1 |
#include <cstdlib> |
2 |
#include <iostream> |
3 |
#include <cmath> |
4 |
|
5 |
#include "SimSetup.hpp" |
6 |
#include "parse_me.h" |
7 |
#include "Integrator.hpp" |
8 |
#include "simError.h" |
9 |
|
10 |
#ifdef IS_MPI |
11 |
#include "mpiBASS.h" |
12 |
#include "mpiSimulation.hpp" |
13 |
#endif |
14 |
|
15 |
SimSetup::SimSetup(){ |
16 |
stamps = new MakeStamps(); |
17 |
globals = new Globals(); |
18 |
|
19 |
#ifdef IS_MPI |
20 |
strcpy( checkPointMsg, "SimSetup creation successful" ); |
21 |
MPIcheckPoint(); |
22 |
#endif // IS_MPI |
23 |
} |
24 |
|
25 |
SimSetup::~SimSetup(){ |
26 |
delete stamps; |
27 |
delete globals; |
28 |
} |
29 |
|
30 |
void SimSetup::parseFile( char* fileName ){ |
31 |
|
32 |
#ifdef IS_MPI |
33 |
if( worldRank == 0 ){ |
34 |
#endif // is_mpi |
35 |
|
36 |
inFileName = fileName; |
37 |
set_interface_stamps( stamps, globals ); |
38 |
|
39 |
#ifdef IS_MPI |
40 |
mpiEventInit(); |
41 |
#endif |
42 |
|
43 |
yacc_BASS( fileName ); |
44 |
|
45 |
#ifdef IS_MPI |
46 |
throwMPIEvent(NULL); |
47 |
} |
48 |
else receiveParse(); |
49 |
#endif |
50 |
|
51 |
} |
52 |
|
53 |
#ifdef IS_MPI |
54 |
void SimSetup::receiveParse(void){ |
55 |
|
56 |
set_interface_stamps( stamps, globals ); |
57 |
mpiEventInit(); |
58 |
MPIcheckPoint(); |
59 |
mpiEventLoop(); |
60 |
|
61 |
} |
62 |
|
63 |
#endif // is_mpi |
64 |
|
65 |
void SimSetup::createSim( void ){ |
66 |
|
67 |
MakeStamps *the_stamps; |
68 |
Globals* the_globals; |
69 |
int i, j; |
70 |
|
71 |
// get the stamps and globals; |
72 |
the_stamps = stamps; |
73 |
the_globals = globals; |
74 |
|
75 |
// set the easy ones first |
76 |
simnfo->target_temp = the_globals->getTargetTemp(); |
77 |
simnfo->dt = the_globals->getDt(); |
78 |
simnfo->run_time = the_globals->getRunTime(); |
79 |
|
80 |
// get the ones we know are there, yet still may need some work. |
81 |
n_components = the_globals->getNComponents(); |
82 |
strcpy( force_field, the_globals->getForceField() ); |
83 |
strcpy( ensemble, the_globals->getEnsemble() ); |
84 |
strcpy( simnfo->ensemble, ensemble ); |
85 |
|
86 |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
87 |
simnfo->usePBC = the_globals->getPBC(); |
88 |
|
89 |
|
90 |
|
91 |
if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
92 |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
93 |
else{ |
94 |
sprintf( painCave.errMsg, |
95 |
"SimSetup Error. Unrecognized force field -> %s\n", |
96 |
force_field ); |
97 |
painCave.isFatal = 1; |
98 |
simError(); |
99 |
} |
100 |
|
101 |
#ifdef IS_MPI |
102 |
strcpy( checkPointMsg, "ForceField creation successful" ); |
103 |
MPIcheckPoint(); |
104 |
#endif // is_mpi |
105 |
|
106 |
|
107 |
|
108 |
// get the components and calculate the tot_nMol and indvidual n_mol |
109 |
the_components = the_globals->getComponents(); |
110 |
components_nmol = new int[n_components]; |
111 |
comp_stamps = new MoleculeStamp*[n_components]; |
112 |
|
113 |
if( !the_globals->haveNMol() ){ |
114 |
// we don't have the total number of molecules, so we assume it is |
115 |
// given in each component |
116 |
|
117 |
tot_nmol = 0; |
118 |
for( i=0; i<n_components; i++ ){ |
119 |
|
120 |
if( !the_components[i]->haveNMol() ){ |
121 |
// we have a problem |
122 |
sprintf( painCave.errMsg, |
123 |
"SimSetup Error. No global NMol or component NMol" |
124 |
" given. Cannot calculate the number of atoms.\n" ); |
125 |
painCave.isFatal = 1; |
126 |
simError(); |
127 |
} |
128 |
|
129 |
tot_nmol += the_components[i]->getNMol(); |
130 |
components_nmol[i] = the_components[i]->getNMol(); |
131 |
} |
132 |
} |
133 |
else{ |
134 |
sprintf( painCave.errMsg, |
135 |
"SimSetup error.\n" |
136 |
"\tSorry, the ability to specify total" |
137 |
" nMols and then give molfractions in the components\n" |
138 |
"\tis not currently supported." |
139 |
" Please give nMol in the components.\n" ); |
140 |
painCave.isFatal = 1; |
