1 |
#include <algorithm> |
2 |
#include <cstdlib> |
3 |
#include <iostream> |
4 |
#include <cmath> |
5 |
#include <string> |
6 |
|
7 |
#include "SimSetup.hpp" |
8 |
#include "ReadWrite.hpp" |
9 |
#include "parse_me.h" |
10 |
#include "Integrator.hpp" |
11 |
#include "simError.h" |
12 |
|
13 |
#ifdef IS_MPI |
14 |
#include "mpiBASS.h" |
15 |
#include "mpiSimulation.hpp" |
16 |
#endif |
17 |
|
18 |
// some defines for ensemble and Forcefield cases |
19 |
|
20 |
#define NVE_ENS 0 |
21 |
#define NVT_ENS 1 |
22 |
#define NPTi_ENS 2 |
23 |
#define NPTf_ENS 3 |
24 |
#define NPTim_ENS 4 |
25 |
#define NPTfm_ENS 5 |
26 |
|
27 |
#define FF_DUFF 0 |
28 |
#define FF_LJ 1 |
29 |
#define FF_EAM 2 |
30 |
|
31 |
using namespace std; |
32 |
|
33 |
SimSetup::SimSetup(){ |
34 |
|
35 |
isInfoArray = 0; |
36 |
nInfo = 1; |
37 |
|
38 |
stamps = new MakeStamps(); |
39 |
globals = new Globals(); |
40 |
|
41 |
|
42 |
#ifdef IS_MPI |
43 |
strcpy( checkPointMsg, "SimSetup creation successful" ); |
44 |
MPIcheckPoint(); |
45 |
#endif // IS_MPI |
46 |
} |
47 |
|
48 |
SimSetup::~SimSetup(){ |
49 |
delete stamps; |
50 |
delete globals; |
51 |
} |
52 |
|
53 |
void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
54 |
info = the_info; |
55 |
nInfo = theNinfo; |
56 |
isInfoArray = 1; |
57 |
} |
58 |
|
59 |
|
60 |
void SimSetup::parseFile( char* fileName ){ |
61 |
|
62 |
#ifdef IS_MPI |
63 |
if( worldRank == 0 ){ |
64 |
#endif // is_mpi |
65 |
|
66 |
inFileName = fileName; |
67 |
set_interface_stamps( stamps, globals ); |
68 |
|
69 |
#ifdef IS_MPI |
70 |
mpiEventInit(); |
71 |
#endif |
72 |
|
73 |
yacc_BASS( fileName ); |
74 |
|
75 |
#ifdef IS_MPI |
76 |
throwMPIEvent(NULL); |
77 |
} |
78 |
else receiveParse(); |
79 |
#endif |
80 |
|
81 |
} |
82 |
|
83 |
#ifdef IS_MPI |
84 |
void SimSetup::receiveParse(void){ |
85 |
|
86 |
set_interface_stamps( stamps, globals ); |
87 |
mpiEventInit(); |
88 |
MPIcheckPoint(); |
89 |
mpiEventLoop(); |
90 |
|
91 |
} |
92 |
|
93 |
#endif // is_mpi |
94 |
|
95 |
void SimSetup::createSim(void){ |
96 |
|
97 |
int i, j, k, globalAtomIndex; |
98 |
|
99 |
// gather all of the information from the Bass file |
100 |
|
101 |
std::cerr << "gathering info\n"; |
102 |
|
103 |
gatherInfo(); |
104 |
|
105 |
// creation of complex system objects |
106 |
|
107 |
std::cerr << "creating system objects\n"; |
108 |
|
109 |
sysObjectsCreation(); |
110 |
|
111 |
// check on the post processing info |
112 |
|
113 |
std::cerr << "performing final info check.\n"; |
114 |
|
115 |
finalInfoCheck(); |
116 |
|
117 |
// initialize the system coordinates |
118 |
|
119 |
std::cerr << "about to init coords\n"; |
120 |
|
121 |
if( !isInfoArray ) initSystemCoords(); |
122 |
|
123 |
// make the output filenames |
124 |
|
125 |
makeOutNames(); |
126 |
|
127 |
// make the integrator |
128 |
|
129 |
makeIntegrator(); |
130 |
|
131 |
#ifdef IS_MPI |
132 |
mpiSim->mpiRefresh(); |
133 |
#endif |
134 |
|
135 |
// initialize the Fortran |
136 |
|
137 |
initFortran(); |
138 |
|
139 |
|
140 |
|
141 |
} |
142 |
|
143 |
|
144 |
void SimSetup::makeMolecules( void ){ |
145 |
|
146 |
int k,l; |
147 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
148 |
molInit molInfo; |
149 |
DirectionalAtom* dAtom; |
150 |
LinkedAssign* extras; |
151 |
LinkedAssign* current_extra; |
152 |
AtomStamp* currentAtom; |
153 |
BondStamp* currentBond; |
154 |
BendStamp* currentBend; |
155 |
TorsionStamp* currentTorsion; |
156 |
|
157 |
bond_pair* theBonds; |
158 |
bend_set* theBends; |
159 |
torsion_set* theTorsions; |
160 |
|
161 |
|
162 |
//init the forceField paramters |
163 |
|
164 |
the_ff->readParams(); |
165 |
|
166 |
|
167 |
// init the atoms |
168 |
|
169 |
double ux, uy, uz, u, uSqr; |
170 |
|
171 |
for(k=0; k<nInfo; k++){ |
172 |
|
173 |
the_ff->setSimInfo( &(info[k]) ); |
174 |
|
175 |
atomOffset = 0; |
176 |
excludeOffset = 0; |
177 |
for(i=0; i<info[k].n_mol; i++){ |
178 |
|
179 |
stampID = info[k].molecules[i].getStampID(); |
180 |
|
181 |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
182 |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
183 |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
184 |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
185 |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
186 |
|
187 |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
188 |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
189 |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
190 |
molInfo.myBends = new Bend*[molInfo.nBends]; |
191 |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
192 |
|
193 |
theBonds = new bond_pair[molInfo.nBonds]; |
194 |
theBends = new bend_set[molInfo.nBends]; |
195 |
theTorsions = new torsion_set[molInfo.nTorsions]; |
196 |
|
197 |
// make the Atoms |
198 |
|
199 |
for(j=0; j<molInfo.nAtoms; j++){ |
200 |
|
201 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
202 |
if( currentAtom->haveOrientation() ){ |
203 |
|
204 |
dAtom = new DirectionalAtom( (j + atomOffset), |
205 |
info[k].getConfiguration() ); |
206 |
info[k].n_oriented++; |
207 |
molInfo.myAtoms[j] = dAtom; |
208 |
|
209 |
ux = currentAtom->getOrntX(); |
210 |
uy = currentAtom->getOrntY(); |
211 |
uz = currentAtom->getOrntZ(); |
212 |
|
213 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
214 |
|
215 |
u = sqrt( uSqr ); |
216 |
ux = ux / u; |
217 |
uy = uy / u; |
218 |
uz = uz / u; |
219 |
|
220 |
dAtom->setSUx( ux ); |
221 |
dAtom->setSUy( uy ); |
222 |
dAtom->setSUz( uz ); |
223 |
} |
224 |
else{ |
225 |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
226 |
info[k].getConfiguration() ); |
227 |
} |
228 |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
229 |
|
230 |
#ifdef IS_MPI |
231 |
|
232 |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
233 |
|
234 |
#endif // is_mpi |
235 |
} |
236 |
|
237 |
// make the bonds |
238 |
for(j=0; j<molInfo.nBonds; j++){ |
239 |
|
240 |
currentBond = comp_stamps[stampID]->getBond( j ); |
241 |
theBonds[j].a = currentBond->getA() + atomOffset; |
242 |
