72 |
|
for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 |
|
|
74 |
|
constrained = theArray[j]->is_constrained(); |
75 |
< |
|
75 |
> |
|
76 |
|
if(constrained){ |
77 |
< |
|
77 |
> |
|
78 |
|
dummy_plug = theArray[j]->get_constraint(); |
79 |
|
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
80 |
|
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
82 |
|
|
83 |
|
nConstrained++; |
84 |
|
constrained = 0; |
85 |
< |
} |
85 |
> |
} |
86 |
|
} |
87 |
|
|
88 |
|
theArray = (SRI**) molecules[i].getMyBends(); |
167 |
|
double currSample; |
168 |
|
double currThermal; |
169 |
|
double currStatus; |
170 |
– |
double currTime; |
170 |
|
|
171 |
|
int calcPot, calcStress; |
172 |
|
int isError; |
173 |
|
|
175 |
– |
|
176 |
– |
|
174 |
|
tStats = new Thermo( info ); |
175 |
|
statOut = new StatWriter( info ); |
176 |
|
dumpOut = new DumpWriter( info ); |
190 |
|
tStats->velocitize(); |
191 |
|
} |
192 |
|
|
196 |
– |
dumpOut->writeDump( 0.0 ); |
197 |
– |
statOut->writeStat( 0.0 ); |
198 |
– |
|
193 |
|
calcPot = 0; |
194 |
|
calcStress = 0; |
195 |
|
currSample = sampleTime; |
196 |
|
currThermal = thermalTime; |
197 |
|
currStatus = statusTime; |
204 |
– |
currTime = 0.0;; |
198 |
|
|
199 |
+ |
dumpOut->writeDump( info->currTime ); |
200 |
+ |
statOut->writeStat( info->currTime ); |
201 |
|
|
202 |
|
readyCheck(); |
203 |
|
|
207 |
|
MPIcheckPoint(); |
208 |
|
#endif // is_mpi |
209 |
|
|
210 |
+ |
while( info->currTime < runTime ){ |
211 |
|
|
212 |
< |
pos = Atom::getPosArray(); |
217 |
< |
vel = Atom::getVelArray(); |
218 |
< |
frc = Atom::getFrcArray(); |
219 |
< |
trq = Atom::getTrqArray(); |
220 |
< |
Amat = Atom::getAmatArray(); |
221 |
< |
|
222 |
< |
while( currTime < runTime ){ |
223 |
< |
|
224 |
< |
if( (currTime+dt) >= currStatus ){ |
212 |
> |
if( (info->currTime+dt) >= currStatus ){ |
213 |
|
calcPot = 1; |
214 |
|
calcStress = 1; |
215 |
|
} |
216 |
|
|
217 |
|
integrateStep( calcPot, calcStress ); |
218 |
|
|
219 |
< |
currTime += dt; |
219 |
> |
info->currTime += dt; |
220 |
> |
info->setTime(info->currTime); |
221 |
|
|
222 |
|
if( info->setTemp ){ |
223 |
< |
if( currTime >= currThermal ){ |
223 |
> |
if( info->currTime >= currThermal ){ |
224 |
|
tStats->velocitize(); |
225 |
|
currThermal += thermalTime; |
226 |
|
} |
227 |
|
} |
228 |
|
|
229 |
< |
if( currTime >= currSample ){ |
230 |
< |
dumpOut->writeDump( currTime ); |
229 |
> |
if( info->currTime >= currSample ){ |
230 |
> |
dumpOut->writeDump( info->currTime ); |
231 |
|
currSample += sampleTime; |
232 |
|
} |
233 |
|
|
234 |
< |
if( currTime >= currStatus ){ |
235 |
< |
statOut->writeStat( currTime ); |
234 |
> |
if( info->currTime >= currStatus ){ |
235 |
> |
statOut->writeStat( info->currTime ); |
236 |
|
calcPot = 0; |
237 |
|
calcStress = 0; |
238 |
|
currStatus += statusTime; |
246 |
|
|
247 |
|
} |
248 |
|
|
249 |
< |
dumpOut->writeFinal(currTime); |
249 |
> |
dumpOut->writeFinal(info->currTime); |
250 |
|
|
251 |
|
delete dumpOut; |
252 |
|
delete statOut; |
262 |
|
moveA(); |
263 |
|
