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 |
// some defines for ensemble and Forcefield cases |
16 |
|
17 |
#define NVE_ENS 0 |
18 |
#define NVT_ENS 1 |
19 |
#define NPT_ENS 2 |
20 |
|
21 |
#define FF_DUFF 0 |
22 |
#define FF_LJ 1 |
23 |
|
24 |
|
25 |
SimSetup::SimSetup(){ |
26 |
stamps = new MakeStamps(); |
27 |
globals = new Globals(); |
28 |
|
29 |
#ifdef IS_MPI |
30 |
strcpy( checkPointMsg, "SimSetup creation successful" ); |
31 |
MPIcheckPoint(); |
32 |
#endif // IS_MPI |
33 |
} |
34 |
|
35 |
SimSetup::~SimSetup(){ |
36 |
delete stamps; |
37 |
delete globals; |
38 |
} |
39 |
|
40 |
void SimSetup::parseFile( char* fileName ){ |
41 |
|
42 |
#ifdef IS_MPI |
43 |
if( worldRank == 0 ){ |
44 |
#endif // is_mpi |
45 |
|
46 |
inFileName = fileName; |
47 |
set_interface_stamps( stamps, globals ); |
48 |
|
49 |
#ifdef IS_MPI |
50 |
mpiEventInit(); |
51 |
#endif |
52 |
|
53 |
yacc_BASS( fileName ); |
54 |
|
55 |
#ifdef IS_MPI |
56 |
throwMPIEvent(NULL); |
57 |
} |
58 |
else receiveParse(); |
59 |
#endif |
60 |
|
61 |
} |
62 |
|
63 |
#ifdef IS_MPI |
64 |
void SimSetup::receiveParse(void){ |
65 |
|
66 |
set_interface_stamps( stamps, globals ); |
67 |
mpiEventInit(); |
68 |
MPIcheckPoint(); |
69 |
mpiEventLoop(); |
70 |
|
71 |
} |
72 |
|
73 |
#endif // is_mpi |
74 |
|
75 |
void SimSetup::createSim( void ){ |
76 |
|
77 |
MakeStamps *the_stamps; |
78 |
Globals* the_globals; |
79 |
int i, j, k, globalAtomIndex; |
80 |
|
81 |
int ensembleCase; |
82 |
int ffCase; |
83 |
|
84 |
ensembleCase = -1; |
85 |
ffCase = -1; |
86 |
|
87 |
// get the stamps and globals; |
88 |
the_stamps = stamps; |
89 |
the_globals = globals; |
90 |
|
91 |
// set the easy ones first |
92 |
simnfo->target_temp = the_globals->getTargetTemp(); |
93 |
simnfo->dt = the_globals->getDt(); |
94 |
simnfo->run_time = the_globals->getRunTime(); |
95 |
|
96 |
// get the ones we know are there, yet still may need some work. |
97 |
n_components = the_globals->getNComponents(); |
98 |
strcpy( force_field, the_globals->getForceField() ); |
99 |
|
100 |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
101 |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
102 |
else{ |
103 |
sprintf( painCave.errMsg, |
104 |
"SimSetup Error. Unrecognized force field -> %s\n", |
105 |
force_field ); |
106 |
painCave.isFatal = 1; |
107 |
simError(); |
108 |
} |
109 |
|
110 |
// get the ensemble: |
111 |
strcpy( ensemble, the_globals->getEnsemble() ); |
112 |
|
113 |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
114 |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
115 |
else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS; |
116 |
else{ |
117 |
sprintf( painCave.errMsg, |
118 |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
119 |
"reverting to NVE for this simulation.\n", |
120 |
ensemble ); |
121 |
painCave.isFatal = 0; |
122 |
simError(); |
123 |
strcpy( ensemble, "NVE" ); |
124 |
ensembleCase = NVE_ENS; |
125 |
} |
126 |
strcpy( simnfo->ensemble, ensemble ); |
127 |
|
128 |
|
129 |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
130 |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
131 |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
132 |
// if (the_globals->haveTargetPressure()) |
133 |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
134 |
// else { |
135 |
// sprintf( painCave.errMsg, |
136 |
// "SimSetup error: If you use the constant pressure\n" |
137 |
// " ensemble, you must set targetPressure.\n" |
138 |
// " This was found in the BASS file.\n"); |
139 |
// painCave.isFatal = 1; |
140 |
// simError(); |
141 |
// } |
142 |
|
143 |
// if (the_globals->haveTauThermostat()) |
144 |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
145 |
// else if (the_globals->haveQmass()) |
146 |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
147 |
// else { |
148 |
// sprintf( painCave.errMsg, |
149 |
// "SimSetup error: If you use one of the constant temperature\n" |
150 |
// " ensembles, you must set either tauThermostat or qMass.\n" |
151 |
// " Neither of these was found in the BASS file.\n"); |
152 |
// painCave.isFatal = 1; |
153 |
// simError(); |
154 |
// } |
155 |
|
156 |
// if (the_globals->haveTauBarostat()) |
157 |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
158 |
// else { |
159 |
// sprintf( painCave.errMsg, |
160 |
// "SimSetup error: If you use the constant pressure\n" |
161 |
// " ensemble, you must set tauBarostat.\n" |
162 |
// " This was found in the BASS file.\n"); |
163 |
// painCave.isFatal = 1; |
164 |
// simError(); |
165 |
// } |
166 |
|
167 |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
168 |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
169 |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
