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 |
gatherInfo(); |
102 |
|
103 |
// creation of complex system objects |
104 |
|
105 |
sysObjectsCreation(); |
106 |
|
107 |
// check on the post processing info |
108 |
|
109 |
finalInfoCheck(); |
110 |
|
111 |
// initialize the system coordinates |
112 |
|
113 |
if( !isInfoArray ) initSystemCoords(); |
114 |
|
115 |
// make the output filenames |
116 |
|
117 |
makeOutNames(); |
118 |
|
119 |
// make the integrator |
120 |
|
121 |
makeIntegrator(); |
122 |
|
123 |
#ifdef IS_MPI |
124 |
mpiSim->mpiRefresh(); |
125 |
#endif |
126 |
|
127 |
// initialize the Fortran |
128 |
|
129 |
initFortran(); |
130 |
|
131 |
|
132 |
|
133 |
} |
134 |
|
135 |
|
136 |
void SimSetup::makeMolecules( void ){ |
137 |
|
138 |
int k,l; |
139 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
140 |
molInit molInfo; |
141 |
DirectionalAtom* dAtom; |
142 |
LinkedAssign* extras; |
143 |
LinkedAssign* current_extra; |
144 |
AtomStamp* currentAtom; |
145 |
BondStamp* currentBond; |
146 |
BendStamp* currentBend; |
147 |
TorsionStamp* currentTorsion; |
148 |
|
149 |
bond_pair* theBonds; |
150 |
bend_set* theBends; |
151 |
torsion_set* theTorsions; |
152 |
|
153 |
|
154 |
//init the forceField paramters |
155 |
|
156 |
the_ff->readParams(); |
157 |
|
158 |
|
159 |
// init the atoms |
160 |
|
161 |
double ux, uy, uz, u, uSqr; |
162 |
|
163 |
for(k=0; k<nInfo; k++){ |
164 |
|
165 |
the_ff->setSimInfo( &(info[k]) ); |
166 |
|
167 |
atomOffset = 0; |
168 |
excludeOffset = 0; |
169 |
for(i=0; i<info[k].n_mol; i++){ |
170 |
|
171 |
stampID = info[k].molecules[i].getStampID(); |
172 |
|
173 |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
174 |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
175 |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
176 |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
177 |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
178 |
|
179 |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
180 |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
181 |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
182 |
molInfo.myBends = new Bend*[molInfo.nBends]; |
183 |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
184 |
|
185 |
theBonds = new bond_pair[molInfo.nBonds]; |
186 |
theBends = new bend_set[molInfo.nBends]; |
187 |
theTorsions = new torsion_set[molInfo.nTorsions]; |
188 |
|
189 |
// make the Atoms |
190 |
|
191 |
for(j=0; j<molInfo.nAtoms; j++){ |
192 |
|
193 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
194 |
if( currentAtom->haveOrientation() ){ |
195 |
|
196 |
dAtom = new DirectionalAtom( (j + atomOffset), |
197 |
info[k].getConfiguration() ); |
198 |
info[k].n_oriented++; |
199 |
molInfo.myAtoms[j] = dAtom; |
200 |
|
201 |
ux = currentAtom->getOrntX(); |
202 |
uy = currentAtom->getOrntY(); |
203 |
uz = currentAtom->getOrntZ(); |
204 |
|
205 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
206 |
|
207 |
u = sqrt( uSqr ); |
208 |
ux = ux / u; |
209 |
uy = uy / u; |
210 |
uz = uz / u; |
211 |
|
212 |
dAtom->setSUx( ux ); |
213 |
dAtom->setSUy( uy ); |
214 |
dAtom->setSUz( uz ); |
215 |
} |
216 |
else{ |
217 |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
218 |
info[k].getConfiguration() ); |
219 |
} |
220 |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
221 |
|
222 |
#ifdef IS_MPI |
223 |
|
224 |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
225 |
|
226 |
#endif // is_mpi |
227 |
} |
228 |
|
229 |
// make the bonds |
230 |
for(j=0; j<molInfo.nBonds; j++){ |
231 |
|
232 |
currentBond = comp_stamps[stampID]->getBond( j ); |
233 |
theBonds[j].a = currentBond->getA() + atomOffset; |
234 |
theBonds[j].b = currentBond->getB() + atomOffset; |
235 |
|
236 |
exI = theBonds[j].a; |
237 |
exJ = theBonds[j].b; |
238 |
|
239 |
// exclude_I must always be the smaller of the pair |
240 |
if( exI > exJ ){ |
241 |
tempEx = exI; |
242 |
exI = exJ; |
243 |
exJ = tempEx; |
244 |
} |
245 |
#ifdef IS_MPI |
246 |
tempEx = exI; |
247 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
248 |
tempEx = exJ; |
249 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
250 |
|
251 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
252 |
#else // isn't MPI |
253 |
|
254 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
255 |
#endif //is_mpi |
256 |
} |
257 |
excludeOffset += molInfo.nBonds; |
258 |
|
259 |
//make the bends |
260 |
for(j=0; j<molInfo.nBends; j++){ |
261 |
|
262 |
currentBend = comp_stamps[stampID]->getBend( j ); |
263 |
theBends[j].a = currentBend->getA() + atomOffset; |
264 |
theBends[j].b = currentBend->getB() + atomOffset; |
265 |
theBends[j].c = currentBend->getC() + atomOffset; |
266 |
|
267 |
if( currentBend->haveExtras() ){ |
268 |
|
269 |
extras = currentBend->getExtras(); |
270 |
current_extra = extras; |
271 |
|
272 |
while( current_extra != NULL ){ |
273 |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
274 |
|
275 |
switch( current_extra->getType() ){ |
276 |
|
277 |
case 0: |
278 |
theBends[j].ghost = |
279 |
current_extra->getInt() + atomOffset; |
280 |
theBends[j].isGhost = 1; |
281 |
break; |
282 |
|
283 |
case 1: |
284 |
theBends[j].ghost = |
285 |
(int)current_extra->getDouble() + atomOffset; |
286 |
theBends[j].isGhost = 1; |
287 |
break; |
288 |
|
289 |
default: |
290 |
sprintf( painCave.errMsg, |
291 |
"SimSetup Error: ghostVectorSource was neither a " |
292 |
"double nor an int.\n" |
293 |
"-->Bend[%d] in %s\n", |
294 |
j, comp_stamps[stampID]->getID() ); |
295 |
painCave.isFatal = 1; |
296 |
simError(); |
297 |
} |
298 |
} |
299 |
|
300 |
else{ |
301 |
|
302 |
sprintf( painCave.errMsg, |
303 |
"SimSetup Error: unhandled bend assignment:\n" |
304 |
" -->%s in Bend[%d] in %s\n", |
305 |
current_extra->getlhs(), |
306 |
j, comp_stamps[stampID]->getID() ); |
307 |