if( nConstrained ) constrainA(); |
264 |
|
|
265 |
+ |
|
266 |
+ |
#ifdef IS_MPI |
267 |
+ |
strcpy( checkPointMsg, "Succesful moveA\n" ); |
268 |
+ |
MPIcheckPoint(); |
269 |
+ |
#endif // is_mpi |
270 |
+ |
|
271 |
+ |
|
272 |
|
// calc forces |
273 |
|
|
274 |
|
myFF->doForces(calcPot,calcStress); |
275 |
|
|
276 |
+ |
#ifdef IS_MPI |
277 |
+ |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
278 |
+ |
MPIcheckPoint(); |
279 |
+ |
#endif // is_mpi |
280 |
+ |
|
281 |
+ |
|
282 |
|
// finish the velocity half step |
283 |
|
|
284 |
|
moveB(); |
285 |
|
if( nConstrained ) constrainB(); |
286 |
< |
|
286 |
> |
|
287 |
> |
#ifdef IS_MPI |
288 |
> |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
289 |
> |
MPIcheckPoint(); |
290 |
> |
#endif // is_mpi |
291 |
> |
|
292 |
> |
|
293 |
|
} |
294 |
|
|
295 |
|
|
296 |
|
void Integrator::moveA( void ){ |
297 |
|
|
298 |
< |
int i,j,k; |
291 |
< |
int atomIndex, aMatIndex; |
298 |
> |
int i, j; |
299 |
|
DirectionalAtom* dAtom; |
300 |
< |
double Tb[3]; |
301 |
< |
double ji[3]; |
300 |
> |
double Tb[3], ji[3]; |
301 |
> |
double A[3][3], I[3][3]; |
302 |
|
double angle; |
303 |
+ |
double vel[3], pos[3], frc[3]; |
304 |
+ |
double mass; |
305 |
|
|
306 |
+ |
for( i=0; i<nAtoms; i++ ){ |
307 |
|
|
308 |
+ |
atoms[i]->getVel( vel ); |
309 |
+ |
atoms[i]->getPos( pos ); |
310 |
+ |
atoms[i]->getFrc( frc ); |
311 |
|
|
312 |
< |
for( i=0; i<nAtoms; i++ ){ |
300 |
< |
atomIndex = i * 3; |
301 |
< |
aMatIndex = i * 9; |
312 |
> |
mass = atoms[i]->getMass(); |
313 |
|
|
314 |
< |
// velocity half step |
315 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
316 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
314 |
> |
for (j=0; j < 3; j++) { |
315 |
> |
// velocity half step |
316 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
317 |
> |
// position whole step |
318 |
> |
pos[j] += dt * vel[j]; |
319 |
> |
} |
320 |
|
|
321 |
< |
// position whole step |
322 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
323 |
< |
|
321 |
> |
atoms[i]->setVel( vel ); |
322 |
> |
atoms[i]->setPos( pos ); |
323 |
> |
|
324 |
|
if( atoms[i]->isDirectional() ){ |
325 |
|
|
326 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
327 |
|
|
328 |
|
// get and convert the torque to body frame |
329 |
|
|
330 |
< |
Tb[0] = dAtom->getTx(); |
317 |
< |
Tb[1] = dAtom->getTy(); |
318 |
< |
Tb[2] = dAtom->getTz(); |
319 |
< |
|
330 |
> |
dAtom->getTrq( Tb ); |
331 |
|
dAtom->lab2Body( Tb ); |
332 |
< |
|
332 |
> |
|
333 |
|
// get the angular momentum, and propagate a half step |
334 |
+ |
|
335 |
+ |
dAtom->getJ( ji ); |
336 |
+ |
|
337 |
+ |
for (j=0; j < 3; j++) |
338 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
339 |
|
|
324 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
325 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
326 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
327 |
– |
|
340 |
|
// use the angular velocities to propagate the rotation matrix a |
341 |
|
// full time step |
342 |
< |
|
342 |
> |
|
343 |
> |
