1 |
#include <algorithm> |
2 |
#include <cstdlib> |
3 |
#include <iostream> |
4 |
#include <cmath> |
5 |
#include <string> |
6 |
#include <sys/time.h> |
7 |
|
8 |
#include "SimSetup.hpp" |
9 |
#include "ReadWrite.hpp" |
10 |
#include "parse_me.h" |
11 |
#include "Integrator.hpp" |
12 |
#include "simError.h" |
13 |
|
14 |
#ifdef IS_MPI |
15 |
#include "mpiBASS.h" |
16 |
#include "mpiSimulation.hpp" |
17 |
#endif |
18 |
|
19 |
// some defines for ensemble and Forcefield cases |
20 |
|
21 |
#define NVE_ENS 0 |
22 |
#define NVT_ENS 1 |
23 |
#define NPTi_ENS 2 |
24 |
#define NPTf_ENS 3 |
25 |
#define NPTim_ENS 4 |
26 |
#define NPTfm_ENS 5 |
27 |
|
28 |
#define FF_DUFF 0 |
29 |
#define FF_LJ 1 |
30 |
#define FF_EAM 2 |
31 |
|
32 |
using namespace std; |
33 |
|
34 |
SimSetup::SimSetup(){ |
35 |
|
36 |
isInfoArray = 0; |
37 |
nInfo = 1; |
38 |
|
39 |
stamps = new MakeStamps(); |
40 |
globals = new Globals(); |
41 |
|
42 |
|
43 |
#ifdef IS_MPI |
44 |
strcpy( checkPointMsg, "SimSetup creation successful" ); |
45 |
MPIcheckPoint(); |
46 |
#endif // IS_MPI |
47 |
} |
48 |
|
49 |
SimSetup::~SimSetup(){ |
50 |
delete stamps; |
51 |
delete globals; |
52 |
} |
53 |
|
54 |
void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
55 |
info = the_info; |
56 |
nInfo = theNinfo; |
57 |
isInfoArray = 1; |
58 |
} |
59 |
|
60 |
|
61 |
void SimSetup::parseFile( char* fileName ){ |
62 |
|
63 |
#ifdef IS_MPI |
64 |
if( worldRank == 0 ){ |
65 |
#endif // is_mpi |
66 |
|
67 |
inFileName = fileName; |
68 |
set_interface_stamps( stamps, globals ); |
69 |
|
70 |
#ifdef IS_MPI |
71 |
mpiEventInit(); |
72 |
#endif |
73 |
|
74 |
yacc_BASS( fileName ); |
75 |
|
76 |
#ifdef IS_MPI |
77 |
throwMPIEvent(NULL); |
78 |
} |
79 |
else receiveParse(); |
80 |
#endif |
81 |
|
82 |
} |
83 |
|
84 |
#ifdef IS_MPI |
85 |
void SimSetup::receiveParse(void){ |
86 |
|
87 |
set_interface_stamps( stamps, globals ); |
88 |
mpiEventInit(); |
89 |
MPIcheckPoint(); |
90 |
mpiEventLoop(); |
91 |
|
92 |
} |
93 |
|
94 |
#endif // is_mpi |
95 |
|
96 |
void SimSetup::createSim(void){ |
97 |
|
98 |
int i, j, k, globalAtomIndex; |
99 |
|
100 |
// gather all of the information from the Bass file |
101 |
|
102 |
gatherInfo(); |
103 |
|
104 |
// creation of complex system objects |
105 |
|
106 |
sysObjectsCreation(); |
107 |
|
108 |
// check on the post processing info |
109 |
|
110 |
finalInfoCheck(); |
111 |
|
112 |
// initialize the system coordinates |
113 |
|
114 |
if( !isInfoArray ) initSystemCoords(); |
115 |
|
116 |
// make the output filenames |
117 |
|
118 |
makeOutNames(); |
119 |
|
120 |
// make the integrator |
121 |
|
122 |
makeIntegrator(); |
123 |
|
124 |
#ifdef IS_MPI |
125 |
mpiSim->mpiRefresh(); |
126 |
#endif |
127 |
|
128 |
// initialize the Fortran |
129 |
|
130 |
initFortran(); |
131 |
|
132 |
|
133 |
|
134 |
} |
135 |
|
136 |
|
137 |
void SimSetup::makeMolecules( void ){ |
138 |
|
139 |
int k,l; |
140 |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
141 |
molInit molInfo; |
142 |
DirectionalAtom* dAtom; |
143 |
LinkedAssign* extras; |
144 |
LinkedAssign* current_extra; |
145 |
AtomStamp* currentAtom; |
146 |
BondStamp* currentBond; |
147 |
BendStamp* currentBend; |
148 |
TorsionStamp* currentTorsion; |
149 |
|
150 |
bond_pair* theBonds; |
151 |
bend_set* theBends; |
152 |
torsion_set* theTorsions; |
153 |
|
154 |
|
155 |
//init the forceField paramters |
156 |
|
157 |
the_ff->readParams(); |
158 |
|
159 |
|
160 |
// init the atoms |
161 |
|
162 |
double ux, uy, uz, u, uSqr; |
163 |
|
164 |
for(k=0; k<nInfo; k++){ |
165 |
|
166 |
the_ff->setSimInfo( &(info[k]) ); |
167 |
|
168 |
atomOffset = 0; |
169 |
excludeOffset = 0; |
170 |
for(i=0; i<info[k].n_mol; i++){ |
171 |
|
172 |
stampID = info[k].molecules[i].getStampID(); |
173 |
|
174 |
molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
175 |
molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
176 |
molInfo.nBends = comp_stamps[stampID]->getNBends(); |
177 |
molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
178 |
molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
179 |
|
180 |
molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
181 |
molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
182 |
molInfo.myBonds = new Bond*[molInfo.nBonds]; |
183 |
molInfo.myBends = new Bend*[molInfo.nBends]; |
184 |
molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
185 |
|
186 |
theBonds = new bond_pair[molInfo.nBonds]; |
187 |
theBends = new bend_set[molInfo.nBends]; |
188 |
theTorsions = new torsion_set[molInfo.nTorsions]; |
189 |
|
190 |
// make the Atoms |
191 |
|
192 |
for(j=0; j<molInfo.nAtoms; j++){ |
193 |
|
194 |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
195 |
if( currentAtom->haveOrientation() ){ |
196 |
|
197 |
dAtom = new DirectionalAtom( (j + atomOffset), |
198 |
info[k].getConfiguration() ); |
199 |
info[k].n_oriented++; |
200 |
molInfo.myAtoms[j] = dAtom; |
201 |
|
202 |
ux = currentAtom->getOrntX(); |
203 |
uy = currentAtom->getOrntY(); |
204 |
uz = currentAtom->getOrntZ(); |
205 |
|
206 |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
207 |
|
208 |
u = sqrt( uSqr ); |
209 |
ux = ux / u; |
210 |
uy = uy / u; |
211 |
uz = uz / u; |
212 |
|
213 |
dAtom->setSUx( ux ); |
214 |
dAtom->setSUy( uy ); |
215 |
dAtom->setSUz( uz ); |
216 |
} |
217 |
else{ |
218 |
molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
219 |
info[k].getConfiguration() ); |
220 |
} |
221 |
molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
222 |
|
223 |
#ifdef IS_MPI |
224 |
|
225 |
molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
226 |
|
227 |
#endif // is_mpi |
228 |
} |
229 |
|
230 |
// make the bonds |
231 |
for(j=0; j<molInfo.nBonds; j++){ |
232 |
|
233 |
currentBond = comp_stamps[stampID]->getBond( j ); |
234 |
theBonds[j].a = currentBond->getA() + atomOffset; |
235 |
theBonds[j].b = currentBond->getB() + atomOffset; |
236 |
|
237 |
exI = theBonds[j].a; |
238 |
exJ = theBonds[j].b; |
239 |
|
240 |
// exclude_I must always be the smaller of the pair |
241 |
if( exI > exJ ){ |
242 |
tempEx = exI; |
243 |
exI = exJ; |
244 |
exJ = tempEx; |
245 |
} |
246 |
#ifdef IS_MPI |
247 |
tempEx = exI; |
248 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