painCave.isFatal = 1; |
308 |
simError(); |
309 |
} |
310 |
|
311 |
current_extra = current_extra->getNext(); |
312 |
} |
313 |
} |
314 |
|
315 |
if( !theBends[j].isGhost ){ |
316 |
|
317 |
exI = theBends[j].a; |
318 |
exJ = theBends[j].c; |
319 |
} |
320 |
else{ |
321 |
|
322 |
exI = theBends[j].a; |
323 |
exJ = theBends[j].b; |
324 |
} |
325 |
|
326 |
// exclude_I must always be the smaller of the pair |
327 |
if( exI > exJ ){ |
328 |
tempEx = exI; |
329 |
exI = exJ; |
330 |
exJ = tempEx; |
331 |
} |
332 |
#ifdef IS_MPI |
333 |
tempEx = exI; |
334 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
335 |
tempEx = exJ; |
336 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
337 |
|
338 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
339 |
#else // isn't MPI |
340 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
341 |
#endif //is_mpi |
342 |
} |
343 |
excludeOffset += molInfo.nBends; |
344 |
|
345 |
for(j=0; j<molInfo.nTorsions; j++){ |
346 |
|
347 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
348 |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
349 |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
350 |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
351 |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
352 |
|
353 |
exI = theTorsions[j].a; |
354 |
exJ = theTorsions[j].d; |
355 |
|
356 |
// exclude_I must always be the smaller of the pair |
357 |
if( exI > exJ ){ |
358 |
tempEx = exI; |
359 |
exI = exJ; |
360 |
exJ = tempEx; |
361 |
} |
362 |
#ifdef IS_MPI |
363 |
tempEx = exI; |
364 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
365 |
tempEx = exJ; |
366 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
367 |
|
368 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
369 |
#else // isn't MPI |
370 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
371 |
#endif //is_mpi |
372 |
} |
373 |
excludeOffset += molInfo.nTorsions; |
374 |
|
375 |
|
376 |
// send the arrays off to the forceField for init. |
377 |
|
378 |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
379 |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
380 |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
381 |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
382 |
|
383 |
|
384 |
info[k].molecules[i].initialize( molInfo ); |
385 |
|
386 |
|
387 |
atomOffset += molInfo.nAtoms; |
388 |
delete[] theBonds; |
389 |
delete[] theBends; |
390 |
delete[] theTorsions; |
391 |
} |
392 |
} |
393 |
|
394 |
#ifdef IS_MPI |
395 |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
396 |
MPIcheckPoint(); |
397 |
#endif // is_mpi |
398 |
|
399 |
// clean up the forcefield |
400 |
|
401 |
the_ff->calcRcut(); |
402 |
the_ff->cleanMe(); |
403 |
|
404 |
} |
405 |
|
406 |
void SimSetup::initFromBass( void ){ |
407 |
|
408 |
int i, j, k; |
409 |
int n_cells; |
410 |
double cellx, celly, cellz; |
411 |
double temp1, temp2, temp3; |
412 |
int n_per_extra; |
413 |
int n_extra; |
414 |
int have_extra, done; |
415 |
|
416 |
double vel[3]; |
417 |
vel[0] = 0.0; |
418 |
vel[1] = 0.0; |
419 |
vel[2] = 0.0; |
420 |
|
421 |
temp1 = (double)tot_nmol / 4.0; |
422 |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
423 |
temp3 = ceil( temp2 ); |
424 |
|
425 |
have_extra =0; |
426 |
if( temp2 < temp3 ){ // we have a non-complete lattice |
427 |
have_extra =1; |
428 |
|
429 |
n_cells = (int)temp3 - 1; |
430 |
cellx = info[0].boxL[0] / temp3; |
431 |
celly = info[0].boxL[1] / temp3; |
432 |
cellz = info[0].boxL[2] / temp3; |
433 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
434 |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
435 |
n_per_extra = (int)ceil( temp1 ); |
436 |
|
437 |
if( n_per_extra > 4){ |
438 |
sprintf( painCave.errMsg, |
439 |
"SimSetup error. There has been an error in constructing" |
440 |
" the non-complete lattice.\n" ); |
441 |
painCave.isFatal = 1; |
442 |
simError(); |
443 |
} |
444 |
} |
445 |
else{ |
446 |
n_cells = (int)temp3; |
447 |
cellx = info[0].boxL[0] / temp3; |
448 |
celly = info[0].boxL[1] / temp3; |
449 |
cellz = info[0].boxL[2] / temp3; |
450 |
} |
451 |
|
452 |
current_mol = 0; |
453 |
current_comp_mol = 0; |
454 |
current_comp = 0; |
455 |
current_atom_ndx = 0; |
456 |
|
457 |
for( i=0; i < n_cells ; i++ ){ |
458 |
for( j=0; j < n_cells; j++ ){ |
459 |
for( k=0; k < n_cells; k++ ){ |
460 |
|
461 |
makeElement( i * cellx, |
462 |
j * celly, |
463 |
k * cellz ); |
464 |
|
465 |
makeElement( i * cellx + 0.5 * cellx, |
466 |
j * celly + 0.5 * celly, |
467 |
k * cellz ); |
468 |
|
469 |
makeElement( i * cellx, |
470 |
j * celly + 0.5 * celly, |
471 |
k * cellz + 0.5 * cellz ); |
472 |
|
473 |
makeElement( i * cellx + 0.5 * cellx, |
474 |
j * celly, |
475 |
k * cellz + 0.5 * cellz ); |
476 |
} |
477 |
} |
478 |
} |
479 |
|
480 |
if( have_extra ){ |
481 |
done = 0; |
482 |
|
483 |
int start_ndx; |
484 |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
485 |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
486 |
|
487 |
if( i < n_cells ){ |
488 |
|
489 |
if( j < n_cells ){ |
490 |
start_ndx = n_cells; |
491 |
} |
492 |
else start_ndx = 0; |
493 |
} |
494 |
else start_ndx = 0; |
495 |
|
496 |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
497 |
|
498 |
makeElement( i * cellx, |
499 |
j * celly, |
500 |
k * cellz ); |
501 |
done = ( current_mol >= tot_nmol ); |
502 |
|
503 |
if( !done && n_per_extra > 1 ){ |
504 |
makeElement( i * cellx + 0.5 * cellx, |
505 |
j * celly + 0.5 * celly, |
506 |
k * cellz ); |
507 |
done = ( current_mol >= tot_nmol ); |
508 |
} |
509 |
|
510 |
if( !done && n_per_extra > 2){ |
511 |
makeElement( i * cellx, |
512 |
j * celly + 0.5 * celly, |
513 |
k * cellz + 0.5 * cellz ); |
514 |
done = ( current_mol >= tot_nmol ); |
515 |
} |
516 |
|
517 |
if( !done && n_per_extra > 3){ |
518 |
makeElement( i * cellx + 0.5 * cellx, |