dAtom->getA(A); |
344 |
> |
dAtom->getI(I); |
345 |
> |
|
346 |
|
// rotate about the x-axis |
347 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
348 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
349 |
< |
|
347 |
> |
angle = dt2 * ji[0] / I[0][0]; |
348 |
> |
this->rotate( 1, 2, angle, ji, A ); |
349 |
> |
|
350 |
|
// rotate about the y-axis |
351 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
352 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
351 |
> |
angle = dt2 * ji[1] / I[1][1]; |
352 |
> |
this->rotate( 2, 0, angle, ji, A ); |
353 |
|
|
354 |
|
// rotate about the z-axis |
355 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
356 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
355 |
> |
angle = dt * ji[2] / I[2][2]; |
356 |
> |
this->rotate( 0, 1, angle, ji, A); |
357 |
|
|
358 |
|
// rotate about the y-axis |
359 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
360 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
359 |
> |
angle = dt2 * ji[1] / I[1][1]; |
360 |
> |
this->rotate( 2, 0, angle, ji, A ); |
361 |
|
|
362 |
|
// rotate about the x-axis |
363 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
364 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
363 |
> |
angle = dt2 * ji[0] / I[0][0]; |
364 |
> |
this->rotate( 1, 2, angle, ji, A ); |
365 |
|
|
366 |
< |
dAtom->setJx( ji[0] ); |
367 |
< |
dAtom->setJy( ji[1] ); |
368 |
< |
dAtom->setJz( ji[2] ); |
369 |
< |
} |
370 |
< |
|
366 |
> |
|
367 |
> |
dAtom->setJ( ji ); |
368 |
> |
dAtom->setA( A ); |
369 |
> |
|
370 |
> |
} |
371 |
|
} |
372 |
|
} |
373 |
|
|
374 |
|
|
375 |
|
void Integrator::moveB( void ){ |
376 |
< |
int i,j,k; |
362 |
< |
int atomIndex; |
376 |
> |
int i, j; |
377 |
|
DirectionalAtom* dAtom; |
378 |
< |
double Tb[3]; |
379 |
< |
double ji[3]; |
378 |
> |
double Tb[3], ji[3]; |
379 |
> |
double vel[3], frc[3]; |
380 |
> |
double mass; |
381 |
|
|
382 |
|
for( i=0; i<nAtoms; i++ ){ |
383 |
< |
atomIndex = i * 3; |
383 |
> |
|
384 |
> |
atoms[i]->getVel( vel ); |
385 |
> |
atoms[i]->getFrc( frc ); |
386 |
|
|
387 |
< |
// velocity half step |
371 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
372 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
387 |
> |
mass = atoms[i]->getMass(); |
388 |
|
|
389 |
+ |
// velocity half step |
390 |
+ |
for (j=0; j < 3; j++) |
391 |
+ |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
392 |
+ |
|
393 |
+ |
atoms[i]->setVel( vel ); |
394 |
+ |
|
395 |
|
if( atoms[i]->isDirectional() ){ |
396 |
< |
|
396 |
> |
|
397 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
398 |
< |
|
399 |
< |
// get and convert the torque to body frame |
400 |
< |
|
401 |
< |
Tb[0] = dAtom->getTx(); |
381 |
< |
Tb[1] = dAtom->getTy(); |
382 |
< |
Tb[2] = dAtom->getTz(); |
383 |
< |
|
398 |
> |
|
399 |
> |
// get and convert the torque to body frame |
400 |
> |
|
401 |
> |
dAtom->getTrq( Tb ); |
402 |
|
dAtom->lab2Body( Tb ); |
403 |
+ |
|
404 |
+ |
// get the angular momentum, and propagate a half step |
405 |
+ |
|
406 |
+ |
