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 |
ExtendedSystem* the_extendedsystem; |
70 |
int i, j; |
71 |
|
72 |
// get the stamps and globals; |
73 |
the_stamps = stamps; |
74 |
the_globals = globals; |
75 |
|
76 |
// set the easy ones first |
77 |
simnfo->target_temp = the_globals->getTargetTemp(); |
78 |
simnfo->dt = the_globals->getDt(); |
79 |
simnfo->run_time = the_globals->getRunTime(); |
80 |
|
81 |
// get the ones we know are there, yet still may need some work. |
82 |
n_components = the_globals->getNComponents(); |
83 |
strcpy( force_field, the_globals->getForceField() ); |
84 |
|
85 |
// get the ensemble and set up an extended system if we need it: |
86 |
strcpy( ensemble, the_globals->getEnsemble() ); |
87 |
if( !strcasecmp( ensemble, "NPT" ) ) { |
88 |
the_extendedsystem = new ExtendedSystem( simnfo ); |
89 |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 |
the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
91 |
the_extendedsystem->setQmass(the_globals->getQmass()); |
92 |
the_extendedsystem->setTauRelax(the_globals->getTauRelax()); |
93 |
} else if ( !strcasecmp( ensemble, "NVT") ) { |
94 |
the_extendedsystem = new ExtendedSystem( simnfo ); |
95 |
the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
96 |
the_extendedsystem->setQmass(the_globals->getQmass()); |
97 |
} else if ( !strcasecmp( ensemble, "NVE") ) { |
98 |
} else { |
99 |
sprintf( painCave.errMsg, |
100 |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
101 |
"reverting to NVE for this simulation.\n", |
102 |
ensemble ); |
103 |
painCave.isFatal = 0; |
104 |
simError(); |
105 |
strcpy( ensemble, "NVE" ); |
106 |
} |
107 |
strcpy( simnfo->ensemble, ensemble ); |
108 |
|
109 |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
110 |
simnfo->usePBC = the_globals->getPBC(); |
111 |
|
112 |
int usesDipoles = 0; |
113 |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
114 |
the_ff = new TraPPE_ExFF(); |
115 |
usesDipoles = 1; |
116 |
} |
117 |
else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
118 |
else{ |
119 |
sprintf( painCave.errMsg, |
120 |
"SimSetup Error. Unrecognized force field -> %s\n", |
121 |
force_field ); |
122 |
painCave.isFatal = 1; |
123 |
simError(); |
124 |
} |
125 |
|
126 |
#ifdef IS_MPI |
127 |
strcpy( checkPointMsg, "ForceField creation successful" ); |
128 |
MPIcheckPoint(); |
129 |
#endif // is_mpi |
130 |
|
131 |
|
132 |
|
133 |
// get the components and calculate the tot_nMol and indvidual n_mol |
134 |
the_components = the_globals->getComponents(); |
135 |
components_nmol = new int[n_components]; |
136 |
comp_stamps = new MoleculeStamp*[n_components]; |
137 |
|
138 |
if( !the_globals->haveNMol() ){ |
139 |
// we don't have the total number of molecules, so we assume it is |
140 |
// given in each component |
141 |
|
142 |
tot_nmol = 0; |
143 |
for( i=0; i<n_components; i++ ){ |
144 |
|
145 |
if( !the_components[i]->haveNMol() ){ |
146 |
// we have a problem |
147 |
sprintf( painCave.errMsg, |
148 |
"SimSetup Error. No global NMol or component NMol" |
149 |
" given. Cannot calculate the number of atoms.\n" ); |
150 |
painCave.isFatal = 1; |
151 |
simError(); |
152 |
} |
153 |
|
154 |
tot_nmol += the_components[i]->getNMol(); |
155 |
components_nmol[i] = the_components[i]->getNMol(); |
156 |
} |
157 |
} |
158 |
else{ |
159 |
sprintf( painCave.errMsg, |
160 |
"SimSetup error.\n" |
161 |
"\tSorry, the ability to specify total" |
162 |
" nMols and then give molfractions in the components\n" |
163 |
"\tis not currently supported." |
164 |
" Please give nMol in the components.\n" ); |
165 |
painCave.isFatal = 1; |
166 |
simError(); |
167 |
|
168 |
|
169 |
// tot_nmol = the_globals->getNMol(); |
170 |
|
171 |
// //we have the total number of molecules, now we check for molfractions |
172 |
// for( i=0; i<n_components; i++ ){ |
173 |
|
174 |
// if( !the_components[i]->haveMolFraction() ){ |
175 |
|
176 |
// if( !the_components[i]->haveNMol() ){ |
177 |
// //we have a problem |
178 |
// std::cerr << "SimSetup error. Neither molFraction nor " |
179 |
// << " nMol was given in component |
180 |
|
181 |
} |
182 |
