > | // get some of the tricky things that may still be in the globals |
708 | ||
709 | < | if( n_per_extra > 4){ |
709 | > | double boxVector[3]; |
710 | > | if( globals->haveBox() ){ |
711 | > | boxVector[0] = globals->getBox(); |
712 | > | boxVector[1] = globals->getBox(); |
713 | > | boxVector[2] = globals->getBox(); |
714 | > | |
715 | > | info->setBox( boxVector ); |
716 | > | } |
717 | > | else if( globals->haveDensity() ){ |
718 | > | |
719 | > | double vol; |
720 | > | vol = (double)tot_nmol / globals->getDensity(); |
721 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
722 | > | boxVector[1] = boxVector[0]; |
723 | > | boxVector[2] = boxVector[0]; |
724 | > | |
725 | > | info->setBox( boxVector ); |
726 | > | } |
727 | > | else{ |
728 | > | if( !globals->haveBoxX() ){ |
729 | sprintf( painCave.errMsg, | |
730 | < | "SimSetup error. There has been an error in constructing" |
1302 | < | " the non-complete lattice.\n" ); |
730 | > | "SimSetup error, no periodic BoxX size given.\n" ); |
731 | painCave.isFatal = 1; | |
732 | simError(); | |
733 | } | |
734 | + | boxVector[0] = globals->getBoxX(); |
735 | + | |
736 | + | if( !globals->haveBoxY() ){ |
737 | + | sprintf( painCave.errMsg, |
738 | + | "SimSetup error, no periodic BoxY size given.\n" ); |
739 | + | painCave.isFatal = 1; |
740 | + | simError(); |
741 | + | } |
742 | + | boxVector[1] = globals->getBoxY(); |
743 | + | |
744 | + | if( !globals->haveBoxZ() ){ |
745 | + | sprintf( painCave.errMsg, |
746 | + | "SimSetup error, no periodic BoxZ size given.\n" ); |
747 | + | painCave.isFatal = 1; |
748 | + | simError(); |
749 | + | } |
750 | + | boxVector[2] = globals->getBoxZ(); |
751 | + | |
752 | + | info->setBox( boxVector ); |
753 | } | |
1307 | – | else{ |
1308 | – | n_cells = (int)temp3; |
1309 | – | cellx = simnfo->box_x / temp3; |
1310 | – | celly = simnfo->box_y / temp3; |
1311 | – | cellz = simnfo->box_z / temp3; |
1312 | – | } |
754 | ||
1314 | – | current_mol = 0; |
1315 | – | current_comp_mol = 0; |
1316 | – | current_comp = 0; |
1317 | – | current_atom_ndx = 0; |
755 | ||
756 | < | for( i=0; i < n_cells ; i++ ){ |
757 | < | for( j=0; j < n_cells; j++ ){ |
758 | < | for( k=0; k < n_cells; k++ ){ |
756 | > | |
757 | > | #ifdef IS_MPI |
758 | > | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
759 | > | MPIcheckPoint(); |
760 | > | #endif // is_mpi |
761 | ||
762 | < | makeElement( i * cellx, |
1324 | < | j * celly, |
1325 | < | k * cellz ); |
762 | > | } |
763 | ||
1327 | – | makeElement( i * cellx + 0.5 * cellx, |
1328 | – | j * celly + 0.5 * celly, |
1329 | – | k * cellz ); |
764 | ||
765 | < | makeElement( i * cellx, |
766 | < | j * celly + 0.5 * celly, |
767 | < | k * cellz + 0.5 * cellz ); |
765 | > | void SimSetup::finalInfoCheck( void ){ |
766 | > | int index; |
767 | > | int usesDipoles; |
768 | > | |
769 | ||
770 | < | makeElement( i * cellx + 0.5 * cellx, |
771 | < | j * celly, |
772 | < | k * cellz + 0.5 * cellz ); |
770 | > | // check electrostatic parameters |
771 | > | |
772 | > | index = 0; |
773 | > | usesDipoles = 0; |
774 | > | while( (index < info->n_atoms) && !usesDipoles ){ |
775 | > | usesDipoles = ((info->atoms)[index])->hasDipole(); |
776 | > | index++; |
777 | > | } |
778 | > | |
779 | > | #ifdef IS_MPI |
780 | > | int myUse = usesDipoles; |
781 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
782 | > | #endif //is_mpi |
783 | > | |
784 | > | double theEcr, theEst; |
785 | > | |
786 | > | if (globals->getUseRF() ) { |
787 | > | info->useReactionField = 1; |
788 | > | |
789 | > | if( !globals->haveECR() ){ |
790 | > | sprintf( painCave.errMsg, |
791 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
792 | > | "box length for the electrostaticCutoffRadius.\n" |
793 | > | "I hope you have a very fast processor!\n"); |
794 | > | painCave.isFatal = 0; |
795 | > | simError(); |
796 | > | double smallest; |
797 | > | smallest = info->boxL[0]; |
798 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
799 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
800 | > | theEcr = 0.5 * smallest; |