141 |
simError(); |
142 |
|
143 |
|
144 |
// tot_nmol = the_globals->getNMol(); |
145 |
|
146 |
// //we have the total number of molecules, now we check for molfractions |
147 |
// for( i=0; i<n_components; i++ ){ |
148 |
|
149 |
// if( !the_components[i]->haveMolFraction() ){ |
150 |
|
151 |
// if( !the_components[i]->haveNMol() ){ |
152 |
// //we have a problem |
153 |
// std::cerr << "SimSetup error. Neither molFraction nor " |
154 |
// << " nMol was given in component |
155 |
|
156 |
} |
157 |
|
158 |
#ifdef IS_MPI |
159 |
strcpy( checkPointMsg, "Have the number of components" ); |
160 |
MPIcheckPoint(); |
161 |
#endif // is_mpi |
162 |
|
163 |
// make an array of molecule stamps that match the components used. |
164 |
// also extract the used stamps out into a separate linked list |
165 |
|
166 |
simnfo->nComponents = n_components; |
167 |
simnfo->componentsNmol = components_nmol; |
168 |
simnfo->compStamps = comp_stamps; |
169 |
simnfo->headStamp = new LinkedMolStamp(); |
170 |
|
171 |
char* id; |
172 |
LinkedMolStamp* headStamp = simnfo->headStamp; |
173 |
LinkedMolStamp* currentStamp = NULL; |
174 |
for( i=0; i<n_components; i++ ){ |
175 |
|
176 |
id = the_components[i]->getType(); |
177 |
comp_stamps[i] = NULL; |
178 |
|
179 |
// check to make sure the component isn't already in the list |
180 |
|
181 |
comp_stamps[i] = headStamp->match( id ); |
182 |
if( comp_stamps[i] == NULL ){ |
183 |
|
184 |
// extract the component from the list; |
185 |
|
186 |
currentStamp = the_stamps->extractMolStamp( id ); |
187 |
if( currentStamp == NULL ){ |
188 |
sprintf( painCave.errMsg, |
189 |
"SimSetup error: Component \"%s\" was not found in the " |
190 |
"list of declared molecules\n", |
191 |
id ); |
192 |
painCave.isFatal = 1; |
193 |
simError(); |
194 |
} |
195 |
|
196 |
headStamp->add( currentStamp ); |
197 |
comp_stamps[i] = headStamp->match( id ); |
198 |
} |
199 |
} |
200 |
|
201 |
#ifdef IS_MPI |
202 |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
203 |
MPIcheckPoint(); |
204 |
#endif // is_mpi |
205 |
|
206 |
|
207 |
|
208 |
|
209 |
// caclulate the number of atoms, bonds, bends and torsions |
210 |
|
211 |
tot_atoms = 0; |
212 |
tot_bonds = 0; |
213 |
tot_bends = 0; |
214 |
tot_torsions = 0; |
215 |
for( i=0; i<n_components; i++ ){ |
216 |
|
217 |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
218 |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
219 |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
220 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
221 |
} |
222 |
|
223 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
224 |
|
225 |
simnfo->n_atoms = tot_atoms; |
226 |
simnfo->n_bonds = tot_bonds; |
227 |
simnfo->n_bends = tot_bends; |
228 |
simnfo->n_torsions = tot_torsions; |
229 |
simnfo->n_SRI = tot_SRI; |
230 |
simnfo->n_mol = tot_nmol; |
231 |
|
232 |
|
233 |
#ifdef IS_MPI |
234 |
|
235 |
// divide the molecules among processors here. |
236 |
|
237 |
mpiSim = new mpiSimulation( simnfo ); |
238 |
|
239 |
|
240 |
|
241 |
globalIndex = mpiSim->divideLabor(); |
242 |
|
243 |
|
244 |
|
245 |
// set up the local variables |
246 |
|
247 |
int localMol, allMol; |
248 |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
249 |
|
250 |
int* mol2proc = mpiSim->getMolToProcMap(); |
251 |
int* molCompType = mpiSim->getMolComponentType(); |
252 |
|
253 |
allMol = 0; |
254 |
localMol = 0; |
255 |
local_atoms = 0; |
256 |
local_bonds = 0; |
257 |
local_bends = 0; |
258 |
local_torsions = 0; |
259 |
for( i=0; i<n_components; i++ ){ |
260 |
|
261 |
for( j=0; j<components_nmol[i]; j++ ){ |
262 |
|
263 |
if( mol2proc[j] == worldRank ){ |
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 not 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 |
int molIndex; |
308 |
|
309 |
// initialize the molecule's stampID's |
310 |
|
311 |
#ifdef IS_MPI |
312 |
|
313 |
|
314 |
molIndex = 0; |