170 |
|
171 |
// if (the_globals->haveTauThermostat()) |
172 |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
173 |
// else if (the_globals->haveQmass()) |
174 |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
175 |
// else { |
176 |
// sprintf( painCave.errMsg, |
177 |
// "SimSetup error: If you use one of the constant temperature\n" |
178 |
// " ensembles, you must set either tauThermostat or qMass.\n" |
179 |
// " Neither of these was found in the BASS file.\n"); |
180 |
// painCave.isFatal = 1; |
181 |
// simError(); |
182 |
// } |
183 |
|
184 |
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
185 |
simnfo->usePBC = the_globals->getPBC(); |
186 |
|
187 |
int usesDipoles = 0; |
188 |
switch( ffCase ){ |
189 |
|
190 |
case FF_DUFF: |
191 |
the_ff = new DUFF(); |
192 |
usesDipoles = 1; |
193 |
break; |
194 |
|
195 |
case FF_LJ: |
196 |
the_ff = new LJFF(); |
197 |
break; |
198 |
|
199 |
default: |
200 |
sprintf( painCave.errMsg, |
201 |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
202 |
painCave.isFatal = 1; |
203 |
simError(); |
204 |
} |
205 |
|
206 |
#ifdef IS_MPI |
207 |
strcpy( checkPointMsg, "ForceField creation successful" ); |
208 |
MPIcheckPoint(); |
209 |
#endif // is_mpi |
210 |
|
211 |
// get the components and calculate the tot_nMol and indvidual n_mol |
212 |
the_components = the_globals->getComponents(); |
213 |
components_nmol = new int[n_components]; |
214 |
comp_stamps = new MoleculeStamp*[n_components]; |
215 |
|
216 |
if( !the_globals->haveNMol() ){ |
217 |
// we don't have the total number of molecules, so we assume it is |
218 |
// given in each component |
219 |
|
220 |
tot_nmol = 0; |
221 |
for( i=0; i<n_components; i++ ){ |
222 |
|
223 |
if( !the_components[i]->haveNMol() ){ |
224 |
// we have a problem |
225 |
sprintf( painCave.errMsg, |
226 |
"SimSetup Error. No global NMol or component NMol" |
227 |
" given. Cannot calculate the number of atoms.\n" ); |
228 |
painCave.isFatal = 1; |
229 |
simError(); |
230 |
} |
231 |
|
232 |
tot_nmol += the_components[i]->getNMol(); |
233 |
components_nmol[i] = the_components[i]->getNMol(); |
234 |
} |
235 |
} |
236 |
else{ |
237 |
sprintf( painCave.errMsg, |
238 |
"SimSetup error.\n" |
239 |
"\tSorry, the ability to specify total" |
240 |
" nMols and then give molfractions in the components\n" |
241 |
"\tis not currently supported." |
242 |
" Please give nMol in the components.\n" ); |
243 |
painCave.isFatal = 1; |
244 |
simError(); |
245 |
|
246 |
|
247 |
// tot_nmol = the_globals->getNMol(); |
248 |
|
249 |
// //we have the total number of molecules, now we check for molfractions |
250 |
// for( i=0; i<n_components; i++ ){ |
251 |
|
252 |
// if( !the_components[i]->haveMolFraction() ){ |
253 |
|
254 |
// if( !the_components[i]->haveNMol() ){ |
255 |
// //we have a problem |
256 |
// std::cerr << "SimSetup error. Neither molFraction nor " |
257 |
// << " nMol was given in component |
258 |
|
259 |
} |
260 |
|
261 |
#ifdef IS_MPI |
262 |
strcpy( checkPointMsg, "Have the number of components" ); |
263 |
MPIcheckPoint(); |
264 |
#endif // is_mpi |
265 |
|
266 |
// make an array of molecule stamps that match the components used. |
267 |
// also extract the used stamps out into a separate linked list |
268 |
|
269 |
simnfo->nComponents = n_components; |
270 |
simnfo->componentsNmol = components_nmol; |
271 |
simnfo->compStamps = comp_stamps; |
272 |
simnfo->headStamp = new LinkedMolStamp(); |
273 |
|
274 |
char* id; |
275 |
LinkedMolStamp* headStamp = simnfo->headStamp; |
276 |
LinkedMolStamp* currentStamp = NULL; |
277 |
for( i=0; i<n_components; i++ ){ |
278 |
|
279 |
id = the_components[i]->getType(); |
280 |
comp_stamps[i] = NULL; |
281 |
|
282 |
// check to make sure the component isn't already in the list |
283 |
|
284 |
comp_stamps[i] = headStamp->match( id ); |
285 |
if( comp_stamps[i] == NULL ){ |
286 |
|
287 |
// extract the component from the list; |
288 |
|
289 |
currentStamp = the_stamps->extractMolStamp( id ); |
290 |
if( currentStamp == NULL ){ |
291 |
sprintf( painCave.errMsg, |
292 |
"SimSetup error: Component \"%s\" was not found in the " |
293 |
"list of declared molecules\n", |
294 |
id ); |
295 |
painCave.isFatal = 1; |
296 |
simError(); |
297 |
} |
298 |
|
299 |
headStamp->add( currentStamp ); |
300 |
comp_stamps[i] = headStamp->match( id ); |
301 |
} |
302 |
} |
303 |
|
304 |
#ifdef IS_MPI |
305 |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
306 |
MPIcheckPoint(); |
307 |
#endif // is_mpi |
308 |
|
309 |
|
310 |
|
311 |
|
312 |
// caclulate the number of atoms, bonds, bends and torsions |
313 |
|
314 |
tot_atoms = 0; |
315 |
tot_bonds = 0; |
316 |
tot_bends = 0; |
317 |