theBonds[j].b = currentBond->getB() + atomOffset; |
243 |
|
244 |
exI = theBonds[j].a; |
245 |
exJ = theBonds[j].b; |
246 |
|
247 |
// exclude_I must always be the smaller of the pair |
248 |
if( exI > exJ ){ |
249 |
tempEx = exI; |
250 |
exI = exJ; |
251 |
exJ = tempEx; |
252 |
} |
253 |
#ifdef IS_MPI |
254 |
tempEx = exI; |
255 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
256 |
tempEx = exJ; |
257 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
258 |
|
259 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
260 |
#else // isn't MPI |
261 |
|
262 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
263 |
#endif //is_mpi |
264 |
} |
265 |
excludeOffset += molInfo.nBonds; |
266 |
|
267 |
//make the bends |
268 |
for(j=0; j<molInfo.nBends; j++){ |
269 |
|
270 |
currentBend = comp_stamps[stampID]->getBend( j ); |
271 |
theBends[j].a = currentBend->getA() + atomOffset; |
272 |
theBends[j].b = currentBend->getB() + atomOffset; |
273 |
theBends[j].c = currentBend->getC() + atomOffset; |
274 |
|
275 |
if( currentBend->haveExtras() ){ |
276 |
|
277 |
extras = currentBend->getExtras(); |
278 |
current_extra = extras; |
279 |
|
280 |
while( current_extra != NULL ){ |
281 |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
282 |
|
283 |
switch( current_extra->getType() ){ |
284 |
|
285 |
case 0: |
286 |
theBends[j].ghost = |
287 |
current_extra->getInt() + atomOffset; |
288 |
theBends[j].isGhost = 1; |
289 |
break; |
290 |
|
291 |
case 1: |
292 |
theBends[j].ghost = |
293 |
(int)current_extra->getDouble() + atomOffset; |
294 |
theBends[j].isGhost = 1; |
295 |
break; |
296 |
|
297 |
default: |
298 |
sprintf( painCave.errMsg, |
299 |
"SimSetup Error: ghostVectorSource was neither a " |
300 |
"double nor an int.\n" |
301 |
"-->Bend[%d] in %s\n", |
302 |
j, comp_stamps[stampID]->getID() ); |
303 |
painCave.isFatal = 1; |
304 |
simError(); |
305 |
} |
306 |
} |
307 |
|
308 |
else{ |
309 |
|
310 |
sprintf( painCave.errMsg, |
311 |
"SimSetup Error: unhandled bend assignment:\n" |
312 |
" -->%s in Bend[%d] in %s\n", |
313 |
current_extra->getlhs(), |
314 |
j, comp_stamps[stampID]->getID() ); |
315 |
painCave.isFatal = 1; |
316 |
simError(); |
317 |
} |
318 |
|
319 |
current_extra = current_extra->getNext(); |
320 |
} |
321 |
} |
322 |
|
323 |
if( !theBends[j].isGhost ){ |
324 |
|
325 |
exI = theBends[j].a; |
326 |
exJ = theBends[j].c; |
327 |
} |
328 |
else{ |
329 |
|
330 |
exI = theBends[j].a; |
331 |
exJ = theBends[j].b; |
332 |
} |
333 |
|
334 |
// exclude_I must always be the smaller of the pair |
335 |
if( exI > exJ ){ |
336 |
tempEx = exI; |
337 |
exI = exJ; |
338 |
exJ = tempEx; |
339 |
} |
340 |
#ifdef IS_MPI |
341 |
tempEx = exI; |
342 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
343 |
tempEx = exJ; |
344 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
345 |
|
346 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
347 |
#else // isn't MPI |
348 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
349 |
#endif //is_mpi |
350 |
} |
351 |
excludeOffset += molInfo.nBends; |
352 |
|
353 |
for(j=0; j<molInfo.nTorsions; j++){ |
354 |
|
355 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
356 |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
357 |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
358 |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
359 |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
360 |
|
361 |
exI = theTorsions[j].a; |
362 |
exJ = theTorsions[j].d; |
363 |
|
364 |
// exclude_I must always be the smaller of the pair |
365 |
if( exI > exJ ){ |
366 |
tempEx = exI; |
367 |
exI = exJ; |
368 |
exJ = tempEx; |
369 |
} |
370 |
#ifdef IS_MPI |
371 |
tempEx = exI; |
372 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
373 |
tempEx = exJ; |
374 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
375 |
|
376 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
377 |
#else // isn't MPI |
378 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
379 |
#endif //is_mpi |
380 |
} |
381 |
excludeOffset += molInfo.nTorsions; |
382 |
|
383 |
|
384 |
// send the arrays off to the forceField for init. |
385 |
|
386 |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
387 |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
388 |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
389 |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
390 |
|
391 |
|
392 |
info[k].molecules[i].initialize( molInfo ); |
393 |
|
394 |
|
395 |
atomOffset += molInfo.nAtoms; |
396 |
delete[] theBonds; |
397 |
delete[] theBends; |
398 |
delete[] theTorsions; |
399 |
} |
400 |
} |
401 |
|
402 |
#ifdef IS_MPI |
403 |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
404 |
MPIcheckPoint(); |
405 |
#endif // is_mpi |
406 |
|
407 |
// clean up the forcefield |
408 |
|
409 |
the_ff->calcRcut(); |
410 |
the_ff->cleanMe(); |
411 |
|
412 |
} |
413 |
|
414 |
void SimSetup::initFromBass( void ){ |
415 |
|
416 |
int i, j, k; |
417 |
int n_cells; |
418 |
double cellx, celly, cellz; |
419 |
double temp1, temp2, temp3; |
420 |
int n_per_extra; |
421 |
int n_extra; |
422 |
int have_extra, done; |
423 |
|
424 |
double vel[3]; |
425 |
vel[0] = 0.0; |
426 |
vel[1] = 0.0; |
427 |
vel[2] = 0.0; |
428 |
|
429 |
temp1 = (double)tot_nmol / 4.0; |
430 |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
431 |
temp3 = ceil( temp2 ); |
432 |
|
433 |
have_extra =0; |
434 |
if( temp2 < temp3 ){ // we have a non-complete lattice |
435 |
have_extra =1; |
436 |
|
437 |
n_cells = (int)temp3 - 1; |
438 |
cellx = info[0].boxL[0] / temp3; |
439 |
celly = info[0].boxL[1] / temp3; |
440 |
cellz = info[0].boxL[2] / temp3; |
441 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
442 |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
443 |
n_per_extra = (int)ceil( temp1 ); |
444 |
|
445 |
if( n_per_extra > 4){ |
446 |
sprintf( painCave.errMsg, |
447 |
"SimSetup error. There has been an error in constructing" |
448 |
" the non-complete lattice.\n" ); |
449 |
painCave.isFatal = 1; |
450 |