|
183 |
#ifdef IS_MPI |
184 |
strcpy( checkPointMsg, "Have the number of components" ); |
185 |
MPIcheckPoint(); |
186 |
#endif // is_mpi |
187 |
|
188 |
// make an array of molecule stamps that match the components used. |
189 |
// also extract the used stamps out into a separate linked list |
190 |
|
191 |
simnfo->nComponents = n_components; |
192 |
simnfo->componentsNmol = components_nmol; |
193 |
simnfo->compStamps = comp_stamps; |
194 |
simnfo->headStamp = new LinkedMolStamp(); |
195 |
|
196 |
char* id; |
197 |
LinkedMolStamp* headStamp = simnfo->headStamp; |
198 |
LinkedMolStamp* currentStamp = NULL; |
199 |
for( i=0; i<n_components; i++ ){ |
200 |
|
201 |
id = the_components[i]->getType(); |
202 |
comp_stamps[i] = NULL; |
203 |
|
204 |
// check to make sure the component isn't already in the list |
205 |
|
206 |
comp_stamps[i] = headStamp->match( id ); |
207 |
if( comp_stamps[i] == NULL ){ |
208 |
|
209 |
// extract the component from the list; |
210 |
|
211 |
currentStamp = the_stamps->extractMolStamp( id ); |
212 |
if( currentStamp == NULL ){ |
213 |
sprintf( painCave.errMsg, |
214 |
"SimSetup error: Component \"%s\" was not found in the " |
215 |
"list of declared molecules\n", |
216 |
id ); |
217 |
painCave.isFatal = 1; |
218 |
simError(); |
219 |
} |
220 |
|
221 |
headStamp->add( currentStamp ); |
222 |
comp_stamps[i] = headStamp->match( id ); |
223 |
} |
224 |
} |
225 |
|
226 |
#ifdef IS_MPI |
227 |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
228 |
MPIcheckPoint(); |
229 |
#endif // is_mpi |
230 |
|
231 |
|
232 |
|
233 |
|
234 |
// caclulate the number of atoms, bonds, bends and torsions |
235 |
|
236 |
tot_atoms = 0; |
237 |
tot_bonds = 0; |
238 |
tot_bends = 0; |
239 |
tot_torsions = 0; |
240 |
for( i=0; i<n_components; i++ ){ |
241 |
|
242 |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
243 |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
244 |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
245 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
246 |
} |
247 |
|
248 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
249 |
|
250 |
simnfo->n_atoms = tot_atoms; |
251 |
simnfo->n_bonds = tot_bonds; |
252 |
simnfo->n_bends = tot_bends; |
253 |
simnfo->n_torsions = tot_torsions; |
254 |
simnfo->n_SRI = tot_SRI; |
255 |
simnfo->n_mol = tot_nmol; |
256 |
|
257 |
|
258 |
#ifdef IS_MPI |
259 |
|
260 |
// divide the molecules among processors here. |
261 |
|
262 |
mpiSim = new mpiSimulation( simnfo ); |
263 |
|
264 |
|
265 |
|
266 |
globalIndex = mpiSim->divideLabor(); |
267 |
|
268 |
// set up the local variables |
269 |
|
270 |
int localMol, allMol; |
271 |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
272 |
|
273 |
int* mol2proc = mpiSim->getMolToProcMap(); |
274 |
int* molCompType = mpiSim->getMolComponentType(); |
275 |
|
276 |
allMol = 0; |
277 |
localMol = 0; |
278 |
local_atoms = 0; |
279 |
local_bonds = 0; |
280 |
local_bends = 0; |
281 |
local_torsions = 0; |
282 |
for( i=0; i<n_components; i++ ){ |
283 |
|
284 |
for( j=0; j<components_nmol[i]; j++ ){ |
285 |
|
286 |
if( mol2proc[j] == worldRank ){ |
287 |
|
288 |
local_atoms += comp_stamps[i]->getNAtoms(); |
289 |
local_bonds += comp_stamps[i]->getNBonds(); |
290 |
local_bends += comp_stamps[i]->getNBends(); |
291 |
local_torsions += comp_stamps[i]->getNTorsions(); |
292 |
localMol++; |
293 |
} |
294 |
allMol++; |
295 |
} |
296 |
} |
297 |
local_SRI = local_bonds + local_bends + local_torsions; |
298 |
|
299 |
|
300 |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
301 |
|
302 |
if( local_atoms != simnfo->n_atoms ){ |
303 |
sprintf( painCave.errMsg, |
304 |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
305 |
" localAtom (%d) are not equal.\n", |
306 |
simnfo->n_atoms, |
307 |
local_atoms ); |
308 |
painCave.isFatal = 1; |
309 |
simError(); |
310 |
} |
311 |
|
312 |
simnfo->n_bonds = local_bonds; |
313 |
simnfo->n_bends = local_bends; |
314 |
simnfo->n_torsions = local_torsions; |
315 |
simnfo->n_SRI = local_SRI; |
316 |
simnfo->n_mol = localMol; |
317 |
|
318 |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
319 |