801 | > | } else { |
802 | > | theEcr = globals->getECR(); |
803 | > | } |
804 | > | |
805 | > | if( !globals->haveEST() ){ |
806 | > | sprintf( painCave.errMsg, |
807 | > | "SimSetup Warning: using default value of 0.05 * the " |
808 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
809 | > | ); |
810 | > | painCave.isFatal = 0; |
811 | > | simError(); |
812 | > | theEst = 0.05 * theEcr; |
813 | > | } else { |
814 | > | theEst= globals->getEST(); |
815 | > | } |
816 | > | |
817 | > | info->setEcr( theEcr, theEst ); |
818 | > | |
819 | > | if(!globals->haveDielectric() ){ |
820 | > | sprintf( painCave.errMsg, |
821 | > | "SimSetup Error: You are trying to use Reaction Field without" |
822 | > | "setting a dielectric constant!\n" |
823 | > | ); |
824 | > | painCave.isFatal = 1; |
825 | > | simError(); |
826 | > | } |
827 | > | info->dielectric = globals->getDielectric(); |
828 | > | } |
829 | > | else { |
830 | > | if (usesDipoles) { |
831 | > | |
832 | > | if( !globals->haveECR() ){ |
833 | > | sprintf( painCave.errMsg, |
834 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
835 | > | "box length for the electrostaticCutoffRadius.\n" |
836 | > | "I hope you have a very fast processor!\n"); |
837 | > | painCave.isFatal = 0; |
838 | > | simError(); |
839 | > | double smallest; |
840 | > | smallest = info->boxL[0]; |
841 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
842 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
843 | > | theEcr = 0.5 * smallest; |
844 | > | } else { |
845 | > | theEcr = globals->getECR(); |
846 | } | |
847 | + | |
848 | + | if( !globals->haveEST() ){ |
849 | + | sprintf( painCave.errMsg, |
850 | + | "SimSetup Warning: using default value of 0.05 * the " |
851 | + | "electrostaticCutoffRadius for the " |
852 | + | "electrostaticSkinThickness\n" |
853 | + | ); |
854 | + | painCave.isFatal = 0; |
855 | + | simError(); |
856 | + | theEst = 0.05 * theEcr; |
857 | + | } else { |
858 | + | theEst= globals->getEST(); |
859 | + | } |
860 | + | |
861 | + | info->setEcr( theEcr, theEst ); |
862 | } | |
863 | < | } |
863 | > | } |
864 | ||
865 | < | if( have_extra ){ |
866 | < | done = 0; |
865 | > | #ifdef IS_MPI |
866 | > | strcpy( checkPointMsg, "post processing checks out" ); |
867 | > | MPIcheckPoint(); |
868 | > | #endif // is_mpi |
869 | ||
870 | < | int start_ndx; |
1346 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1347 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
870 | > | } |
871 | ||
872 | < | if( i < n_cells ){ |
872 | > | void SimSetup::initSystemCoords( void ){ |
873 | ||
874 | < | if( j < n_cells ){ |
875 | < | start_ndx = n_cells; |
876 | < | } |
877 | < | else start_ndx = 0; |
874 | > | if( globals->haveInitialConfig() ){ |
875 | > | |
876 | > | InitializeFromFile* fileInit; |
877 | > | #ifdef IS_MPI // is_mpi |
878 | > | if( worldRank == 0 ){ |
879 | > | #endif //is_mpi |
880 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
881 | > | #ifdef IS_MPI |
882 | > | }else fileInit = new InitializeFromFile( NULL ); |
883 | > | #endif |
884 | > | fileInit->readInit( info ); // default velocities on |
885 | > | |
886 | > | delete fileInit; |
887 | > | } |
888 | > | else{ |
889 | > | |
890 | > | #ifdef IS_MPI |
891 | > | |
892 | > | // no init from bass |
893 | > | |
894 | > | sprintf( painCave.errMsg, |
895 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
896 | > | painCave.isFatal; |
897 | > | simError(); |
898 | > | |
899 | > | #else |
900 | > | |
901 | > | initFromBass(); |
902 | > | |
903 | > | |
904 | > | #endif |
905 | > | } |
906 | > | |
907 | > | #ifdef IS_MPI |
908 | > | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
909 | > | MPIcheckPoint(); |
910 | > | #endif // is_mpi |
911 | > | |
912 | > | } |
913 | > | |
914 | > | |
915 | > | void SimSetup::makeOutNames( void ){ |
916 | > | |
917 | > | #ifdef IS_MPI |
918 | > | if( worldRank == 0 ){ |
919 | > | #endif // is_mpi |
920 | > | |
921 | > | if( globals->haveFinalConfig() ){ |
922 | > | strcpy( info->finalName, globals->getFinalConfig() ); |
923 | > | } |
924 | > | else{ |
