27 |
|
|
28 |
|
nAtoms = info->n_atoms; |
29 |
|
|
30 |
– |
std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
31 |
– |
|
30 |
|
// check for constraints |
31 |
|
|
32 |
|
constrainedA = NULL; |
178 |
|
int calcPot, calcStress; |
179 |
|
int isError; |
180 |
|
|
183 |
– |
|
184 |
– |
|
181 |
|
tStats = new Thermo( info ); |
182 |
|
statOut = new StatWriter( info ); |
183 |
|
dumpOut = new DumpWriter( info ); |
216 |
|
MPIcheckPoint(); |
217 |
|
#endif // is_mpi |
218 |
|
|
223 |
– |
|
224 |
– |
pos = Atom::getPosArray(); |
225 |
– |
vel = Atom::getVelArray(); |
226 |
– |
frc = Atom::getFrcArray(); |
227 |
– |
|
219 |
|
while( currTime < runTime ){ |
220 |
|
|
221 |
|
if( (currTime+dt) >= currStatus ){ |
223 |
|
calcStress = 1; |
224 |
|
} |
225 |
|
|
235 |
– |
std::cerr << currTime << "\n"; |
236 |
– |
|
226 |
|
integrateStep( calcPot, calcStress ); |
227 |
|
|
228 |
|
currTime += dt; |
268 |
|
|
269 |
|
preMove(); |
270 |
|
moveA(); |
271 |
< |
//if( nConstrained ) constrainA(); |
271 |
> |
if( nConstrained ) constrainA(); |
272 |
|
|
273 |
|
// calc forces |
274 |
|
|
284 |
|
|
285 |
|
void Integrator::moveA( void ){ |
286 |
|
|
287 |
< |
int i,j,k; |
299 |
< |
int atomIndex, aMatIndex; |
287 |
> |
int i, j; |
288 |
|
DirectionalAtom* dAtom; |
289 |
< |
double Tb[3]; |
290 |
< |
double ji[3]; |
289 |
> |
double Tb[3], ji[3]; |
290 |
> |
double A[3][3], I[3][3]; |
291 |
|
double angle; |
292 |
< |
double A[3][3], At[3][3]; |
292 |
> |
double vel[3], pos[3], frc[3]; |
293 |
> |
double mass; |
294 |
|
|
306 |
– |
|
295 |
|
for( i=0; i<nAtoms; i++ ){ |
308 |
– |
atomIndex = i * 3; |
309 |
– |
aMatIndex = i * 9; |
296 |
|
|
297 |
< |
// velocity half step |
298 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
299 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
297 |
> |
atoms[i]->getVel( vel ); |
298 |
> |
atoms[i]->getPos( pos ); |
299 |
> |
atoms[i]->getFrc( frc ); |
300 |
|
|
301 |
+ |
mass = atoms[i]->getMass(); |
302 |
|
|
303 |
< |
// position whole step |
304 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
305 |
< |
|
303 |
> |
for (j=0; j < 3; j++) { |
304 |
> |
// velocity half step |
305 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
306 |
> |
// position whole step |
307 |
> |
pos[j] += dt * vel[j]; |
308 |
> |
} |
309 |
|
|
310 |
+ |
atoms[i]->setVel( vel ); |
311 |
+ |
atoms[i]->setPos( pos ); |
312 |
+ |
|
313 |
|
if( atoms[i]->isDirectional() ){ |
314 |
|
|
315 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
316 |
|
|
317 |
|
// get and convert the torque to body frame |
318 |
|
|
319 |
< |
Tb[0] = dAtom->getTx(); |
327 |
< |
Tb[1] = dAtom->getTy(); |
328 |
< |
Tb[2] = dAtom->getTz(); |
329 |
< |
|
319 |
> |
dAtom->getTrq( Tb ); |
320 |
|
dAtom->lab2Body( Tb ); |
321 |
|
|
322 |
|
// get the angular momentum, and propagate a half step |
323 |
+ |
|
324 |
+ |
dAtom->getJ( ji ); |
325 |
+ |
|
326 |
+ |
for (j=0; j < 3; j++) |
327 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
328 |
|
|
334 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
335 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
336 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
337 |
– |
|
329 |
|
// use the angular velocities to propagate the rotation matrix a |
330 |
|
// full time step |
331 |
< |