249 |
tempEx = exJ; |
250 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
251 |
|
252 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
253 |
#else // isn't MPI |
254 |
|
255 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
256 |
#endif //is_mpi |
257 |
} |
258 |
excludeOffset += molInfo.nBonds; |
259 |
|
260 |
//make the bends |
261 |
for(j=0; j<molInfo.nBends; j++){ |
262 |
|
263 |
currentBend = comp_stamps[stampID]->getBend( j ); |
264 |
theBends[j].a = currentBend->getA() + atomOffset; |
265 |
theBends[j].b = currentBend->getB() + atomOffset; |
266 |
theBends[j].c = currentBend->getC() + atomOffset; |
267 |
|
268 |
if( currentBend->haveExtras() ){ |
269 |
|
270 |
extras = currentBend->getExtras(); |
271 |
current_extra = extras; |
272 |
|
273 |
while( current_extra != NULL ){ |
274 |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
275 |
|
276 |
switch( current_extra->getType() ){ |
277 |
|
278 |
case 0: |
279 |
theBends[j].ghost = |
280 |
current_extra->getInt() + atomOffset; |
281 |
theBends[j].isGhost = 1; |
282 |
break; |
283 |
|
284 |
case 1: |
285 |
theBends[j].ghost = |
286 |
(int)current_extra->getDouble() + atomOffset; |
287 |
theBends[j].isGhost = 1; |
288 |
break; |
289 |
|
290 |
default: |
291 |
sprintf( painCave.errMsg, |
292 |
"SimSetup Error: ghostVectorSource was neither a " |
293 |
"double nor an int.\n" |
294 |
"-->Bend[%d] in %s\n", |
295 |
j, comp_stamps[stampID]->getID() ); |
296 |
painCave.isFatal = 1; |
297 |
simError(); |
298 |
} |
299 |
} |
300 |
|
301 |
else{ |
302 |
|
303 |
sprintf( painCave.errMsg, |
304 |
"SimSetup Error: unhandled bend assignment:\n" |
305 |
" -->%s in Bend[%d] in %s\n", |
306 |
current_extra->getlhs(), |
307 |
j, comp_stamps[stampID]->getID() ); |
308 |
painCave.isFatal = 1; |
309 |
simError(); |
310 |
} |
311 |
|
312 |
current_extra = current_extra->getNext(); |
313 |
} |
314 |
} |
315 |
|
316 |
if( !theBends[j].isGhost ){ |
317 |
|
318 |
exI = theBends[j].a; |
319 |
exJ = theBends[j].c; |
320 |
} |
321 |
else{ |
322 |
|
323 |
exI = theBends[j].a; |
324 |
exJ = theBends[j].b; |
325 |
} |
326 |
|
327 |
// exclude_I must always be the smaller of the pair |
328 |
if( exI > exJ ){ |
329 |
tempEx = exI; |
330 |
exI = exJ; |
331 |
exJ = tempEx; |
332 |
} |
333 |
#ifdef IS_MPI |
334 |
tempEx = exI; |
335 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
336 |
tempEx = exJ; |
337 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
338 |
|
339 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
340 |
#else // isn't MPI |
341 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
342 |
#endif //is_mpi |
343 |
} |
344 |
excludeOffset += molInfo.nBends; |
345 |
|
346 |
for(j=0; j<molInfo.nTorsions; j++){ |
347 |
|
348 |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
349 |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
350 |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
351 |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
352 |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
353 |
|
354 |
exI = theTorsions[j].a; |
355 |
exJ = theTorsions[j].d; |
356 |
|
357 |
// exclude_I must always be the smaller of the pair |
358 |
if( exI > exJ ){ |
359 |
tempEx = exI; |
360 |
exI = exJ; |
361 |
exJ = tempEx; |
362 |
} |
363 |
#ifdef IS_MPI |
364 |
tempEx = exI; |
365 |
exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
366 |
tempEx = exJ; |
367 |
exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
368 |
|
369 |
info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
370 |
#else // isn't MPI |
371 |
info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
372 |
#endif //is_mpi |
373 |
} |
374 |
excludeOffset += molInfo.nTorsions; |
375 |
|
376 |
|
377 |
// send the arrays off to the forceField for init. |
378 |
|
379 |
the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
380 |
the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
381 |
the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
382 |
the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
383 |
|
384 |
|
385 |
info[k].molecules[i].initialize( molInfo ); |
386 |
|
387 |
|
388 |
atomOffset += molInfo.nAtoms; |
389 |
delete[] theBonds; |
390 |
delete[] theBends; |
391 |
delete[] theTorsions; |
392 |
} |
393 |
} |
394 |
|
395 |
#ifdef IS_MPI |
396 |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
397 |
MPIcheckPoint(); |
398 |
#endif // is_mpi |
399 |
|
400 |
// clean up the forcefield |
401 |
|
402 |
the_ff->calcRcut(); |
403 |
the_ff->cleanMe(); |
404 |
|
405 |
} |
406 |
|
407 |
void SimSetup::initFromBass( void ){ |
408 |
|
409 |
int i, j, k; |
410 |
int n_cells; |
411 |
double cellx, celly, cellz; |
412 |
double temp1, temp2, temp3; |
413 |
int n_per_extra; |
414 |
int n_extra; |
415 |
int have_extra, done; |
416 |
|
417 |
double vel[3]; |
418 |
vel[0] = 0.0; |
419 |
vel[1] = 0.0; |
420 |
vel[2] = 0.0; |
421 |
|
422 |
temp1 = (double)tot_nmol / 4.0; |
423 |
temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
424 |
temp3 = ceil( temp2 ); |
425 |
|
426 |
have_extra =0; |
427 |
if( temp2 < temp3 ){ // we have a non-complete lattice |
428 |
have_extra =1; |
429 |
|
430 |
n_cells = (int)temp3 - 1; |
431 |
cellx = info[0].boxL[0] / temp3; |
432 |
celly = info[0].boxL[1] / temp3; |
433 |
cellz = info[0].boxL[2] / temp3; |
434 |
n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
435 |
temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
436 |
n_per_extra = (int)ceil( temp1 ); |
437 |
|
438 |
if( n_per_extra > 4){ |
439 |
sprintf( painCave.errMsg, |
440 |
"SimSetup error. There has been an error in constructing" |
441 |
" the non-complete lattice.\n" ); |
442 |
painCave.isFatal = 1; |
443 |
simError(); |
444 |
} |
445 |
} |
446 |
else{ |
447 |
n_cells = (int)temp3; |
448 |
cellx = info[0].boxL[0] / temp3; |
449 |
celly = info[0].boxL[1] / temp3; |
450 |
cellz = info[0].boxL[2] / temp3; |
451 |
} |
452 |
|
453 |
current_mol = 0; |
454 |
current_comp_mol = 0; |
455 |
current_comp = 0; |
456 |
current_atom_ndx = 0; |
457 |
|
458 |
for( i=0; i < n_cells ; i++ ){ |
459 |
for( j=0; j < n_cells; j++ ){ |
460 |
for( k=0; k < n_cells; k++ ){ |
461 |
|
462 |
makeElement( i * cellx, |
463 |
j * celly, |
464 |