925 | > | strcpy( info->finalName, inFileName ); |
926 | > | char* endTest; |
927 | > | int nameLength = strlen( info->finalName ); |
928 | > | endTest = &(info->finalName[nameLength - 5]); |
929 | > | if( !strcmp( endTest, ".bass" ) ){ |
930 | > | strcpy( endTest, ".eor" ); |
931 | > | } |
932 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
933 | > | strcpy( endTest, ".eor" ); |
934 | > | } |
935 | > | else{ |
936 | > | endTest = &(info->finalName[nameLength - 4]); |
937 | > | if( !strcmp( endTest, ".bss" ) ){ |
938 | > | strcpy( endTest, ".eor" ); |
939 | } | |
940 | < | else start_ndx = 0; |
940 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
941 | > | strcpy( endTest, ".eor" ); |
942 | > | } |
943 | > | else{ |
944 | > | strcat( info->finalName, ".eor" ); |
945 | > | } |
946 | > | } |
947 | > | } |
948 | > | |
949 | > | // make the sample and status out names |
950 | > | |
951 | > | strcpy( info->sampleName, inFileName ); |
952 | > | char* endTest; |
953 | > | int nameLength = strlen( info->sampleName ); |
954 | > | endTest = &(info->sampleName[nameLength - 5]); |
955 | > | if( !strcmp( endTest, ".bass" ) ){ |
956 | > | strcpy( endTest, ".dump" ); |
957 | > | } |
958 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
959 | > | strcpy( endTest, ".dump" ); |
960 | > | } |
961 | > | else{ |
962 | > | endTest = &(info->sampleName[nameLength - 4]); |
963 | > | if( !strcmp( endTest, ".bss" ) ){ |
964 | > | strcpy( endTest, ".dump" ); |
965 | > | } |
966 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
967 | > | strcpy( endTest, ".dump" ); |
968 | > | } |
969 | > | else{ |
970 | > | strcat( info->sampleName, ".dump" ); |
971 | > | } |
972 | > | } |
973 | > | |
974 | > | strcpy( info->statusName, inFileName ); |
975 | > | nameLength = strlen( info->statusName ); |
976 | > | endTest = &(info->statusName[nameLength - 5]); |
977 | > | if( !strcmp( endTest, ".bass" ) ){ |
978 | > | strcpy( endTest, ".stat" ); |
979 | > | } |
980 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
981 | > | strcpy( endTest, ".stat" ); |
982 | > | } |
983 | > | else{ |
984 | > | endTest = &(info->statusName[nameLength - 4]); |
985 | > | if( !strcmp( endTest, ".bss" ) ){ |
986 | > | strcpy( endTest, ".stat" ); |
987 | > | } |
988 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
989 | > | strcpy( endTest, ".stat" ); |
990 | > | } |
991 | > | else{ |
992 | > | strcat( info->statusName, ".stat" ); |
993 | > | } |
994 | > | } |
995 | > | |
996 | > | #ifdef IS_MPI |
997 | > | } |
998 | > | #endif // is_mpi |
999 | ||
1000 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1000 | > | } |
1001 | ||
1360 | – | makeElement( i * cellx, |
1361 | – | j * celly, |
1362 | – | k * cellz ); |
1363 | – | done = ( current_mol >= tot_nmol ); |
1002 | ||
1003 | < | if( !done && n_per_extra > 1 ){ |
1366 | < | makeElement( i * cellx + 0.5 * cellx, |
1367 | < | j * celly + 0.5 * celly, |
1368 | < | k * cellz ); |
1369 | < | done = ( current_mol >= tot_nmol ); |
1370 | < | } |
1003 | > | void SimSetup::sysObjectsCreation( void ){ |
1004 | ||
1005 | < | if( !done && n_per_extra > 2){ |
1006 | < | makeElement( i * cellx, |
1007 | < | j * celly + 0.5 * celly, |
1008 | < | k * cellz + 0.5 * cellz ); |
1009 | < | done = ( current_mol >= tot_nmol ); |
1010 | < | } |
1005 | > | int i; |
1006 | > | |
1007 | > | // create the forceField |
1008 | > | |
1009 | > | createFF(); |
1010 | > | |
1011 | > | // extract componentList |
1012 | ||
1013 | < | if( !done && n_per_extra > 3){ |
1014 | < | makeElement( i * cellx + 0.5 * cellx, |
1015 | < | j * celly, |
1016 | < | k * cellz + 0.5 * cellz ); |
1017 | < | done = ( current_mol >= tot_nmol ); |
1018 | < | } |
1019 | < | } |
1013 | > | compList(); |
1014 | > | |
1015 | > | // calc the number of atoms, bond, bends, and torsions |
1016 | > | |
1017 | > | calcSysValues(); |
1018 | > | |
1019 | > | #ifdef IS_MPI |
1020 | > | // divide the molecules among the processors |
1021 | > | |
1022 | > | mpiMolDivide(); |
1023 | > | #endif //is_mpi |
1024 | > | |
1025 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1026 | > | |