simError(); |
451 |
} |
452 |
} |
453 |
else{ |
454 |
n_cells = (int)temp3; |
455 |
cellx = info[0].boxL[0] / temp3; |
456 |
celly = info[0].boxL[1] / temp3; |
457 |
cellz = info[0].boxL[2] / temp3; |
458 |
} |
459 |
|
460 |
current_mol = 0; |
461 |
current_comp_mol = 0; |
462 |
current_comp = 0; |
463 |
current_atom_ndx = 0; |
464 |
|
465 |
for( i=0; i < n_cells ; i++ ){ |
466 |
for( j=0; j < n_cells; j++ ){ |
467 |
for( k=0; k < n_cells; k++ ){ |
468 |
|
469 |
makeElement( i * cellx, |
470 |
j * celly, |
471 |
k * cellz ); |
472 |
|
473 |
makeElement( i * cellx + 0.5 * cellx, |
474 |
j * celly + 0.5 * celly, |
475 |
k * cellz ); |
476 |
|
477 |
makeElement( i * cellx, |
478 |
j * celly + 0.5 * celly, |
479 |
k * cellz + 0.5 * cellz ); |
480 |
|
481 |
makeElement( i * cellx + 0.5 * cellx, |
482 |
j * celly, |
483 |
k * cellz + 0.5 * cellz ); |
484 |
} |
485 |
} |
486 |
} |
487 |
|
488 |
if( have_extra ){ |
489 |
done = 0; |
490 |
|
491 |
int start_ndx; |
492 |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
493 |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
494 |
|
495 |
if( i < n_cells ){ |
496 |
|
497 |
if( j < n_cells ){ |
498 |
start_ndx = n_cells; |
499 |
} |
500 |
else start_ndx = 0; |
501 |
} |
502 |
else start_ndx = 0; |
503 |
|
504 |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
505 |
|
506 |
makeElement( i * cellx, |
507 |
j * celly, |
508 |
k * cellz ); |
509 |
done = ( current_mol >= tot_nmol ); |
510 |
|
511 |
if( !done && n_per_extra > 1 ){ |
512 |
makeElement( i * cellx + 0.5 * cellx, |
513 |
j * celly + 0.5 * celly, |
514 |
k * cellz ); |
515 |
done = ( current_mol >= tot_nmol ); |
516 |
} |
517 |
|
518 |
if( !done && n_per_extra > 2){ |
519 |
makeElement( i * cellx, |
520 |
j * celly + 0.5 * celly, |
521 |
k * cellz + 0.5 * cellz ); |
522 |
done = ( current_mol >= tot_nmol ); |
523 |
} |
524 |
|
525 |
if( !done && n_per_extra > 3){ |
526 |
makeElement( i * cellx + 0.5 * cellx, |
527 |
j * celly, |
528 |
k * cellz + 0.5 * cellz ); |
529 |
done = ( current_mol >= tot_nmol ); |
530 |
} |
531 |
} |
532 |
} |
533 |
} |
534 |
} |
535 |
|
536 |
for( i=0; i<info[0].n_atoms; i++ ){ |
537 |
info[0].atoms[i]->setVel( vel ); |
538 |
} |
539 |
} |
540 |
|
541 |
void SimSetup::makeElement( double x, double y, double z ){ |
542 |
|
543 |
int k; |
544 |
AtomStamp* current_atom; |
545 |
DirectionalAtom* dAtom; |
546 |
double rotMat[3][3]; |
547 |
double pos[3]; |
548 |
|
549 |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
550 |
|
551 |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
552 |
if( !current_atom->havePosition() ){ |
553 |
sprintf( painCave.errMsg, |
554 |
"SimSetup:initFromBass error.\n" |
555 |
"\tComponent %s, atom %s does not have a position specified.\n" |
556 |
"\tThe initialization routine is unable to give a start" |
557 |
" position.\n", |
558 |
comp_stamps[current_comp]->getID(), |
559 |
current_atom->getType() ); |
560 |
painCave.isFatal = 1; |
561 |
simError(); |
562 |
} |
563 |
|
564 |
pos[0] = x + current_atom->getPosX(); |
565 |
pos[1] = y + current_atom->getPosY(); |
566 |
pos[2] = z + current_atom->getPosZ(); |
567 |
|
568 |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
569 |
|
570 |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
571 |
|
572 |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
573 |
|
574 |
rotMat[0][0] = 1.0; |
575 |
rotMat[0][1] = 0.0; |
576 |
rotMat[0][2] = 0.0; |
577 |
|
578 |
rotMat[1][0] = 0.0; |
579 |
rotMat[1][1] = 1.0; |
580 |
rotMat[1][2] = 0.0; |
581 |
|
582 |
rotMat[2][0] = 0.0; |
583 |
rotMat[2][1] = 0.0; |
584 |
rotMat[2][2] = 1.0; |
585 |
|
586 |
dAtom->setA( rotMat ); |
587 |
} |
588 |
|
589 |
current_atom_ndx++; |
590 |
} |
591 |
|
592 |
current_mol++; |
593 |
current_comp_mol++; |
594 |
|
595 |
if( current_comp_mol >= components_nmol[current_comp] ){ |
596 |
|
597 |
current_comp_mol = 0; |
598 |
current_comp++; |
599 |
} |
600 |
} |
601 |
|
602 |
|
603 |
void SimSetup::gatherInfo( void ){ |
604 |
int i,j,k; |
605 |
|
606 |
ensembleCase = -1; |
607 |
ffCase = -1; |
608 |
|
609 |
// set the easy ones first |
610 |
|
611 |
for( i=0; i<nInfo; i++){ |
612 |
info[i].target_temp = globals->getTargetTemp(); |
613 |
info[i].dt = globals->getDt(); |
614 |
info[i].run_time = globals->getRunTime(); |
615 |
} |
616 |
n_components = globals->getNComponents(); |
617 |
|
618 |
|
619 |
// get the forceField |
620 |
|
621 |
strcpy( force_field, globals->getForceField() ); |
622 |
|
623 |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
624 |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
625 |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
626 |
else{ |
627 |
sprintf( painCave.errMsg, |
628 |
"SimSetup Error. Unrecognized force field -> %s\n", |
629 |
force_field ); |
630 |
painCave.isFatal = 1; |
631 |
simError(); |
632 |
} |
633 |
|
634 |
// get the ensemble |
635 |
|
636 |
strcpy( ensemble, globals->getEnsemble() ); |
637 |
|
638 |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
639 |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
640 |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
641 |
ensembleCase = NPTi_ENS; |
642 |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
643 |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
644 |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
645 |
else{ |
646 |
sprintf( painCave.errMsg, |
647 |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
648 |
"reverting to NVE for this simulation.\n", |
649 |
ensemble ); |
650 |
painCave.isFatal = 0; |
651 |
simError(); |
652 |
strcpy( ensemble, "NVE" ); |
653 |
ensembleCase = NVE_ENS; |
654 |
} |
655 |
|
656 |
for(i=0; i<nInfo; i++){ |
657 |
|
658 |
strcpy( info[i].ensemble, ensemble ); |
659 |
|
660 |
// get the mixing rule |
661 |
|
662 |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
663 |
info[i].usePBC = globals->getPBC(); |
664 |
} |
665 |
|
666 |
// get the components and calculate the tot_nMol and indvidual n_mol |
667 |
|
668 |
the_components = globals->getComponents(); |