k * cellz ); |
465 |
|
466 |
makeElement( i * cellx + 0.5 * cellx, |
467 |
j * celly + 0.5 * celly, |
468 |
k * cellz ); |
469 |
|
470 |
makeElement( i * cellx, |
471 |
j * celly + 0.5 * celly, |
472 |
k * cellz + 0.5 * cellz ); |
473 |
|
474 |
makeElement( i * cellx + 0.5 * cellx, |
475 |
j * celly, |
476 |
k * cellz + 0.5 * cellz ); |
477 |
} |
478 |
} |
479 |
} |
480 |
|
481 |
if( have_extra ){ |
482 |
done = 0; |
483 |
|
484 |
int start_ndx; |
485 |
for( i=0; i < (n_cells+1) && !done; i++ ){ |
486 |
for( j=0; j < (n_cells+1) && !done; j++ ){ |
487 |
|
488 |
if( i < n_cells ){ |
489 |
|
490 |
if( j < n_cells ){ |
491 |
start_ndx = n_cells; |
492 |
} |
493 |
else start_ndx = 0; |
494 |
} |
495 |
else start_ndx = 0; |
496 |
|
497 |
for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
498 |
|
499 |
makeElement( i * cellx, |
500 |
j * celly, |
501 |
k * cellz ); |
502 |
done = ( current_mol >= tot_nmol ); |
503 |
|
504 |
if( !done && n_per_extra > 1 ){ |
505 |
makeElement( i * cellx + 0.5 * cellx, |
506 |
j * celly + 0.5 * celly, |
507 |
k * cellz ); |
508 |
done = ( current_mol >= tot_nmol ); |
509 |
} |
510 |
|
511 |
if( !done && n_per_extra > 2){ |
512 |
makeElement( i * cellx, |
513 |
j * celly + 0.5 * celly, |
514 |
k * cellz + 0.5 * cellz ); |
515 |
done = ( current_mol >= tot_nmol ); |
516 |
} |
517 |
|
518 |
if( !done && n_per_extra > 3){ |
519 |
makeElement( i * cellx + 0.5 * cellx, |
520 |
j * celly, |
521 |
k * cellz + 0.5 * cellz ); |
522 |
done = ( current_mol >= tot_nmol ); |
523 |
} |
524 |
} |
525 |
} |
526 |
} |
527 |
} |
528 |
|
529 |
for( i=0; i<info[0].n_atoms; i++ ){ |
530 |
info[0].atoms[i]->setVel( vel ); |
531 |
} |
532 |
} |
533 |
|
534 |
void SimSetup::makeElement( double x, double y, double z ){ |
535 |
|
536 |
int k; |
537 |
AtomStamp* current_atom; |
538 |
DirectionalAtom* dAtom; |
539 |
double rotMat[3][3]; |
540 |
double pos[3]; |
541 |
|
542 |
for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
543 |
|
544 |
current_atom = comp_stamps[current_comp]->getAtom( k ); |
545 |
if( !current_atom->havePosition() ){ |
546 |
sprintf( painCave.errMsg, |
547 |
"SimSetup:initFromBass error.\n" |
548 |
"\tComponent %s, atom %s does not have a position specified.\n" |
549 |
"\tThe initialization routine is unable to give a start" |
550 |
" position.\n", |
551 |
comp_stamps[current_comp]->getID(), |
552 |
current_atom->getType() ); |
553 |
painCave.isFatal = 1; |
554 |
simError(); |
555 |
} |
556 |
|
557 |
pos[0] = x + current_atom->getPosX(); |
558 |
pos[1] = y + current_atom->getPosY(); |
559 |
pos[2] = z + current_atom->getPosZ(); |
560 |
|
561 |
info[0].atoms[current_atom_ndx]->setPos( pos ); |
562 |
|
563 |
if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
564 |
|
565 |
dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
566 |
|
567 |
rotMat[0][0] = 1.0; |
568 |
rotMat[0][1] = 0.0; |
569 |
rotMat[0][2] = 0.0; |
570 |
|
571 |
rotMat[1][0] = 0.0; |
572 |
rotMat[1][1] = 1.0; |
573 |
rotMat[1][2] = 0.0; |
574 |
|
575 |
rotMat[2][0] = 0.0; |
576 |
rotMat[2][1] = 0.0; |
577 |
rotMat[2][2] = 1.0; |
578 |
|
579 |
dAtom->setA( rotMat ); |
580 |
} |
581 |
|
582 |
current_atom_ndx++; |
583 |
} |
584 |
|
585 |
current_mol++; |
586 |
current_comp_mol++; |
587 |
|
588 |
if( current_comp_mol >= components_nmol[current_comp] ){ |
589 |
|
590 |
current_comp_mol = 0; |
591 |
current_comp++; |
592 |
} |
593 |
} |
594 |
|
595 |
|
596 |
void SimSetup::gatherInfo( void ){ |
597 |
int i,j,k; |
598 |
|
599 |
ensembleCase = -1; |
600 |
ffCase = -1; |
601 |
|
602 |
// set the easy ones first |
603 |
|
604 |
for( i=0; i<nInfo; i++){ |
605 |
info[i].target_temp = globals->getTargetTemp(); |
606 |
info[i].dt = globals->getDt(); |
607 |
info[i].run_time = globals->getRunTime(); |
608 |
} |
609 |
n_components = globals->getNComponents(); |
610 |
|
611 |
|
612 |
// get the forceField |
613 |
|
614 |
strcpy( force_field, globals->getForceField() ); |
615 |
|
616 |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
617 |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
618 |
else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
619 |
else{ |
620 |
sprintf( painCave.errMsg, |
621 |
"SimSetup Error. Unrecognized force field -> %s\n", |
622 |
force_field ); |
623 |
painCave.isFatal = 1; |
624 |
simError(); |
625 |
} |
626 |
|
627 |
// get the ensemble |
628 |
|
629 |
strcpy( ensemble, globals->getEnsemble() ); |
630 |
|
631 |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
632 |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
633 |
else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
634 |
ensembleCase = NPTi_ENS; |
635 |
else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
636 |
else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
637 |
else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
638 |
else{ |
639 |
sprintf( painCave.errMsg, |
640 |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
641 |
"reverting to NVE for this simulation.\n", |
642 |
ensemble ); |
643 |
painCave.isFatal = 0; |
644 |
simError(); |
645 |
strcpy( ensemble, "NVE" ); |
646 |
ensembleCase = NVE_ENS; |
647 |
} |
648 |
|
649 |
for(i=0; i<nInfo; i++){ |
650 |
|
651 |
strcpy( info[i].ensemble, ensemble ); |
652 |
|
653 |
// get the mixing rule |
654 |
|
655 |
strcpy( info[i].mixingRule, globals->getMixingRule() ); |
656 |
info[i].usePBC = globals->getPBC(); |
657 |
} |
658 |
|
659 |
// get the components and calculate the tot_nMol and indvidual n_mol |
660 |
|
661 |
the_components = globals->getComponents(); |
662 |
components_nmol = new int[n_components]; |
663 |
|
664 |
|
665 |
if( !globals->haveNMol() ){ |
666 |
// we don't have the total number of molecules, so we assume it is |
667 |
// given in each component |
668 |
|
669 |
tot_nmol = 0; |
670 |
for( i=0; i<n_components; i++ ){ |
671 |
|
672 |
if( !the_components[i]->haveNMol() ){ |
673 |
// we have a problem |
674 |
sprintf( painCave.errMsg, |
675 |
"SimSetup Error. No global NMol or component NMol" |
676 |
" given. Cannot calculate the number of atoms.\n" ); |
677 |
painCave.isFatal = 1; |
678 |
simError(); |
679 |
} |
680 |
|
681 |
tot_nmol += the_components[i]->getNMol(); |
682 |
components_nmol[i] = the_components[i]->getNMol(); |