1027 | > | makeSysArrays(); |
1028 | > | |
1029 | > | // make and initialize the molecules (all but atomic coordinates) |
1030 | > | |
1031 | > | makeMolecules(); |
1032 | > | info->identArray = new int[info->n_atoms]; |
1033 | > | for(i=0; i<info->n_atoms; i++){ |
1034 | > | info->identArray[i] = the_atoms[i]->getIdent(); |
1035 | > | } |
1036 | > | |
1037 | > | |
1038 | > | |
1039 | > | } |
1040 | > | |
1041 | > | |
1042 | > | void SimSetup::createFF( void ){ |
1043 | > | |
1044 | > | switch( ffCase ){ |
1045 | > | |
1046 | > | case FF_DUFF: |
1047 | > | the_ff = new DUFF(); |
1048 | > | break; |
1049 | > | |
1050 | > | case FF_LJ: |
1051 | > | the_ff = new LJFF(); |
1052 | > | break; |
1053 | > | |
1054 | > | case FF_EAM: |
1055 | > | the_ff = new EAM_FF(); |
1056 | > | break; |
1057 | > | |
1058 | > | default: |
1059 | > | sprintf( painCave.errMsg, |
1060 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1061 | > | painCave.isFatal = 1; |
1062 | > | simError(); |
1063 | > | } |
1064 | > | |
1065 | > | #ifdef IS_MPI |
1066 | > | strcpy( checkPointMsg, "ForceField creation successful" ); |
1067 | > | MPIcheckPoint(); |
1068 | > | #endif // is_mpi |
1069 | > | |
1070 | > | } |
1071 | > | |
1072 | > | |
1073 | > | void SimSetup::compList( void ){ |
1074 | > | |
1075 | > | int i; |
1076 | > | |
1077 | > | comp_stamps = new MoleculeStamp*[n_components]; |
1078 | > | |
1079 | > | // make an array of molecule stamps that match the components used. |
1080 | > | // also extract the used stamps out into a separate linked list |
1081 | > | |
1082 | > | info->nComponents = n_components; |
1083 | > | info->componentsNmol = components_nmol; |
1084 | > | info->compStamps = comp_stamps; |
1085 | > | info->headStamp = new LinkedMolStamp(); |
1086 | > | |
1087 | > | char* id; |
1088 | > | LinkedMolStamp* headStamp = info->headStamp; |
1089 | > | LinkedMolStamp* currentStamp = NULL; |
1090 | > | for( i=0; i<n_components; i++ ){ |
1091 | > | |
1092 | > | id = the_components[i]->getType(); |
1093 | > | comp_stamps[i] = NULL; |
1094 | > | |
1095 | > | // check to make sure the component isn't already in the list |
1096 | > | |
1097 | > | comp_stamps[i] = headStamp->match( id ); |
1098 | > | if( comp_stamps[i] == NULL ){ |
1099 | > | |
1100 | > | // extract the component from the list; |
1101 | > | |
1102 | > | currentStamp = stamps->extractMolStamp( id ); |
1103 | > | if( currentStamp == NULL ){ |
1104 | > | sprintf( painCave.errMsg, |
1105 | > | "SimSetup error: Component \"%s\" was not found in the " |
1106 | > | "list of declared molecules\n", |
1107 | > | id ); |
1108 | > | painCave.isFatal = 1; |
1109 | > | simError(); |
1110 | } | |
1111 | + | |
1112 | + | headStamp->add( currentStamp ); |
1113 | + | comp_stamps[i] = headStamp->match( id ); |
1114 | } | |
1115 | } | |
1116 | ||
1117 | + | #ifdef IS_MPI |
1118 | + | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1119 | + | MPIcheckPoint(); |
1120 | + | #endif // is_mpi |
1121 | ||
1122 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1123 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1124 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1125 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
1122 | > | |
1123 | > | } |
1124 | > | |
1125 | > | void SimSetup::calcSysValues( void ){ |
1126 | > | int i, j, k; |
1127 | > | |
1128 | > | |
1129 | > | tot_atoms = 0; |
1130 | > | tot_bonds = 0; |
1131 | > | tot_bends = 0; |
1132 | > | tot_torsions = 0; |
1133 | > | for( i=0; i<n_components; i++ ){ |
1134 | > | |
1135 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1136 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1137 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1138 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1139 | } | |
1140 | + | |
1141 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1142 | + | |
1143 | + | info->n_atoms = tot_atoms; |
1144 | + | info->n_bonds = tot_bonds; |
1145 | + | info->n_bends = tot_bends; |
1146 | + | info->n_torsions = tot_torsions; |
1147 | + | info->n_SRI = tot_SRI; |