MPIcheckPoint(); |
320 |
|
321 |
|
322 |
#endif // is_mpi |
323 |
|
324 |
|
325 |
// create the atom and short range interaction arrays |
326 |
|
327 |
Atom::createArrays(simnfo->n_atoms); |
328 |
the_atoms = new Atom*[simnfo->n_atoms]; |
329 |
the_molecules = new Molecule[simnfo->n_mol]; |
330 |
int molIndex; |
331 |
|
332 |
// initialize the molecule's stampID's |
333 |
|
334 |
#ifdef IS_MPI |
335 |
|
336 |
|
337 |
molIndex = 0; |
338 |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
339 |
|
340 |
if(mol2proc[i] == worldRank ){ |
341 |
the_molecules[molIndex].setStampID( molCompType[i] ); |
342 |
the_molecules[molIndex].setMyIndex( molIndex ); |
343 |
molIndex++; |
344 |
} |
345 |
} |
346 |
|
347 |
#else // is_mpi |
348 |
|
349 |
molIndex = 0; |
350 |
for(i=0; i<n_components; i++){ |
351 |
for(j=0; j<components_nmol[i]; j++ ){ |
352 |
the_molecules[molIndex].setStampID( i ); |
353 |
the_molecules[molIndex].setMyIndex( molIndex ); |
354 |
molIndex++; |
355 |
} |
356 |
} |
357 |
|
358 |
|
359 |
#endif // is_mpi |
360 |
|
361 |
|
362 |
if( simnfo->n_SRI ){ |
363 |
|
364 |
Exclude::createArray(simnfo->n_SRI); |
365 |
the_excludes = new Exclude*[simnfo->n_SRI]; |
366 |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
367 |
simnfo->globalExcludes = new int; |
368 |
simnfo->n_exclude = simnfo->n_SRI; |
369 |
} |
370 |
else{ |
371 |
|
372 |
Exclude::createArray( 1 ); |
373 |
the_excludes = new Exclude*; |
374 |
the_excludes[0] = new Exclude(0); |
375 |
the_excludes[0]->setPair( 0,0 ); |
376 |
simnfo->globalExcludes = new int; |
377 |
simnfo->globalExcludes[0] = 0; |
378 |
simnfo->n_exclude = 0; |
379 |
} |
380 |
|
381 |
// set the arrays into the SimInfo object |
382 |
|
383 |
simnfo->atoms = the_atoms; |
384 |
simnfo->molecules = the_molecules; |
385 |
simnfo->nGlobalExcludes = 0; |
386 |
simnfo->excludes = the_excludes; |
387 |
|
388 |
|
389 |
// get some of the tricky things that may still be in the globals |
390 |
|
391 |
|
392 |
if( the_globals->haveBox() ){ |
393 |
simnfo->box_x = the_globals->getBox(); |
394 |
simnfo->box_y = the_globals->getBox(); |
395 |
simnfo->box_z = the_globals->getBox(); |
396 |
} |
397 |
else if( the_globals->haveDensity() ){ |
398 |
|
399 |
double vol; |
400 |
vol = (double)tot_nmol / the_globals->getDensity(); |
401 |
simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
402 |
simnfo->box_y = simnfo->box_x; |
403 |
simnfo->box_z = simnfo->box_x; |
404 |
} |
405 |
else{ |
406 |
if( !the_globals->haveBoxX() ){ |
407 |
sprintf( painCave.errMsg, |
408 |
"SimSetup error, no periodic BoxX size given.\n" ); |
409 |
painCave.isFatal = 1; |
410 |
simError(); |
411 |
} |
412 |
simnfo->box_x = the_globals->getBoxX(); |
413 |
|
414 |
if( !the_globals->haveBoxY() ){ |
415 |
sprintf( painCave.errMsg, |
416 |
"SimSetup error, no periodic BoxY size given.\n" ); |
417 |
painCave.isFatal = 1; |
418 |
simError(); |
419 |
} |
420 |
simnfo->box_y = the_globals->getBoxY(); |
421 |
|
422 |
if( !the_globals->haveBoxZ() ){ |
423 |
sprintf( painCave.errMsg, |
424 |
"SimSetup error, no periodic BoxZ size given.\n" ); |
425 |
painCave.isFatal = 1; |
426 |
simError(); |
427 |
} |
428 |
simnfo->box_z = the_globals->getBoxZ(); |
429 |
} |
430 |
|
431 |
#ifdef IS_MPI |
432 |
strcpy( checkPointMsg, "Box size set up" ); |
433 |
MPIcheckPoint(); |
434 |
#endif // is_mpi |
435 |
|
436 |
|
437 |
// initialize the arrays |
438 |
|
439 |
the_ff->setSimInfo( simnfo ); |
440 |
|
441 |
makeMolecules(); |
442 |
simnfo->identArray = new int[simnfo->n_atoms]; |
443 |
for(i=0; i<simnfo->n_atoms; i++){ |
444 |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
445 |
} |
446 |
|
447 |
if (the_globals->getUseRF() ) { |
448 |
simnfo->useReactionField = 1; |
449 |
|
450 |
if( !the_globals->haveECR() ){ |
451 |
sprintf( painCave.errMsg, |
452 |
"SimSetup Warning: using default value of 1/2 the smallest " |
453 |
"box length for the electrostaticCutoffRadius.\n" |
454 |
"I hope you have a very fast processor!\n"); |
455 |
painCave.isFatal = 0; |
456 |
simError(); |
457 |
double smallest; |
458 |
smallest = simnfo->box_x; |