683 |
} |
684 |
} |
685 |
else{ |
686 |
sprintf( painCave.errMsg, |
687 |
"SimSetup error.\n" |
688 |
"\tSorry, the ability to specify total" |
689 |
" nMols and then give molfractions in the components\n" |
690 |
"\tis not currently supported." |
691 |
" Please give nMol in the components.\n" ); |
692 |
painCave.isFatal = 1; |
693 |
simError(); |
694 |
} |
695 |
|
696 |
// set the status, sample, and thermal kick times |
697 |
|
698 |
for(i=0; i<nInfo; i++){ |
699 |
|
700 |
if( globals->haveSampleTime() ){ |
701 |
info[i].sampleTime = globals->getSampleTime(); |
702 |
info[i].statusTime = info[i].sampleTime; |
703 |
info[i].thermalTime = info[i].sampleTime; |
704 |
} |
705 |
else{ |
706 |
info[i].sampleTime = globals->getRunTime(); |
707 |
info[i].statusTime = info[i].sampleTime; |
708 |
info[i].thermalTime = info[i].sampleTime; |
709 |
} |
710 |
|
711 |
if( globals->haveStatusTime() ){ |
712 |
info[i].statusTime = globals->getStatusTime(); |
713 |
} |
714 |
|
715 |
if( globals->haveThermalTime() ){ |
716 |
info[i].thermalTime = globals->getThermalTime(); |
717 |
} |
718 |
|
719 |
// check for the temperature set flag |
720 |
|
721 |
if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
722 |
|
723 |
// get some of the tricky things that may still be in the globals |
724 |
|
725 |
double boxVector[3]; |
726 |
if( globals->haveBox() ){ |
727 |
boxVector[0] = globals->getBox(); |
728 |
boxVector[1] = globals->getBox(); |
729 |
boxVector[2] = globals->getBox(); |
730 |
|
731 |
info[i].setBox( boxVector ); |
732 |
} |
733 |
else if( globals->haveDensity() ){ |
734 |
|
735 |
double vol; |
736 |
vol = (double)tot_nmol / globals->getDensity(); |
737 |
boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
738 |
boxVector[1] = boxVector[0]; |
739 |
boxVector[2] = boxVector[0]; |
740 |
|
741 |
info[i].setBox( boxVector ); |
742 |
} |
743 |
else{ |
744 |
if( !globals->haveBoxX() ){ |
745 |
sprintf( painCave.errMsg, |
746 |
"SimSetup error, no periodic BoxX size given.\n" ); |
747 |
painCave.isFatal = 1; |
748 |
simError(); |
749 |
} |
750 |
boxVector[0] = globals->getBoxX(); |
751 |
|
752 |
if( !globals->haveBoxY() ){ |
753 |
sprintf( painCave.errMsg, |
754 |
"SimSetup error, no periodic BoxY size given.\n" ); |
755 |
painCave.isFatal = 1; |
756 |
simError(); |
757 |
} |
758 |
boxVector[1] = globals->getBoxY(); |
759 |
|
760 |
if( !globals->haveBoxZ() ){ |
761 |
sprintf( painCave.errMsg, |
762 |
"SimSetup error, no periodic BoxZ size given.\n" ); |
763 |
painCave.isFatal = 1; |
764 |
simError(); |
765 |
} |
766 |
boxVector[2] = globals->getBoxZ(); |
767 |
|
768 |
info[i].setBox( boxVector ); |
769 |
} |
770 |
} |
771 |
|
772 |
int seedValue; |
773 |
struct timeval now_time_val; |
774 |
struct timezone time_zone; |
775 |
|
776 |
if(globals->haveSeed()){ |
777 |
seedValue = globals->getSeed(); |
778 |
} |
779 |
else{ |
780 |
#ifndef IS_MPI |
781 |
gettimeofday(&now_time_val, &time_zone); // get the time now |
782 |
seedValue = (int) now_time_val.tv_sec; // convert to epoch time |
783 |
#else |
784 |
if(worldRank == 0){ |
785 |
gettimeofday(&now_time_val, &time_zone); // get the time now |
786 |
seedValue = (int) now_time_val.tv_sec; // convert to epoch time |
787 |
} |
788 |
MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
789 |
#endif |
790 |
} |
791 |
|
792 |
for(int i = 0; i < nInfo; i++){ |
793 |
info[i].setSeed(seedValue); |
794 |
} |
795 |
|
796 |
#ifdef IS_MPI |
797 |
strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
798 |
MPIcheckPoint(); |
799 |
#endif // is_mpi |
800 |
|
801 |
} |
802 |
|
803 |
|
804 |
void SimSetup::finalInfoCheck( void ){ |
805 |
int index; |
806 |
int usesDipoles; |
807 |
int i; |
808 |
|
809 |
for(i=0; i<nInfo; i++){ |
810 |
// check electrostatic parameters |
811 |
|
812 |
index = 0; |
813 |
usesDipoles = 0; |
814 |
while( (index < info[i].n_atoms) && !usesDipoles ){ |
815 |
usesDipoles = (info[i].atoms[index])->hasDipole(); |
816 |
index++; |
817 |
} |
818 |
|
819 |
#ifdef IS_MPI |
820 |
int myUse = usesDipoles; |
821 |
MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
822 |
#endif //is_mpi |
823 |
|
824 |
double theEcr, theEst; |
825 |
|
826 |
if (globals->getUseRF() ) { |
827 |
info[i].useReactionField = 1; |
828 |
|
829 |
if( !globals->haveECR() ){ |
830 |
sprintf( painCave.errMsg, |
831 |
"SimSetup Warning: using default value of 1/2 the smallest " |
832 |
"box length for the electrostaticCutoffRadius.\n" |
833 |
"I hope you have a very fast processor!\n"); |
834 |
painCave.isFatal = 0; |
835 |
simError(); |
836 |
double smallest; |
837 |
smallest = info[i].boxL[0]; |
838 |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
839 |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
840 |
theEcr = 0.5 * smallest; |
841 |
} else { |
842 |
theEcr = globals->getECR(); |
843 |
} |
844 |
|
845 |
if( !globals->haveEST() ){ |
846 |
sprintf( painCave.errMsg, |
847 |
"SimSetup Warning: using default value of 0.05 * the " |
848 |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
849 |
); |
850 |
painCave.isFatal = 0; |
851 |
simError(); |
852 |
theEst = 0.05 * theEcr; |
853 |
} else { |
854 |
theEst= globals->getEST(); |
855 |
} |
856 |
|
857 |
info[i].setEcr( theEcr, theEst ); |
858 |
|
859 |
if(!globals->haveDielectric() ){ |
860 |
sprintf( painCave.errMsg, |
861 |
"SimSetup Error: You are trying to use Reaction Field without" |
862 |
"setting a dielectric constant!\n" |
863 |
); |
864 |
painCave.isFatal = 1; |
865 |
simError(); |
866 |
} |
867 |
info[i].dielectric = globals->getDielectric(); |
868 |
} |
869 |
else { |
870 |
if (usesDipoles) { |
871 |
|
872 |
if( !globals->haveECR() ){ |
873 |
sprintf( painCave.errMsg, |
874 |
"SimSetup Warning: using default value of 1/2 the smallest " |
875 |
"box length for the electrostaticCutoffRadius.\n" |
876 |
"I hope you have a very fast processor!\n"); |
877 |
painCave.isFatal = 0; |
878 |
simError(); |
879 |
double smallest; |
880 |
smallest = info[i].boxL[0]; |
881 |
if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
882 |
if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
883 |
theEcr = 0.5 * smallest; |
884 |
} else { |
885 |
theEcr = globals->getECR(); |
886 |
} |
887 |
|
888 |