519 |
j * celly, |
520 |
k * cellz + 0.5 * cellz ); |
521 |
done = ( current_mol >= tot_nmol ); |
522 |
} |
523 |
} |
524 |
} |
525 |
} |
526 |
} |
527 |
|
528 |
for( i=0; i<info[0].n_atoms; i++ ){ |
529 |
info[0].atoms[i]->setVel( vel ); |
530 |
} |
531 |
} |
532 |
|
533 |
void SimSetup::makeElement( double x, double y, double z ){ |
534 |
|
535 |
int k; |
536 |
AtomStamp* current_atom; |
537 |
DirectionalAtom* dAtom; |
538 |
double rotMat[3][3]; |
539 |
double pos[3]; |
540 |
|
541 |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
542 |
|
543 |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
544 |
if( !current_atom->havePosition() ){ |
545 |
sprintf( painCave.errMsg, |
546 |
"SimSetup:initFromBass error.\n" |
547 |
"\tComponent %s, atom %s does not have a position specified.\n" |
548 |
"\tThe initialization routine is unable to give a start" |
549 |
" position.\n", |
550 |
comp_stamps[current_comp]->getID(), |
551 |
current_atom->getType() ); |
552 |
painCave.isFatal = 1; |
553 |
simError(); |
554 |
} |
555 |
|
556 |
pos[0] = x + current_atom->getPosX(); |
557 |
pos[1] = y + current_atom->getPosY(); |
558 |
pos[2] = z + current_atom->getPosZ(); |
559 |
|
560 |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
561 |
|
562 |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
563 |
|
564 |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
565 |
|
566 |
rotMat[0][0] = 1.0; |
567 |
rotMat[0][1] = 0.0; |
568 |
rotMat[0][2] = 0.0; |
569 |
|
570 |
rotMat[1][0] = 0.0; |
571 |
rotMat[1][1] = 1.0; |
572 |
rotMat[1][2] = 0.0; |
573 |
|
574 |
rotMat[2][0] = 0.0; |
575 |
rotMat[2][1] = 0.0; |
576 |
rotMat[2][2] = 1.0; |
577 |
|
578 |
dAtom->setA( rotMat ); |
579 |
} |
580 |
|
581 |
current_atom_ndx++; |
582 |
} |
583 |
|
584 |
current_mol++; |
585 |
current_comp_mol++; |
586 |
|
587 |
if( current_comp_mol >= components_nmol[current_comp] ){ |
588 |
|
589 |
current_comp_mol = 0; |
590 |
current_comp++; |
591 |
} |
592 |
} |
593 |
|
594 |
|
595 |
void SimSetup::gatherInfo( void ){ |
596 |
int i,j,k; |
597 |
|
598 |
ensembleCase = -1; |
599 |
ffCase = -1; |
600 |
|
601 |
// set the easy ones first |
602 |
|
603 |
for( i=0; i<nInfo; i++){ |
604 |
info[i].target_temp = globals->getTargetTemp(); |
605 |
info[i].dt = globals->getDt(); |
606 |
info[i].run_time = globals->getRunTime(); |
607 |
} |
608 |
n_components = globals->getNComponents(); |
609 |
|
610 |
|
611 |
// get the forceField |
612 |
|
613 |
strcpy( force_field, globals->getForceField() ); |
614 |
|
615 |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
616 |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
617 |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
618 |
else{ |
619 |
sprintf( painCave.errMsg, |
620 |
"SimSetup Error. Unrecognized force field -> %s\n", |
621 |
force_field ); |
622 |
painCave.isFatal = 1; |
623 |
simError(); |
624 |
} |
625 |
|
626 |
// get the ensemble |
627 |
|
628 |
strcpy( ensemble, globals->getEnsemble() ); |
629 |
|
630 |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
631 |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
632 |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
633 |
ensembleCase = NPTi_ENS; |
634 |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
635 |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
636 |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
637 |
else{ |
638 |
sprintf( painCave.errMsg, |
639 |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
640 |
"reverting to NVE for this simulation.\n", |
641 |
ensemble ); |
642 |
painCave.isFatal = 0; |
643 |
simError(); |
644 |
strcpy( ensemble, "NVE" ); |
645 |
ensembleCase = NVE_ENS; |
646 |
} |
647 |
|
648 |
for(i=0; i<nInfo; i++){ |
649 |
|
650 |
strcpy( info[i].ensemble, ensemble ); |
651 |
|
652 |
// get the mixing rule |
653 |
|
654 |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
655 |
info[i].usePBC = globals->getPBC(); |
656 |
} |
657 |
|
658 |
// get the components and calculate the tot_nMol and indvidual n_mol |
659 |
|
660 |
the_components = globals->getComponents(); |
661 |
components_nmol = new int[n_components]; |
662 |
|
663 |
|
664 |
if( !globals->haveNMol() ){ |
665 |
// we don't have the total number of molecules, so we assume it is |
666 |
// given in each component |
667 |
|
668 |
tot_nmol = 0; |
669 |
for( i=0; i<n_components; i++ ){ |
670 |
|
671 |
if( !the_components[i]->haveNMol() ){ |
672 |
// we have a problem |
673 |
sprintf( painCave.errMsg, |
674 |
"SimSetup Error. No global NMol or component NMol" |
675 |
" given. Cannot calculate the number of atoms.\n" ); |
676 |
painCave.isFatal = 1; |
677 |
simError(); |
678 |
} |
679 |
|
680 |
tot_nmol += the_components[i]->getNMol(); |
681 |
components_nmol[i] = the_components[i]->getNMol(); |
682 |
} |
683 |
} |
684 |
else{ |
685 |
sprintf( painCave.errMsg, |
686 |
"SimSetup error.\n" |
687 |
"\tSorry, the ability to specify total" |
688 |
" nMols and then give molfractions in the components\n" |
689 |
"\tis not currently supported." |
690 |
" Please give nMol in the components.\n" ); |
691 |
painCave.isFatal = 1; |
692 |
simError(); |
693 |
} |
694 |
|
695 |
// set the status, sample, and thermal kick times |
696 |
|
697 |
for(i=0; i<nInfo; i++){ |
698 |
|
699 |
if( globals->haveSampleTime() ){ |
700 |
info[i].sampleTime = globals->getSampleTime(); |
701 |
info[i].statusTime = info[i].sampleTime; |
702 |
info[i].thermalTime = info[i].sampleTime; |
703 |
} |
704 |
else{ |
705 |
info[i].sampleTime = globals->getRunTime(); |
706 |
info[i].statusTime = info[i].sampleTime; |
707 |
info[i].thermalTime = info[i].sampleTime; |
708 |
} |
709 |
|
710 |
if( globals->haveStatusTime() ){ |
711 |
info[i].statusTime = globals->getStatusTime(); |
712 |
} |
713 |
|
714 |
if( globals->haveThermalTime() ){ |
715 |