459 |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
460 |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
461 |
simnfo->ecr = 0.5 * smallest; |
462 |
} else { |
463 |
simnfo->ecr = the_globals->getECR(); |
464 |
} |
465 |
|
466 |
if( !the_globals->haveEST() ){ |
467 |
sprintf( painCave.errMsg, |
468 |
"SimSetup Warning: using default value of 0.05 * the " |
469 |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
470 |
); |
471 |
painCave.isFatal = 0; |
472 |
simError(); |
473 |
simnfo->est = 0.05 * simnfo->ecr; |
474 |
} else { |
475 |
simnfo->est = the_globals->getEST(); |
476 |
} |
477 |
|
478 |
if(!the_globals->haveDielectric() ){ |
479 |
sprintf( painCave.errMsg, |
480 |
"SimSetup Error: You are trying to use Reaction Field without" |
481 |
"setting a dielectric constant!\n" |
482 |
); |
483 |
painCave.isFatal = 1; |
484 |
simError(); |
485 |
} |
486 |
simnfo->dielectric = the_globals->getDielectric(); |
487 |
} else { |
488 |
if (usesDipoles) { |
489 |
|
490 |
if( !the_globals->haveECR() ){ |
491 |
sprintf( painCave.errMsg, |
492 |
"SimSetup Warning: using default value of 1/2 the smallest " |
493 |
"box length for the electrostaticCutoffRadius.\n" |
494 |
"I hope you have a very fast processor!\n"); |
495 |
painCave.isFatal = 0; |
496 |
simError(); |
497 |
double smallest; |
498 |
smallest = simnfo->box_x; |
499 |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
500 |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
501 |
simnfo->ecr = 0.5 * smallest; |
502 |
} else { |
503 |
simnfo->ecr = the_globals->getECR(); |
504 |
} |
505 |
|
506 |
if( !the_globals->haveEST() ){ |
507 |
sprintf( painCave.errMsg, |
508 |
"SimSetup Warning: using default value of 5%% of the " |
509 |
"electrostaticCutoffRadius for the " |
510 |
"electrostaticSkinThickness\n" |
511 |
); |
512 |
painCave.isFatal = 0; |
513 |
simError(); |
514 |
simnfo->est = 0.05 * simnfo->ecr; |
515 |
} else { |
516 |
simnfo->est = the_globals->getEST(); |
517 |
} |
518 |
} |
519 |
} |
520 |
|
521 |
#ifdef IS_MPI |
522 |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
523 |
MPIcheckPoint(); |
524 |
#endif // is_mpi |
525 |
|
526 |
if( the_globals->haveInitialConfig() ){ |
527 |
|
528 |
InitializeFromFile* fileInit; |
529 |
#ifdef IS_MPI // is_mpi |
530 |
if( worldRank == 0 ){ |
531 |
#endif //is_mpi |
532 |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
533 |
#ifdef IS_MPI |
534 |
}else fileInit = new InitializeFromFile( NULL ); |
535 |
#endif |
536 |
fileInit->read_xyz( simnfo ); // default velocities on |
537 |
|
538 |
delete fileInit; |
539 |
} |
540 |
else{ |
541 |
|
542 |
#ifdef IS_MPI |
543 |
|
544 |
// no init from bass |
545 |
|
546 |
sprintf( painCave.errMsg, |
547 |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
548 |
painCave.isFatal; |
549 |
simError(); |
550 |
|
551 |
#else |
552 |
|
553 |
initFromBass(); |
554 |
|
555 |
|
556 |
#endif |
557 |
} |
558 |
|
559 |
#ifdef IS_MPI |
560 |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
561 |
MPIcheckPoint(); |
562 |
#endif // is_mpi |
563 |
|
564 |
|
565 |
|
566 |
|
567 |
|
568 |
|
569 |
|
570 |
#ifdef IS_MPI |
571 |
if( worldRank == 0 ){ |
572 |
#endif // is_mpi |
573 |
|
574 |
if( the_globals->haveFinalConfig() ){ |
575 |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
576 |
} |
577 |
else{ |
578 |
strcpy( simnfo->finalName, inFileName ); |
579 |
char* endTest; |
580 |
int nameLength = strlen( simnfo->finalName ); |
581 |
endTest = &(simnfo->finalName[nameLength - 5]); |
582 |
if( !strcmp( endTest, ".bass" ) ){ |
583 |
strcpy( endTest, ".eor" ); |
584 |
} |
585 |
else if( !strcmp( endTest, ".BASS" ) ){ |
586 |
strcpy( endTest, ".eor" ); |
587 |
} |
588 |
else{ |
589 |
endTest = &(simnfo->finalName[nameLength - 4]); |
590 |
if( !strcmp( endTest, ".bss" ) ){ |
591 |
strcpy( endTest, ".eor" ); |
592 |
} |
593 |
else if( !strcmp( endTest, ".mdl" ) ){ |
594 |
strcpy( endTest, ".eor" ); |
595 |
} |
596 |
else{ |
597 |
strcat( simnfo->finalName, ".eor" ); |
598 |
} |
599 |
} |
600 |
} |
601 |
|
602 |
// make the sample and status out names |
603 |
|
604 |
strcpy( simnfo->sampleName, inFileName ); |