if( !globals->haveEST() ){ |
889 |
sprintf( painCave.errMsg, |
890 |
"SimSetup Warning: using default value of 0.05 * the " |
891 |
"electrostaticCutoffRadius for the " |
892 |
"electrostaticSkinThickness\n" |
893 |
); |
894 |
painCave.isFatal = 0; |
895 |
simError(); |
896 |
theEst = 0.05 * theEcr; |
897 |
} else { |
898 |
theEst= globals->getEST(); |
899 |
} |
900 |
|
901 |
info[i].setEcr( theEcr, theEst ); |
902 |
} |
903 |
} |
904 |
} |
905 |
|
906 |
#ifdef IS_MPI |
907 |
strcpy( checkPointMsg, "post processing checks out" ); |
908 |
MPIcheckPoint(); |
909 |
#endif // is_mpi |
910 |
|
911 |
} |
912 |
|
913 |
void SimSetup::initSystemCoords( void ){ |
914 |
int i; |
915 |
|
916 |
char* inName; |
917 |
|
918 |
(info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
919 |
|
920 |
for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
921 |
|
922 |
if( globals->haveInitialConfig() ){ |
923 |
|
924 |
InitializeFromFile* fileInit; |
925 |
#ifdef IS_MPI // is_mpi |
926 |
if( worldRank == 0 ){ |
927 |
#endif //is_mpi |
928 |
inName = globals->getInitialConfig(); |
929 |
double* tempDouble = new double[1000000]; |
930 |
fileInit = new InitializeFromFile( inName ); |
931 |
#ifdef IS_MPI |
932 |
}else fileInit = new InitializeFromFile( NULL ); |
933 |
#endif |
934 |
fileInit->readInit( info ); // default velocities on |
935 |
|
936 |
delete fileInit; |
937 |
} |
938 |
else{ |
939 |
|
940 |
#ifdef IS_MPI |
941 |
|
942 |
// no init from bass |
943 |
|
944 |
sprintf( painCave.errMsg, |
945 |
"Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
946 |
painCave.isFatal; |
947 |
simError(); |
948 |
|
949 |
#else |
950 |
|
951 |
initFromBass(); |
952 |
|
953 |
|
954 |
#endif |
955 |
} |
956 |
|
957 |
#ifdef IS_MPI |
958 |
strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
959 |
MPIcheckPoint(); |
960 |
#endif // is_mpi |
961 |
|
962 |
} |
963 |
|
964 |
|
965 |
void SimSetup::makeOutNames( void ){ |
966 |
|
967 |
int k; |
968 |
|
969 |
|
970 |
for(k=0; k<nInfo; k++){ |
971 |
|
972 |
#ifdef IS_MPI |
973 |
if( worldRank == 0 ){ |
974 |
#endif // is_mpi |
975 |
|
976 |
if( globals->haveFinalConfig() ){ |
977 |
strcpy( info[k].finalName, globals->getFinalConfig() ); |
978 |
} |
979 |
else{ |
980 |
strcpy( info[k].finalName, inFileName ); |
981 |
char* endTest; |
982 |
int nameLength = strlen( info[k].finalName ); |
983 |
endTest = &(info[k].finalName[nameLength - 5]); |
984 |
if( !strcmp( endTest, ".bass" ) ){ |
985 |
strcpy( endTest, ".eor" ); |
986 |
} |
987 |
else if( !strcmp( endTest, ".BASS" ) ){ |
988 |
strcpy( endTest, ".eor" ); |
989 |
} |
990 |
else{ |
991 |
endTest = &(info[k].finalName[nameLength - 4]); |
992 |
if( !strcmp( endTest, ".bss" ) ){ |
993 |
strcpy( endTest, ".eor" ); |
994 |
} |
995 |
else if( !strcmp( endTest, ".mdl" ) ){ |
996 |
strcpy( endTest, ".eor" ); |
997 |
} |
998 |
else{ |
999 |
strcat( info[k].finalName, ".eor" ); |
1000 |
} |
1001 |
} |
1002 |
} |
1003 |
|
1004 |
// make the sample and status out names |
1005 |
|
1006 |
strcpy( info[k].sampleName, inFileName ); |
1007 |
char* endTest; |
1008 |
int nameLength = strlen( info[k].sampleName ); |
1009 |
endTest = &(info[k].sampleName[nameLength - 5]); |
1010 |
if( !strcmp( endTest, ".bass" ) ){ |
1011 |
strcpy( endTest, ".dump" ); |
1012 |
} |
1013 |
else if( !strcmp( endTest, ".BASS" ) ){ |
1014 |
strcpy( endTest, ".dump" ); |
1015 |
} |
1016 |
else{ |
1017 |
endTest = &(info[k].sampleName[nameLength - 4]); |
1018 |
if( !strcmp( endTest, ".bss" ) ){ |
1019 |
strcpy( endTest, ".dump" ); |
1020 |
} |
1021 |
else if( !strcmp( endTest, ".mdl" ) ){ |
1022 |
strcpy( endTest, ".dump" ); |
1023 |
} |
1024 |
else{ |
1025 |
strcat( info[k].sampleName, ".dump" ); |
1026 |
} |
1027 |
} |
1028 |
|
1029 |
strcpy( info[k].statusName, inFileName ); |
1030 |
nameLength = strlen( info[k].statusName ); |
1031 |
endTest = &(info[k].statusName[nameLength - 5]); |
1032 |
if( !strcmp( endTest, ".bass" ) ){ |
1033 |
strcpy( endTest, ".stat" ); |
1034 |
} |
1035 |
else if( !strcmp( endTest, ".BASS" ) ){ |
1036 |
strcpy( endTest, ".stat" ); |
1037 |
} |
1038 |
else{ |
1039 |
endTest = &(info[k].statusName[nameLength - 4]); |
1040 |
if( !strcmp( endTest, ".bss" ) ){ |
1041 |
strcpy( endTest, ".stat" ); |
1042 |
} |
1043 |
else if( !strcmp( endTest, ".mdl" ) ){ |
1044 |
strcpy( endTest, ".stat" ); |
1045 |
} |
1046 |
else{ |
1047 |
strcat( info[k].statusName, ".stat" ); |
1048 |
} |
1049 |
} |
1050 |
|
1051 |
#ifdef IS_MPI |
1052 |
} |
1053 |
#endif // is_mpi |
1054 |
} |
1055 |
} |
1056 |
|
1057 |
|
1058 |
void SimSetup::sysObjectsCreation( void ){ |
1059 |
|
1060 |
int i,k; |
1061 |
|
1062 |
// create the forceField |
1063 |
|
1064 |
createFF(); |
1065 |
|
1066 |
// extract componentList |
1067 |
|
1068 |
compList(); |
1069 |
|
1070 |
// calc the number of atoms, bond, bends, and torsions |
1071 |
|
1072 |
calcSysValues(); |
1073 |
|
1074 |
#ifdef IS_MPI |
1075 |
// divide the molecules among the processors |
1076 |
|
1077 |
mpiMolDivide(); |
1078 |
#endif //is_mpi |
1079 |
|
1080 |
// create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1081 |
|
1082 |
makeSysArrays(); |
1083 |
|
1084 |
// make and initialize the molecules (all but atomic coordinates) |
1085 |
|
1086 |
makeMolecules(); |
1087 |
|
1088 |
for(k=0; k<nInfo; k++){ |
1089 |
info[k].identArray = new int[info[k].n_atoms]; |
1090 |
for(i=0; i<info[k].n_atoms; i++){ |
1091 |
info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1092 |
} |
1093 |
} |
1094 |
} |
1095 |
|
1096 |
|
1097 |
void SimSetup::createFF( void ){ |
1098 |
|
1099 |
switch( ffCase ){ |
1100 |
|
1101 |
case FF_DUFF: |
1102 |
the_ff = new DUFF(); |
1103 |
break; |
1104 |
|
1105 |
case FF_LJ: |
1106 |
the_ff = new LJFF(); |
1107 |
break; |
1108 |
|
1109 |
case FF_EAM: |
1110 |
the_ff = new EAM_FF(); |
1111 |
break; |
1112 |
|
1113 |
default: |
1114 |
sprintf( painCave.errMsg, |
1115 |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
1116 |
painCave.isFatal = 1; |
1117 |
simError(); |
1118 |
} |
1119 |
|
1120 |
#ifdef IS_MPI |
1121 |
strcpy( checkPointMsg, "ForceField creation successful" ); |
1122 |
MPIcheckPoint(); |
1123 |
#endif // is_mpi |
1124 |
|
1125 |
} |
1126 |
|
1127 |
|
1128 |