|
331 |
> |
|
332 |
> |
dAtom->getA(A); |
333 |
> |
dAtom->getI(I); |
334 |
> |
|
335 |
|
// rotate about the x-axis |
336 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
337 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
336 |
> |
angle = dt2 * ji[0] / I[0][0]; |
337 |
> |
this->rotate( 1, 2, angle, ji, A ); |
338 |
|
|
339 |
|
// rotate about the y-axis |
340 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
341 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
340 |
> |
angle = dt2 * ji[1] / I[1][1]; |
341 |
> |
this->rotate( 2, 0, angle, ji, A ); |
342 |
|
|
343 |
|
// rotate about the z-axis |
344 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
345 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
344 |
> |
angle = dt * ji[2] / I[2][2]; |
345 |
> |
this->rotate( 0, 1, angle, ji, A); |
346 |
|
|
347 |
|
// rotate about the y-axis |
348 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
349 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
348 |
> |
angle = dt2 * ji[1] / I[1][1]; |
349 |
> |
this->rotate( 2, 0, angle, ji, A ); |
350 |
|
|
351 |
|
// rotate about the x-axis |
352 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
353 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
352 |
> |
angle = dt2 * ji[0] / I[0][0]; |
353 |
> |
this->rotate( 1, 2, angle, ji, A ); |
354 |
|
|
361 |
– |
dAtom->setJx( ji[0] ); |
362 |
– |
dAtom->setJy( ji[1] ); |
363 |
– |
dAtom->setJz( ji[2] ); |
355 |
|
|
356 |
< |
std::cerr << "Amat[" << i << "]\n"; |
357 |
< |
info->printMat9( &Amat[aMatIndex] ); |
356 |
> |
dAtom->setJ( ji ); |
357 |
> |
dAtom->setA( A ); |
358 |
|
|
359 |
< |
std::cerr << "ji[" << i << "]\t" |
369 |
< |
<< ji[0] << "\t" |
370 |
< |
<< ji[1] << "\t" |
371 |
< |
<< ji[2] << "\n"; |
372 |
< |
|
373 |
< |
} |
374 |
< |
|
359 |
> |
} |
360 |
|
} |
361 |
|
} |
362 |
|
|
363 |
|
|
364 |
|
void Integrator::moveB( void ){ |
365 |
< |
int i,j,k; |
381 |
< |
int atomIndex, aMatIndex; |
365 |
> |
int i, j; |
366 |
|
DirectionalAtom* dAtom; |
367 |
< |
double Tb[3]; |
368 |
< |
double ji[3]; |
367 |
> |
double Tb[3], ji[3]; |
368 |
> |
double vel[3], frc[3]; |
369 |
> |
double mass; |
370 |
|
|
371 |
|
for( i=0; i<nAtoms; i++ ){ |
372 |
< |
atomIndex = i * 3; |
373 |
< |
aMatIndex = i * 9; |
372 |
> |
|
373 |
> |
atoms[i]->getVel( vel ); |
374 |
> |
atoms[i]->getFrc( frc ); |
375 |
|
|
376 |
< |
// velocity half step |
391 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
392 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
376 |
> |
mass = atoms[i]->getMass(); |
377 |
|
|
378 |
+ |
// velocity half step |
379 |
+ |
for (j=0; j < 3; j++) |
380 |
+ |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
381 |
+ |
|
382 |
+ |
atoms[i]->setVel( vel ); |
383 |
|
|
384 |
|
if( atoms[i]->isDirectional() ){ |
385 |
< |
|
385 |
> |
|
386 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
398 |
– |
|
399 |
– |
// get and convert the torque to body frame |
400 |
– |
|
401 |
– |
Tb[0] = dAtom->getTx(); |
402 |
– |
Tb[1] = dAtom->getTy(); |
403 |
– |
Tb[2] = dAtom->getTz(); |
404 |
– |
|
405 |
– |
std::cerr << "TrqB[" << i << "]\t" |
406 |
– |
<< Tb[0] << "\t" |
407 |
– |
<< Tb[1] << "\t" |
408 |
– |
<< Tb[2] << "\n"; |
387 |
|
|
388 |
+ |
// get and convert the torque to body frame |