605 |
char* endTest; |
606 |
int nameLength = strlen( simnfo->sampleName ); |
607 |
endTest = &(simnfo->sampleName[nameLength - 5]); |
608 |
if( !strcmp( endTest, ".bass" ) ){ |
609 |
strcpy( endTest, ".dump" ); |
610 |
} |
611 |
else if( !strcmp( endTest, ".BASS" ) ){ |
612 |
strcpy( endTest, ".dump" ); |
613 |
} |
614 |
else{ |
615 |
endTest = &(simnfo->sampleName[nameLength - 4]); |
616 |
if( !strcmp( endTest, ".bss" ) ){ |
617 |
strcpy( endTest, ".dump" ); |
618 |
} |
619 |
else if( !strcmp( endTest, ".mdl" ) ){ |
620 |
strcpy( endTest, ".dump" ); |
621 |
} |
622 |
else{ |
623 |
strcat( simnfo->sampleName, ".dump" ); |
624 |
} |
625 |
} |
626 |
|
627 |
strcpy( simnfo->statusName, inFileName ); |
628 |
nameLength = strlen( simnfo->statusName ); |
629 |
endTest = &(simnfo->statusName[nameLength - 5]); |
630 |
if( !strcmp( endTest, ".bass" ) ){ |
631 |
strcpy( endTest, ".stat" ); |
632 |
} |
633 |
else if( !strcmp( endTest, ".BASS" ) ){ |
634 |
strcpy( endTest, ".stat" ); |
635 |
} |
636 |
else{ |
637 |
endTest = &(simnfo->statusName[nameLength - 4]); |
638 |
if( !strcmp( endTest, ".bss" ) ){ |
639 |
strcpy( endTest, ".stat" ); |
640 |
} |
641 |
else if( !strcmp( endTest, ".mdl" ) ){ |
642 |
strcpy( endTest, ".stat" ); |
643 |
} |
644 |
else{ |
645 |
strcat( simnfo->statusName, ".stat" ); |
646 |
} |
647 |
} |
648 |
|
649 |
#ifdef IS_MPI |
650 |
} |
651 |
#endif // is_mpi |
652 |
|
653 |
// set the status, sample, and themal kick times |
654 |
|
655 |
if( the_globals->haveSampleTime() ){ |
656 |
simnfo->sampleTime = the_globals->getSampleTime(); |
657 |
simnfo->statusTime = simnfo->sampleTime; |
658 |
simnfo->thermalTime = simnfo->sampleTime; |
659 |
} |
660 |
else{ |
661 |
simnfo->sampleTime = the_globals->getRunTime(); |
662 |
simnfo->statusTime = simnfo->sampleTime; |
663 |
simnfo->thermalTime = simnfo->sampleTime; |
664 |
} |
665 |
|
666 |
if( the_globals->haveStatusTime() ){ |
667 |
simnfo->statusTime = the_globals->getStatusTime(); |
668 |
} |
669 |
|
670 |
if( the_globals->haveThermalTime() ){ |
671 |
simnfo->thermalTime = the_globals->getThermalTime(); |
672 |
} |
673 |
|
674 |
// check for the temperature set flag |
675 |
|
676 |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
677 |
|
678 |
|
679 |
// // make the longe range forces and the integrator |
680 |
|
681 |
// new AllLong( simnfo ); |
682 |
|
683 |
|
684 |
if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
685 |
new Symplectic(simnfo, the_ff, the_extendedsystem); |
686 |
std::cerr << "called new Symplecic\n"; |
687 |
fprintf( stderr, "called new Symplectic. stderr\n" ); |
688 |
} |
689 |
else if( !strcmp( force_field, "LJ" ) ){ |
690 |
new Verlet( *simnfo, the_ff, the_extendedsystem ); |
691 |
std::cerr << "called new Verlet\n"; |
692 |
fprintf( stderr, "called new Verlet. stderr\n" ); |
693 |
} |
694 |
else { |
695 |
std::cerr << "I'm a bug.\n"; |
696 |
fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
697 |
} |
698 |
#ifdef IS_MPI |
699 |
mpiSim->mpiRefresh(); |
700 |
#endif |
701 |
|
702 |
// initialize the Fortran |
703 |
|
704 |
|
705 |
simnfo->refreshSim(); |
706 |
|
707 |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
708 |
the_ff->initForceField( LB_MIXING_RULE ); |
709 |
} |
710 |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
711 |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
712 |
} |
713 |
else{ |
714 |
sprintf( painCave.errMsg, |
715 |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
716 |
simnfo->mixingRule ); |
717 |
painCave.isFatal = 1; |
718 |
simError(); |
719 |
} |
720 |
|
721 |
|
722 |
#ifdef IS_MPI |
723 |
strcpy( checkPointMsg, |
724 |
"Successfully intialized the mixingRule for Fortran." ); |
725 |
MPIcheckPoint(); |
726 |
#endif // is_mpi |
727 |
} |
728 |
|
729 |
|
730 |
void SimSetup::makeMolecules( void ){ |
731 |
|
732 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
733 |
molInit info; |
734 |
DirectionalAtom* dAtom; |
735 |
LinkedAssign* extras; |
736 |
LinkedAssign* current_extra; |
737 |
AtomStamp* currentAtom; |
738 |
BondStamp* currentBond; |
739 |
BendStamp* currentBend; |
740 |