669 |
components_nmol = new int[n_components]; |
670 |
|
671 |
|
672 |
if( !globals->haveNMol() ){ |
673 |
// we don't have the total number of molecules, so we assume it is |
674 |
// given in each component |
675 |
|
676 |
tot_nmol = 0; |
677 |
for( i=0; i<n_components; i++ ){ |
678 |
|
679 |
if( !the_components[i]->haveNMol() ){ |
680 |
// we have a problem |
681 |
sprintf( painCave.errMsg, |
682 |
"SimSetup Error. No global NMol or component NMol" |
683 |
" given. Cannot calculate the number of atoms.\n" ); |
684 |
painCave.isFatal = 1; |
685 |
simError(); |
686 |
} |
687 |
|
688 |
tot_nmol += the_components[i]->getNMol(); |
689 |
components_nmol[i] = the_components[i]->getNMol(); |
690 |
} |
691 |
} |
692 |
else{ |
693 |
sprintf( painCave.errMsg, |
694 |
"SimSetup error.\n" |
695 |
"\tSorry, the ability to specify total" |
696 |
" nMols and then give molfractions in the components\n" |
697 |
"\tis not currently supported." |
698 |
" Please give nMol in the components.\n" ); |
699 |
painCave.isFatal = 1; |
700 |
simError(); |
701 |
} |
702 |
|
703 |
// set the status, sample, and thermal kick times |
704 |
|
705 |
for(i=0; i<nInfo; i++){ |
706 |
|
707 |
if( globals->haveSampleTime() ){ |
708 |
info[i].sampleTime = globals->getSampleTime(); |
709 |
info[i].statusTime = info[i].sampleTime; |
710 |
info[i].thermalTime = info[i].sampleTime; |
711 |
} |
712 |
else{ |
713 |
info[i].sampleTime = globals->getRunTime(); |
714 |
info[i].statusTime = info[i].sampleTime; |
715 |
info[i].thermalTime = info[i].sampleTime; |
716 |
} |
717 |
|
718 |
if( globals->haveStatusTime() ){ |
719 |
info[i].statusTime = globals->getStatusTime(); |
720 |
} |
721 |
|
722 |
if( globals->haveThermalTime() ){ |
723 |
info[i].thermalTime = globals->getThermalTime(); |
724 |
} |
725 |
|
726 |
// check for the temperature set flag |
727 |
|
728 |
if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
729 |
|
730 |
// get some of the tricky things that may still be in the globals |
731 |
|
732 |
double boxVector[3]; |
733 |
if( globals->haveBox() ){ |
734 |
boxVector[0] = globals->getBox(); |
735 |
boxVector[1] = globals->getBox(); |
736 |
boxVector[2] = globals->getBox(); |
737 |
|
738 |
info[i].setBox( boxVector ); |
739 |
} |
740 |
else if( globals->haveDensity() ){ |
741 |
|
742 |
double vol; |
743 |
vol = (double)tot_nmol / globals->getDensity(); |
744 |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
745 |
boxVector[1] = boxVector[0]; |
746 |
boxVector[2] = boxVector[0]; |
747 |
|
748 |
info[i].setBox( boxVector ); |
749 |
} |
750 |
else{ |
751 |
if( !globals->haveBoxX() ){ |
752 |
sprintf( painCave.errMsg, |
753 |
"SimSetup error, no periodic BoxX size given.\n" ); |
754 |
painCave.isFatal = 1; |
755 |
simError(); |
756 |
} |
757 |
boxVector[0] = globals->getBoxX(); |
758 |
|
759 |
if( !globals->haveBoxY() ){ |
760 |
sprintf( painCave.errMsg, |
761 |
"SimSetup error, no periodic BoxY size given.\n" ); |
762 |
painCave.isFatal = 1; |
763 |
simError(); |
764 |
} |
765 |
boxVector[1] = globals->getBoxY(); |
766 |
|
767 |
if( !globals->haveBoxZ() ){ |
768 |
sprintf( painCave.errMsg, |
769 |
"SimSetup error, no periodic BoxZ size given.\n" ); |
770 |
painCave.isFatal = 1; |
771 |
simError(); |
772 |
} |
773 |
boxVector[2] = globals->getBoxZ(); |
774 |
|
775 |
info[i].setBox( boxVector ); |
776 |
} |
777 |
|
778 |
} |
779 |
|
780 |
#ifdef IS_MPI |
781 |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
782 |
MPIcheckPoint(); |
783 |
#endif // is_mpi |
784 |
|
785 |
} |
786 |
|
787 |
|
788 |
void SimSetup::finalInfoCheck( void ){ |
789 |
int index; |
790 |
int usesDipoles; |
791 |
int i; |
792 |
|
793 |
for(i=0; i<nInfo; i++){ |
794 |
// check electrostatic parameters |
795 |
|
796 |
index = 0; |
797 |
usesDipoles = 0; |
798 |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
799 |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
800 |
index++; |
801 |
} |
802 |
|
803 |
#ifdef IS_MPI |
804 |
int myUse = usesDipoles; |
805 |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
806 |
#endif //is_mpi |
807 |
|
808 |
double theEcr, theEst; |
809 |
|
810 |
if (globals->getUseRF() ) { |
811 |
info[i].useReactionField = 1; |
812 |
|
813 |
if( !globals->haveECR() ){ |
814 |
sprintf( painCave.errMsg, |
815 |
"SimSetup Warning: using default value of 1/2 the smallest " |
816 |
"box length for the electrostaticCutoffRadius.\n" |
817 |
"I hope you have a very fast processor!\n"); |
818 |
painCave.isFatal = 0; |
819 |
simError(); |
820 |
double smallest; |
821 |
smallest = info[i].boxL[0]; |
822 |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
823 |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
824 |
theEcr = 0.5 * smallest; |
825 |
} else { |
826 |
theEcr = globals->getECR(); |
827 |
} |
828 |
|
829 |
if( !globals->haveEST() ){ |
830 |
sprintf( painCave.errMsg, |
831 |
"SimSetup Warning: using default value of 0.05 * the " |
832 |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
833 |
); |
834 |
painCave.isFatal = 0; |
835 |
simError(); |
836 |
theEst = 0.05 * theEcr; |
837 |
} else { |
838 |
theEst= globals->getEST(); |
839 |
} |
840 |
|
841 |
info[i].setEcr( theEcr, theEst ); |
842 |
|
843 |
if(!globals->haveDielectric() ){ |
844 |
sprintf( painCave.errMsg, |
845 |
"SimSetup Error: You are trying to use Reaction Field without" |
846 |
"setting a dielectric constant!\n" |
847 |
); |
848 |
painCave.isFatal = 1; |
849 |
simError(); |
850 |
} |
851 |
info[i].dielectric = globals->getDielectric(); |
852 |
} |
853 |
else { |
854 |
if (usesDipoles) { |
855 |
|
856 |
if( !globals->haveECR() ){ |
857 |
sprintf( painCave.errMsg, |
858 |
"SimSetup Warning: using default value of 1/2 the smallest " |
859 |
"box length for the electrostaticCutoffRadius.\n" |
860 |
"I hope you have a very fast processor!\n"); |
861 |
painCave.isFatal = 0; |
862 |
simError(); |
863 |
double smallest; |
864 |
smallest = info[i].boxL[0]; |
865 |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