315 |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
316 |
|
317 |
if(mol2proc[i] == worldRank ){ |
318 |
the_molecules[molIndex].setStampID( molCompType[i] ); |
319 |
molIndex++; |
320 |
} |
321 |
} |
322 |
|
323 |
#else // is_mpi |
324 |
|
325 |
molIndex = 0; |
326 |
for(i=0; i<n_components; i++){ |
327 |
for(j=0; j<components_nmol[i]; j++ ){ |
328 |
the_molecules[molIndex].setStampID( i ); |
329 |
molIndex++; |
330 |
} |
331 |
} |
332 |
|
333 |
|
334 |
#endif // is_mpi |
335 |
|
336 |
|
337 |
if( simnfo->n_SRI ){ |
338 |
Exclude::createArray(simnfo->n_SRI); |
339 |
the_excludes = new Exclude*[simnfo->n_SRI]; |
340 |
simnfo->globalExcludes = new int; |
341 |
simnfo->n_exclude = tot_SRI; |
342 |
} |
343 |
else{ |
344 |
|
345 |
Exclude::createArray( 1 ); |
346 |
the_excludes = new Exclude*; |
347 |
the_excludes[0] = new Exclude(0); |
348 |
the_excludes[0]->setPair( 0,0 ); |
349 |
simnfo->globalExcludes = new int; |
350 |
simnfo->globalExcludes[0] = 0; |
351 |
simnfo->n_exclude = 0; |
352 |
} |
353 |
|
354 |
// set the arrays into the SimInfo object |
355 |
|
356 |
simnfo->atoms = the_atoms; |
357 |
simnfo->nGlobalExcludes = 0; |
358 |
simnfo->excludes = the_excludes; |
359 |
|
360 |
|
361 |
// get some of the tricky things that may still be in the globals |
362 |
|
363 |
|
364 |
if( the_globals->haveBox() ){ |
365 |
simnfo->box_x = the_globals->getBox(); |
366 |
simnfo->box_y = the_globals->getBox(); |
367 |
simnfo->box_z = the_globals->getBox(); |
368 |
} |
369 |
else if( the_globals->haveDensity() ){ |
370 |
|
371 |
double vol; |
372 |
vol = (double)tot_nmol / the_globals->getDensity(); |
373 |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
374 |
simnfo->box_y = simnfo->box_x; |
375 |
simnfo->box_z = simnfo->box_x; |
376 |
} |
377 |
else{ |
378 |
if( !the_globals->haveBoxX() ){ |
379 |
sprintf( painCave.errMsg, |
380 |
"SimSetup error, no periodic BoxX size given.\n" ); |
381 |
painCave.isFatal = 1; |
382 |
simError(); |
383 |
} |
384 |
simnfo->box_x = the_globals->getBoxX(); |
385 |
|
386 |
if( !the_globals->haveBoxY() ){ |
387 |
sprintf( painCave.errMsg, |
388 |
"SimSetup error, no periodic BoxY size given.\n" ); |
389 |
painCave.isFatal = 1; |
390 |
simError(); |
391 |
} |
392 |
simnfo->box_y = the_globals->getBoxY(); |
393 |
|
394 |
if( !the_globals->haveBoxZ() ){ |
395 |
sprintf( painCave.errMsg, |
396 |
"SimSetup error, no periodic BoxZ size given.\n" ); |
397 |
painCave.isFatal = 1; |
398 |
simError(); |
399 |
} |
400 |
simnfo->box_z = the_globals->getBoxZ(); |
401 |
} |
402 |
|
403 |
#ifdef IS_MPI |
404 |
strcpy( checkPointMsg, "Box size set up" ); |
405 |
MPIcheckPoint(); |
406 |
#endif // is_mpi |
407 |
|
408 |
|
409 |
// initialize the arrays |
410 |
|
411 |
the_ff->setSimInfo( simnfo ); |
412 |
|
413 |
makeMolecules(); |
414 |
simnfo->identArray = new int[simnfo->n_atoms]; |
415 |
for(i=0; i<simnfo->n_atoms; i++){ |
416 |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
417 |
} |
418 |
|
419 |
if (the_globals->getUseRF() ) { |
420 |
simnfo->useReactionField = 1; |
421 |
|
422 |
if( !the_globals->haveECR() ){ |
423 |
sprintf( painCave.errMsg, |
424 |
"SimSetup Warning: using default value of 1/2 the smallest " |
425 |
"box length for the electrostaticCutoffRadius.\n" |
426 |
"I hope you have a very fast processor!\n"); |
427 |
painCave.isFatal = 0; |
428 |
simError(); |
429 |
double smallest; |
430 |
smallest = simnfo->box_x; |
431 |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
432 |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
433 |
simnfo->ecr = 0.5 * smallest; |
434 |
} else { |
435 |
simnfo->ecr = the_globals->getECR(); |
436 |
} |
437 |
|
438 |
if( !the_globals->haveEST() ){ |
439 |
sprintf( painCave.errMsg, |
440 |
"SimSetup Warning: using default value of 0.05 * the " |
441 |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
442 |
); |
443 |