TorsionStamp* currentTorsion; |
741 |
|
742 |
bond_pair* theBonds; |
743 |
bend_set* theBends; |
744 |
torsion_set* theTorsions; |
745 |
|
746 |
|
747 |
//init the forceField paramters |
748 |
|
749 |
the_ff->readParams(); |
750 |
|
751 |
|
752 |
// init the atoms |
753 |
|
754 |
double ux, uy, uz, u, uSqr; |
755 |
|
756 |
atomOffset = 0; |
757 |
excludeOffset = 0; |
758 |
for(i=0; i<simnfo->n_mol; i++){ |
759 |
|
760 |
stampID = the_molecules[i].getStampID(); |
761 |
|
762 |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
763 |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
764 |
info.nBends = comp_stamps[stampID]->getNBends(); |
765 |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
766 |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
767 |
|
768 |
info.myAtoms = &the_atoms[atomOffset]; |
769 |
info.myExcludes = &the_excludes[excludeOffset]; |
770 |
info.myBonds = new Bond*[info.nBonds]; |
771 |
info.myBends = new Bend*[info.nBends]; |
772 |
info.myTorsions = new Torsion*[info.nTorsions]; |
773 |
|
774 |
theBonds = new bond_pair[info.nBonds]; |
775 |
theBends = new bend_set[info.nBends]; |
776 |
theTorsions = new torsion_set[info.nTorsions]; |
777 |
|
778 |
// make the Atoms |
779 |
|
780 |
for(j=0; j<info.nAtoms; j++){ |
781 |
|
782 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
783 |
if( currentAtom->haveOrientation() ){ |
784 |
|
785 |
dAtom = new DirectionalAtom(j + atomOffset); |
786 |
simnfo->n_oriented++; |
787 |
info.myAtoms[j] = dAtom; |
788 |
|
789 |
ux = currentAtom->getOrntX(); |
790 |
uy = currentAtom->getOrntY(); |
791 |
uz = currentAtom->getOrntZ(); |
792 |
|
793 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
794 |
|
795 |
u = sqrt( uSqr ); |
796 |
ux = ux / u; |
797 |
uy = uy / u; |
798 |
uz = uz / u; |
799 |
|
800 |
dAtom->setSUx( ux ); |
801 |
dAtom->setSUy( uy ); |
802 |
dAtom->setSUz( uz ); |
803 |
} |
804 |
else{ |
805 |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
806 |
} |
807 |
info.myAtoms[j]->setType( currentAtom->getType() ); |
808 |
|
809 |
#ifdef IS_MPI |
810 |
|
811 |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
812 |
|
813 |
#endif // is_mpi |
814 |
} |
815 |
|
816 |
// make the bonds |
817 |
for(j=0; j<info.nBonds; j++){ |
818 |
|
819 |
currentBond = comp_stamps[stampID]->getBond( j ); |
820 |
theBonds[j].a = currentBond->getA() + atomOffset; |
821 |
theBonds[j].b = currentBond->getB() + atomOffset; |
822 |
|
823 |
exI = theBonds[j].a; |
824 |
exJ = theBonds[j].b; |
825 |
|
826 |
// exclude_I must always be the smaller of the pair |
827 |
if( exI > exJ ){ |
828 |
tempEx = exI; |
829 |
exI = exJ; |
830 |
exJ = tempEx; |
831 |
} |
832 |
#ifdef IS_MPI |
833 |
tempEx = exI; |
834 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
835 |
tempEx = exJ; |
836 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
837 |
|
838 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
839 |
#else // isn't MPI |
840 |
|
841 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
842 |
#endif //is_mpi |
843 |
} |
844 |
excludeOffset += info.nBonds; |
845 |
|
846 |
//make the bends |
847 |
for(j=0; j<info.nBends; j++){ |
848 |
|
849 |
currentBend = comp_stamps[stampID]->getBend( j ); |
850 |
theBends[j].a = currentBend->getA() + atomOffset; |
851 |
theBends[j].b = currentBend->getB() + atomOffset; |
852 |
theBends[j].c = currentBend->getC() + atomOffset; |
853 |
|
854 |
if( currentBend->haveExtras() ){ |
855 |
|
856 |
extras = currentBend->getExtras(); |
857 |
current_extra = extras; |
858 |
|
859 |
while( current_extra != NULL ){ |
860 |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
861 |
|
862 |
switch( current_extra->getType() ){ |
863 |
|
864 |
case 0: |
865 |
theBends[j].ghost = |
866 |
current_extra->getInt() + atomOffset; |
867 |
theBends[j].isGhost = 1; |
868 |
break; |
869 |
|
870 |
case 1: |
871 |
theBends[j].ghost = |
872 |
(int)current_extra->getDouble() + atomOffset; |
873 |
theBends[j].isGhost = 1; |
874 |
break; |
875 |
|
876 |
default: |
877 |
sprintf( painCave.errMsg, |
878 |
"SimSetup Error: ghostVectorSource was neither a " |
879 |
"double nor an int.\n" |