866 |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
867 |
theEcr = 0.5 * smallest; |
868 |
} else { |
869 |
theEcr = globals->getECR(); |
870 |
} |
871 |
|
872 |
if( !globals->haveEST() ){ |
873 |
sprintf( painCave.errMsg, |
874 |
"SimSetup Warning: using default value of 0.05 * the " |
875 |
"electrostaticCutoffRadius for the " |
876 |
"electrostaticSkinThickness\n" |
877 |
); |
878 |
painCave.isFatal = 0; |
879 |
simError(); |
880 |
theEst = 0.05 * theEcr; |
881 |
} else { |
882 |
theEst= globals->getEST(); |
883 |
} |
884 |
|
885 |
info[i].setEcr( theEcr, theEst ); |
886 |
} |
887 |
} |
888 |
} |
889 |
|
890 |
#ifdef IS_MPI |
891 |
strcpy( checkPointMsg, "post processing checks out" ); |
892 |
MPIcheckPoint(); |
893 |
#endif // is_mpi |
894 |
|
895 |
} |
896 |
|
897 |
void SimSetup::initSystemCoords( void ){ |
898 |
int i; |
899 |
|
900 |
char* inName; |
901 |
|
902 |
std::cerr << "Setting atom Coords\n"; |
903 |
|
904 |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
905 |
|
906 |
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
907 |
|
908 |
if( globals->haveInitialConfig() ){ |
909 |
|
910 |
InitializeFromFile* fileInit; |
911 |
#ifdef IS_MPI // is_mpi |
912 |
if( worldRank == 0 ){ |
913 |
#endif //is_mpi |
914 |
inName = globals->getInitialConfig(); |
915 |
fileInit = new InitializeFromFile( inName ); |
916 |
#ifdef IS_MPI |
917 |
}else fileInit = new InitializeFromFile( NULL ); |
918 |
#endif |
919 |
fileInit->readInit( info ); // default velocities on |
920 |
|
921 |
delete fileInit; |
922 |
} |
923 |
else{ |
924 |
|
925 |
#ifdef IS_MPI |
926 |
|
927 |
// no init from bass |
928 |
|
929 |
sprintf( painCave.errMsg, |
930 |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
931 |
painCave.isFatal; |
932 |
simError(); |
933 |
|
934 |
#else |
935 |
|
936 |
initFromBass(); |
937 |
|
938 |
|
939 |
#endif |
940 |
} |
941 |
|
942 |
#ifdef IS_MPI |
943 |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
944 |
MPIcheckPoint(); |
945 |
#endif // is_mpi |
946 |
|
947 |
} |
948 |
|
949 |
|
950 |
void SimSetup::makeOutNames( void ){ |
951 |
|
952 |
int k; |
953 |
|
954 |
|
955 |
for(k=0; k<nInfo; k++){ |
956 |
|
957 |
#ifdef IS_MPI |
958 |
if( worldRank == 0 ){ |
959 |
#endif // is_mpi |
960 |
|
961 |
if( globals->haveFinalConfig() ){ |
962 |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
963 |
} |
964 |
else{ |
965 |
strcpy( info[k].finalName, inFileName ); |
966 |
char* endTest; |
967 |
int nameLength = strlen( info[k].finalName ); |
968 |
endTest = &(info[k].finalName[nameLength - 5]); |
969 |
if( !strcmp( endTest, ".bass" ) ){ |
970 |
strcpy( endTest, ".eor" ); |
971 |
} |
972 |
else if( !strcmp( endTest, ".BASS" ) ){ |
973 |
strcpy( endTest, ".eor" ); |
974 |
} |
975 |
else{ |
976 |
endTest = &(info[k].finalName[nameLength - 4]); |
977 |
if( !strcmp( endTest, ".bss" ) ){ |
978 |
strcpy( endTest, ".eor" ); |
979 |
} |
980 |
else if( !strcmp( endTest, ".mdl" ) ){ |
981 |
strcpy( endTest, ".eor" ); |
982 |
} |
983 |
else{ |
984 |
strcat( info[k].finalName, ".eor" ); |
985 |
} |
986 |
} |
987 |
} |
988 |
|
989 |
// make the sample and status out names |
990 |
|
991 |
strcpy( info[k].sampleName, inFileName ); |
992 |
char* endTest; |
993 |
int nameLength = strlen( info[k].sampleName ); |
994 |
endTest = &(info[k].sampleName[nameLength - 5]); |
995 |
if( !strcmp( endTest, ".bass" ) ){ |
996 |
strcpy( endTest, ".dump" ); |
997 |
} |
998 |
else if( !strcmp( endTest, ".BASS" ) ){ |
999 |
strcpy( endTest, ".dump" ); |
1000 |
} |
1001 |
else{ |
1002 |
endTest = &(info[k].sampleName[nameLength - 4]); |
1003 |
if( !strcmp( endTest, ".bss" ) ){ |
1004 |
strcpy( endTest, ".dump" ); |
1005 |
} |
1006 |
else if( !strcmp( endTest, ".mdl" ) ){ |
1007 |
strcpy( endTest, ".dump" ); |
1008 |
} |
1009 |
else{ |
1010 |
strcat( info[k].sampleName, ".dump" ); |
1011 |
} |
1012 |
} |
1013 |
|
1014 |
strcpy( info[k].statusName, inFileName ); |
1015 |
nameLength = strlen( info[k].statusName ); |
1016 |
endTest = &(info[k].statusName[nameLength - 5]); |
1017 |
if( !strcmp( endTest, ".bass" ) ){ |
1018 |
strcpy( endTest, ".stat" ); |
1019 |
} |
1020 |
else if( !strcmp( endTest, ".BASS" ) ){ |
1021 |
strcpy( endTest, ".stat" ); |
1022 |
} |
1023 |
else{ |
1024 |
endTest = &(info[k].statusName[nameLength - 4]); |
1025 |
if( !strcmp( endTest, ".bss" ) ){ |
1026 |
strcpy( endTest, ".stat" ); |
1027 |
} |
1028 |
else if( !strcmp( endTest, ".mdl" ) ){ |
1029 |
strcpy( endTest, ".stat" ); |
1030 |
} |
1031 |
else{ |
1032 |
strcat( info[k].statusName, ".stat" ); |
1033 |
} |
1034 |
} |
1035 |
|
1036 |
#ifdef IS_MPI |
1037 |
} |
1038 |
#endif // is_mpi |
1039 |
} |
1040 |
} |
1041 |
|
1042 |
|
1043 |
void SimSetup::sysObjectsCreation( void ){ |
1044 |
|
1045 |
int i,k; |
1046 |
|
1047 |
// create the forceField |
1048 |
|
1049 |
createFF(); |
1050 |
|
1051 |
// extract componentList |
1052 |
|
1053 |
compList(); |
1054 |
|
1055 |
// calc the number of atoms, bond, bends, and torsions |
1056 |
|
1057 |
calcSysValues(); |
1058 |
|
1059 |
#ifdef IS_MPI |
1060 |
// divide the molecules among the processors |
1061 |
|
1062 |
mpiMolDivide(); |
1063 |
#endif //is_mpi |
1064 |
|
1065 |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1066 |
|
1067 |
makeSysArrays(); |
1068 |
|
1069 |
// make and initialize the molecules (all but atomic coordinates) |
1070 |
|
1071 |
makeMolecules(); |
1072 |
|
1073 |
for(k=0; k<nInfo; k++){ |
1074 |
info[k].identArray = new int[info[k].n_atoms]; |
1075 |
for(i=0; i<info[k].n_atoms; i++){ |
1076 |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1077 |
} |
1078 |
} |
1079 |
} |
1080 |
|
1081 |
|
1082 |
void SimSetup::createFF( void ){ |
1083 |
|
1084 |
switch( ffCase ){ |
1085 |
|
1086 |
case FF_DUFF: |
1087 |
the_ff = new DUFF(); |
1088 |
break; |
1089 |
|
1090 |
case FF_LJ: |
1091 |
the_ff = new LJFF(); |
1092 |
break; |
1093 |
|
1094 |
case FF_EAM: |
1095 |
the_ff = new EAM_FF(); |
1096 |
break; |
1097 |
|
1098 |
default: |
1099 |
sprintf( painCave.errMsg, |