painCave.isFatal = 0; |
444 |
simError(); |
445 |
simnfo->est = 0.05 * simnfo->ecr; |
446 |
} else { |
447 |
simnfo->est = the_globals->getEST(); |
448 |
} |
449 |
|
450 |
if(!the_globals->haveDielectric() ){ |
451 |
sprintf( painCave.errMsg, |
452 |
"SimSetup Error: You are trying to use Reaction Field without" |
453 |
"setting a dielectric constant!\n" |
454 |
); |
455 |
painCave.isFatal = 1; |
456 |
simError(); |
457 |
} |
458 |
simnfo->dielectric = the_globals->getDielectric(); |
459 |
} else { |
460 |
if (simnfo->n_dipoles) { |
461 |
|
462 |
if( !the_globals->haveECR() ){ |
463 |
sprintf( painCave.errMsg, |
464 |
"SimSetup Warning: using default value of 1/2 the smallest" |
465 |
"box length for the electrostaticCutoffRadius.\n" |
466 |
"I hope you have a very fast processor!\n"); |
467 |
painCave.isFatal = 0; |
468 |
simError(); |
469 |
double smallest; |
470 |
smallest = simnfo->box_x; |
471 |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
472 |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
473 |
simnfo->ecr = 0.5 * smallest; |
474 |
} else { |
475 |
simnfo->ecr = the_globals->getECR(); |
476 |
} |
477 |
|
478 |
if( !the_globals->haveEST() ){ |
479 |
sprintf( painCave.errMsg, |
480 |
"SimSetup Warning: using default value of 5% of the" |
481 |
"electrostaticCutoffRadius for the " |
482 |
"electrostaticSkinThickness\n" |
483 |
); |
484 |
painCave.isFatal = 0; |
485 |
simError(); |
486 |
simnfo->est = 0.05 * simnfo->ecr; |
487 |
} else { |
488 |
simnfo->est = the_globals->getEST(); |
489 |
} |
490 |
} |
491 |
} |
492 |
|
493 |
#ifdef IS_MPI |
494 |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
495 |
MPIcheckPoint(); |
496 |
#endif // is_mpi |
497 |
|
498 |
if( the_globals->haveInitialConfig() ){ |
499 |
|
500 |
InitializeFromFile* fileInit; |
501 |
#ifdef IS_MPI // is_mpi |
502 |
if( worldRank == 0 ){ |
503 |
#endif //is_mpi |
504 |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
505 |
#ifdef IS_MPI |
506 |
}else fileInit = new InitializeFromFile( NULL ); |
507 |
#endif |
508 |
fileInit->read_xyz( simnfo ); // default velocities on |
509 |
|
510 |
delete fileInit; |
511 |
} |
512 |
else{ |
513 |
|
514 |
#ifdef IS_MPI |
515 |
|
516 |
// no init from bass |
517 |
|
518 |
sprintf( painCave.errMsg, |
519 |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
520 |
painCave.isFatal; |
521 |
simError(); |
522 |
|
523 |
#else |
524 |
|
525 |
initFromBass(); |
526 |
|
527 |
|
528 |
#endif |
529 |
} |
530 |
|
531 |
#ifdef IS_MPI |
532 |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
533 |
MPIcheckPoint(); |
534 |
#endif // is_mpi |
535 |
|
536 |
|
537 |
|
538 |
|
539 |
|
540 |
|
541 |
|
542 |
#ifdef IS_MPI |
543 |
if( worldRank == 0 ){ |
544 |
#endif // is_mpi |
545 |
|
546 |
if( the_globals->haveFinalConfig() ){ |
547 |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
548 |
} |
549 |
else{ |
550 |
strcpy( simnfo->finalName, inFileName ); |
551 |
char* endTest; |
552 |
int nameLength = strlen( simnfo->finalName ); |
553 |
endTest = &(simnfo->finalName[nameLength - 5]); |
554 |
if( !strcmp( endTest, ".bass" ) ){ |
555 |
strcpy( endTest, ".eor" ); |
556 |
} |
557 |
else if( !strcmp( endTest, ".BASS" ) ){ |
558 |
strcpy( endTest, ".eor" ); |
559 |
} |
560 |
else{ |
561 |
endTest = &(simnfo->finalName[nameLength - 4]); |
562 |
if( !strcmp( endTest, ".bss" ) ){ |
563 |
strcpy( endTest, ".eor" ); |
564 |
} |
565 |
else if( !strcmp( endTest, ".mdl" ) ){ |
566 |
strcpy( endTest, ".eor" ); |
567 |
} |
568 |
else{ |
569 |
strcat( simnfo->finalName, ".eor" ); |
570 |
} |
571 |
} |
572 |
} |
573 |
|
574 |
// make the sample and status out names |
575 |
|
576 |
strcpy( simnfo->sampleName, inFileName ); |
577 |
char* endTest; |
578 |
int nameLength = strlen( simnfo->sampleName ); |
579 |
endTest = &(simnfo->sampleName[nameLength - 5]); |
580 |
if( !strcmp( endTest, ".bass" ) ){ |
581 |