tot_torsions = 0; |
318 |
for( i=0; i<n_components; i++ ){ |
319 |
|
320 |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
321 |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
322 |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
323 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
324 |
} |
325 |
|
326 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
327 |
|
328 |
simnfo->n_atoms = tot_atoms; |
329 |
simnfo->n_bonds = tot_bonds; |
330 |
simnfo->n_bends = tot_bends; |
331 |
simnfo->n_torsions = tot_torsions; |
332 |
simnfo->n_SRI = tot_SRI; |
333 |
simnfo->n_mol = tot_nmol; |
334 |
|
335 |
simnfo->molMembershipArray = new int[tot_atoms]; |
336 |
|
337 |
#ifdef IS_MPI |
338 |
|
339 |
// divide the molecules among processors here. |
340 |
|
341 |
mpiSim = new mpiSimulation( simnfo ); |
342 |
|
343 |
globalIndex = mpiSim->divideLabor(); |
344 |
|
345 |
// set up the local variables |
346 |
|
347 |
int localMol, allMol; |
348 |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
349 |
|
350 |
int* mol2proc = mpiSim->getMolToProcMap(); |
351 |
int* molCompType = mpiSim->getMolComponentType(); |
352 |
|
353 |
allMol = 0; |
354 |
localMol = 0; |
355 |
local_atoms = 0; |
356 |
local_bonds = 0; |
357 |
local_bends = 0; |
358 |
local_torsions = 0; |
359 |
globalAtomIndex = 0; |
360 |
|
361 |
|
362 |
for( i=0; i<n_components; i++ ){ |
363 |
|
364 |
for( j=0; j<components_nmol[i]; j++ ){ |
365 |
|
366 |
if( mol2proc[allMol] == worldRank ){ |
367 |
|
368 |
local_atoms += comp_stamps[i]->getNAtoms(); |
369 |
local_bonds += comp_stamps[i]->getNBonds(); |
370 |
local_bends += comp_stamps[i]->getNBends(); |
371 |
local_torsions += comp_stamps[i]->getNTorsions(); |
372 |
localMol++; |
373 |
} |
374 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
375 |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
376 |
globalAtomIndex++; |
377 |
} |
378 |
|
379 |
allMol++; |
380 |
} |
381 |
} |
382 |
local_SRI = local_bonds + local_bends + local_torsions; |
383 |
|
384 |
simnfo->n_atoms = mpiSim->getMyNlocal(); |
385 |
|
386 |
if( local_atoms != simnfo->n_atoms ){ |
387 |
sprintf( painCave.errMsg, |
388 |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
389 |
" localAtom (%d) are not equal.\n", |
390 |
simnfo->n_atoms, |
391 |
local_atoms ); |
392 |
painCave.isFatal = 1; |
393 |
simError(); |
394 |
} |
395 |
|
396 |
simnfo->n_bonds = local_bonds; |
397 |
simnfo->n_bends = local_bends; |
398 |
simnfo->n_torsions = local_torsions; |
399 |
simnfo->n_SRI = local_SRI; |
400 |
simnfo->n_mol = localMol; |
401 |
|
402 |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
403 |
MPIcheckPoint(); |
404 |
|
405 |
|
406 |
#endif // is_mpi |
407 |
|
408 |
|
409 |
// create the atom and short range interaction arrays |
410 |
|
411 |
Atom::createArrays(simnfo->n_atoms); |
412 |
the_atoms = new Atom*[simnfo->n_atoms]; |
413 |
the_molecules = new Molecule[simnfo->n_mol]; |
414 |
int molIndex; |
415 |
|
416 |
// initialize the molecule's stampID's |
417 |
|
418 |
#ifdef IS_MPI |
419 |
|
420 |
|
421 |
molIndex = 0; |
422 |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
423 |
|
424 |
if(mol2proc[i] == worldRank ){ |
425 |
the_molecules[molIndex].setStampID( molCompType[i] ); |
426 |
the_molecules[molIndex].setMyIndex( molIndex ); |
427 |
the_molecules[molIndex].setGlobalIndex( i ); |
428 |
molIndex++; |
429 |
} |
430 |
} |
431 |
|
432 |
#else // is_mpi |
433 |
|
434 |
molIndex = 0; |
435 |
globalAtomIndex = 0; |
436 |
for(i=0; i<n_components; i++){ |
437 |
for(j=0; j<components_nmol[i]; j++ ){ |
438 |
the_molecules[molIndex].setStampID( i ); |
439 |
the_molecules[molIndex].setMyIndex( molIndex ); |
440 |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
441 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
442 |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
443 |
globalAtomIndex++; |
444 |
} |
445 |
molIndex++; |
446 |
} |
447 |
} |
448 |
|
449 |
|
450 |
#endif // is_mpi |
451 |
|
452 |
|
453 |
if( simnfo->n_SRI ){ |
454 |
|
455 |
Exclude::createArray(simnfo->n_SRI); |
456 |
the_excludes = new Exclude*[simnfo->n_SRI]; |
457 |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
458 |
simnfo->globalExcludes = new int; |
459 |
simnfo->n_exclude = simnfo->n_SRI; |
460 |
} |
461 |
else{ |
462 |
|
463 |
Exclude::createArray( 1 ); |
464 |
the_excludes = new Exclude*; |
465 |
the_excludes[0] = new Exclude(0); |
466 |
the_excludes[0]->setPair( 0,0 ); |
467 |
simnfo->globalExcludes = new int; |
468 |
simnfo->globalExcludes[0] = 0; |
469 |
simnfo->n_exclude = 0; |
470 |
} |
471 |
|
472 |
// set the arrays into the SimInfo object |
473 |
|
474 |
simnfo->atoms = the_atoms; |
475 |
simnfo->molecules = the_molecules; |