880 |
"-->Bend[%d] in %s\n", |
881 |
j, comp_stamps[stampID]->getID() ); |
882 |
painCave.isFatal = 1; |
883 |
simError(); |
884 |
} |
885 |
} |
886 |
|
887 |
else{ |
888 |
|
889 |
sprintf( painCave.errMsg, |
890 |
"SimSetup Error: unhandled bend assignment:\n" |
891 |
" -->%s in Bend[%d] in %s\n", |
892 |
current_extra->getlhs(), |
893 |
j, comp_stamps[stampID]->getID() ); |
894 |
painCave.isFatal = 1; |
895 |
simError(); |
896 |
} |
897 |
|
898 |
current_extra = current_extra->getNext(); |
899 |
} |
900 |
} |
901 |
|
902 |
if( !theBends[j].isGhost ){ |
903 |
|
904 |
exI = theBends[j].a; |
905 |
exJ = theBends[j].c; |
906 |
} |
907 |
else{ |
908 |
|
909 |
exI = theBends[j].a; |
910 |
exJ = theBends[j].b; |
911 |
} |
912 |
|
913 |
// exclude_I must always be the smaller of the pair |
914 |
if( exI > exJ ){ |
915 |
tempEx = exI; |
916 |
exI = exJ; |
917 |
exJ = tempEx; |
918 |
} |
919 |
#ifdef IS_MPI |
920 |
tempEx = exI; |
921 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
922 |
tempEx = exJ; |
923 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
924 |
|
925 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
926 |
#else // isn't MPI |
927 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
928 |
#endif //is_mpi |
929 |
} |
930 |
excludeOffset += info.nBends; |
931 |
|
932 |
for(j=0; j<info.nTorsions; j++){ |
933 |
|
934 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
935 |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
936 |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
937 |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
938 |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
939 |
|
940 |
exI = theTorsions[j].a; |
941 |
exJ = theTorsions[j].d; |
942 |
|
943 |
// exclude_I must always be the smaller of the pair |
944 |
if( exI > exJ ){ |
945 |
tempEx = exI; |
946 |
exI = exJ; |
947 |
exJ = tempEx; |
948 |
} |
949 |
#ifdef IS_MPI |
950 |
tempEx = exI; |
951 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
952 |
tempEx = exJ; |
953 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
954 |
|
955 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
956 |
#else // isn't MPI |
957 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
958 |
#endif //is_mpi |
959 |
} |
960 |
excludeOffset += info.nTorsions; |
961 |
|
962 |
|
963 |
// send the arrays off to the forceField for init. |
964 |
|
965 |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
966 |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
967 |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
968 |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
969 |
|
970 |
|
971 |
the_molecules[i].initialize( info ); |
972 |
|
973 |
|
974 |
atomOffset += info.nAtoms; |
975 |
delete[] theBonds; |
976 |
delete[] theBends; |
977 |
delete[] theTorsions; |
978 |
} |
979 |
|
980 |
#ifdef IS_MPI |
981 |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
982 |
MPIcheckPoint(); |
983 |
#endif // is_mpi |
984 |
|
985 |
// clean up the forcefield |
986 |
the_ff->calcRcut(); |
987 |
the_ff->cleanMe(); |
988 |
|
989 |
} |
990 |
|
991 |
void SimSetup::initFromBass( void ){ |
992 |
|
993 |
int i, j, k; |
994 |
int n_cells; |
995 |
double cellx, celly, cellz; |
996 |
double temp1, temp2, temp3; |
997 |
int n_per_extra; |
998 |
int n_extra; |
999 |
int have_extra, done; |
1000 |
|
1001 |
temp1 = (double)tot_nmol / 4.0; |
1002 |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1003 |
temp3 = ceil( temp2 ); |
1004 |
|
1005 |
have_extra =0; |
1006 |
if( temp2 < temp3 ){ // we have a non-complete lattice |
1007 |
have_extra =1; |
1008 |
|
1009 |
n_cells = (int)temp3 - 1; |
1010 |
cellx = simnfo->box_x / temp3; |
1011 |
celly = simnfo->box_y / temp3; |
1012 |
cellz = simnfo->box_z / temp3; |
1013 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1014 |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1015 |
n_per_extra = (int)ceil( temp1 ); |
1016 |
|
1017 |
if( n_per_extra > 4){ |
1018 |
sprintf( painCave.errMsg, |
1019 |
"SimSetup error. There has been an error in constructing" |
1020 |
" the non-complete lattice.\n" ); |
1021 |