strcpy( endTest, ".dump" ); |
582 |
} |
583 |
else if( !strcmp( endTest, ".BASS" ) ){ |
584 |
strcpy( endTest, ".dump" ); |
585 |
} |
586 |
else{ |
587 |
endTest = &(simnfo->sampleName[nameLength - 4]); |
588 |
if( !strcmp( endTest, ".bss" ) ){ |
589 |
strcpy( endTest, ".dump" ); |
590 |
} |
591 |
else if( !strcmp( endTest, ".mdl" ) ){ |
592 |
strcpy( endTest, ".dump" ); |
593 |
} |
594 |
else{ |
595 |
strcat( simnfo->sampleName, ".dump" ); |
596 |
} |
597 |
} |
598 |
|
599 |
strcpy( simnfo->statusName, inFileName ); |
600 |
nameLength = strlen( simnfo->statusName ); |
601 |
endTest = &(simnfo->statusName[nameLength - 5]); |
602 |
if( !strcmp( endTest, ".bass" ) ){ |
603 |
strcpy( endTest, ".stat" ); |
604 |
} |
605 |
else if( !strcmp( endTest, ".BASS" ) ){ |
606 |
strcpy( endTest, ".stat" ); |
607 |
} |
608 |
else{ |
609 |
endTest = &(simnfo->statusName[nameLength - 4]); |
610 |
if( !strcmp( endTest, ".bss" ) ){ |
611 |
strcpy( endTest, ".stat" ); |
612 |
} |
613 |
else if( !strcmp( endTest, ".mdl" ) ){ |
614 |
strcpy( endTest, ".stat" ); |
615 |
} |
616 |
else{ |
617 |
strcat( simnfo->statusName, ".stat" ); |
618 |
} |
619 |
} |
620 |
|
621 |
#ifdef IS_MPI |
622 |
} |
623 |
#endif // is_mpi |
624 |
|
625 |
// set the status, sample, and themal kick times |
626 |
|
627 |
if( the_globals->haveSampleTime() ){ |
628 |
simnfo->sampleTime = the_globals->getSampleTime(); |
629 |
simnfo->statusTime = simnfo->sampleTime; |
630 |
simnfo->thermalTime = simnfo->sampleTime; |
631 |
} |
632 |
else{ |
633 |
simnfo->sampleTime = the_globals->getRunTime(); |
634 |
simnfo->statusTime = simnfo->sampleTime; |
635 |
simnfo->thermalTime = simnfo->sampleTime; |
636 |
} |
637 |
|
638 |
if( the_globals->haveStatusTime() ){ |
639 |
simnfo->statusTime = the_globals->getStatusTime(); |
640 |
} |
641 |
|
642 |
if( the_globals->haveThermalTime() ){ |
643 |
simnfo->thermalTime = the_globals->getThermalTime(); |
644 |
} |
645 |
|
646 |
// check for the temperature set flag |
647 |
|
648 |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
649 |
|
650 |
|
651 |
// // make the longe range forces and the integrator |
652 |
|
653 |
// new AllLong( simnfo ); |
654 |
|
655 |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
656 |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
657 |
|
658 |
|
659 |
|
660 |
// initialize the Fortran |
661 |
|
662 |
simnfo->refreshSim(); |
663 |
|
664 |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
665 |
the_ff->initForceField( LB_MIXING_RULE ); |
666 |
} |
667 |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
668 |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
669 |
} |
670 |
else{ |
671 |
sprintf( painCave.errMsg, |
672 |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
673 |
simnfo->mixingRule ); |
674 |
painCave.isFatal = 1; |
675 |
simError(); |
676 |
} |
677 |
|
678 |
|
679 |
#ifdef IS_MPI |
680 |
strcpy( checkPointMsg, |
681 |
"Successfully intialized the mixingRule for Fortran." ); |
682 |
MPIcheckPoint(); |
683 |
#endif // is_mpi |
684 |
} |
685 |
|
686 |
|
687 |
void SimSetup::makeMolecules( void ){ |
688 |
|
689 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
690 |
molInit info; |
691 |
DirectionalAtom* dAtom; |
692 |
LinkedAssign* extras; |
693 |
LinkedAssign* current_extra; |
694 |
AtomStamp* currentAtom; |
695 |
BondStamp* currentBond; |
696 |
BendStamp* currentBend; |
697 |
TorsionStamp* currentTorsion; |
698 |
|
699 |
bond_pair* theBonds; |
700 |
bend_set* theBends; |
701 |
torsion_set* theTorsions; |
702 |
|
703 |
|
704 |
//init the forceField paramters |
705 |
|
706 |
the_ff->readParams(); |
707 |
|
708 |
|
709 |
// init the atoms |
710 |
|
711 |
double ux, uy, uz, u, uSqr; |
712 |
|
713 |
atomOffset = 0; |
714 |
excludeOffset = 0; |
715 |
for(i=0; i<simnfo->n_mol; i++){ |
716 |
|
717 |
stampID = the_molecules[i].getStampID(); |
718 |
|