void SimSetup::compList( void ){ |
1129 |
|
1130 |
int i; |
1131 |
char* id; |
1132 |
LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1133 |
LinkedMolStamp* currentStamp = NULL; |
1134 |
comp_stamps = new MoleculeStamp*[n_components]; |
1135 |
|
1136 |
// make an array of molecule stamps that match the components used. |
1137 |
// also extract the used stamps out into a separate linked list |
1138 |
|
1139 |
for(i=0; i<nInfo; i++){ |
1140 |
info[i].nComponents = n_components; |
1141 |
info[i].componentsNmol = components_nmol; |
1142 |
info[i].compStamps = comp_stamps; |
1143 |
info[i].headStamp = headStamp; |
1144 |
} |
1145 |
|
1146 |
|
1147 |
for( i=0; i<n_components; i++ ){ |
1148 |
|
1149 |
id = the_components[i]->getType(); |
1150 |
comp_stamps[i] = NULL; |
1151 |
|
1152 |
// check to make sure the component isn't already in the list |
1153 |
|
1154 |
comp_stamps[i] = headStamp->match( id ); |
1155 |
if( comp_stamps[i] == NULL ){ |
1156 |
|
1157 |
// extract the component from the list; |
1158 |
|
1159 |
currentStamp = stamps->extractMolStamp( id ); |
1160 |
if( currentStamp == NULL ){ |
1161 |
sprintf( painCave.errMsg, |
1162 |
"SimSetup error: Component \"%s\" was not found in the " |
1163 |
"list of declared molecules\n", |
1164 |
id ); |
1165 |
painCave.isFatal = 1; |
1166 |
simError(); |
1167 |
} |
1168 |
|
1169 |
headStamp->add( currentStamp ); |
1170 |
comp_stamps[i] = headStamp->match( id ); |
1171 |
} |
1172 |
} |
1173 |
|
1174 |
#ifdef IS_MPI |
1175 |
strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1176 |
MPIcheckPoint(); |
1177 |
#endif // is_mpi |
1178 |
|
1179 |
|
1180 |
} |
1181 |
|
1182 |
void SimSetup::calcSysValues( void ){ |
1183 |
int i, j, k; |
1184 |
|
1185 |
int *molMembershipArray; |
1186 |
|
1187 |
tot_atoms = 0; |
1188 |
tot_bonds = 0; |
1189 |
tot_bends = 0; |
1190 |
tot_torsions = 0; |
1191 |
for( i=0; i<n_components; i++ ){ |
1192 |
|
1193 |
tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1194 |
tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1195 |
tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1196 |
tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1197 |
} |
1198 |
|
1199 |
tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1200 |
molMembershipArray = new int[tot_atoms]; |
1201 |
|
1202 |
for(i=0; i<nInfo; i++){ |
1203 |
info[i].n_atoms = tot_atoms; |
1204 |
info[i].n_bonds = tot_bonds; |
1205 |
info[i].n_bends = tot_bends; |
1206 |
info[i].n_torsions = tot_torsions; |
1207 |
info[i].n_SRI = tot_SRI; |
1208 |
info[i].n_mol = tot_nmol; |
1209 |
|
1210 |
info[i].molMembershipArray = molMembershipArray; |
1211 |
} |
1212 |
} |
1213 |
|
1214 |
#ifdef IS_MPI |
1215 |
|
1216 |
void SimSetup::mpiMolDivide( void ){ |
1217 |
|
1218 |
int i, j, k; |
1219 |
int localMol, allMol; |
1220 |
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1221 |
|
1222 |
mpiSim = new mpiSimulation( info ); |
1223 |
|
1224 |
globalIndex = mpiSim->divideLabor(); |
1225 |
|
1226 |
// set up the local variables |
1227 |
|
1228 |
mol2proc = mpiSim->getMolToProcMap(); |
1229 |
molCompType = mpiSim->getMolComponentType(); |
1230 |
|
1231 |
allMol = 0; |
1232 |
localMol = 0; |
1233 |
local_atoms = 0; |
1234 |
local_bonds = 0; |
1235 |
local_bends = 0; |
1236 |
local_torsions = 0; |
1237 |
globalAtomIndex = 0; |
1238 |
|
1239 |
|
1240 |
for( i=0; i<n_components; i++ ){ |
1241 |
|
1242 |
for( j=0; j<components_nmol[i]; j++ ){ |
1243 |
|
1244 |
if( mol2proc[allMol] == worldRank ){ |
1245 |
|
1246 |
local_atoms += comp_stamps[i]->getNAtoms(); |
1247 |
local_bonds += comp_stamps[i]->getNBonds(); |
1248 |
local_bends += comp_stamps[i]->getNBends(); |
1249 |
local_torsions += comp_stamps[i]->getNTorsions(); |
1250 |
localMol++; |
1251 |
} |
1252 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1253 |
info[0].molMembershipArray[globalAtomIndex] = allMol; |
1254 |
globalAtomIndex++; |
1255 |
} |
1256 |
|
1257 |
allMol++; |
1258 |
} |
1259 |
} |
1260 |
local_SRI = local_bonds + local_bends + local_torsions; |
1261 |
|
1262 |
info[0].n_atoms = mpiSim->getMyNlocal(); |
1263 |
|
1264 |
if( local_atoms != info[0].n_atoms ){ |
1265 |
sprintf( painCave.errMsg, |
1266 |
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1267 |
" localAtom (%d) are not equal.\n", |
1268 |
info[0].n_atoms, |
1269 |
local_atoms ); |
1270 |
painCave.isFatal = 1; |
1271 |
simError(); |
1272 |
} |
1273 |
|
1274 |
info[0].n_bonds = local_bonds; |
1275 |
info[0].n_bends = local_bends; |
1276 |
info[0].n_torsions = local_torsions; |
1277 |
info[0].n_SRI = local_SRI; |
1278 |
info[0].n_mol = localMol; |
1279 |
|
1280 |
strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1281 |
MPIcheckPoint(); |
1282 |
} |
1283 |
|
1284 |
#endif // is_mpi |
1285 |
|
1286 |
|
1287 |
void SimSetup::makeSysArrays( void ){ |
1288 |
int i, j, k, l; |
1289 |
|
1290 |
Atom** the_atoms; |
1291 |
Molecule* the_molecules; |
1292 |
Exclude** the_excludes; |
1293 |
|
1294 |
|
1295 |
for(l=0; l<nInfo; l++){ |
1296 |
|
1297 |
// create the atom and short range interaction arrays |
1298 |
|
1299 |
the_atoms = new Atom*[info[l].n_atoms]; |
1300 |
the_molecules = new Molecule[info[l].n_mol]; |
1301 |
int molIndex; |
1302 |
|
1303 |
// initialize the molecule's stampID's |
1304 |
|
1305 |
#ifdef IS_MPI |
1306 |
|
1307 |
|
1308 |
molIndex = 0; |
1309 |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
1310 |
|
1311 |
if(mol2proc[i] == worldRank ){ |
1312 |
the_molecules[molIndex].setStampID( molCompType[i] ); |
1313 |
the_molecules[molIndex].setMyIndex( molIndex ); |
1314 |
the_molecules[molIndex].setGlobalIndex( i ); |
1315 |
molIndex++; |
1316 |
} |
1317 |
} |
1318 |
|
1319 |
#else // is_mpi |
1320 |
|
1321 |
molIndex = 0; |
1322 |
globalAtomIndex = 0; |
1323 |
for(i=0; i<n_components; i++){ |
1324 |
for(j=0; j<components_nmol[i]; j++ ){ |
1325 |
the_molecules[molIndex].setStampID( i ); |
1326 |
the_molecules[molIndex].setMyIndex( molIndex ); |
1327 |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
1328 |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1329 |
info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1330 |
globalAtomIndex++; |
1331 |
} |
1332 |
molIndex++; |
1333 |
} |
1334 |
} |
1335 |
|
1336 |
|
1337 |