dAtom->getJ( ji ); |
407 |
+ |
|
408 |
+ |
for (j=0; j < 3; j++) |
409 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
410 |
|
|
411 |
< |
// get the angular momentum, and complete the angular momentum |
412 |
< |
// half step |
388 |
< |
|
389 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
390 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
391 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
392 |
< |
|
393 |
< |
dAtom->setJx( ji[0] ); |
394 |
< |
dAtom->setJy( ji[1] ); |
395 |
< |
dAtom->setJz( ji[2] ); |
411 |
> |
|
412 |
> |
dAtom->setJ( ji ); |
413 |
|
} |
414 |
|
} |
398 |
– |
|
415 |
|
} |
416 |
|
|
417 |
|
void Integrator::preMove( void ){ |
418 |
< |
int i; |
418 |
> |
int i, j; |
419 |
> |
double pos[3]; |
420 |
|
|
421 |
|
if( nConstrained ){ |
422 |
|
|
423 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
424 |
< |
} |
425 |
< |
} |
423 |
> |
for(i=0; i < nAtoms; i++) { |
424 |
> |
|
425 |
> |
atoms[i]->getPos( pos ); |
426 |
|
|
427 |
+ |
for (j = 0; j < 3; j++) { |
428 |
+ |
oldPos[3*i + j] = pos[j]; |
429 |
+ |
} |
430 |
+ |
|
431 |
+ |
} |
432 |
+ |
} |
433 |
+ |
} |
434 |
+ |
|
435 |
|
void Integrator::constrainA(){ |
436 |
|
|
437 |
|
int i,j,k; |
438 |
|
int done; |
439 |
+ |
double posA[3], posB[3]; |
440 |
+ |
double velA[3], velB[3]; |
441 |
|
double pab[3]; |
442 |
|
double rab[3]; |
443 |
|
int a, b, ax, ay, az, bx, by, bz; |
449 |
|
double gab; |
450 |
|
int iteration; |
451 |
|
|
452 |
< |
|
426 |
< |
|
427 |
< |
for( i=0; i<nAtoms; i++){ |
428 |
< |
|
452 |
> |
for( i=0; i<nAtoms; i++){ |
453 |
|
moving[i] = 0; |
454 |
|
moved[i] = 1; |
455 |
|
} |
473 |
|
bz = (b*3) + 2; |
474 |
|
|
475 |
|
if( moved[a] || moved[b] ){ |
476 |
< |
|
477 |
< |
pab[0] = pos[ax] - pos[bx]; |
478 |
< |
pab[1] = pos[ay] - pos[by]; |
479 |
< |
pab[2] = pos[az] - pos[bz]; |
480 |
< |
|
476 |
> |
|
477 |
> |
atoms[a]->getPos( posA ); |
478 |
> |
atoms[b]->getPos( posB ); |
479 |
> |
|
480 |
> |
for (j = 0; j < 3; j++ ) |
481 |
> |
pab[j] = posA[j] - posB[j]; |
482 |
> |
|
483 |
|
//periodic boundary condition |
484 |
|
|
485 |
|
info->wrapVector( pab ); |
524 |
|
dy = rab[1] * gab; |
525 |
|
dz = rab[2] * gab; |
526 |
|
|
527 |
< |
pos[ax] += rma * dx; |
528 |
< |
pos[ay] += rma * dy; |
529 |
< |
pos[az] += rma * dz; |
527 |
> |
posA[0] += rma * dx; |
528 |
> |
posA[1] += rma * dy; |
529 |
> |
posA[2] += rma * dz; |
530 |
|
|
531 |
< |
pos[bx] -= rmb * dx; |
506 |
< |
pos[by] -= rmb * dy; |
507 |
< |
pos[bz] -= rmb * dz; |
531 |
> |
atoms[a]->setPos( posA ); |
532 |
|
|
533 |
+ |
posB[0] -= rmb * dx; |
534 |
+ |
posB[1] -= rmb * dy; |
535 |
+ |
posB[2] -= rmb * dz; |
536 |
+ |
|
537 |
+ |
atoms[b]->setPos( posB ); |
538 |
+ |
|
539 |
|
dx = dx / dt; |
540 |
|
dy = dy / dt; |
541 |
|
dz = dz / dt; |
542 |
|
|
543 |
< |
vel[ax] += rma * dx; |
514 |
< |
vel[ay] += rma * dy; |
515 |
< |
vel[az] += rma * dz; |
543 |
> |
atoms[a]->getVel( velA ); |
544 |
|
|
545 |
< |
vel[bx] -= rmb * dx; |
546 |
< |
vel[by] -= rmb * dy; |
547 |
< |
vel[bz] -= rmb * dz; |
545 |