719 |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
720 |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
721 |
info.nBends = comp_stamps[stampID]->getNBends(); |
722 |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
723 |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
724 |
|
725 |
info.myAtoms = &the_atoms[atomOffset]; |
726 |
info.myExcludes = &the_excludes[excludeOffset]; |
727 |
info.myBonds = new Bond*[info.nBonds]; |
728 |
info.myBends = new Bend*[info.nBends]; |
729 |
info.myTorsions = new Torsion*[info.nTorsions]; |
730 |
|
731 |
theBonds = new bond_pair[info.nBonds]; |
732 |
theBends = new bend_set[info.nBends]; |
733 |
theTorsions = new torsion_set[info.nTorsions]; |
734 |
|
735 |
// make the Atoms |
736 |
|
737 |
for(j=0; j<info.nAtoms; j++){ |
738 |
|
739 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
740 |
if( currentAtom->haveOrientation() ){ |
741 |
|
742 |
dAtom = new DirectionalAtom(j + atomOffset); |
743 |
simnfo->n_oriented++; |
744 |
info.myAtoms[j] = dAtom; |
745 |
|
746 |
ux = currentAtom->getOrntX(); |
747 |
uy = currentAtom->getOrntY(); |
748 |
uz = currentAtom->getOrntZ(); |
749 |
|
750 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
751 |
|
752 |
u = sqrt( uSqr ); |
753 |
ux = ux / u; |
754 |
uy = uy / u; |
755 |
uz = uz / u; |
756 |
|
757 |
dAtom->setSUx( ux ); |
758 |
dAtom->setSUy( uy ); |
759 |
dAtom->setSUz( uz ); |
760 |
} |
761 |
else{ |
762 |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
763 |
} |
764 |
info.myAtoms[j]->setType( currentAtom->getType() ); |
765 |
|
766 |
#ifdef IS_MPI |
767 |
|
768 |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
769 |
|
770 |
#endif // is_mpi |
771 |
} |
772 |
|
773 |
// make the bonds |
774 |
for(j=0; j<info.nBonds; j++){ |
775 |
|
776 |
currentBond = comp_stamps[stampID]->getBond( j ); |
777 |
theBonds[j].a = currentBond->getA() + atomOffset; |
778 |
theBonds[j].b = currentBond->getB() + atomOffset; |
779 |
|
780 |
exI = theBonds[i].a; |
781 |
exJ = theBonds[i].b; |
782 |
|
783 |
// exclude_I must always be the smaller of the pair |
784 |
if( exI > exJ ){ |
785 |
tempEx = exI; |
786 |
exI = exJ; |
787 |
exJ = tempEx; |
788 |
} |
789 |
#ifdef IS_MPI |
790 |
tempEx = exI; |
791 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
792 |
tempEx = exJ; |
793 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
794 |
|
795 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
796 |
#else // isn't MPI |
797 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
798 |
#endif //is_mpi |
799 |
} |
800 |
excludeOffset += info.nBonds; |
801 |
|
802 |
//make the bends |
803 |
for(j=0; j<info.nBends; j++){ |
804 |
|
805 |
currentBend = comp_stamps[stampID]->getBend( j ); |
806 |
theBends[j].a = currentBend->getA() + atomOffset; |
807 |
theBends[j].b = currentBend->getB() + atomOffset; |
808 |
theBends[j].c = currentBend->getC() + atomOffset; |
809 |
|
810 |
if( currentBend->haveExtras() ){ |
811 |
|
812 |
extras = currentBend->getExtras(); |
813 |
current_extra = extras; |
814 |
|
815 |
while( current_extra != NULL ){ |
816 |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
817 |
|
818 |
switch( current_extra->getType() ){ |
819 |
|
820 |
case 0: |
821 |
theBends[j].ghost = |
822 |
current_extra->getInt() + atomOffset; |
823 |
theBends[j].isGhost = 1; |
824 |
break; |
825 |
|
826 |
case 1: |
827 |
theBends[j].ghost = |
828 |
(int)current_extra->getDouble() + atomOffset; |
829 |
theBends[j].isGhost = 1; |
830 |
break; |
831 |
|
832 |
default: |
833 |
sprintf( painCave.errMsg, |
834 |
"SimSetup Error: ghostVectorSource was neiter a " |
835 |
"double nor an int.\n" |
836 |
"-->Bend[%d] in %s\n", |
837 |
j, comp_stamps[stampID]->getID() ); |
838 |
painCave.isFatal = 1; |
839 |
simError(); |
840 |
} |
841 |
} |
842 |
|
843 |
else{ |
844 |
|
845 |
sprintf( painCave.errMsg, |
846 |
"SimSetup Error: unhandled bend assignment:\n" |