#endif // is_mpi |
1338 |
|
1339 |
|
1340 |
if( info[l].n_SRI ){ |
1341 |
|
1342 |
Exclude::createArray(info[l].n_SRI); |
1343 |
the_excludes = new Exclude*[info[l].n_SRI]; |
1344 |
for( int ex=0; ex<info[l].n_SRI; ex++){ |
1345 |
the_excludes[ex] = new Exclude(ex); |
1346 |
} |
1347 |
info[l].globalExcludes = new int; |
1348 |
info[l].n_exclude = info[l].n_SRI; |
1349 |
} |
1350 |
else{ |
1351 |
|
1352 |
Exclude::createArray( 1 ); |
1353 |
the_excludes = new Exclude*; |
1354 |
the_excludes[0] = new Exclude(0); |
1355 |
the_excludes[0]->setPair( 0,0 ); |
1356 |
info[l].globalExcludes = new int; |
1357 |
info[l].globalExcludes[0] = 0; |
1358 |
info[l].n_exclude = 0; |
1359 |
} |
1360 |
|
1361 |
// set the arrays into the SimInfo object |
1362 |
|
1363 |
info[l].atoms = the_atoms; |
1364 |
info[l].molecules = the_molecules; |
1365 |
info[l].nGlobalExcludes = 0; |
1366 |
info[l].excludes = the_excludes; |
1367 |
|
1368 |
the_ff->setSimInfo( info ); |
1369 |
|
1370 |
} |
1371 |
} |
1372 |
|
1373 |
void SimSetup::makeIntegrator( void ){ |
1374 |
|
1375 |
int k; |
1376 |
|
1377 |
NVT<RealIntegrator>* myNVT = NULL; |
1378 |
NPTi<RealIntegrator>* myNPTi = NULL; |
1379 |
NPTf<RealIntegrator>* myNPTf = NULL; |
1380 |
NPTim<RealIntegrator>* myNPTim = NULL; |
1381 |
NPTfm<RealIntegrator>* myNPTfm = NULL; |
1382 |
|
1383 |
for(k=0; k<nInfo; k++){ |
1384 |
|
1385 |
switch( ensembleCase ){ |
1386 |
|
1387 |
case NVE_ENS: |
1388 |
if (globals->haveZconstraints()){ |
1389 |
setupZConstraint(info[k]); |
1390 |
new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1391 |
} |
1392 |
|
1393 |
else |
1394 |
new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1395 |
break; |
1396 |
|
1397 |
case NVT_ENS: |
1398 |
if (globals->haveZconstraints()){ |
1399 |
setupZConstraint(info[k]); |
1400 |
myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1401 |
} |
1402 |
else |
1403 |
myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1404 |
|
1405 |
myNVT->setTargetTemp(globals->getTargetTemp()); |
1406 |
|
1407 |
if (globals->haveTauThermostat()) |
1408 |
myNVT->setTauThermostat(globals->getTauThermostat()); |
1409 |
|
1410 |
else { |
1411 |
sprintf( painCave.errMsg, |
1412 |
"SimSetup error: If you use the NVT\n" |
1413 |
" ensemble, you must set tauThermostat.\n"); |
1414 |
painCave.isFatal = 1; |
1415 |
simError(); |
1416 |
} |
1417 |
break; |
1418 |
|
1419 |
case NPTi_ENS: |
1420 |
if (globals->haveZconstraints()){ |
1421 |
setupZConstraint(info[k]); |
1422 |
myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1423 |
} |
1424 |
else |
1425 |
myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1426 |
|
1427 |
myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1428 |
|
1429 |
if (globals->haveTargetPressure()) |
1430 |
myNPTi->setTargetPressure(globals->getTargetPressure()); |
1431 |
else { |
1432 |
sprintf( painCave.errMsg, |
1433 |
"SimSetup error: If you use a constant pressure\n" |
1434 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1435 |
painCave.isFatal = 1; |
1436 |
simError(); |
1437 |
} |
1438 |
|
1439 |
if( globals->haveTauThermostat() ) |
1440 |
myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1441 |
else{ |
1442 |
sprintf( painCave.errMsg, |
1443 |
"SimSetup error: If you use an NPT\n" |
1444 |
" ensemble, you must set tauThermostat.\n"); |
1445 |
painCave.isFatal = 1; |
1446 |
simError(); |
1447 |
} |
1448 |
|
1449 |
if( globals->haveTauBarostat() ) |
1450 |
myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1451 |
else{ |
1452 |
sprintf( painCave.errMsg, |
1453 |
"SimSetup error: If you use an NPT\n" |
1454 |
" ensemble, you must set tauBarostat.\n"); |
1455 |
painCave.isFatal = 1; |
1456 |
simError(); |
1457 |
} |
1458 |
break; |
1459 |
|
1460 |
case NPTf_ENS: |
1461 |
if (globals->haveZconstraints()){ |
1462 |
setupZConstraint(info[k]); |
1463 |
myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1464 |
} |
1465 |
else |
1466 |
myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1467 |
|
1468 |
myNPTf->setTargetTemp( globals->getTargetTemp()); |
1469 |
|
1470 |
if (globals->haveTargetPressure()) |
1471 |
myNPTf->setTargetPressure(globals->getTargetPressure()); |
1472 |
else { |
1473 |
sprintf( painCave.errMsg, |
1474 |
"SimSetup error: If you use a constant pressure\n" |
1475 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1476 |
painCave.isFatal = 1; |
1477 |
simError(); |
1478 |
} |
1479 |
|
1480 |
if( globals->haveTauThermostat() ) |
1481 |
myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1482 |
else{ |
1483 |
sprintf( painCave.errMsg, |
1484 |
"SimSetup error: If you use an NPT\n" |
1485 |
" ensemble, you must set tauThermostat.\n"); |
1486 |
painCave.isFatal = 1; |
1487 |
simError(); |
1488 |
} |
1489 |
|
1490 |
if( globals->haveTauBarostat() ) |
1491 |
myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1492 |
else{ |
1493 |
sprintf( painCave.errMsg, |
1494 |
"SimSetup error: If you use an NPT\n" |
1495 |
" ensemble, you must set tauBarostat.\n"); |
1496 |
painCave.isFatal = 1; |
1497 |
simError(); |
1498 |
} |
1499 |
break; |
1500 |
|
1501 |
case NPTim_ENS: |
1502 |
if (globals->haveZconstraints()){ |
1503 |
setupZConstraint(info[k]); |
1504 |
myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1505 |
} |
1506 |
else |
1507 |
myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1508 |
|
1509 |
myNPTim->setTargetTemp( globals->getTargetTemp()); |
1510 |
|
1511 |
if (globals->haveTargetPressure()) |
1512 |
myNPTim->setTargetPressure(globals->getTargetPressure()); |
1513 |
else { |
1514 |
sprintf( painCave.errMsg, |
1515 |
"SimSetup error: If you use a constant pressure\n" |
1516 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1517 |
painCave.isFatal = 1; |
1518 |
simError(); |
1519 |
} |
1520 |
|
1521 |
if( globals->haveTauThermostat() ) |
1522 |
myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1523 |
else{ |
1524 |
sprintf( painCave.errMsg, |
1525 |
"SimSetup error: If you use an NPT\n" |
1526 |
" ensemble, you must set tauThermostat.\n"); |
1527 |
painCave.isFatal = 1; |
1528 |
simError(); |
1529 |
} |
1530 |
|
1531 |
if( globals->haveTauBarostat() ) |
1532 |
myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1533 |