> |
velA[0] += rma * dx; |
546 |
> |
velA[1] += rma * dy; |
547 |
> |
velA[2] += rma * dz; |
548 |
|
|
549 |
+ |
atoms[a]->setVel( velA ); |
550 |
+ |
|
551 |
+ |
atoms[b]->getVel( velB ); |
552 |
+ |
|
553 |
+ |
velB[0] -= rmb * dx; |
554 |
+ |
velB[1] -= rmb * dy; |
555 |
+ |
velB[2] -= rmb * dz; |
556 |
+ |
|
557 |
+ |
atoms[b]->setVel( velB ); |
558 |
+ |
|
559 |
|
moving[a] = 1; |
560 |
|
moving[b] = 1; |
561 |
|
done = 0; |
587 |
|
|
588 |
|
int i,j,k; |
589 |
|
int done; |
590 |
+ |
double posA[3], posB[3]; |
591 |
+ |
double velA[3], velB[3]; |
592 |
|
double vxab, vyab, vzab; |
593 |
|
double rab[3]; |
594 |
|
int a, b, ax, ay, az, bx, by, bz; |
624 |
|
bz = (b*3) + 2; |
625 |
|
|
626 |
|
if( moved[a] || moved[b] ){ |
587 |
– |
|
588 |
– |
vxab = vel[ax] - vel[bx]; |
589 |
– |
vyab = vel[ay] - vel[by]; |
590 |
– |
vzab = vel[az] - vel[bz]; |
627 |
|
|
628 |
< |
rab[0] = pos[ax] - pos[bx]; |
629 |
< |
rab[1] = pos[ay] - pos[by]; |
630 |
< |
rab[2] = pos[az] - pos[bz]; |
631 |
< |
|
628 |
> |
atoms[a]->getVel( velA ); |
629 |
> |
atoms[b]->getVel( velB ); |
630 |
> |
|
631 |
> |
vxab = velA[0] - velB[0]; |
632 |
> |
vyab = velA[1] - velB[1]; |
633 |
> |
vzab = velA[2] - velB[2]; |
634 |
> |
|
635 |
> |
atoms[a]->getPos( posA ); |
636 |
> |
atoms[b]->getPos( posB ); |
637 |
> |
|
638 |
> |
for (j = 0; j < 3; j++) |
639 |
> |
rab[j] = posA[j] - posB[j]; |
640 |
> |
|
641 |
|
info->wrapVector( rab ); |
642 |
|
|
643 |
|
rma = 1.0 / atoms[a]->getMass(); |
652 |
|
dx = rab[0] * gab; |
653 |
|
dy = rab[1] * gab; |
654 |
|
dz = rab[2] * gab; |
655 |
< |
|
656 |
< |
vel[ax] += rma * dx; |
657 |
< |
vel[ay] += rma * dy; |
658 |
< |
vel[az] += rma * dz; |
655 |
> |
|
656 |
> |
velA[0] += rma * dx; |
657 |
> |
velA[1] += rma * dy; |
658 |
> |
velA[2] += rma * dz; |
659 |
|
|
660 |
< |
vel[bx] -= rmb * dx; |
661 |
< |
vel[by] -= rmb * dy; |
662 |
< |
vel[bz] -= rmb * dz; |
660 |
> |
atoms[a]->setVel( velA ); |
661 |
> |
|
662 |
> |
velB[0] -= rmb * dx; |
663 |
> |
velB[1] -= rmb * dy; |
664 |
> |
velB[2] -= rmb * dz; |
665 |
> |
|
666 |
> |
atoms[b]->setVel( velB ); |
667 |
|
|
668 |
|
moving[a] = 1; |
669 |
|
moving[b] = 1; |
679 |
|
|
680 |
|
iteration++; |
681 |
|
} |
682 |
< |
|
682 |
> |
|
683 |
|
if( !done ){ |
684 |
|
|
685 |
|
|
692 |
|
|
693 |
|
} |
694 |
|
|
646 |
– |
|
647 |
– |
|
648 |
– |
|
649 |
– |
|
650 |
– |
|
651 |
– |
|
695 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
696 |
< |
double A[9] ){ |
696 |
> |
double A[3][3] ){ |
697 |
|
|
698 |
|
int i,j,k; |
699 |
|
double sinAngle; |
709 |
|
|
710 |
|
for(i=0; i<3; i++){ |
711 |
|
for(j=0; j<3; j++){ |
712 |
< |
tempA[j][i] = A[3*i + j]; |
712 |
> |
tempA[j][i] = A[i][j]; |
713 |
|
} |
714 |
|
} |
715 |
|
|
766 |
|
|
767 |
|
for(i=0; i<3; i++){ |
768 |
|
for(j=0; j<3; j++){ |
769 |
< |
A[3*j + i] = 0.0; |
769 |
> |
A[j][i] = 0.0; |
770 |
|
for(k=0; k<3; k++){ |
771 |
< |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
771 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
772 |
|
} |
773 |
|
} |
774 |
|
} |