1100 |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1101 |
painCave.isFatal = 1; |
1102 |
simError(); |
1103 |
} |
1104 |
|
1105 |
#ifdef IS_MPI |
1106 |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1107 |
MPIcheckPoint(); |
1108 |
#endif // is_mpi |
1109 |
|
1110 |
} |
1111 |
|
1112 |
|
1113 |
void SimSetup::compList( void ){ |
1114 |
|
1115 |
int i; |
1116 |
char* id; |
1117 |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1118 |
LinkedMolStamp* currentStamp = NULL; |
1119 |
comp_stamps = new MoleculeStamp*[n_components]; |
1120 |
|
1121 |
// make an array of molecule stamps that match the components used. |
1122 |
// also extract the used stamps out into a separate linked list |
1123 |
|
1124 |
for(i=0; i<nInfo; i++){ |
1125 |
info[i].nComponents = n_components; |
1126 |
info[i].componentsNmol = components_nmol; |
1127 |
info[i].compStamps = comp_stamps; |
1128 |
info[i].headStamp = headStamp; |
1129 |
} |
1130 |
|
1131 |
|
1132 |
for( i=0; i<n_components; i++ ){ |
1133 |
|
1134 |
id = the_components[i]->getType(); |
1135 |
comp_stamps[i] = NULL; |
1136 |
|
1137 |
// check to make sure the component isn't already in the list |
1138 |
|
1139 |
comp_stamps[i] = headStamp->match( id ); |
1140 |
if( comp_stamps[i] == NULL ){ |
1141 |
|
1142 |
// extract the component from the list; |
1143 |
|
1144 |
currentStamp = stamps->extractMolStamp( id ); |
1145 |
if( currentStamp == NULL ){ |
1146 |
sprintf( painCave.errMsg, |
1147 |
"SimSetup error: Component \"%s\" was not found in the " |
1148 |
"list of declared molecules\n", |
1149 |
id ); |
1150 |
painCave.isFatal = 1; |
1151 |
simError(); |
1152 |
} |
1153 |
|
1154 |
headStamp->add( currentStamp ); |
1155 |
comp_stamps[i] = headStamp->match( id ); |
1156 |
} |
1157 |
} |
1158 |
|
1159 |
#ifdef IS_MPI |
1160 |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1161 |
MPIcheckPoint(); |
1162 |
#endif // is_mpi |
1163 |
|
1164 |
|
1165 |
} |
1166 |
|
1167 |
void SimSetup::calcSysValues( void ){ |
1168 |
int i, j, k; |
1169 |
|
1170 |
int *molMembershipArray; |
1171 |
|
1172 |
tot_atoms = 0; |
1173 |
tot_bonds = 0; |
1174 |
tot_bends = 0; |
1175 |
tot_torsions = 0; |
1176 |
for( i=0; i<n_components; i++ ){ |
1177 |
|
1178 |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1179 |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1180 |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1181 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1182 |
} |
1183 |
|
1184 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1185 |
molMembershipArray = new int[tot_atoms]; |
1186 |
|
1187 |
for(i=0; i<nInfo; i++){ |
1188 |
info[i].n_atoms = tot_atoms; |
1189 |
info[i].n_bonds = tot_bonds; |
1190 |
info[i].n_bends = tot_bends; |
1191 |
info[i].n_torsions = tot_torsions; |
1192 |
info[i].n_SRI = tot_SRI; |
1193 |
info[i].n_mol = tot_nmol; |
1194 |
|
1195 |
info[i].molMembershipArray = molMembershipArray; |
1196 |
} |
1197 |
} |
1198 |
|
1199 |
#ifdef IS_MPI |
1200 |
|
1201 |
void SimSetup::mpiMolDivide( void ){ |
1202 |
|
1203 |
int i, j, k; |
1204 |
int localMol, allMol; |
1205 |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1206 |
|
1207 |
mpiSim = new mpiSimulation( info ); |
1208 |
|
1209 |
globalIndex = mpiSim->divideLabor(); |
1210 |
|
1211 |
// set up the local variables |
1212 |
|
1213 |
mol2proc = mpiSim->getMolToProcMap(); |
1214 |
molCompType = mpiSim->getMolComponentType(); |
1215 |
|
1216 |
allMol = 0; |
1217 |
localMol = 0; |
1218 |
local_atoms = 0; |
1219 |
local_bonds = 0; |
1220 |
local_bends = 0; |
1221 |
local_torsions = 0; |
1222 |
globalAtomIndex = 0; |
1223 |
|
1224 |
|
1225 |
for( i=0; i<n_components; i++ ){ |
1226 |
|
1227 |
for( j=0; j<components_nmol[i]; j++ ){ |
1228 |
|
1229 |
if( mol2proc[allMol] == worldRank ){ |
1230 |
|
1231 |
local_atoms += comp_stamps[i]->getNAtoms(); |
1232 |
local_bonds += comp_stamps[i]->getNBonds(); |
1233 |
local_bends += comp_stamps[i]->getNBends(); |
1234 |
local_torsions += comp_stamps[i]->getNTorsions(); |
1235 |
localMol++; |
1236 |
} |
1237 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1238 |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1239 |
globalAtomIndex++; |
1240 |
} |
1241 |
|
1242 |
allMol++; |
1243 |
} |
1244 |
} |
1245 |
local_SRI = local_bonds + local_bends + local_torsions; |
1246 |
|
1247 |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1248 |
|
1249 |
if( local_atoms != info[0].n_atoms ){ |
1250 |
sprintf( painCave.errMsg, |
1251 |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1252 |
" localAtom (%d) are not equal.\n", |
1253 |
info[0].n_atoms, |
1254 |
local_atoms ); |
1255 |
painCave.isFatal = 1; |
1256 |
simError(); |
1257 |
} |
1258 |
|
1259 |
info[0].n_bonds = local_bonds; |
1260 |
info[0].n_bends = local_bends; |
1261 |
info[0].n_torsions = local_torsions; |
1262 |
info[0].n_SRI = local_SRI; |
1263 |
info[0].n_mol = localMol; |
1264 |
|
1265 |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1266 |
MPIcheckPoint(); |
1267 |
} |
1268 |
|
1269 |
#endif // is_mpi |
1270 |
|
1271 |
|
1272 |
void SimSetup::makeSysArrays( void ){ |
1273 |
int i, j, k, l; |
1274 |
|
1275 |
Atom** the_atoms; |
1276 |
Molecule* the_molecules; |
1277 |
Exclude** the_excludes; |
1278 |
|
1279 |
|
1280 |
for(l=0; l<nInfo; l++){ |
1281 |
|
1282 |
// create the atom and short range interaction arrays |
1283 |
|
1284 |
the_atoms = new Atom*[info[l].n_atoms]; |
1285 |
the_molecules = new Molecule[info[l].n_mol]; |
1286 |
int molIndex; |
1287 |
|
1288 |
// initialize the molecule's stampID's |
1289 |
|
1290 |
#ifdef IS_MPI |
1291 |
|
1292 |
|
1293 |
molIndex = 0; |
1294 |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1295 |
|
1296 |
if(mol2proc[i] == worldRank ){ |
1297 |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1298 |
the_molecules[molIndex].setMyIndex( molIndex ); |
1299 |
the_molecules[molIndex].setGlobalIndex( i ); |
1300 |
molIndex++; |
1301 |
} |
1302 |
} |
1303 |
|
1304 |
#else // is_mpi |
1305 |
|
1306 |
molIndex = 0; |
1307 |
globalAtomIndex = 0; |
1308 |