847 |
" -->%s in Bend[%d] in %s\n", |
848 |
current_extra->getlhs(), |
849 |
j, comp_stamps[stampID]->getID() ); |
850 |
painCave.isFatal = 1; |
851 |
simError(); |
852 |
} |
853 |
|
854 |
current_extra = current_extra->getNext(); |
855 |
} |
856 |
} |
857 |
|
858 |
if( !theBends[j].isGhost ){ |
859 |
|
860 |
exI = theBends[j].a; |
861 |
exJ = theBends[j].c; |
862 |
} |
863 |
else{ |
864 |
|
865 |
exI = theBends[j].a; |
866 |
exJ = theBends[j].b; |
867 |
} |
868 |
|
869 |
// exclude_I must always be the smaller of the pair |
870 |
if( exI > exJ ){ |
871 |
tempEx = exI; |
872 |
exI = exJ; |
873 |
exJ = tempEx; |
874 |
} |
875 |
#ifdef IS_MPI |
876 |
tempEx = exI; |
877 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
878 |
tempEx = exJ; |
879 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
880 |
|
881 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
882 |
#else // isn't MPI |
883 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
884 |
#endif //is_mpi |
885 |
} |
886 |
excludeOffset += info.nBends; |
887 |
|
888 |
for(j=0; j<info.nTorsions; j++){ |
889 |
|
890 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
891 |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
892 |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
893 |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
894 |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
895 |
|
896 |
exI = theTorsions[j].a; |
897 |
exJ = theTorsions[j].d; |
898 |
|
899 |
// exclude_I must always be the smaller of the pair |
900 |
if( exI > exJ ){ |
901 |
tempEx = exI; |
902 |
exI = exJ; |
903 |
exJ = tempEx; |
904 |
} |
905 |
#ifdef IS_MPI |
906 |
tempEx = exI; |
907 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
908 |
tempEx = exJ; |
909 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
910 |
|
911 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
912 |
#else // isn't MPI |
913 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
914 |
#endif //is_mpi |
915 |
} |
916 |
excludeOffset += info.nTorsions; |
917 |
|
918 |
|
919 |
// send the arrays off to the forceField for init. |
920 |
|
921 |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
922 |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
923 |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
924 |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
925 |
|
926 |
|
927 |
the_molecules[i].initialize( info ); |
928 |
atomOffset += info.nAtoms; |
929 |
delete[] theBonds; |
930 |
delete[] theBends; |
931 |
delete[] theTorsions; |
932 |
} |
933 |
|
934 |
// clean up the forcefield |
935 |
the_ff->calcRcut(); |
936 |
the_ff->cleanMe(); |
937 |
} |
938 |
|
939 |
void SimSetup::initFromBass( void ){ |
940 |
|
941 |
int i, j, k; |
942 |
int n_cells; |
943 |
double cellx, celly, cellz; |
944 |
double temp1, temp2, temp3; |
945 |
int n_per_extra; |
946 |
int n_extra; |
947 |
int have_extra, done; |
948 |
|
949 |
temp1 = (double)tot_nmol / 4.0; |
950 |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
951 |
temp3 = ceil( temp2 ); |
952 |
|
953 |
have_extra =0; |
954 |
if( temp2 < temp3 ){ // we have a non-complete lattice |
955 |
have_extra =1; |
956 |
|
957 |
n_cells = (int)temp3 - 1; |
958 |
cellx = simnfo->box_x / temp3; |
959 |
celly = simnfo->box_y / temp3; |
960 |
cellz = simnfo->box_z / temp3; |
961 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
962 |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
963 |
n_per_extra = (int)ceil( temp1 ); |
964 |
|
965 |
if( n_per_extra > 4){ |
966 |
sprintf( painCave.errMsg, |
967 |
"SimSetup error. There has been an error in constructing" |
968 |
" the non-complete lattice.\n" ); |
969 |
painCave.isFatal = 1; |
970 |
simError(); |
971 |
} |
972 |
} |
973 |
else{ |
974 |
n_cells = (int)temp3; |
975 |
cellx = simnfo->box_x / temp3; |
976 |
celly = simnfo->box_y / temp3; |
977 |
cellz = simnfo->box_z / temp3; |