info[i].thermalTime = globals->getThermalTime(); |
716 |
} |
717 |
|
718 |
// check for the temperature set flag |
719 |
|
720 |
if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
721 |
|
722 |
// get some of the tricky things that may still be in the globals |
723 |
|
724 |
double boxVector[3]; |
725 |
if( globals->haveBox() ){ |
726 |
boxVector[0] = globals->getBox(); |
727 |
boxVector[1] = globals->getBox(); |
728 |
boxVector[2] = globals->getBox(); |
729 |
|
730 |
info[i].setBox( boxVector ); |
731 |
} |
732 |
else if( globals->haveDensity() ){ |
733 |
|
734 |
double vol; |
735 |
vol = (double)tot_nmol / globals->getDensity(); |
736 |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
737 |
boxVector[1] = boxVector[0]; |
738 |
boxVector[2] = boxVector[0]; |
739 |
|
740 |
info[i].setBox( boxVector ); |
741 |
} |
742 |
else{ |
743 |
if( !globals->haveBoxX() ){ |
744 |
sprintf( painCave.errMsg, |
745 |
"SimSetup error, no periodic BoxX size given.\n" ); |
746 |
painCave.isFatal = 1; |
747 |
simError(); |
748 |
} |
749 |
boxVector[0] = globals->getBoxX(); |
750 |
|
751 |
if( !globals->haveBoxY() ){ |
752 |
sprintf( painCave.errMsg, |
753 |
"SimSetup error, no periodic BoxY size given.\n" ); |
754 |
painCave.isFatal = 1; |
755 |
simError(); |
756 |
} |
757 |
boxVector[1] = globals->getBoxY(); |
758 |
|
759 |
if( !globals->haveBoxZ() ){ |
760 |
sprintf( painCave.errMsg, |
761 |
"SimSetup error, no periodic BoxZ size given.\n" ); |
762 |
painCave.isFatal = 1; |
763 |
simError(); |
764 |
} |
765 |
boxVector[2] = globals->getBoxZ(); |
766 |
|
767 |
info[i].setBox( boxVector ); |
768 |
} |
769 |
|
770 |
} |
771 |
|
772 |
#ifdef IS_MPI |
773 |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
774 |
MPIcheckPoint(); |
775 |
#endif // is_mpi |
776 |
|
777 |
} |
778 |
|
779 |
|
780 |
void SimSetup::finalInfoCheck( void ){ |
781 |
int index; |
782 |
int usesDipoles; |
783 |
int i; |
784 |
|
785 |
for(i=0; i<nInfo; i++){ |
786 |
// check electrostatic parameters |
787 |
|
788 |
index = 0; |
789 |
usesDipoles = 0; |
790 |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
791 |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
792 |
index++; |
793 |
} |
794 |
|
795 |
#ifdef IS_MPI |
796 |
int myUse = usesDipoles; |
797 |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
798 |
#endif //is_mpi |
799 |
|
800 |
double theEcr, theEst; |
801 |
|
802 |
if (globals->getUseRF() ) { |
803 |
info[i].useReactionField = 1; |
804 |
|
805 |
if( !globals->haveECR() ){ |
806 |
sprintf( painCave.errMsg, |
807 |
"SimSetup Warning: using default value of 1/2 the smallest " |
808 |
"box length for the electrostaticCutoffRadius.\n" |
809 |
"I hope you have a very fast processor!\n"); |
810 |
painCave.isFatal = 0; |
811 |
simError(); |
812 |
double smallest; |
813 |
smallest = info[i].boxL[0]; |
814 |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
815 |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
816 |
theEcr = 0.5 * smallest; |
817 |
} else { |
818 |
theEcr = globals->getECR(); |
819 |
} |
820 |
|
821 |
if( !globals->haveEST() ){ |
822 |
sprintf( painCave.errMsg, |
823 |
"SimSetup Warning: using default value of 0.05 * the " |
824 |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 |
); |
826 |
painCave.isFatal = 0; |
827 |
simError(); |
828 |
theEst = 0.05 * theEcr; |
829 |
} else { |
830 |
theEst= globals->getEST(); |
831 |
} |
832 |
|
833 |
info[i].setEcr( theEcr, theEst ); |
834 |
|
835 |
if(!globals->haveDielectric() ){ |
836 |
sprintf( painCave.errMsg, |
837 |
"SimSetup Error: You are trying to use Reaction Field without" |
838 |
"setting a dielectric constant!\n" |
839 |
); |
840 |
painCave.isFatal = 1; |
841 |
simError(); |
842 |
} |
843 |
info[i].dielectric = globals->getDielectric(); |
844 |
} |
845 |
else { |
846 |
if (usesDipoles) { |
847 |
|
848 |
if( !globals->haveECR() ){ |
849 |
sprintf( painCave.errMsg, |
850 |
"SimSetup Warning: using default value of 1/2 the smallest " |
851 |
"box length for the electrostaticCutoffRadius.\n" |
852 |
"I hope you have a very fast processor!\n"); |
853 |
painCave.isFatal = 0; |
854 |
simError(); |
855 |
double smallest; |
856 |
smallest = info[i].boxL[0]; |
857 |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
858 |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
859 |
theEcr = 0.5 * smallest; |
860 |
} else { |
861 |
theEcr = globals->getECR(); |
862 |
} |
863 |
|
864 |
if( !globals->haveEST() ){ |
865 |
sprintf( painCave.errMsg, |
866 |
"SimSetup Warning: using default value of 0.05 * the " |
867 |
"electrostaticCutoffRadius for the " |
868 |
"electrostaticSkinThickness\n" |
869 |
); |
870 |
painCave.isFatal = 0; |
871 |
simError(); |
872 |
theEst = 0.05 * theEcr; |
873 |
} else { |
874 |
theEst= globals->getEST(); |
875 |
} |
876 |
|
877 |
info[i].setEcr( theEcr, theEst ); |
878 |
} |
879 |
} |
880 |
} |
881 |
|
882 |
#ifdef IS_MPI |
883 |
strcpy( checkPointMsg, "post processing checks out" ); |
884 |
MPIcheckPoint(); |
885 |
#endif // is_mpi |
886 |
|
887 |
} |
888 |
|
889 |
void SimSetup::initSystemCoords( void ){ |
890 |
int i; |
891 |
|
892 |
char* inName; |
893 |
|
894 |
|
895 |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
896 |
|
897 |
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
898 |
|
899 |
if( globals->haveInitialConfig() ){ |
900 |
|
901 |
InitializeFromFile* fileInit; |
902 |
#ifdef IS_MPI // is_mpi |
903 |
if( worldRank == 0 ){ |
904 |
#endif //is_mpi |
905 |
inName = globals->getInitialConfig(); |
906 |
double* tempDouble = new double[1000000]; |
907 |
fileInit = new InitializeFromFile( inName ); |
908 |
#ifdef IS_MPI |
909 |
}else fileInit = new InitializeFromFile( NULL ); |
910 |
#endif |
911 |
fileInit->readInit( info ); // default velocities on |
912 |
|
913 |
delete fileInit; |
914 |
} |
915 |
else{ |
916 |
|