476 |
simnfo->nGlobalExcludes = 0; |
477 |
simnfo->excludes = the_excludes; |
478 |
|
479 |
|
480 |
// get some of the tricky things that may still be in the globals |
481 |
|
482 |
double boxVector[3]; |
483 |
if( the_globals->haveBox() ){ |
484 |
boxVector[0] = the_globals->getBox(); |
485 |
boxVector[1] = the_globals->getBox(); |
486 |
boxVector[2] = the_globals->getBox(); |
487 |
|
488 |
simnfo->setBox( boxVector ); |
489 |
} |
490 |
else if( the_globals->haveDensity() ){ |
491 |
|
492 |
double vol; |
493 |
vol = (double)tot_nmol / the_globals->getDensity(); |
494 |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
495 |
boxVector[1] = boxVector[0]; |
496 |
boxVector[2] = boxVector[0]; |
497 |
|
498 |
simnfo->setBox( boxVector ); |
499 |
} |
500 |
else{ |
501 |
if( !the_globals->haveBoxX() ){ |
502 |
sprintf( painCave.errMsg, |
503 |
"SimSetup error, no periodic BoxX size given.\n" ); |
504 |
painCave.isFatal = 1; |
505 |
simError(); |
506 |
} |
507 |
boxVector[0] = the_globals->getBoxX(); |
508 |
|
509 |
if( !the_globals->haveBoxY() ){ |
510 |
sprintf( painCave.errMsg, |
511 |
"SimSetup error, no periodic BoxY size given.\n" ); |
512 |
painCave.isFatal = 1; |
513 |
simError(); |
514 |
} |
515 |
boxVector[1] = the_globals->getBoxY(); |
516 |
|
517 |
if( !the_globals->haveBoxZ() ){ |
518 |
sprintf( painCave.errMsg, |
519 |
"SimSetup error, no periodic BoxZ size given.\n" ); |
520 |
painCave.isFatal = 1; |
521 |
simError(); |
522 |
} |
523 |
boxVector[2] = the_globals->getBoxZ(); |
524 |
|
525 |
simnfo->setBox( boxVector ); |
526 |
} |
527 |
|
528 |
#ifdef IS_MPI |
529 |
strcpy( checkPointMsg, "Box size set up" ); |
530 |
MPIcheckPoint(); |
531 |
#endif // is_mpi |
532 |
|
533 |
|
534 |
// initialize the arrays |
535 |
|
536 |
the_ff->setSimInfo( simnfo ); |
537 |
|
538 |
makeMolecules(); |
539 |
simnfo->identArray = new int[simnfo->n_atoms]; |
540 |
for(i=0; i<simnfo->n_atoms; i++){ |
541 |
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
542 |
} |
543 |
|
544 |
if (the_globals->getUseRF() ) { |
545 |
simnfo->useReactionField = 1; |
546 |
|
547 |
if( !the_globals->haveECR() ){ |
548 |
sprintf( painCave.errMsg, |
549 |
"SimSetup Warning: using default value of 1/2 the smallest " |
550 |
"box length for the electrostaticCutoffRadius.\n" |
551 |
"I hope you have a very fast processor!\n"); |
552 |
painCave.isFatal = 0; |
553 |
simError(); |
554 |
double smallest; |
555 |
smallest = simnfo->boxLx; |
556 |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
557 |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
558 |
simnfo->ecr = 0.5 * smallest; |
559 |
} else { |
560 |
simnfo->ecr = the_globals->getECR(); |
561 |
} |
562 |
|
563 |
if( !the_globals->haveEST() ){ |
564 |
sprintf( painCave.errMsg, |
565 |
"SimSetup Warning: using default value of 0.05 * the " |
566 |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
567 |
); |
568 |
painCave.isFatal = 0; |
569 |
simError(); |
570 |
simnfo->est = 0.05 * simnfo->ecr; |
571 |
} else { |
572 |
simnfo->est = the_globals->getEST(); |
573 |
} |
574 |
|
575 |
if(!the_globals->haveDielectric() ){ |
576 |
sprintf( painCave.errMsg, |
577 |
"SimSetup Error: You are trying to use Reaction Field without" |
578 |
"setting a dielectric constant!\n" |
579 |
); |
580 |
painCave.isFatal = 1; |
581 |
simError(); |
582 |
} |
583 |
simnfo->dielectric = the_globals->getDielectric(); |
584 |
} else { |
585 |
if (usesDipoles) { |
586 |
|
587 |
if( !the_globals->haveECR() ){ |
588 |
sprintf( painCave.errMsg, |
589 |
"SimSetup Warning: using default value of 1/2 the smallest " |
590 |
"box length for the electrostaticCutoffRadius.\n" |
591 |
"I hope you have a very fast processor!\n"); |
592 |
painCave.isFatal = 0; |
593 |
simError(); |
594 |
double smallest; |
595 |
smallest = simnfo->boxLx; |
596 |
if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
597 |
if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
598 |
simnfo->ecr = 0.5 * smallest; |
599 |
} else { |
600 |
simnfo->ecr = the_globals->getECR(); |
601 |
} |
602 |
|
603 |
if( !the_globals->haveEST() ){ |
604 |
sprintf( painCave.errMsg, |
605 |
"SimSetup Warning: using default value of 5%% of the " |
606 |
"electrostaticCutoffRadius for the " |
607 |
"electrostaticSkinThickness\n" |
608 |
); |
609 |
painCave.isFatal = 0; |
610 |
simError(); |
611 |
simnfo->est = 0.05 * simnfo->ecr; |
612 |
} else { |
613 |
simnfo->est = the_globals->getEST(); |
614 |
} |
615 |
} |
616 |
} |
617 |
|
618 |
#ifdef IS_MPI |
619 |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
620 |
MPIcheckPoint(); |
621 |
#endif // is_mpi |
622 |
|
623 |
if( the_globals->haveInitialConfig() ){ |
624 |
|
625 |
InitializeFromFile* fileInit; |