1148 | + | info->n_mol = tot_nmol; |
1149 | + | |
1150 | + | info->molMembershipArray = new int[tot_atoms]; |
1151 | } | |
1152 | ||
1398 | – | void SimSetup::makeElement( double x, double y, double z ){ |
1153 | ||
1154 | < | int k; |
1401 | < | AtomStamp* current_atom; |
1402 | < | DirectionalAtom* dAtom; |
1403 | < | double rotMat[3][3]; |
1154 | > | #ifdef IS_MPI |
1155 | ||
1156 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1156 | > | void SimSetup::mpiMolDivide( void ){ |
1157 | > | |
1158 | > | int i, j, k; |
1159 | > | int localMol, allMol; |
1160 | > | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1161 | ||
1162 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1163 | < | if( !current_atom->havePosition() ){ |
1164 | < | sprintf( painCave.errMsg, |
1165 | < | "SimSetup:initFromBass error.\n" |
1166 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
1167 | < | "\tThe initialization routine is unable to give a start" |
1168 | < | " position.\n", |
1169 | < | comp_stamps[current_comp]->getID(), |
1170 | < | current_atom->getType() ); |
1171 | < | painCave.isFatal = 1; |
1172 | < | simError(); |
1162 | > | mpiSim = new mpiSimulation( info ); |
1163 | > | |
1164 | > | globalIndex = mpiSim->divideLabor(); |
1165 | > | |
1166 | > | // set up the local variables |
1167 | > | |
1168 | > | mol2proc = mpiSim->getMolToProcMap(); |
1169 | > | molCompType = mpiSim->getMolComponentType(); |
1170 | > | |
1171 | > | allMol = 0; |
1172 | > | localMol = 0; |
1173 | > | local_atoms = 0; |
1174 | > | local_bonds = 0; |
1175 | > | local_bends = 0; |
1176 | > | local_torsions = 0; |
1177 | > | globalAtomIndex = 0; |
1178 | > | |
1179 | > | |
1180 | > | for( i=0; i<n_components; i++ ){ |
1181 | > | |
1182 | > | for( j=0; j<components_nmol[i]; j++ ){ |
1183 | > | |
1184 | > | if( mol2proc[allMol] == worldRank ){ |
1185 | > | |
1186 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1187 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1188 | > | local_bends += comp_stamps[i]->getNBends(); |
1189 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1190 | > | localMol++; |
1191 | > | } |
1192 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1193 | > | info->molMembershipArray[globalAtomIndex] = allMol; |
1194 | > | globalAtomIndex++; |
1195 | > | } |
1196 | > | |
1197 | > | allMol++; |
1198 | } | |
1199 | + | } |
1200 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1201 | + | |
1202 | + | info->n_atoms = mpiSim->getMyNlocal(); |
1203 | + | |
1204 | + | if( local_atoms != info->n_atoms ){ |
1205 | + | sprintf( painCave.errMsg, |
1206 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1207 | + | " localAtom (%d) are not equal.\n", |
1208 | + | info->n_atoms, |
1209 | + | local_atoms ); |
1210 | + | painCave.isFatal = 1; |
1211 | + | simError(); |
1212 | + | } |
1213 | ||
1214 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1215 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1216 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1214 | > | info->n_bonds = local_bonds; |
1215 | > | info->n_bends = local_bends; |
1216 | > | info->n_torsions = local_torsions; |
1217 | > | info->n_SRI = local_SRI; |
1218 | > | info->n_mol = localMol; |
1219 | ||
1220 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1220 | > | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1221 | > | MPIcheckPoint(); |
1222 | > | } |
1223 | > | |
1224 | > | #endif // is_mpi |
1225 | ||
1426 | – | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1226 | ||
1227 | < | rotMat[0][0] = 1.0; |
1228 | < | rotMat[0][1] = 0.0; |
1430 | < | rotMat[0][2] = 0.0; |
1227 | > | void SimSetup::makeSysArrays( void ){ |
1228 | > | int i, j, k; |
1229 | ||
1432 | – | rotMat[1][0] = 0.0; |
1433 | – | rotMat[1][1] = 1.0; |
1434 | – | rotMat[1][2] = 0.0; |
1230 | ||
1231 | < | rotMat[2][0] = 0.0; |
1437 | < | rotMat[2][1] = 0.0; |
1438 | < | rotMat[2][2] = 1.0; |
1231 | > | // create the atom and short range interaction arrays |
1232 | ||
1233 | < | dAtom->setA( rotMat ); |
1233 | > | Atom::createArrays(info->n_atoms); |