389 |
+ |
|
390 |
+ |
dAtom->getTrq( Tb ); |
391 |
|
dAtom->lab2Body( Tb ); |
411 |
– |
|
412 |
– |
// get the angular momentum, and complete the angular momentum |
413 |
– |
// half step |
414 |
– |
|
415 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
416 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
417 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
418 |
– |
|
419 |
– |
dAtom->setJx( ji[0] ); |
420 |
– |
dAtom->setJy( ji[1] ); |
421 |
– |
dAtom->setJz( ji[2] ); |
392 |
|
|
393 |
+ |
// get the angular momentum, and propagate a half step |
394 |
|
|
395 |
< |
std::cerr << "Amat[" << i << "]\n"; |
396 |
< |
info->printMat9( &Amat[aMatIndex] ); |
397 |
< |
|
398 |
< |
std::cerr << "ji[" << i << "]\t" |
399 |
< |
<< ji[0] << "\t" |
400 |
< |
<< ji[1] << "\t" |
401 |
< |
<< ji[2] << "\n"; |
395 |
> |
dAtom->getJ( ji ); |
396 |
> |
|
397 |
> |
for (j=0; j < 3; j++) |
398 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
399 |
> |
|
400 |
> |
|
401 |
> |
dAtom->setJ( ji ); |
402 |
|
} |
403 |
|
} |
433 |
– |
|
404 |
|
} |
405 |
|
|
406 |
|
void Integrator::preMove( void ){ |
407 |
< |
int i; |
407 |
> |
int i, j; |
408 |
> |
double pos[3]; |
409 |
|
|
410 |
|
if( nConstrained ){ |
411 |
|
|
412 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
413 |
< |
} |
414 |
< |
} |
412 |
> |
for(i=0; i < nAtoms; i++) { |
413 |
> |
|
414 |
> |
atoms[i]->getPos( pos ); |
415 |
|
|
416 |
+ |
for (j = 0; j < 3; j++) { |
417 |
+ |
oldPos[3*i + j] = pos[j]; |
418 |
+ |
} |
419 |
+ |
|
420 |
+ |
} |
421 |
+ |
} |
422 |
+ |
} |
423 |
+ |
|
424 |
|
void Integrator::constrainA(){ |
425 |
|
|
426 |
|
int i,j,k; |
427 |
|
int done; |
428 |
+ |
double posA[3], posB[3]; |
429 |
+ |
double velA[3], velB[3]; |
430 |
|
double pab[3]; |
431 |
|
double rab[3]; |
432 |
|
int a, b, ax, ay, az, bx, by, bz; |
438 |
|
double gab; |
439 |
|
int iteration; |
440 |
|
|
441 |
< |
for( i=0; i<nAtoms; i++){ |
461 |
< |
|
441 |
> |
for( i=0; i<nAtoms; i++){ |
442 |
|
moving[i] = 0; |
443 |
|
moved[i] = 1; |
444 |
|
} |
462 |
|
bz = (b*3) + 2; |
463 |
|
|
464 |
|
if( moved[a] || moved[b] ){ |
465 |
< |
|
466 |
< |
pab[0] = pos[ax] - pos[bx]; |
467 |
< |
pab[1] = pos[ay] - pos[by]; |
468 |
< |
pab[2] = pos[az] - pos[bz]; |
469 |
< |
|
465 |
> |
|
466 |
> |
atoms[a]->getPos( posA ); |
467 |
> |
atoms[b]->getPos( posB ); |
468 |
> |
|
469 |
> |
for (j = 0; j < 3; j++ ) |
470 |
> |
pab[j] = posA[j] - posB[j]; |
471 |
> |
|
472 |
|
//periodic boundary condition |
473 |
|
|
474 |
|
info->wrapVector( pab ); |
513 |
|
dy = rab[1] * gab; |
514 |
|
dz = rab[2] * gab; |
515 |
|
|
516 |
< |
pos[ax] += rma * dx; |
517 |
< |
pos[ay] += rma * dy; |
518 |
< |
pos[az] += rma * dz; |
516 |
> |
posA[0] += rma * dx; |
517 |
> |
posA[1] += rma * dy; |
518 |
> |
posA[2] += rma * dz; |
519 |
|
|
520 |
< |
pos[bx] -= rmb * dx; |
539 |
< |
pos[by] -= rmb * dy; |
540 |
< |
pos[bz] -= rmb * dz; |
520 |
> |
atoms[a]->setPos( posA ); |
521 |
|
|
522 |
+ |
posB[0] -= rmb * dx; |
523 |
+ |
posB[1] -= rmb * dy; |
524 |
+ |
posB[2] -= rmb * dz; |
525 |
+ |
|
526 |
+ |
atoms[b]->setPos( posB ); |
527 |
+ |
|
528 |
|
dx = dx / dt; |
529 |
|
dy = dy / dt; |
530 |
|
dz = dz / dt; |
531 |
|
|
532 |
< |
vel[ax] += rma * dx; |
547 |
< |
vel[ay] += rma * dy; |
548 |
< |
vel[az] += rma * dz; |