978 |
} |
979 |
|
980 |
current_mol = 0; |
981 |
current_comp_mol = 0; |
982 |
current_comp = 0; |
983 |
current_atom_ndx = 0; |
984 |
|
985 |
for( i=0; i < n_cells ; i++ ){ |
986 |
for( j=0; j < n_cells; j++ ){ |
987 |
for( k=0; k < n_cells; k++ ){ |
988 |
|
989 |
makeElement( i * cellx, |
990 |
j * celly, |
991 |
k * cellz ); |
992 |
|
993 |
makeElement( i * cellx + 0.5 * cellx, |
994 |
j * celly + 0.5 * celly, |
995 |
k * cellz ); |
996 |
|
997 |
makeElement( i * cellx, |
998 |
j * celly + 0.5 * celly, |
999 |
k * cellz + 0.5 * cellz ); |
1000 |
|
1001 |
makeElement( i * cellx + 0.5 * cellx, |
1002 |
j * celly, |
1003 |
k * cellz + 0.5 * cellz ); |
1004 |
} |
1005 |
} |
1006 |
} |
1007 |
|
1008 |
if( have_extra ){ |
1009 |
done = 0; |
1010 |
|
1011 |
int start_ndx; |
1012 |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1013 |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1014 |
|
1015 |
if( i < n_cells ){ |
1016 |
|
1017 |
if( j < n_cells ){ |
1018 |
start_ndx = n_cells; |
1019 |
} |
1020 |
else start_ndx = 0; |
1021 |
} |
1022 |
else start_ndx = 0; |
1023 |
|
1024 |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1025 |
|
1026 |
makeElement( i * cellx, |
1027 |
j * celly, |
1028 |
k * cellz ); |
1029 |
done = ( current_mol >= tot_nmol ); |
1030 |
|
1031 |
if( !done && n_per_extra > 1 ){ |
1032 |
makeElement( i * cellx + 0.5 * cellx, |
1033 |
j * celly + 0.5 * celly, |
1034 |
k * cellz ); |
1035 |
done = ( current_mol >= tot_nmol ); |
1036 |
} |
1037 |
|
1038 |
if( !done && n_per_extra > 2){ |
1039 |
makeElement( i * cellx, |
1040 |
j * celly + 0.5 * celly, |
1041 |
k * cellz + 0.5 * cellz ); |
1042 |
done = ( current_mol >= tot_nmol ); |
1043 |
} |
1044 |
|
1045 |
if( !done && n_per_extra > 3){ |
1046 |
makeElement( i * cellx + 0.5 * cellx, |
1047 |
j * celly, |
1048 |
k * cellz + 0.5 * cellz ); |
1049 |
done = ( current_mol >= tot_nmol ); |
1050 |
} |
1051 |
} |
1052 |
} |
1053 |
} |
1054 |
} |
1055 |
|
1056 |
|
1057 |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1058 |
simnfo->atoms[i]->set_vx( 0.0 ); |
1059 |
simnfo->atoms[i]->set_vy( 0.0 ); |
1060 |
simnfo->atoms[i]->set_vz( 0.0 ); |
1061 |
} |
1062 |
} |
1063 |
|
1064 |
void SimSetup::makeElement( double x, double y, double z ){ |
1065 |
|
1066 |
int k; |
1067 |
AtomStamp* current_atom; |
1068 |
DirectionalAtom* dAtom; |
1069 |
double rotMat[3][3]; |
1070 |
|
1071 |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1072 |
|
1073 |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1074 |
if( !current_atom->havePosition() ){ |
1075 |
sprintf( painCave.errMsg, |
1076 |
"SimSetup:initFromBass error.\n" |
1077 |
"\tComponent %s, atom %s does not have a position specified.\n" |
1078 |
"\tThe initialization routine is unable to give a start" |
1079 |
" position.\n", |
1080 |
comp_stamps[current_comp]->getID(), |
1081 |
current_atom->getType() ); |
1082 |
painCave.isFatal = 1; |
1083 |
simError(); |
1084 |
} |
1085 |
|
1086 |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1087 |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1088 |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1089 |
|
1090 |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1091 |
|
1092 |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1093 |
|
1094 |
rotMat[0][0] = 1.0; |
1095 |
rotMat[0][1] = 0.0; |
1096 |
rotMat[0][2] = 0.0; |
1097 |
|
1098 |
rotMat[1][0] = 0.0; |
1099 |
rotMat[1][1] = 1.0; |
1100 |
rotMat[1][2] = 0.0; |
1101 |
|
1102 |
rotMat[2][0] = 0.0; |
1103 |
rotMat[2][1] = 0.0; |
1104 |
rotMat[2][2] = 1.0; |
1105 |
|
1106 |
dAtom->setA( rotMat ); |
1107 |
} |
1108 |
|
1109 |
current_atom_ndx++; |
1110 |
} |
1111 |
|
1112 |
current_mol++; |
1113 |
current_comp_mol++; |
1114 |
|
1115 |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1116 |
|
1117 |
current_comp_mol = 0; |
1118 |
current_comp++; |
1119 |
} |
1120 |
} |