1234 | > | the_atoms = new Atom*[info->n_atoms]; |
1235 | > | the_molecules = new Molecule[info->n_mol]; |
1236 | > | int molIndex; |
1237 | > | |
1238 | > | // initialize the molecule's stampID's |
1239 | > | |
1240 | > | #ifdef IS_MPI |
1241 | > | |
1242 | > | |
1243 | > | molIndex = 0; |
1244 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1245 | > | |
1246 | > | if(mol2proc[i] == worldRank ){ |
1247 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
1248 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1249 | > | the_molecules[molIndex].setGlobalIndex( i ); |
1250 | > | molIndex++; |
1251 | } | |
1252 | + | } |
1253 | ||
1254 | < | current_atom_ndx++; |
1254 | > | #else // is_mpi |
1255 | > | |
1256 | > | molIndex = 0; |
1257 | > | globalAtomIndex = 0; |
1258 | > | for(i=0; i<n_components; i++){ |
1259 | > | for(j=0; j<components_nmol[i]; j++ ){ |
1260 | > | the_molecules[molIndex].setStampID( i ); |
1261 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1262 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1263 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1264 | > | info->molMembershipArray[globalAtomIndex] = molIndex; |
1265 | > | globalAtomIndex++; |
1266 | > | } |
1267 | > | molIndex++; |
1268 | > | } |
1269 | } | |
1270 | + | |
1271 | ||
1272 | < | current_mol++; |
1447 | < | current_comp_mol++; |
1272 | > | #endif // is_mpi |
1273 | ||
1449 | – | if( current_comp_mol >= components_nmol[current_comp] ){ |
1274 | ||
1275 | < | current_comp_mol = 0; |
1276 | < | current_comp++; |
1275 | > | if( info->n_SRI ){ |
1276 | > | |
1277 | > | Exclude::createArray(info->n_SRI); |
1278 | > | the_excludes = new Exclude*[info->n_SRI]; |
1279 | > | for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1280 | > | info->globalExcludes = new int; |
1281 | > | info->n_exclude = info->n_SRI; |
1282 | } | |
1283 | + | else{ |
1284 | + | |
1285 | + | Exclude::createArray( 1 ); |
1286 | + | the_excludes = new Exclude*; |
1287 | + | the_excludes[0] = new Exclude(0); |
1288 | + | the_excludes[0]->setPair( 0,0 ); |
1289 | + | info->globalExcludes = new int; |
1290 | + | info->globalExcludes[0] = 0; |
1291 | + | info->n_exclude = 0; |
1292 | + | } |
1293 | + | |
1294 | + | // set the arrays into the SimInfo object |
1295 | + | |
1296 | + | info->atoms = the_atoms; |
1297 | + | info->molecules = the_molecules; |
1298 | + | info->nGlobalExcludes = 0; |
1299 | + | info->excludes = the_excludes; |
1300 | + | |
1301 | + | the_ff->setSimInfo( info ); |
1302 | + | |
1303 | } | |
1304 | + | |
1305 | + | void SimSetup::makeIntegrator( void ){ |
1306 | + | |
1307 | + | NVT<RealIntegrator>* myNVT = NULL; |
1308 | + | NPTi<RealIntegrator>* myNPTi = NULL; |
1309 | + | NPTf<RealIntegrator>* myNPTf = NULL; |
1310 | + | NPTim<RealIntegrator>* myNPTim = NULL; |
1311 | + | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1312 | + | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1313 | + | |
1314 | + | cerr << "setting integrator" <<endl; |
1315 | + | |
1316 | + | switch( ensembleCase ){ |
1317 | + | |
1318 | + | case NVE_ENS: |
1319 | + | new NVE<RealIntegrator>( info, the_ff ); |
1320 | + | break; |
1321 | + | |
1322 | + | case NVT_ENS: |
1323 | + | myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1324 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1325 | + | |
1326 | + | if (globals->haveTauThermostat()) |
1327 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1328 | + | |
1329 | + | else { |
1330 | + | sprintf( painCave.errMsg, |
1331 | + | "SimSetup error: If you use the NVT\n" |
1332 | + | " ensemble, you must set tauThermostat.\n"); |
1333 | + | painCave.isFatal = 1; |
1334 | + | simError(); |
1335 | + | } |
1336 | + | break; |
1337 | + | |
1338 | + | case NPTi_ENS: |
1339 | + | myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1340 | + | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1341 | + | |
1342 | + | if (globals->haveTargetPressure()) |
1343 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1344 | + | else { |
1345 | + | sprintf( painCave.errMsg, |