917 |
#ifdef IS_MPI |
918 |
|
919 |
// no init from bass |
920 |
|
921 |
sprintf( painCave.errMsg, |
922 |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
923 |
painCave.isFatal; |
924 |
simError(); |
925 |
|
926 |
#else |
927 |
|
928 |
initFromBass(); |
929 |
|
930 |
|
931 |
#endif |
932 |
} |
933 |
|
934 |
#ifdef IS_MPI |
935 |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
936 |
MPIcheckPoint(); |
937 |
#endif // is_mpi |
938 |
|
939 |
} |
940 |
|
941 |
|
942 |
void SimSetup::makeOutNames( void ){ |
943 |
|
944 |
int k; |
945 |
|
946 |
|
947 |
for(k=0; k<nInfo; k++){ |
948 |
|
949 |
#ifdef IS_MPI |
950 |
if( worldRank == 0 ){ |
951 |
#endif // is_mpi |
952 |
|
953 |
if( globals->haveFinalConfig() ){ |
954 |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
955 |
} |
956 |
else{ |
957 |
strcpy( info[k].finalName, inFileName ); |
958 |
char* endTest; |
959 |
int nameLength = strlen( info[k].finalName ); |
960 |
endTest = &(info[k].finalName[nameLength - 5]); |
961 |
if( !strcmp( endTest, ".bass" ) ){ |
962 |
strcpy( endTest, ".eor" ); |
963 |
} |
964 |
else if( !strcmp( endTest, ".BASS" ) ){ |
965 |
strcpy( endTest, ".eor" ); |
966 |
} |
967 |
else{ |
968 |
endTest = &(info[k].finalName[nameLength - 4]); |
969 |
if( !strcmp( endTest, ".bss" ) ){ |
970 |
strcpy( endTest, ".eor" ); |
971 |
} |
972 |
else if( !strcmp( endTest, ".mdl" ) ){ |
973 |
strcpy( endTest, ".eor" ); |
974 |
} |
975 |
else{ |
976 |
strcat( info[k].finalName, ".eor" ); |
977 |
} |
978 |
} |
979 |
} |
980 |
|
981 |
// make the sample and status out names |
982 |
|
983 |
strcpy( info[k].sampleName, inFileName ); |
984 |
char* endTest; |
985 |
int nameLength = strlen( info[k].sampleName ); |
986 |
endTest = &(info[k].sampleName[nameLength - 5]); |
987 |
if( !strcmp( endTest, ".bass" ) ){ |
988 |
strcpy( endTest, ".dump" ); |
989 |
} |
990 |
else if( !strcmp( endTest, ".BASS" ) ){ |
991 |
strcpy( endTest, ".dump" ); |
992 |
} |
993 |
else{ |
994 |
endTest = &(info[k].sampleName[nameLength - 4]); |
995 |
if( !strcmp( endTest, ".bss" ) ){ |
996 |
strcpy( endTest, ".dump" ); |
997 |
} |
998 |
else if( !strcmp( endTest, ".mdl" ) ){ |
999 |
strcpy( endTest, ".dump" ); |
1000 |
} |
1001 |
else{ |
1002 |
strcat( info[k].sampleName, ".dump" ); |
1003 |
} |
1004 |
} |
1005 |
|
1006 |
strcpy( info[k].statusName, inFileName ); |
1007 |
nameLength = strlen( info[k].statusName ); |
1008 |
endTest = &(info[k].statusName[nameLength - 5]); |
1009 |
if( !strcmp( endTest, ".bass" ) ){ |
1010 |
strcpy( endTest, ".stat" ); |
1011 |
} |
1012 |
else if( !strcmp( endTest, ".BASS" ) ){ |
1013 |
strcpy( endTest, ".stat" ); |
1014 |
} |
1015 |
else{ |
1016 |
endTest = &(info[k].statusName[nameLength - 4]); |
1017 |
if( !strcmp( endTest, ".bss" ) ){ |
1018 |
strcpy( endTest, ".stat" ); |
1019 |
} |
1020 |
else if( !strcmp( endTest, ".mdl" ) ){ |
1021 |
strcpy( endTest, ".stat" ); |
1022 |
} |
1023 |
else{ |
1024 |
strcat( info[k].statusName, ".stat" ); |
1025 |
} |
1026 |
} |
1027 |
|
1028 |
#ifdef IS_MPI |
1029 |
} |
1030 |
#endif // is_mpi |
1031 |
} |
1032 |
} |
1033 |
|
1034 |
|
1035 |
void SimSetup::sysObjectsCreation( void ){ |
1036 |
|
1037 |
int i,k; |
1038 |
|
1039 |
// create the forceField |
1040 |
|
1041 |
createFF(); |
1042 |
|
1043 |
// extract componentList |
1044 |
|
1045 |
compList(); |
1046 |
|
1047 |
// calc the number of atoms, bond, bends, and torsions |
1048 |
|
1049 |
calcSysValues(); |
1050 |
|
1051 |
#ifdef IS_MPI |
1052 |
// divide the molecules among the processors |
1053 |
|
1054 |
mpiMolDivide(); |
1055 |
#endif //is_mpi |
1056 |
|
1057 |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1058 |
|
1059 |
makeSysArrays(); |
1060 |
|
1061 |
// make and initialize the molecules (all but atomic coordinates) |
1062 |
|
1063 |
makeMolecules(); |
1064 |
|
1065 |
for(k=0; k<nInfo; k++){ |
1066 |
info[k].identArray = new int[info[k].n_atoms]; |
1067 |
for(i=0; i<info[k].n_atoms; i++){ |
1068 |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1069 |
} |
1070 |
} |
1071 |
} |
1072 |
|
1073 |
|
1074 |
void SimSetup::createFF( void ){ |
1075 |
|
1076 |
switch( ffCase ){ |
1077 |
|
1078 |
case FF_DUFF: |
1079 |
the_ff = new DUFF(); |
1080 |
break; |
1081 |
|
1082 |
case FF_LJ: |
1083 |
the_ff = new LJFF(); |
1084 |
break; |
1085 |
|
1086 |
case FF_EAM: |
1087 |
the_ff = new EAM_FF(); |
1088 |
break; |
1089 |
|
1090 |
default: |
1091 |
sprintf( painCave.errMsg, |
1092 |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1093 |
painCave.isFatal = 1; |
1094 |
simError(); |
1095 |
} |
1096 |
|
1097 |
#ifdef IS_MPI |
1098 |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1099 |
MPIcheckPoint(); |
1100 |
#endif // is_mpi |
1101 |
|
1102 |
} |
1103 |
|
1104 |
|
1105 |
void SimSetup::compList( void ){ |
1106 |
|
1107 |
int i; |
1108 |
char* id; |
1109 |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1110 |
LinkedMolStamp* currentStamp = NULL; |
1111 |
comp_stamps = new MoleculeStamp*[n_components]; |
1112 |
|
1113 |
// make an array of molecule stamps that match the components used. |
1114 |
// also extract the used stamps out into a separate linked list |
1115 |
|
1116 |
for(i=0; i<nInfo; i++){ |
1117 |
info[i].nComponents = n_components; |
1118 |
info[i].componentsNmol = components_nmol; |
1119 |
info[i].compStamps = comp_stamps; |
1120 |
info[i].headStamp = headStamp; |
1121 |
} |
1122 |
|
1123 |
|
1124 |
for( i=0; i<n_components; i++ ){ |
1125 |
|
1126 |
id = the_components[i]->getType(); |
1127 |
comp_stamps[i] = NULL; |
1128 |
|
1129 |
// check to make sure the component isn't already in the list |
1130 |
|
1131 |
comp_stamps[i] = headStamp->match( id ); |
1132 |
if( comp_stamps[i] == NULL ){ |
1133 |
|
1134 |
// extract the component from the list; |
1135 |
|
1136 |
currentStamp = stamps->extractMolStamp( id ); |
1137 |