626 |
#ifdef IS_MPI // is_mpi |
627 |
if( worldRank == 0 ){ |
628 |
#endif //is_mpi |
629 |
fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
630 |
#ifdef IS_MPI |
631 |
}else fileInit = new InitializeFromFile( NULL ); |
632 |
#endif |
633 |
fileInit->read_xyz( simnfo ); // default velocities on |
634 |
|
635 |
delete fileInit; |
636 |
} |
637 |
else{ |
638 |
|
639 |
#ifdef IS_MPI |
640 |
|
641 |
// no init from bass |
642 |
|
643 |
sprintf( painCave.errMsg, |
644 |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
645 |
painCave.isFatal; |
646 |
simError(); |
647 |
|
648 |
#else |
649 |
|
650 |
initFromBass(); |
651 |
|
652 |
|
653 |
#endif |
654 |
} |
655 |
|
656 |
#ifdef IS_MPI |
657 |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
658 |
MPIcheckPoint(); |
659 |
#endif // is_mpi |
660 |
|
661 |
|
662 |
|
663 |
|
664 |
|
665 |
|
666 |
|
667 |
#ifdef IS_MPI |
668 |
if( worldRank == 0 ){ |
669 |
#endif // is_mpi |
670 |
|
671 |
if( the_globals->haveFinalConfig() ){ |
672 |
strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
673 |
} |
674 |
else{ |
675 |
strcpy( simnfo->finalName, inFileName ); |
676 |
char* endTest; |
677 |
int nameLength = strlen( simnfo->finalName ); |
678 |
endTest = &(simnfo->finalName[nameLength - 5]); |
679 |
if( !strcmp( endTest, ".bass" ) ){ |
680 |
strcpy( endTest, ".eor" ); |
681 |
} |
682 |
else if( !strcmp( endTest, ".BASS" ) ){ |
683 |
strcpy( endTest, ".eor" ); |
684 |
} |
685 |
else{ |
686 |
endTest = &(simnfo->finalName[nameLength - 4]); |
687 |
if( !strcmp( endTest, ".bss" ) ){ |
688 |
strcpy( endTest, ".eor" ); |
689 |
} |
690 |
else if( !strcmp( endTest, ".mdl" ) ){ |
691 |
strcpy( endTest, ".eor" ); |
692 |
} |
693 |
else{ |
694 |
strcat( simnfo->finalName, ".eor" ); |
695 |
} |
696 |
} |
697 |
} |
698 |
|
699 |
// make the sample and status out names |
700 |
|
701 |
strcpy( simnfo->sampleName, inFileName ); |
702 |
char* endTest; |
703 |
int nameLength = strlen( simnfo->sampleName ); |
704 |
endTest = &(simnfo->sampleName[nameLength - 5]); |
705 |
if( !strcmp( endTest, ".bass" ) ){ |
706 |
strcpy( endTest, ".dump" ); |
707 |
} |
708 |
else if( !strcmp( endTest, ".BASS" ) ){ |
709 |
strcpy( endTest, ".dump" ); |
710 |
} |
711 |
else{ |
712 |
endTest = &(simnfo->sampleName[nameLength - 4]); |
713 |
if( !strcmp( endTest, ".bss" ) ){ |
714 |
strcpy( endTest, ".dump" ); |
715 |
} |
716 |
else if( !strcmp( endTest, ".mdl" ) ){ |
717 |
strcpy( endTest, ".dump" ); |
718 |
} |
719 |
else{ |
720 |
strcat( simnfo->sampleName, ".dump" ); |
721 |
} |
722 |
} |
723 |
|
724 |
strcpy( simnfo->statusName, inFileName ); |
725 |
nameLength = strlen( simnfo->statusName ); |
726 |
endTest = &(simnfo->statusName[nameLength - 5]); |
727 |
if( !strcmp( endTest, ".bass" ) ){ |
728 |
strcpy( endTest, ".stat" ); |
729 |
} |
730 |
else if( !strcmp( endTest, ".BASS" ) ){ |
731 |
strcpy( endTest, ".stat" ); |
732 |
} |
733 |
else{ |
734 |
endTest = &(simnfo->statusName[nameLength - 4]); |
735 |
if( !strcmp( endTest, ".bss" ) ){ |
736 |
strcpy( endTest, ".stat" ); |
737 |
} |
738 |
else if( !strcmp( endTest, ".mdl" ) ){ |
739 |
strcpy( endTest, ".stat" ); |
740 |
} |
741 |
else{ |
742 |
strcat( simnfo->statusName, ".stat" ); |
743 |
} |
744 |
} |
745 |
|
746 |
#ifdef IS_MPI |
747 |
} |
748 |
#endif // is_mpi |
749 |
|
750 |
// set the status, sample, and themal kick times |
751 |
|
752 |
if( the_globals->haveSampleTime() ){ |
753 |
simnfo->sampleTime = the_globals->getSampleTime(); |
754 |
simnfo->statusTime = simnfo->sampleTime; |
755 |
simnfo->thermalTime = simnfo->sampleTime; |
756 |
} |
757 |
else{ |
758 |
simnfo->sampleTime = the_globals->getRunTime(); |
759 |
simnfo->statusTime = simnfo->sampleTime; |
760 |
simnfo->thermalTime = simnfo->sampleTime; |
761 |
} |
762 |
|
763 |
if( the_globals->haveStatusTime() ){ |
764 |
simnfo->statusTime = the_globals->getStatusTime(); |
765 |
} |
766 |
|
767 |
if( the_globals->haveThermalTime() ){ |
768 |
simnfo->thermalTime = the_globals->getThermalTime(); |
769 |
} |
770 |
|
771 |
// check for the temperature set flag |
772 |
|
773 |
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
774 |
|
775 |
|
776 |
// make the integrator |
777 |
|
778 |
|
779 |
NVT* myNVT = NULL; |
780 |
switch( ensembleCase ){ |
781 |
|
782 |
case NVE_ENS: |
783 |
new NVE( simnfo, the_ff ); |
784 |
break; |
785 |
|
786 |
case NVT_ENS: |
787 |
myNVT = new NVT( simnfo, the_ff ); |
788 |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
789 |
|
790 |
if (the_globals->haveTauThermostat()) |
791 |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
792 |
// else if (the_globals->haveQmass()) |
793 |
// myNVT->setQmass(the_globals->getQmass()); |
794 |
else { |