1346 | + | "SimSetup error: If you use a constant pressure\n" |
1347 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1348 | + | painCave.isFatal = 1; |
1349 | + | simError(); |
1350 | + | } |
1351 | + | |
1352 | + | if( globals->haveTauThermostat() ) |
1353 | + | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1354 | + | else{ |
1355 | + | sprintf( painCave.errMsg, |
1356 | + | "SimSetup error: If you use an NPT\n" |
1357 | + | " ensemble, you must set tauThermostat.\n"); |
1358 | + | painCave.isFatal = 1; |
1359 | + | simError(); |
1360 | + | } |
1361 | + | |
1362 | + | if( globals->haveTauBarostat() ) |
1363 | + | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1364 | + | else{ |
1365 | + | sprintf( painCave.errMsg, |
1366 | + | "SimSetup error: If you use an NPT\n" |
1367 | + | " ensemble, you must set tauBarostat.\n"); |
1368 | + | painCave.isFatal = 1; |
1369 | + | simError(); |
1370 | + | } |
1371 | + | break; |
1372 | + | |
1373 | + | case NPTf_ENS: |
1374 | + | myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1375 | + | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1376 | + | |
1377 | + | if (globals->haveTargetPressure()) |
1378 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1379 | + | else { |
1380 | + | sprintf( painCave.errMsg, |
1381 | + | "SimSetup error: If you use a constant pressure\n" |
1382 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1383 | + | painCave.isFatal = 1; |
1384 | + | simError(); |
1385 | + | } |
1386 | + | |
1387 | + | if( globals->haveTauThermostat() ) |
1388 | + | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1389 | + | else{ |
1390 | + | sprintf( painCave.errMsg, |
1391 | + | "SimSetup error: If you use an NPT\n" |
1392 | + | " ensemble, you must set tauThermostat.\n"); |
1393 | + | painCave.isFatal = 1; |
1394 | + | simError(); |
1395 | + | } |
1396 | + | |
1397 | + | if( globals->haveTauBarostat() ) |
1398 | + | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1399 | + | else{ |
1400 | + | sprintf( painCave.errMsg, |
1401 | + | "SimSetup error: If you use an NPT\n" |
1402 | + | " ensemble, you must set tauBarostat.\n"); |
1403 | + | painCave.isFatal = 1; |
1404 | + | simError(); |
1405 | + | } |
1406 | + | break; |
1407 | + | |
1408 | + | case NPTim_ENS: |
1409 | + | myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1410 | + | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1411 | + | |
1412 | + | if (globals->haveTargetPressure()) |
1413 | + | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1414 | + | else { |
1415 | + | sprintf( painCave.errMsg, |
1416 | + | "SimSetup error: If you use a constant pressure\n" |
1417 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1418 | + | painCave.isFatal = 1; |
1419 | + | simError(); |
1420 | + | } |
1421 | + | |
1422 | + | if( globals->haveTauThermostat() ) |
1423 | + | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1424 | + | else{ |
1425 | + | sprintf( painCave.errMsg, |
1426 | + | "SimSetup error: If you use an NPT\n" |
1427 | + | " ensemble, you must set tauThermostat.\n"); |
1428 | + | painCave.isFatal = 1; |
1429 | + | simError(); |
1430 | + | } |
1431 | + | |
1432 | + | if( globals->haveTauBarostat() ) |
1433 | + | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1434 | + | else{ |
1435 | + | sprintf( painCave.errMsg, |
1436 | + | "SimSetup error: If you use an NPT\n" |
1437 | + | " ensemble, you must set tauBarostat.\n"); |
1438 | + | painCave.isFatal = 1; |
1439 | + | simError(); |
1440 | + | } |
1441 | + | break; |
1442 | + | |
1443 | + | case NPTfm_ENS: |
1444 | + | myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1445 | + | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1446 | + | |
1447 | + | if (globals->haveTargetPressure()) |
1448 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1449 | + | else { |
1450 | + | sprintf( painCave.errMsg, |
1451 | + | "SimSetup error: If you use a constant pressure\n" |
1452 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1453 | + | painCave.isFatal = 1; |
1454 | + | simError(); |
1455 | + | } |