if( currentStamp == NULL ){ |
1138 |
sprintf( painCave.errMsg, |
1139 |
"SimSetup error: Component \"%s\" was not found in the " |
1140 |
"list of declared molecules\n", |
1141 |
id ); |
1142 |
painCave.isFatal = 1; |
1143 |
simError(); |
1144 |
} |
1145 |
|
1146 |
headStamp->add( currentStamp ); |
1147 |
comp_stamps[i] = headStamp->match( id ); |
1148 |
} |
1149 |
} |
1150 |
|
1151 |
#ifdef IS_MPI |
1152 |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1153 |
MPIcheckPoint(); |
1154 |
#endif // is_mpi |
1155 |
|
1156 |
|
1157 |
} |
1158 |
|
1159 |
void SimSetup::calcSysValues( void ){ |
1160 |
int i, j, k; |
1161 |
|
1162 |
int *molMembershipArray; |
1163 |
|
1164 |
tot_atoms = 0; |
1165 |
tot_bonds = 0; |
1166 |
tot_bends = 0; |
1167 |
tot_torsions = 0; |
1168 |
for( i=0; i<n_components; i++ ){ |
1169 |
|
1170 |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1171 |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1172 |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1173 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1174 |
} |
1175 |
|
1176 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1177 |
molMembershipArray = new int[tot_atoms]; |
1178 |
|
1179 |
for(i=0; i<nInfo; i++){ |
1180 |
info[i].n_atoms = tot_atoms; |
1181 |
info[i].n_bonds = tot_bonds; |
1182 |
info[i].n_bends = tot_bends; |
1183 |
info[i].n_torsions = tot_torsions; |
1184 |
info[i].n_SRI = tot_SRI; |
1185 |
info[i].n_mol = tot_nmol; |
1186 |
|
1187 |
info[i].molMembershipArray = molMembershipArray; |
1188 |
} |
1189 |
} |
1190 |
|
1191 |
#ifdef IS_MPI |
1192 |
|
1193 |
void SimSetup::mpiMolDivide( void ){ |
1194 |
|
1195 |
int i, j, k; |
1196 |
int localMol, allMol; |
1197 |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1198 |
|
1199 |
mpiSim = new mpiSimulation( info ); |
1200 |
|
1201 |
globalIndex = mpiSim->divideLabor(); |
1202 |
|
1203 |
// set up the local variables |
1204 |
|
1205 |
mol2proc = mpiSim->getMolToProcMap(); |
1206 |
molCompType = mpiSim->getMolComponentType(); |
1207 |
|
1208 |
allMol = 0; |
1209 |
localMol = 0; |
1210 |
local_atoms = 0; |
1211 |
local_bonds = 0; |
1212 |
local_bends = 0; |
1213 |
local_torsions = 0; |
1214 |
globalAtomIndex = 0; |
1215 |
|
1216 |
|
1217 |
for( i=0; i<n_components; i++ ){ |
1218 |
|
1219 |
for( j=0; j<components_nmol[i]; j++ ){ |
1220 |
|
1221 |
if( mol2proc[allMol] == worldRank ){ |
1222 |
|
1223 |
local_atoms += comp_stamps[i]->getNAtoms(); |
1224 |
local_bonds += comp_stamps[i]->getNBonds(); |
1225 |
local_bends += comp_stamps[i]->getNBends(); |
1226 |
local_torsions += comp_stamps[i]->getNTorsions(); |
1227 |
localMol++; |
1228 |
} |
1229 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1230 |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1231 |
globalAtomIndex++; |
1232 |
} |
1233 |
|
1234 |
allMol++; |
1235 |
} |
1236 |
} |
1237 |
local_SRI = local_bonds + local_bends + local_torsions; |
1238 |
|
1239 |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1240 |
|
1241 |
if( local_atoms != info[0].n_atoms ){ |
1242 |
sprintf( painCave.errMsg, |
1243 |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1244 |
" localAtom (%d) are not equal.\n", |
1245 |
info[0].n_atoms, |
1246 |
local_atoms ); |
1247 |
painCave.isFatal = 1; |
1248 |
simError(); |
1249 |
} |
1250 |
|
1251 |
info[0].n_bonds = local_bonds; |
1252 |
info[0].n_bends = local_bends; |
1253 |
info[0].n_torsions = local_torsions; |
1254 |
info[0].n_SRI = local_SRI; |
1255 |
info[0].n_mol = localMol; |
1256 |
|
1257 |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1258 |
MPIcheckPoint(); |
1259 |
} |
1260 |
|
1261 |
#endif // is_mpi |
1262 |
|
1263 |
|
1264 |
void SimSetup::makeSysArrays( void ){ |
1265 |
int i, j, k, l; |
1266 |
|
1267 |
Atom** the_atoms; |
1268 |
Molecule* the_molecules; |
1269 |
Exclude** the_excludes; |
1270 |
|
1271 |
|
1272 |
for(l=0; l<nInfo; l++){ |
1273 |
|
1274 |
// create the atom and short range interaction arrays |
1275 |
|
1276 |
the_atoms = new Atom*[info[l].n_atoms]; |
1277 |
the_molecules = new Molecule[info[l].n_mol]; |
1278 |
int molIndex; |
1279 |
|
1280 |
// initialize the molecule's stampID's |
1281 |
|
1282 |
#ifdef IS_MPI |
1283 |
|
1284 |
|
1285 |
molIndex = 0; |
1286 |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1287 |
|
1288 |
if(mol2proc[i] == worldRank ){ |
1289 |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1290 |
the_molecules[molIndex].setMyIndex( molIndex ); |
1291 |
the_molecules[molIndex].setGlobalIndex( i ); |
1292 |
molIndex++; |
1293 |
} |
1294 |
} |
1295 |
|
1296 |
#else // is_mpi |
1297 |
|
1298 |
molIndex = 0; |
1299 |
globalAtomIndex = 0; |
1300 |
for(i=0; i<n_components; i++){ |
1301 |
for(j=0; j<components_nmol[i]; j++ ){ |
1302 |
the_molecules[molIndex].setStampID( i ); |
1303 |
the_molecules[molIndex].setMyIndex( molIndex ); |
1304 |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1305 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1306 |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1307 |
globalAtomIndex++; |
1308 |
} |
1309 |
molIndex++; |
1310 |
} |
1311 |
} |
1312 |
|
1313 |
|
1314 |
#endif // is_mpi |
1315 |
|
1316 |
|
1317 |
if( info[l].n_SRI ){ |
1318 |
|
1319 |
Exclude::createArray(info[l].n_SRI); |
1320 |
the_excludes = new Exclude*[info[l].n_SRI]; |
1321 |
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1322 |
the_excludes[ex] = new Exclude(ex); |
1323 |
} |
1324 |
info[l].globalExcludes = new int; |
1325 |
info[l].n_exclude = info[l].n_SRI; |
1326 |
} |
1327 |
else{ |
1328 |
|
1329 |
Exclude::createArray( 1 ); |
1330 |
the_excludes = new Exclude*; |
1331 |
the_excludes[0] = new Exclude(0); |
1332 |
the_excludes[0]->setPair( 0,0 ); |
1333 |
info[l].globalExcludes = new int; |
1334 |
info[l].globalExcludes[0] = 0; |
1335 |
info[l].n_exclude = 0; |
1336 |