795 |
sprintf( painCave.errMsg, |
796 |
"SimSetup error: If you use the NVT\n" |
797 |
" ensemble, you must set either tauThermostat or qMass.\n" |
798 |
" Neither of these was found in the BASS file.\n"); |
799 |
painCave.isFatal = 1; |
800 |
simError(); |
801 |
} |
802 |
break; |
803 |
|
804 |
default: |
805 |
sprintf( painCave.errMsg, |
806 |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
807 |
painCave.isFatal = 1; |
808 |
simError(); |
809 |
} |
810 |
|
811 |
|
812 |
#ifdef IS_MPI |
813 |
mpiSim->mpiRefresh(); |
814 |
#endif |
815 |
|
816 |
// initialize the Fortran |
817 |
|
818 |
|
819 |
simnfo->refreshSim(); |
820 |
|
821 |
if( !strcmp( simnfo->mixingRule, "standard") ){ |
822 |
the_ff->initForceField( LB_MIXING_RULE ); |
823 |
} |
824 |
else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
825 |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
826 |
} |
827 |
else{ |
828 |
sprintf( painCave.errMsg, |
829 |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
830 |
simnfo->mixingRule ); |
831 |
painCave.isFatal = 1; |
832 |
simError(); |
833 |
} |
834 |
|
835 |
|
836 |
#ifdef IS_MPI |
837 |
strcpy( checkPointMsg, |
838 |
"Successfully intialized the mixingRule for Fortran." ); |
839 |
MPIcheckPoint(); |
840 |
#endif // is_mpi |
841 |
} |
842 |
|
843 |
|
844 |
void SimSetup::makeMolecules( void ){ |
845 |
|
846 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
847 |
molInit info; |
848 |
DirectionalAtom* dAtom; |
849 |
LinkedAssign* extras; |
850 |
LinkedAssign* current_extra; |
851 |
AtomStamp* currentAtom; |
852 |
BondStamp* currentBond; |
853 |
BendStamp* currentBend; |
854 |
TorsionStamp* currentTorsion; |
855 |
|
856 |
bond_pair* theBonds; |
857 |
bend_set* theBends; |
858 |
torsion_set* theTorsions; |
859 |
|
860 |
|
861 |
//init the forceField paramters |
862 |
|
863 |
the_ff->readParams(); |
864 |
|
865 |
|
866 |
// init the atoms |
867 |
|
868 |
double ux, uy, uz, u, uSqr; |
869 |
|
870 |
atomOffset = 0; |
871 |
excludeOffset = 0; |
872 |
for(i=0; i<simnfo->n_mol; i++){ |
873 |
|
874 |
stampID = the_molecules[i].getStampID(); |
875 |
|
876 |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
877 |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
878 |
info.nBends = comp_stamps[stampID]->getNBends(); |
879 |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
880 |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
881 |
|
882 |
info.myAtoms = &the_atoms[atomOffset]; |
883 |
info.myExcludes = &the_excludes[excludeOffset]; |
884 |
info.myBonds = new Bond*[info.nBonds]; |
885 |
info.myBends = new Bend*[info.nBends]; |
886 |
info.myTorsions = new Torsion*[info.nTorsions]; |
887 |
|
888 |
theBonds = new bond_pair[info.nBonds]; |
889 |
theBends = new bend_set[info.nBends]; |
890 |
theTorsions = new torsion_set[info.nTorsions]; |
891 |
|
892 |
// make the Atoms |
893 |
|
894 |
for(j=0; j<info.nAtoms; j++){ |
895 |
|
896 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
897 |
if( currentAtom->haveOrientation() ){ |
898 |
|
899 |
dAtom = new DirectionalAtom(j + atomOffset); |
900 |
simnfo->n_oriented++; |
901 |
info.myAtoms[j] = dAtom; |
902 |
|
903 |
ux = currentAtom->getOrntX(); |
904 |
uy = currentAtom->getOrntY(); |
905 |
uz = currentAtom->getOrntZ(); |
906 |
|
907 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
908 |
|
909 |
u = sqrt( uSqr ); |
910 |
ux = ux / u; |
911 |
uy = uy / u; |
912 |
uz = uz / u; |
913 |
|
914 |
dAtom->setSUx( ux ); |
915 |
dAtom->setSUy( uy ); |
916 |
dAtom->setSUz( uz ); |
917 |
} |
918 |
else{ |
919 |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
920 |
} |
921 |
info.myAtoms[j]->setType( currentAtom->getType() ); |
922 |
|
923 |
#ifdef IS_MPI |
924 |
|
925 |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
926 |
|
927 |
#endif // is_mpi |
928 |
} |
929 |
|
930 |
// make the bonds |
931 |
for(j=0; j<info.nBonds; j++){ |
932 |
|
933 |
currentBond = comp_stamps[stampID]->getBond( j ); |
934 |
theBonds[j].a = currentBond->getA() + atomOffset; |
935 |
theBonds[j].b = currentBond->getB() + atomOffset; |
936 |
|
937 |
exI = theBonds[j].a; |
938 |
exJ = theBonds[j].b; |
939 |
|
940 |
// exclude_I must always be the smaller of the pair |
941 |
if( exI > exJ ){ |
942 |
tempEx = exI; |
943 |
exI = exJ; |
944 |
exJ = tempEx; |
945 |
} |
946 |
#ifdef IS_MPI |
947 |
tempEx = exI; |
948 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
949 |
tempEx = exJ; |
950 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
951 |
|
952 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
953 |
#else // isn't MPI |
954 |
|
955 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
956 |
#endif //is_mpi |
957 |
} |
958 |
excludeOffset += info.nBonds; |