1456 | + | |
1457 | + | if( globals->haveTauThermostat() ) |
1458 | + | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1459 | + | else{ |
1460 | + | sprintf( painCave.errMsg, |
1461 | + | "SimSetup error: If you use an NPT\n" |
1462 | + | " ensemble, you must set tauThermostat.\n"); |
1463 | + | painCave.isFatal = 1; |
1464 | + | simError(); |
1465 | + | } |
1466 | + | |
1467 | + | if( globals->haveTauBarostat() ) |
1468 | + | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1469 | + | else{ |
1470 | + | sprintf( painCave.errMsg, |
1471 | + | "SimSetup error: If you use an NPT\n" |
1472 | + | " ensemble, you must set tauBarostat.\n"); |
1473 | + | painCave.isFatal = 1; |
1474 | + | simError(); |
1475 | + | } |
1476 | + | break; |
1477 | + | |
1478 | + | case NVEZCONS_ENS: |
1479 | + | { |
1480 | + | |
1481 | + | if(globals->haveZConsTime()){ |
1482 | + | |
1483 | + | //add sample time of z-constraint into SimInfo's property list |
1484 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1485 | + | zconsTimeProp->setID("zconstime"); |
1486 | + | zconsTimeProp->setData(globals->getZConsTime()); |
1487 | + | info->addProperty(zconsTimeProp); |
1488 | + | } |
1489 | + | else{ |
1490 | + | sprintf( painCave.errMsg, |
1491 | + | "ZConstraint error: If you use an ZConstraint\n" |
1492 | + | " , you must set sample time.\n"); |
1493 | + | painCave.isFatal = 1; |
1494 | + | simError(); |
1495 | + | } |
1496 | + | |
1497 | + | if(globals->haveIndexOfAllZConsMols()){ |
1498 | + | |
1499 | + | //add index of z-constraint molecules into SimInfo's property list |
1500 | + | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1501 | + | sort(tempIndex.begin(), tempIndex.end()); |
1502 | + | |
1503 | + | IndexData* zconsIndex = new IndexData(); |
1504 | + | zconsIndex->setID("zconsindex"); |
1505 | + | zconsIndex->setIndexData(tempIndex); |
1506 | + | info->addProperty(zconsIndex); |
1507 | + | } |
1508 | + | else{ |
1509 | + | sprintf( painCave.errMsg, |
1510 | + | "SimSetup error: If you use an ZConstraint\n" |
1511 | + | " , you must set index of z-constraint molecules.\n"); |
1512 | + | painCave.isFatal = 1; |
1513 | + | simError(); |
1514 | + | |
1515 | + | } |
1516 | + | |
1517 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1518 | + | //Be careful, do not use inFileName, since it is a pointer which |
1519 | + | //point to a string at master node, and slave nodes do not contain that string |
1520 | + | |
1521 | + | string zconsOutput(info->finalName); |
1522 | + | |
1523 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1524 | + | |
1525 | + | StringData* zconsFilename = new StringData(); |
1526 | + | zconsFilename->setID("zconsfilename"); |
1527 | + | zconsFilename->setData(zconsOutput); |
1528 | + | |
1529 | + | info->addProperty(zconsFilename); |
1530 | + | |
1531 | + | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1532 | + | |
1533 | + | break; |
1534 | + | } |
1535 | + | |
1536 | + | default: |
1537 | + | sprintf( painCave.errMsg, |
1538 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1539 | + | painCave.isFatal = 1; |
1540 | + | simError(); |
1541 | + | } |
1542 | + | |
1543 | + | } |
1544 | + | |
1545 | + | void SimSetup::initFortran( void ){ |
1546 | + | |
1547 | + | info->refreshSim(); |
1548 | + | |
1549 | + | if( !strcmp( info->mixingRule, "standard") ){ |
1550 | + | the_ff->initForceField( LB_MIXING_RULE ); |
1551 | + | } |
1552 | + | else if( !strcmp( info->mixingRule, "explicit") ){ |
1553 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1554 | + | } |
1555 | + | else{ |
1556 | + | sprintf( painCave.errMsg, |
1557 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1558 | + | info->mixingRule ); |
1559 | + | painCave.isFatal = 1; |
1560 | + | simError(); |
1561 | + | } |
1562 | + | |
1563 | + | |
1564 | + | #ifdef IS_MPI |
1565 | + | strcpy( checkPointMsg, |
1566 | + | "Successfully intialized the mixingRule for Fortran." ); |
1567 | + | MPIcheckPoint(); |
1568 | + | #endif // is_mpi |
1569 | + | |
1570 | + | } |
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