for(i=0; i<n_components; i++){ |
1309 |
for(j=0; j<components_nmol[i]; j++ ){ |
1310 |
the_molecules[molIndex].setStampID( i ); |
1311 |
the_molecules[molIndex].setMyIndex( molIndex ); |
1312 |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1313 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1314 |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1315 |
globalAtomIndex++; |
1316 |
} |
1317 |
molIndex++; |
1318 |
} |
1319 |
} |
1320 |
|
1321 |
|
1322 |
#endif // is_mpi |
1323 |
|
1324 |
|
1325 |
if( info[l].n_SRI ){ |
1326 |
|
1327 |
Exclude::createArray(info[l].n_SRI); |
1328 |
the_excludes = new Exclude*[info[l].n_SRI]; |
1329 |
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1330 |
the_excludes[ex] = new Exclude(ex); |
1331 |
} |
1332 |
info[l].globalExcludes = new int; |
1333 |
info[l].n_exclude = info[l].n_SRI; |
1334 |
} |
1335 |
else{ |
1336 |
|
1337 |
Exclude::createArray( 1 ); |
1338 |
the_excludes = new Exclude*; |
1339 |
the_excludes[0] = new Exclude(0); |
1340 |
the_excludes[0]->setPair( 0,0 ); |
1341 |
info[l].globalExcludes = new int; |
1342 |
info[l].globalExcludes[0] = 0; |
1343 |
info[l].n_exclude = 0; |
1344 |
} |
1345 |
|
1346 |
// set the arrays into the SimInfo object |
1347 |
|
1348 |
info[l].atoms = the_atoms; |
1349 |
info[l].molecules = the_molecules; |
1350 |
info[l].nGlobalExcludes = 0; |
1351 |
info[l].excludes = the_excludes; |
1352 |
|
1353 |
the_ff->setSimInfo( info ); |
1354 |
|
1355 |
} |
1356 |
} |
1357 |
|
1358 |
void SimSetup::makeIntegrator( void ){ |
1359 |
|
1360 |
int k; |
1361 |
|
1362 |
NVT<RealIntegrator>* myNVT = NULL; |
1363 |
NPTi<RealIntegrator>* myNPTi = NULL; |
1364 |
NPTf<RealIntegrator>* myNPTf = NULL; |
1365 |
NPTim<RealIntegrator>* myNPTim = NULL; |
1366 |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1367 |
|
1368 |
for(k=0; k<nInfo; k++){ |
1369 |
|
1370 |
switch( ensembleCase ){ |
1371 |
|
1372 |
case NVE_ENS: |
1373 |
if (globals->haveZconstraints()){ |
1374 |
setupZConstraint(info[k]); |
1375 |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1376 |
} |
1377 |
|
1378 |
else |
1379 |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1380 |
break; |
1381 |
|
1382 |
case NVT_ENS: |
1383 |
if (globals->haveZconstraints()){ |
1384 |
setupZConstraint(info[k]); |
1385 |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1386 |
} |
1387 |
else |
1388 |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1389 |
|
1390 |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1391 |
|
1392 |
if (globals->haveTauThermostat()) |
1393 |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1394 |
|
1395 |
else { |
1396 |
sprintf( painCave.errMsg, |
1397 |
"SimSetup error: If you use the NVT\n" |
1398 |
" ensemble, you must set tauThermostat.\n"); |
1399 |
painCave.isFatal = 1; |
1400 |
simError(); |
1401 |
} |
1402 |
break; |
1403 |
|
1404 |
case NPTi_ENS: |
1405 |
if (globals->haveZconstraints()){ |
1406 |
setupZConstraint(info[k]); |
1407 |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1408 |
} |
1409 |
else |
1410 |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1411 |
|
1412 |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1413 |
|
1414 |
if (globals->haveTargetPressure()) |
1415 |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1416 |
else { |
1417 |
sprintf( painCave.errMsg, |
1418 |
"SimSetup error: If you use a constant pressure\n" |
1419 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1420 |
painCave.isFatal = 1; |
1421 |
simError(); |
1422 |
} |
1423 |
|
1424 |
if( globals->haveTauThermostat() ) |
1425 |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1426 |
else{ |
1427 |
sprintf( painCave.errMsg, |
1428 |
"SimSetup error: If you use an NPT\n" |
1429 |
" ensemble, you must set tauThermostat.\n"); |
1430 |
painCave.isFatal = 1; |
1431 |
simError(); |
1432 |
} |
1433 |
|
1434 |
if( globals->haveTauBarostat() ) |
1435 |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1436 |
else{ |
1437 |
sprintf( painCave.errMsg, |
1438 |
"SimSetup error: If you use an NPT\n" |
1439 |
" ensemble, you must set tauBarostat.\n"); |
1440 |
painCave.isFatal = 1; |
1441 |
simError(); |
1442 |
} |
1443 |
break; |
1444 |
|
1445 |
case NPTf_ENS: |
1446 |
if (globals->haveZconstraints()){ |
1447 |
setupZConstraint(info[k]); |
1448 |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1449 |
} |
1450 |
else |
1451 |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1452 |
|
1453 |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1454 |
|
1455 |
if (globals->haveTargetPressure()) |
1456 |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1457 |
else { |
1458 |
sprintf( painCave.errMsg, |
1459 |
"SimSetup error: If you use a constant pressure\n" |
1460 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1461 |
painCave.isFatal = 1; |
1462 |
simError(); |
1463 |
} |
1464 |
|
1465 |
if( globals->haveTauThermostat() ) |
1466 |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1467 |
else{ |
1468 |
sprintf( painCave.errMsg, |
1469 |
"SimSetup error: If you use an NPT\n" |
1470 |
" ensemble, you must set tauThermostat.\n"); |
1471 |
painCave.isFatal = 1; |
1472 |
simError(); |
1473 |
} |
1474 |
|
1475 |
if( globals->haveTauBarostat() ) |
1476 |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1477 |
else{ |
1478 |
sprintf( painCave.errMsg, |
1479 |
"SimSetup error: If you use an NPT\n" |
1480 |
" ensemble, you must set tauBarostat.\n"); |
1481 |
painCave.isFatal = 1; |
1482 |
simError(); |
1483 |
} |
1484 |
break; |
1485 |
|
1486 |
case NPTim_ENS: |
1487 |
if (globals->haveZconstraints()){ |
1488 |
setupZConstraint(info[k]); |
1489 |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1490 |
} |
1491 |
else |
1492 |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1493 |
|
1494 |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1495 |
|
1496 |
if (globals->haveTargetPressure()) |
1497 |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1498 |
else { |
1499 |
sprintf( painCave.errMsg, |
1500 |