painCave.isFatal = 1; |
1022 |
simError(); |
1023 |
} |
1024 |
} |
1025 |
else{ |
1026 |
n_cells = (int)temp3; |
1027 |
cellx = simnfo->box_x / temp3; |
1028 |
celly = simnfo->box_y / temp3; |
1029 |
cellz = simnfo->box_z / temp3; |
1030 |
} |
1031 |
|
1032 |
current_mol = 0; |
1033 |
current_comp_mol = 0; |
1034 |
current_comp = 0; |
1035 |
current_atom_ndx = 0; |
1036 |
|
1037 |
for( i=0; i < n_cells ; i++ ){ |
1038 |
for( j=0; j < n_cells; j++ ){ |
1039 |
for( k=0; k < n_cells; k++ ){ |
1040 |
|
1041 |
makeElement( i * cellx, |
1042 |
j * celly, |
1043 |
k * cellz ); |
1044 |
|
1045 |
makeElement( i * cellx + 0.5 * cellx, |
1046 |
j * celly + 0.5 * celly, |
1047 |
k * cellz ); |
1048 |
|
1049 |
makeElement( i * cellx, |
1050 |
j * celly + 0.5 * celly, |
1051 |
k * cellz + 0.5 * cellz ); |
1052 |
|
1053 |
makeElement( i * cellx + 0.5 * cellx, |
1054 |
j * celly, |
1055 |
k * cellz + 0.5 * cellz ); |
1056 |
} |
1057 |
} |
1058 |
} |
1059 |
|
1060 |
if( have_extra ){ |
1061 |
done = 0; |
1062 |
|
1063 |
int start_ndx; |
1064 |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1065 |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1066 |
|
1067 |
if( i < n_cells ){ |
1068 |
|
1069 |
if( j < n_cells ){ |
1070 |
start_ndx = n_cells; |
1071 |
} |
1072 |
else start_ndx = 0; |
1073 |
} |
1074 |
else start_ndx = 0; |
1075 |
|
1076 |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1077 |
|
1078 |
makeElement( i * cellx, |
1079 |
j * celly, |
1080 |
k * cellz ); |
1081 |
done = ( current_mol >= tot_nmol ); |
1082 |
|
1083 |
if( !done && n_per_extra > 1 ){ |
1084 |
makeElement( i * cellx + 0.5 * cellx, |
1085 |
j * celly + 0.5 * celly, |
1086 |
k * cellz ); |
1087 |
done = ( current_mol >= tot_nmol ); |
1088 |
} |
1089 |
|
1090 |
if( !done && n_per_extra > 2){ |
1091 |
makeElement( i * cellx, |
1092 |
j * celly + 0.5 * celly, |
1093 |
k * cellz + 0.5 * cellz ); |
1094 |
done = ( current_mol >= tot_nmol ); |
1095 |
} |
1096 |
|
1097 |
if( !done && n_per_extra > 3){ |
1098 |
makeElement( i * cellx + 0.5 * cellx, |
1099 |
j * celly, |
1100 |
k * cellz + 0.5 * cellz ); |
1101 |
done = ( current_mol >= tot_nmol ); |
1102 |
} |
1103 |
} |
1104 |
} |
1105 |
} |
1106 |
} |
1107 |
|
1108 |
|
1109 |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1110 |
simnfo->atoms[i]->set_vx( 0.0 ); |
1111 |
simnfo->atoms[i]->set_vy( 0.0 ); |
1112 |
simnfo->atoms[i]->set_vz( 0.0 ); |
1113 |
} |
1114 |
} |
1115 |
|
1116 |
void SimSetup::makeElement( double x, double y, double z ){ |
1117 |
|
1118 |
int k; |
1119 |
AtomStamp* current_atom; |
1120 |
DirectionalAtom* dAtom; |
1121 |
double rotMat[3][3]; |
1122 |
|
1123 |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1124 |
|
1125 |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1126 |
if( !current_atom->havePosition() ){ |
1127 |
sprintf( painCave.errMsg, |
1128 |
"SimSetup:initFromBass error.\n" |
1129 |
"\tComponent %s, atom %s does not have a position specified.\n" |
1130 |
"\tThe initialization routine is unable to give a start" |
1131 |
" position.\n", |
1132 |
comp_stamps[current_comp]->getID(), |
1133 |
current_atom->getType() ); |
1134 |
painCave.isFatal = 1; |
1135 |
simError(); |
1136 |
} |
1137 |
|
1138 |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1139 |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1140 |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1141 |
|
1142 |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1143 |
|
1144 |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1145 |
|
1146 |
rotMat[0][0] = 1.0; |
1147 |
rotMat[0][1] = 0.0; |
1148 |
rotMat[0][2] = 0.0; |
1149 |
|
1150 |
rotMat[1][0] = 0.0; |
1151 |
rotMat[1][1] = 1.0; |
1152 |
rotMat[1][2] = 0.0; |
1153 |
|
1154 |
rotMat[2][0] = 0.0; |
1155 |
rotMat[2][1] = 0.0; |
1156 |
rotMat[2][2] = 1.0; |
1157 |
|
1158 |
dAtom->setA( rotMat ); |
1159 |
} |
1160 |
|
1161 |
current_atom_ndx++; |
1162 |
} |
1163 |
|
1164 |
current_mol++; |
1165 |
current_comp_mol++; |
1166 |
|
1167 |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1168 |
|
1169 |
current_comp_mol = 0; |
1170 |
current_comp++; |
1171 |
} |
1172 |
} |