959 |
|
960 |
//make the bends |
961 |
for(j=0; j<info.nBends; j++){ |
962 |
|
963 |
currentBend = comp_stamps[stampID]->getBend( j ); |
964 |
theBends[j].a = currentBend->getA() + atomOffset; |
965 |
theBends[j].b = currentBend->getB() + atomOffset; |
966 |
theBends[j].c = currentBend->getC() + atomOffset; |
967 |
|
968 |
if( currentBend->haveExtras() ){ |
969 |
|
970 |
extras = currentBend->getExtras(); |
971 |
current_extra = extras; |
972 |
|
973 |
while( current_extra != NULL ){ |
974 |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
975 |
|
976 |
switch( current_extra->getType() ){ |
977 |
|
978 |
case 0: |
979 |
theBends[j].ghost = |
980 |
current_extra->getInt() + atomOffset; |
981 |
theBends[j].isGhost = 1; |
982 |
break; |
983 |
|
984 |
case 1: |
985 |
theBends[j].ghost = |
986 |
(int)current_extra->getDouble() + atomOffset; |
987 |
theBends[j].isGhost = 1; |
988 |
break; |
989 |
|
990 |
default: |
991 |
sprintf( painCave.errMsg, |
992 |
"SimSetup Error: ghostVectorSource was neither a " |
993 |
"double nor an int.\n" |
994 |
"-->Bend[%d] in %s\n", |
995 |
j, comp_stamps[stampID]->getID() ); |
996 |
painCave.isFatal = 1; |
997 |
simError(); |
998 |
} |
999 |
} |
1000 |
|
1001 |
else{ |
1002 |
|
1003 |
sprintf( painCave.errMsg, |
1004 |
"SimSetup Error: unhandled bend assignment:\n" |
1005 |
" -->%s in Bend[%d] in %s\n", |
1006 |
current_extra->getlhs(), |
1007 |
j, comp_stamps[stampID]->getID() ); |
1008 |
painCave.isFatal = 1; |
1009 |
simError(); |
1010 |
} |
1011 |
|
1012 |
current_extra = current_extra->getNext(); |
1013 |
} |
1014 |
} |
1015 |
|
1016 |
if( !theBends[j].isGhost ){ |
1017 |
|
1018 |
exI = theBends[j].a; |
1019 |
exJ = theBends[j].c; |
1020 |
} |
1021 |
else{ |
1022 |
|
1023 |
exI = theBends[j].a; |
1024 |
exJ = theBends[j].b; |
1025 |
} |
1026 |
|
1027 |
// exclude_I must always be the smaller of the pair |
1028 |
if( exI > exJ ){ |
1029 |
tempEx = exI; |
1030 |
exI = exJ; |
1031 |
exJ = tempEx; |
1032 |
} |
1033 |
#ifdef IS_MPI |
1034 |
tempEx = exI; |
1035 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1036 |
tempEx = exJ; |
1037 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1038 |
|
1039 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1040 |
#else // isn't MPI |
1041 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1042 |
#endif //is_mpi |
1043 |
} |
1044 |
excludeOffset += info.nBends; |
1045 |
|
1046 |
for(j=0; j<info.nTorsions; j++){ |
1047 |
|
1048 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1049 |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1050 |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1051 |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1052 |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1053 |
|
1054 |
exI = theTorsions[j].a; |
1055 |
exJ = theTorsions[j].d; |
1056 |
|
1057 |
// exclude_I must always be the smaller of the pair |
1058 |
if( exI > exJ ){ |
1059 |
tempEx = exI; |
1060 |
exI = exJ; |
1061 |
exJ = tempEx; |
1062 |
} |
1063 |
#ifdef IS_MPI |
1064 |
tempEx = exI; |
1065 |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1066 |
tempEx = exJ; |
1067 |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1068 |
|
1069 |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1070 |
#else // isn't MPI |
1071 |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1072 |
#endif //is_mpi |
1073 |
} |
1074 |
excludeOffset += info.nTorsions; |
1075 |
|
1076 |
|
1077 |
// send the arrays off to the forceField for init. |
1078 |
|
1079 |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1080 |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1081 |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1082 |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1083 |
|
1084 |
|
1085 |
the_molecules[i].initialize( info ); |
1086 |
|
1087 |
|
1088 |
atomOffset += info.nAtoms; |
1089 |
delete[] theBonds; |
1090 |
delete[] theBends; |
1091 |
delete[] theTorsions; |
1092 |
} |
1093 |
|
1094 |
#ifdef IS_MPI |
1095 |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1096 |
MPIcheckPoint(); |
1097 |
#endif // is_mpi |
1098 |
|
1099 |
// clean up the forcefield |
1100 |
the_ff->calcRcut(); |
1101 |
the_ff->cleanMe(); |
1102 |
|
1103 |
} |
1104 |
|
1105 |
void SimSetup::initFromBass( void ){ |
1106 |
|
1107 |
int i, j, k; |
1108 |
int n_cells; |
1109 |
double cellx, celly, cellz; |
1110 |
double temp1, temp2, temp3; |
1111 |
int n_per_extra; |
1112 |
int n_extra; |
1113 |
int have_extra, done; |
1114 |
|
1115 |
temp1 = (double)tot_nmol / 4.0; |
1116 |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1117 |
temp3 = ceil( temp2 ); |
1118 |
|
1119 |
have_extra =0; |
1120 |
if( temp2 < temp3 ){ // we have a non-complete lattice |