532 |
> |
atoms[a]->getVel( velA ); |
533 |
|
|
534 |
< |
vel[bx] -= rmb * dx; |
535 |
< |
vel[by] -= rmb * dy; |
536 |
< |
vel[bz] -= rmb * dz; |
534 |
> |
velA[0] += rma * dx; |
535 |
> |
velA[1] += rma * dy; |
536 |
> |
velA[2] += rma * dz; |
537 |
> |
|
538 |
> |
atoms[a]->setVel( velA ); |
539 |
|
|
540 |
+ |
atoms[b]->getVel( velB ); |
541 |
+ |
|
542 |
+ |
velB[0] -= rmb * dx; |
543 |
+ |
velB[1] -= rmb * dy; |
544 |
+ |
velB[2] -= rmb * dz; |
545 |
+ |
|
546 |
+ |
atoms[b]->setVel( velB ); |
547 |
+ |
|
548 |
|
moving[a] = 1; |
549 |
|
moving[b] = 1; |
550 |
|
done = 0; |
576 |
|
|
577 |
|
int i,j,k; |
578 |
|
int done; |
579 |
+ |
double posA[3], posB[3]; |
580 |
+ |
double velA[3], velB[3]; |
581 |
|
double vxab, vyab, vzab; |
582 |
|
double rab[3]; |
583 |
|
int a, b, ax, ay, az, bx, by, bz; |
613 |
|
bz = (b*3) + 2; |
614 |
|
|
615 |
|
if( moved[a] || moved[b] ){ |
620 |
– |
|
621 |
– |
vxab = vel[ax] - vel[bx]; |
622 |
– |
vyab = vel[ay] - vel[by]; |
623 |
– |
vzab = vel[az] - vel[bz]; |
616 |
|
|
617 |
< |
rab[0] = pos[ax] - pos[bx]; |
618 |
< |
rab[1] = pos[ay] - pos[by]; |
619 |
< |
rab[2] = pos[az] - pos[bz]; |
620 |
< |
|
617 |
> |
atoms[a]->getVel( velA ); |
618 |
> |
atoms[b]->getVel( velB ); |
619 |
> |
|
620 |
> |
vxab = velA[0] - velB[0]; |
621 |
> |
vyab = velA[1] - velB[1]; |
622 |
> |
vzab = velA[2] - velB[2]; |
623 |
> |
|
624 |
> |
atoms[a]->getPos( posA ); |
625 |
> |
atoms[b]->getPos( posB ); |
626 |
> |
|
627 |
> |
for (j = 0; j < 3; j++) |
628 |
> |
rab[j] = posA[j] - posB[j]; |
629 |
> |
|
630 |
|
info->wrapVector( rab ); |
631 |
|
|
632 |
|
rma = 1.0 / atoms[a]->getMass(); |
641 |
|
dx = rab[0] * gab; |
642 |
|
dy = rab[1] * gab; |
643 |
|
dz = rab[2] * gab; |
644 |
< |
|
645 |
< |
vel[ax] += rma * dx; |
646 |
< |
vel[ay] += rma * dy; |
647 |
< |
vel[az] += rma * dz; |
644 |
> |
|
645 |
> |
velA[0] += rma * dx; |
646 |
> |
velA[1] += rma * dy; |
647 |
> |
velA[2] += rma * dz; |
648 |
|
|
649 |
< |
vel[bx] -= rmb * dx; |
650 |
< |
vel[by] -= rmb * dy; |
651 |
< |
vel[bz] -= rmb * dz; |
649 |
> |
atoms[a]->setVel( velA ); |
650 |
> |
|
651 |
> |
velB[0] -= rmb * dx; |
652 |
> |
velB[1] -= rmb * dy; |
653 |
> |
velB[2] -= rmb * dz; |
654 |
> |
|
655 |
> |
atoms[b]->setVel( velB ); |
656 |
|
|
657 |
|
moving[a] = 1; |
658 |
|
moving[b] = 1; |
668 |
|
|
669 |
|
iteration++; |
670 |
|
} |
671 |
< |
|
671 |
> |
|
672 |
|
if( !done ){ |
673 |
|
|
674 |
|
|
681 |
|
|
682 |
|
} |
683 |
|
|
679 |
– |
|
680 |
– |
|
681 |
– |
|
682 |
– |
|
683 |
– |
|
684 |
– |
|
684 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
685 |
< |
double A[9] ){ |
685 |
> |
double A[3][3] ){ |
686 |
|
|
687 |
|
int i,j,k; |
688 |
|
double sinAngle; |
694 |
|
double tempA[3][3]; |
695 |
|
double tempJ[3]; |
696 |
|
|
698 |
– |
|
697 |
|
// initialize the tempA |
698 |
|
|
699 |
|
for(i=0; i<3; i++){ |
700 |
|
for(j=0; j<3; j++){ |
701 |
< |
tempA[j][i] = A[3*i+j]; |
701 |
> |
tempA[j][i] = A[i][j]; |
702 |
|
} |
703 |
|
} |
704 |
|
|
755 |
|
|
756 |
|
for(i=0; i<3; i++){ |
757 |
|
for(j=0; j<3; j++){ |
758 |
< |
A[3*j+i] = 0.0; |
758 |
> |
A[j][i] = 0.0; |
759 |
|
for(k=0; k<3; k++){ |
760 |
< |
A[3*j+i] += tempA[i][k] * rot[j][k]; |
760 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
761 |
|
} |
762 |
|
} |
763 |
|
} |