} |
1337 |
|
1338 |
// set the arrays into the SimInfo object |
1339 |
|
1340 |
info[l].atoms = the_atoms; |
1341 |
info[l].molecules = the_molecules; |
1342 |
info[l].nGlobalExcludes = 0; |
1343 |
info[l].excludes = the_excludes; |
1344 |
|
1345 |
the_ff->setSimInfo( info ); |
1346 |
|
1347 |
} |
1348 |
} |
1349 |
|
1350 |
void SimSetup::makeIntegrator( void ){ |
1351 |
|
1352 |
int k; |
1353 |
|
1354 |
NVT<RealIntegrator>* myNVT = NULL; |
1355 |
NPTi<RealIntegrator>* myNPTi = NULL; |
1356 |
NPTf<RealIntegrator>* myNPTf = NULL; |
1357 |
NPTim<RealIntegrator>* myNPTim = NULL; |
1358 |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1359 |
|
1360 |
for(k=0; k<nInfo; k++){ |
1361 |
|
1362 |
switch( ensembleCase ){ |
1363 |
|
1364 |
case NVE_ENS: |
1365 |
if (globals->haveZconstraints()){ |
1366 |
setupZConstraint(info[k]); |
1367 |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1368 |
} |
1369 |
|
1370 |
else |
1371 |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1372 |
break; |
1373 |
|
1374 |
case NVT_ENS: |
1375 |
if (globals->haveZconstraints()){ |
1376 |
setupZConstraint(info[k]); |
1377 |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1378 |
} |
1379 |
else |
1380 |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1381 |
|
1382 |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1383 |
|
1384 |
if (globals->haveTauThermostat()) |
1385 |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1386 |
|
1387 |
else { |
1388 |
sprintf( painCave.errMsg, |
1389 |
"SimSetup error: If you use the NVT\n" |
1390 |
" ensemble, you must set tauThermostat.\n"); |
1391 |
painCave.isFatal = 1; |
1392 |
simError(); |
1393 |
} |
1394 |
break; |
1395 |
|
1396 |
case NPTi_ENS: |
1397 |
if (globals->haveZconstraints()){ |
1398 |
setupZConstraint(info[k]); |
1399 |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1400 |
} |
1401 |
else |
1402 |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1403 |
|
1404 |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1405 |
|
1406 |
if (globals->haveTargetPressure()) |
1407 |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1408 |
else { |
1409 |
sprintf( painCave.errMsg, |
1410 |
"SimSetup error: If you use a constant pressure\n" |
1411 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1412 |
painCave.isFatal = 1; |
1413 |
simError(); |
1414 |
} |
1415 |
|
1416 |
if( globals->haveTauThermostat() ) |
1417 |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1418 |
else{ |
1419 |
sprintf( painCave.errMsg, |
1420 |
"SimSetup error: If you use an NPT\n" |
1421 |
" ensemble, you must set tauThermostat.\n"); |
1422 |
painCave.isFatal = 1; |
1423 |
simError(); |
1424 |
} |
1425 |
|
1426 |
if( globals->haveTauBarostat() ) |
1427 |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1428 |
else{ |
1429 |
sprintf( painCave.errMsg, |
1430 |
"SimSetup error: If you use an NPT\n" |
1431 |
" ensemble, you must set tauBarostat.\n"); |
1432 |
painCave.isFatal = 1; |
1433 |
simError(); |
1434 |
} |
1435 |
break; |
1436 |
|
1437 |
case NPTf_ENS: |
1438 |
if (globals->haveZconstraints()){ |
1439 |
setupZConstraint(info[k]); |
1440 |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1441 |
} |
1442 |
else |
1443 |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1444 |
|
1445 |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1446 |
|
1447 |
if (globals->haveTargetPressure()) |
1448 |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1449 |
else { |
1450 |
sprintf( painCave.errMsg, |
1451 |
"SimSetup error: If you use a constant pressure\n" |
1452 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1453 |
painCave.isFatal = 1; |
1454 |
simError(); |
1455 |
} |
1456 |
|
1457 |
if( globals->haveTauThermostat() ) |
1458 |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1459 |
else{ |
1460 |
sprintf( painCave.errMsg, |
1461 |
"SimSetup error: If you use an NPT\n" |
1462 |
" ensemble, you must set tauThermostat.\n"); |
1463 |
painCave.isFatal = 1; |
1464 |
simError(); |
1465 |
} |
1466 |
|
1467 |
if( globals->haveTauBarostat() ) |
1468 |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1469 |
else{ |
1470 |
sprintf( painCave.errMsg, |
1471 |
"SimSetup error: If you use an NPT\n" |
1472 |
" ensemble, you must set tauBarostat.\n"); |
1473 |
painCave.isFatal = 1; |
1474 |
simError(); |
1475 |
} |
1476 |
break; |
1477 |
|
1478 |
case NPTim_ENS: |
1479 |
if (globals->haveZconstraints()){ |
1480 |
setupZConstraint(info[k]); |
1481 |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1482 |
} |
1483 |
else |
1484 |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1485 |
|
1486 |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1487 |
|
1488 |
if (globals->haveTargetPressure()) |
1489 |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1490 |
else { |
1491 |
sprintf( painCave.errMsg, |
1492 |
"SimSetup error: If you use a constant pressure\n" |
1493 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1494 |
painCave.isFatal = 1; |
1495 |
simError(); |
1496 |
} |
1497 |
|
1498 |
if( globals->haveTauThermostat() ) |
1499 |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1500 |
else{ |
1501 |
sprintf( painCave.errMsg, |
1502 |
"SimSetup error: If you use an NPT\n" |
1503 |
" ensemble, you must set tauThermostat.\n"); |
1504 |
painCave.isFatal = 1; |
1505 |
simError(); |
1506 |
} |
1507 |
|
1508 |
if( globals->haveTauBarostat() ) |
1509 |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1510 |
else{ |
1511 |
sprintf( painCave.errMsg, |
1512 |
"SimSetup error: If you use an NPT\n" |
1513 |
" ensemble, you must set tauBarostat.\n"); |
1514 |
painCave.isFatal = 1; |
1515 |
simError(); |
1516 |
} |
1517 |
break; |
1518 |
|
1519 |
case NPTfm_ENS: |
1520 |
if (globals->haveZconstraints()){ |
1521 |
setupZConstraint(info[k]); |