"SimSetup error: If you use a constant pressure\n" |
1501 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1502 |
painCave.isFatal = 1; |
1503 |
simError(); |
1504 |
} |
1505 |
|
1506 |
if( globals->haveTauThermostat() ) |
1507 |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1508 |
else{ |
1509 |
sprintf( painCave.errMsg, |
1510 |
"SimSetup error: If you use an NPT\n" |
1511 |
" ensemble, you must set tauThermostat.\n"); |
1512 |
painCave.isFatal = 1; |
1513 |
simError(); |
1514 |
} |
1515 |
|
1516 |
if( globals->haveTauBarostat() ) |
1517 |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1518 |
else{ |
1519 |
sprintf( painCave.errMsg, |
1520 |
"SimSetup error: If you use an NPT\n" |
1521 |
" ensemble, you must set tauBarostat.\n"); |
1522 |
painCave.isFatal = 1; |
1523 |
simError(); |
1524 |
} |
1525 |
break; |
1526 |
|
1527 |
case NPTfm_ENS: |
1528 |
if (globals->haveZconstraints()){ |
1529 |
setupZConstraint(info[k]); |
1530 |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1531 |
} |
1532 |
else |
1533 |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1534 |
|
1535 |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1536 |
|
1537 |
if (globals->haveTargetPressure()) |
1538 |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1539 |
else { |
1540 |
sprintf( painCave.errMsg, |
1541 |
"SimSetup error: If you use a constant pressure\n" |
1542 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1543 |
painCave.isFatal = 1; |
1544 |
simError(); |
1545 |
} |
1546 |
|
1547 |
if( globals->haveTauThermostat() ) |
1548 |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1549 |
else{ |
1550 |
sprintf( painCave.errMsg, |
1551 |
"SimSetup error: If you use an NPT\n" |
1552 |
" ensemble, you must set tauThermostat.\n"); |
1553 |
painCave.isFatal = 1; |
1554 |
simError(); |
1555 |
} |
1556 |
|
1557 |
if( globals->haveTauBarostat() ) |
1558 |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1559 |
else{ |
1560 |
sprintf( painCave.errMsg, |
1561 |
"SimSetup error: If you use an NPT\n" |
1562 |
" ensemble, you must set tauBarostat.\n"); |
1563 |
painCave.isFatal = 1; |
1564 |
simError(); |
1565 |
} |
1566 |
break; |
1567 |
|
1568 |
default: |
1569 |
sprintf( painCave.errMsg, |
1570 |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1571 |
painCave.isFatal = 1; |
1572 |
simError(); |
1573 |
} |
1574 |
} |
1575 |
} |
1576 |
|
1577 |
void SimSetup::initFortran( void ){ |
1578 |
|
1579 |
info[0].refreshSim(); |
1580 |
|
1581 |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1582 |
the_ff->initForceField( LB_MIXING_RULE ); |
1583 |
} |
1584 |
else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1585 |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1586 |
} |
1587 |
else{ |
1588 |
sprintf( painCave.errMsg, |
1589 |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1590 |
info[0].mixingRule ); |
1591 |
painCave.isFatal = 1; |
1592 |
simError(); |
1593 |
} |
1594 |
|
1595 |
|
1596 |
#ifdef IS_MPI |
1597 |
strcpy( checkPointMsg, |
1598 |
"Successfully intialized the mixingRule for Fortran." ); |
1599 |
MPIcheckPoint(); |
1600 |
#endif // is_mpi |
1601 |
|
1602 |
} |
1603 |
|
1604 |
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1605 |
{ |
1606 |
int nZConstraints; |
1607 |
ZconStamp** zconStamp; |
1608 |
|
1609 |
if(globals->haveZconstraintTime()){ |
1610 |
|
1611 |
//add sample time of z-constraint into SimInfo's property list |
1612 |
DoubleData* zconsTimeProp = new DoubleData(); |
1613 |
zconsTimeProp->setID(ZCONSTIME_ID); |
1614 |
zconsTimeProp->setData(globals->getZconsTime()); |
1615 |
theInfo.addProperty(zconsTimeProp); |
1616 |
} |
1617 |
else{ |
1618 |
sprintf( painCave.errMsg, |
1619 |
"ZConstraint error: If you use an ZConstraint\n" |
1620 |
" , you must set sample time.\n"); |
1621 |
painCave.isFatal = 1; |
1622 |
simError(); |
1623 |
} |
1624 |
|
1625 |
// |
1626 |
nZConstraints = globals->getNzConstraints(); |
1627 |
zconStamp = globals->getZconStamp(); |
1628 |
ZConsParaItem tempParaItem; |
1629 |
|
1630 |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1631 |
zconsParaData->setID(ZCONSPARADATA_ID); |
1632 |
|
1633 |
for(int i = 0; i < nZConstraints; i++){ |
1634 |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1635 |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1636 |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1637 |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1638 |
|
1639 |
zconsParaData->addItem(tempParaItem); |
1640 |
} |
1641 |
|
1642 |
//sort the parameters by index of molecules |
1643 |
zconsParaData->sortByIndex(); |
1644 |
|
1645 |
//push data into siminfo, therefore, we can retrieve later |
1646 |
theInfo.addProperty(zconsParaData); |
1647 |
|
1648 |
//push zconsTol into siminfo, if user does not specify |
1649 |
//value for zconsTol, a default value will be used |
1650 |
DoubleData* zconsTol = new DoubleData(); |
1651 |
zconsTol->setID(ZCONSTOL_ID); |
1652 |
if(globals->haveZconsTol()){ |
1653 |
zconsTol->setData(globals->getZconsTol()); |
1654 |
} |
1655 |
else{ |
1656 |
double defaultZConsTol = 1E-6; |
1657 |
sprintf( painCave.errMsg, |
1658 |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1659 |
" , default value %f is used.\n", defaultZConsTol); |
1660 |
painCave.isFatal = 0; |
1661 |
simError(); |
1662 |
|
1663 |
zconsTol->setData(defaultZConsTol); |
1664 |
} |
1665 |
theInfo.addProperty(zconsTol); |
1666 |
|
1667 |
//Determine the name of ouput file and add it into SimInfo's property list |
1668 |
//Be careful, do not use inFileName, since it is a pointer which |
1669 |
//point to a string at master node, and slave nodes do not contain that string |
1670 |
|
1671 |
string zconsOutput(theInfo.finalName); |
1672 |
|
1673 |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1674 |
|
1675 |
StringData* zconsFilename = new StringData(); |
1676 |
zconsFilename->setID(ZCONSFILENAME_ID); |
1677 |
zconsFilename->setData(zconsOutput); |
1678 |
|
1679 |
theInfo.addProperty(zconsFilename); |
1680 |
} |