1121 |
have_extra =1; |
1122 |
|
1123 |
n_cells = (int)temp3 - 1; |
1124 |
cellx = simnfo->boxLx / temp3; |
1125 |
celly = simnfo->boxLy / temp3; |
1126 |
cellz = simnfo->boxLz / temp3; |
1127 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1128 |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1129 |
n_per_extra = (int)ceil( temp1 ); |
1130 |
|
1131 |
if( n_per_extra > 4){ |
1132 |
sprintf( painCave.errMsg, |
1133 |
"SimSetup error. There has been an error in constructing" |
1134 |
" the non-complete lattice.\n" ); |
1135 |
painCave.isFatal = 1; |
1136 |
simError(); |
1137 |
} |
1138 |
} |
1139 |
else{ |
1140 |
n_cells = (int)temp3; |
1141 |
cellx = simnfo->boxLx / temp3; |
1142 |
celly = simnfo->boxLy / temp3; |
1143 |
cellz = simnfo->boxLz / temp3; |
1144 |
} |
1145 |
|
1146 |
current_mol = 0; |
1147 |
current_comp_mol = 0; |
1148 |
current_comp = 0; |
1149 |
current_atom_ndx = 0; |
1150 |
|
1151 |
for( i=0; i < n_cells ; i++ ){ |
1152 |
for( j=0; j < n_cells; j++ ){ |
1153 |
for( k=0; k < n_cells; k++ ){ |
1154 |
|
1155 |
makeElement( i * cellx, |
1156 |
j * celly, |
1157 |
k * cellz ); |
1158 |
|
1159 |
makeElement( i * cellx + 0.5 * cellx, |
1160 |
j * celly + 0.5 * celly, |
1161 |
k * cellz ); |
1162 |
|
1163 |
makeElement( i * cellx, |
1164 |
j * celly + 0.5 * celly, |
1165 |
k * cellz + 0.5 * cellz ); |
1166 |
|
1167 |
makeElement( i * cellx + 0.5 * cellx, |
1168 |
j * celly, |
1169 |
k * cellz + 0.5 * cellz ); |
1170 |
} |
1171 |
} |
1172 |
} |
1173 |
|
1174 |
if( have_extra ){ |
1175 |
done = 0; |
1176 |
|
1177 |
int start_ndx; |
1178 |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
1179 |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
1180 |
|
1181 |
if( i < n_cells ){ |
1182 |
|
1183 |
if( j < n_cells ){ |
1184 |
start_ndx = n_cells; |
1185 |
} |
1186 |
else start_ndx = 0; |
1187 |
} |
1188 |
else start_ndx = 0; |
1189 |
|
1190 |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1191 |
|
1192 |
makeElement( i * cellx, |
1193 |
j * celly, |
1194 |
k * cellz ); |
1195 |
done = ( current_mol >= tot_nmol ); |
1196 |
|
1197 |
if( !done && n_per_extra > 1 ){ |
1198 |
makeElement( i * cellx + 0.5 * cellx, |
1199 |
j * celly + 0.5 * celly, |
1200 |
k * cellz ); |
1201 |
done = ( current_mol >= tot_nmol ); |
1202 |
} |
1203 |
|
1204 |
if( !done && n_per_extra > 2){ |
1205 |
makeElement( i * cellx, |
1206 |
j * celly + 0.5 * celly, |
1207 |
k * cellz + 0.5 * cellz ); |
1208 |
done = ( current_mol >= tot_nmol ); |
1209 |
} |
1210 |
|
1211 |
if( !done && n_per_extra > 3){ |
1212 |
makeElement( i * cellx + 0.5 * cellx, |
1213 |
j * celly, |
1214 |
k * cellz + 0.5 * cellz ); |
1215 |
done = ( current_mol >= tot_nmol ); |
1216 |
} |
1217 |
} |
1218 |
} |
1219 |
} |
1220 |
} |
1221 |
|
1222 |
|
1223 |
for( i=0; i<simnfo->n_atoms; i++ ){ |
1224 |
simnfo->atoms[i]->set_vx( 0.0 ); |
1225 |
simnfo->atoms[i]->set_vy( 0.0 ); |
1226 |
simnfo->atoms[i]->set_vz( 0.0 ); |
1227 |
} |
1228 |
} |
1229 |
|
1230 |
void SimSetup::makeElement( double x, double y, double z ){ |
1231 |
|
1232 |
int k; |
1233 |
AtomStamp* current_atom; |
1234 |
DirectionalAtom* dAtom; |
1235 |
double rotMat[3][3]; |
1236 |
|
1237 |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1238 |
|
1239 |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
1240 |
if( !current_atom->havePosition() ){ |
1241 |
sprintf( painCave.errMsg, |
1242 |
"SimSetup:initFromBass error.\n" |
1243 |
"\tComponent %s, atom %s does not have a position specified.\n" |
1244 |
"\tThe initialization routine is unable to give a start" |
1245 |
" position.\n", |
1246 |
comp_stamps[current_comp]->getID(), |
1247 |
current_atom->getType() ); |
1248 |
painCave.isFatal = 1; |
1249 |
simError(); |
1250 |
} |
1251 |
|
1252 |
the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1253 |
the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1254 |
the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1255 |
|
1256 |
if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1257 |
|
1258 |
dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1259 |
|
1260 |
rotMat[0][0] = 1.0; |
1261 |
rotMat[0][1] = 0.0; |
1262 |
rotMat[0][2] = 0.0; |
1263 |
|
1264 |
rotMat[1][0] = 0.0; |
1265 |
rotMat[1][1] = 1.0; |
1266 |
rotMat[1][2] = 0.0; |
1267 |
|
1268 |
rotMat[2][0] = 0.0; |
1269 |
rotMat[2][1] = 0.0; |
1270 |
rotMat[2][2] = 1.0; |
1271 |
|
1272 |
dAtom->setA( rotMat ); |
1273 |
} |
1274 |
|
1275 |
current_atom_ndx++; |
1276 |
} |
1277 |
|
1278 |
current_mol++; |
1279 |
current_comp_mol++; |
1280 |
|
1281 |
if( current_comp_mol >= components_nmol[current_comp] ){ |
1282 |
|
1283 |
current_comp_mol = 0; |
1284 |
current_comp++; |
1285 |
} |
1286 |
} |