else{ |
1534 |
sprintf( painCave.errMsg, |
1535 |
"SimSetup error: If you use an NPT\n" |
1536 |
" ensemble, you must set tauBarostat.\n"); |
1537 |
painCave.isFatal = 1; |
1538 |
simError(); |
1539 |
} |
1540 |
break; |
1541 |
|
1542 |
case NPTfm_ENS: |
1543 |
if (globals->haveZconstraints()){ |
1544 |
setupZConstraint(info[k]); |
1545 |
myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1546 |
} |
1547 |
else |
1548 |
myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1549 |
|
1550 |
myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1551 |
|
1552 |
if (globals->haveTargetPressure()) |
1553 |
myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1554 |
else { |
1555 |
sprintf( painCave.errMsg, |
1556 |
"SimSetup error: If you use a constant pressure\n" |
1557 |
" ensemble, you must set targetPressure in the BASS file.\n"); |
1558 |
painCave.isFatal = 1; |
1559 |
simError(); |
1560 |
} |
1561 |
|
1562 |
if( globals->haveTauThermostat() ) |
1563 |
myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1564 |
else{ |
1565 |
sprintf( painCave.errMsg, |
1566 |
"SimSetup error: If you use an NPT\n" |
1567 |
" ensemble, you must set tauThermostat.\n"); |
1568 |
painCave.isFatal = 1; |
1569 |
simError(); |
1570 |
} |
1571 |
|
1572 |
if( globals->haveTauBarostat() ) |
1573 |
myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1574 |
else{ |
1575 |
sprintf( painCave.errMsg, |
1576 |
"SimSetup error: If you use an NPT\n" |
1577 |
" ensemble, you must set tauBarostat.\n"); |
1578 |
painCave.isFatal = 1; |
1579 |
simError(); |
1580 |
} |
1581 |
break; |
1582 |
|
1583 |
default: |
1584 |
sprintf( painCave.errMsg, |
1585 |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1586 |
painCave.isFatal = 1; |
1587 |
simError(); |
1588 |
} |
1589 |
} |
1590 |
} |
1591 |
|
1592 |
void SimSetup::initFortran( void ){ |
1593 |
|
1594 |
info[0].refreshSim(); |
1595 |
|
1596 |
if( !strcmp( info[0].mixingRule, "standard") ){ |
1597 |
the_ff->initForceField( LB_MIXING_RULE ); |
1598 |
} |
1599 |
else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1600 |
the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1601 |
} |
1602 |
else{ |
1603 |
sprintf( painCave.errMsg, |
1604 |
"SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1605 |
info[0].mixingRule ); |
1606 |
painCave.isFatal = 1; |
1607 |
simError(); |
1608 |
} |
1609 |
|
1610 |
|
1611 |
#ifdef IS_MPI |
1612 |
strcpy( checkPointMsg, |
1613 |
"Successfully intialized the mixingRule for Fortran." ); |
1614 |
MPIcheckPoint(); |
1615 |
#endif // is_mpi |
1616 |
|
1617 |
} |
1618 |
|
1619 |
void SimSetup::setupZConstraint(SimInfo& theInfo) |
1620 |
{ |
1621 |
int nZConstraints; |
1622 |
ZconStamp** zconStamp; |
1623 |
|
1624 |
if(globals->haveZconstraintTime()){ |
1625 |
|
1626 |
//add sample time of z-constraint into SimInfo's property list |
1627 |
DoubleData* zconsTimeProp = new DoubleData(); |
1628 |
zconsTimeProp->setID(ZCONSTIME_ID); |
1629 |
zconsTimeProp->setData(globals->getZconsTime()); |
1630 |
theInfo.addProperty(zconsTimeProp); |
1631 |
} |
1632 |
else{ |
1633 |
sprintf( painCave.errMsg, |
1634 |
"ZConstraint error: If you use an ZConstraint\n" |
1635 |
" , you must set sample time.\n"); |
1636 |
painCave.isFatal = 1; |
1637 |
simError(); |
1638 |
} |
1639 |
|
1640 |
//push zconsTol into siminfo, if user does not specify |
1641 |
//value for zconsTol, a default value will be used |
1642 |
DoubleData* zconsTol = new DoubleData(); |
1643 |
zconsTol->setID(ZCONSTOL_ID); |
1644 |
if(globals->haveZconsTol()){ |
1645 |
zconsTol->setData(globals->getZconsTol()); |
1646 |
} |
1647 |
else{ |
1648 |
double defaultZConsTol = 0.01; |
1649 |
sprintf( painCave.errMsg, |
1650 |
"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1651 |
" , default value %f is used.\n", defaultZConsTol); |
1652 |
painCave.isFatal = 0; |
1653 |
simError(); |
1654 |
|
1655 |
zconsTol->setData(defaultZConsTol); |
1656 |
} |
1657 |
theInfo.addProperty(zconsTol); |
1658 |
|
1659 |
//set Force Substraction Policy |
1660 |
StringData* zconsForcePolicy = new StringData(); |
1661 |
zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1662 |
|
1663 |
if(globals->haveZconsForcePolicy()){ |
1664 |
zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1665 |
} |
1666 |
else{ |
1667 |
sprintf( painCave.errMsg, |
1668 |
"ZConstraint Warning: User does not set force substraction policy, " |
1669 |
"average force substraction policy is used\n"); |
1670 |
painCave.isFatal = 0; |
1671 |
simError(); |
1672 |
zconsForcePolicy->setData("BYNUMBER"); |
1673 |
} |
1674 |
|
1675 |
theInfo.addProperty(zconsForcePolicy); |
1676 |
|
1677 |
//Determine the name of ouput file and add it into SimInfo's property list |
1678 |
//Be careful, do not use inFileName, since it is a pointer which |
1679 |
//point to a string at master node, and slave nodes do not contain that string |
1680 |
|
1681 |
string zconsOutput(theInfo.finalName); |
1682 |
|
1683 |
zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1684 |
|
1685 |
StringData* zconsFilename = new StringData(); |
1686 |
zconsFilename->setID(ZCONSFILENAME_ID); |
1687 |
zconsFilename->setData(zconsOutput); |
1688 |
|
1689 |
theInfo.addProperty(zconsFilename); |
1690 |
|
1691 |
//setup index, pos and other parameters of z-constraint molecules |
1692 |
nZConstraints = globals->getNzConstraints(); |
1693 |
theInfo.nZconstraints = nZConstraints; |
1694 |
|
1695 |
zconStamp = globals->getZconStamp(); |
1696 |
ZConsParaItem tempParaItem; |
1697 |
|
1698 |
ZConsParaData* zconsParaData = new ZConsParaData(); |
1699 |
zconsParaData->setID(ZCONSPARADATA_ID); |
1700 |
|
1701 |
for(int i = 0; i < nZConstraints; i++){ |
1702 |
tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1703 |
tempParaItem.zPos = zconStamp[i]->getZpos(); |
1704 |
tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1705 |
tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1706 |
|
1707 |
zconsParaData->addItem(tempParaItem); |
1708 |
} |
1709 |
|
1710 |
//sort the parameters by index of molecules |
1711 |
zconsParaData->sortByIndex(); |
1712 |
|
1713 |
//push data into siminfo, therefore, we can retrieve later |
1714 |
theInfo.addProperty(zconsParaData); |
1715 |
|
1716 |
} |