1522 |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1523 |
} |
1524 |
else |
1525 |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1526 |
|
1527 |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1528 |
|
1529 |
if (globals->haveTargetPressure()) |
1530 |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1531 |
else { |
1532 |
sprintf( painCave.errMsg, |
1533 |
"SimSetup error: If you use a constant pressure\n" |
1534 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1535 |
painCave.isFatal = 1; |
1536 |
simError(); |
1537 |
} |
1538 |
|
1539 |
if( globals->haveTauThermostat() ) |
1540 |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1541 |
else{ |
1542 |
sprintf( painCave.errMsg, |
1543 |
"SimSetup error: If you use an NPT\n" |
1544 |
" ensemble, you must set tauThermostat.\n"); |
1545 |
painCave.isFatal = 1; |
1546 |
simError(); |
1547 |
} |
1548 |
|
1549 |
if( globals->haveTauBarostat() ) |
1550 |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1551 |
else{ |
1552 |
sprintf( painCave.errMsg, |
1553 |
"SimSetup error: If you use an NPT\n" |
1554 |
" ensemble, you must set tauBarostat.\n"); |
1555 |
painCave.isFatal = 1; |
1556 |
simError(); |
1557 |
} |
1558 |
break; |
1559 |
|
1560 |
default: |
1561 |
sprintf( painCave.errMsg, |
1562 |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1563 |
painCave.isFatal = 1; |
1564 |
simError(); |
1565 |
} |
1566 |
} |
1567 |
} |
1568 |
|
1569 |
void SimSetup::initFortran( void ){ |
1570 |
|
1571 |
info[0].refreshSim(); |
1572 |
|
1573 |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1574 |
the_ff->initForceField( LB_MIXING_RULE ); |
1575 |
} |
1576 |
else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1577 |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1578 |
} |
1579 |
else{ |
1580 |
sprintf( painCave.errMsg, |
1581 |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1582 |
info[0].mixingRule ); |
1583 |
painCave.isFatal = 1; |
1584 |
simError(); |
1585 |
} |
1586 |
|
1587 |
|
1588 |
#ifdef IS_MPI |
1589 |
strcpy( checkPointMsg, |
1590 |
"Successfully intialized the mixingRule for Fortran." ); |
1591 |
MPIcheckPoint(); |
1592 |
#endif // is_mpi |
1593 |
|
1594 |
} |
1595 |
|
1596 |
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1597 |
{ |
1598 |
int nZConstraints; |
1599 |
ZconStamp** zconStamp; |
1600 |
|
1601 |
if(globals->haveZconstraintTime()){ |
1602 |
|
1603 |
//add sample time of z-constraint into SimInfo's property list |
1604 |
DoubleData* zconsTimeProp = new DoubleData(); |
1605 |
zconsTimeProp->setID(ZCONSTIME_ID); |
1606 |
zconsTimeProp->setData(globals->getZconsTime()); |
1607 |
theInfo.addProperty(zconsTimeProp); |
1608 |
} |
1609 |
else{ |
1610 |
sprintf( painCave.errMsg, |
1611 |
"ZConstraint error: If you use an ZConstraint\n" |
1612 |
" , you must set sample time.\n"); |
1613 |
painCave.isFatal = 1; |
1614 |
simError(); |
1615 |
} |
1616 |
|
1617 |
//push zconsTol into siminfo, if user does not specify |
1618 |
//value for zconsTol, a default value will be used |
1619 |
DoubleData* zconsTol = new DoubleData(); |
1620 |
zconsTol->setID(ZCONSTOL_ID); |
1621 |
if(globals->haveZconsTol()){ |
1622 |
zconsTol->setData(globals->getZconsTol()); |
1623 |
} |
1624 |
else{ |
1625 |
double defaultZConsTol = 0.01; |
1626 |
sprintf( painCave.errMsg, |
1627 |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1628 |
" , default value %f is used.\n", defaultZConsTol); |
1629 |
painCave.isFatal = 0; |
1630 |
simError(); |
1631 |
|
1632 |
zconsTol->setData(defaultZConsTol); |
1633 |
} |
1634 |
theInfo.addProperty(zconsTol); |
1635 |
|
1636 |
//set Force Substraction Policy |
1637 |
StringData* zconsForcePolicy = new StringData(); |
1638 |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1639 |
|
1640 |
if(globals->haveZconsForcePolicy()){ |
1641 |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1642 |
} |
1643 |
else{ |
1644 |
sprintf( painCave.errMsg, |
1645 |
"ZConstraint Warning: User does not set force substraction policy, " |
1646 |
"average force substraction policy is used\n"); |
1647 |
painCave.isFatal = 0; |
1648 |
simError(); |
1649 |
zconsForcePolicy->setData("BYNUMBER"); |
1650 |
} |
1651 |
|
1652 |
theInfo.addProperty(zconsForcePolicy); |
1653 |
|
1654 |
//Determine the name of ouput file and add it into SimInfo's property list |
1655 |
//Be careful, do not use inFileName, since it is a pointer which |
1656 |
//point to a string at master node, and slave nodes do not contain that string |
1657 |
|
1658 |
string zconsOutput(theInfo.finalName); |
1659 |
|
1660 |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1661 |
|
1662 |
StringData* zconsFilename = new StringData(); |
1663 |
zconsFilename->setID(ZCONSFILENAME_ID); |
1664 |
zconsFilename->setData(zconsOutput); |
1665 |
|
1666 |
theInfo.addProperty(zconsFilename); |
1667 |
|
1668 |
//setup index, pos and other parameters of z-constraint molecules |
1669 |
nZConstraints = globals->getNzConstraints(); |
1670 |
theInfo.nZconstraints = nZConstraints; |
1671 |
|
1672 |
zconStamp = globals->getZconStamp(); |
1673 |
ZConsParaItem tempParaItem; |
1674 |
|
1675 |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1676 |
zconsParaData->setID(ZCONSPARADATA_ID); |
1677 |
|
1678 |
for(int i = 0; i < nZConstraints; i++){ |
1679 |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1680 |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1681 |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1682 |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1683 |
|
1684 |
zconsParaData->addItem(tempParaItem); |
1685 |
} |
1686 |
|
1687 |
//sort the parameters by index of molecules |
1688 |
zconsParaData->sortByIndex(); |
1689 |
|
1690 |
//push data into siminfo, therefore, we can retrieve later |
1691 |
theInfo.addProperty(zconsParaData); |
1692 |
|
1693 |
} |