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