180 |
|
int calcPot, calcStress; |
181 |
|
int isError; |
182 |
|
|
183 |
– |
|
184 |
– |
|
183 |
|
tStats = new Thermo( info ); |
184 |
|
statOut = new StatWriter( info ); |
185 |
|
dumpOut = new DumpWriter( info ); |
217 |
|
"The integrator is ready to go." ); |
218 |
|
MPIcheckPoint(); |
219 |
|
#endif // is_mpi |
222 |
– |
|
223 |
– |
|
224 |
– |
pos = Atom::getPosArray(); |
225 |
– |
vel = Atom::getVelArray(); |
226 |
– |
frc = Atom::getFrcArray(); |
227 |
– |
trq = Atom::getTrqArray(); |
228 |
– |
Amat = Atom::getAmatArray(); |
220 |
|
|
221 |
|
while( currTime < runTime ){ |
222 |
|
|
225 |
|
calcStress = 1; |
226 |
|
} |
227 |
|
|
228 |
< |
std::cerr << "calcPot = " << calcPot << "; calcStress = " |
238 |
< |
<< calcStress << "\n"; |
228 |
> |
std::cerr << currTime << "\n"; |
229 |
|
|
230 |
|
integrateStep( calcPot, calcStress ); |
231 |
|
|
288 |
|
|
289 |
|
void Integrator::moveA( void ){ |
290 |
|
|
291 |
< |
int i,j,k; |
302 |
< |
int atomIndex, aMatIndex; |
291 |
> |
int i, j; |
292 |
|
DirectionalAtom* dAtom; |
293 |
< |
double Tb[3]; |
294 |
< |
double ji[3]; |
293 |
> |
double Tb[3], ji[3]; |
294 |
> |
double A[3][3], I[3][3]; |
295 |
|
double angle; |
296 |
< |
double A[3][3]; |
296 |
> |
double vel[3], pos[3], frc[3]; |
297 |
> |
double mass; |
298 |
|
|
309 |
– |
|
299 |
|
for( i=0; i<nAtoms; i++ ){ |
300 |
< |
atomIndex = i * 3; |
301 |
< |
aMatIndex = i * 9; |
300 |
> |
|
301 |
> |
atoms[i]->getVel( vel ); |
302 |
> |
atoms[i]->getPos( pos ); |
303 |
> |
atoms[i]->getFrc( frc ); |
304 |
|
|
305 |
< |
// velocity half step |
315 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
316 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
305 |
> |
mass = atoms[i]->getMass(); |
306 |
|
|
307 |
< |
std::cerr<< "MoveA vel[" << i << "] = " |
308 |
< |
<< vel[atomIndex] << "\t" |
309 |
< |
<< vel[atomIndex+1]<< "\t" |
310 |
< |
<< vel[atomIndex+2]<< "\n"; |
311 |
< |
|
312 |
< |
// position whole step |
324 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
325 |
< |
|
307 |
> |
for (j=0; j < 3; j++) { |
308 |
> |
// velocity half step |
309 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
310 |
> |
// position whole step |
311 |
> |
pos[j] += dt * vel[j]; |
312 |
> |
} |
313 |
|
|
314 |
< |
std::cerr<< "MoveA pos[" << i << "] = " |
315 |
< |
<< pos[atomIndex] << "\t" |
329 |
< |
<< pos[atomIndex+1]<< "\t" |
330 |
< |
<< pos[atomIndex+2]<< "\n"; |
314 |
> |
atoms[i]->setVel( vel ); |
315 |
> |
atoms[i]->setPos( pos ); |
316 |
|
|
317 |
|
if( atoms[i]->isDirectional() ){ |
318 |
|
|
320 |
|
|
321 |
|
// get and convert the torque to body frame |
322 |
|
|
323 |
< |
Tb[0] = dAtom->getTx(); |
339 |
< |
Tb[1] = dAtom->getTy(); |
340 |
< |
Tb[2] = dAtom->getTz(); |
341 |
< |
|
323 |
> |
dAtom->getTrq( Tb ); |
324 |
|
dAtom->lab2Body( Tb ); |
325 |
< |
|
325 |
> |
|
326 |
|
// get the angular momentum, and propagate a half step |
327 |
+ |
|
328 |
+ |
dAtom->getJ( ji ); |
329 |
+ |
|
330 |
+ |
for (j=0; j < 3; j++) |
331 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
332 |
|
|
346 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
347 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
348 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
349 |
– |
|
333 |
|
// use the angular velocities to propagate the rotation matrix a |
334 |
|
// full time step |
335 |
< |
|
336 |
< |
// get the atom's rotation matrix |
337 |
< |
|
338 |
< |
A[0][0] = dAtom->getAxx(); |
356 |
< |
A[0][1] = dAtom->getAxy(); |
357 |
< |
A[0][2] = dAtom->getAxz(); |
358 |
< |
|
359 |
< |
A[1][0] = dAtom->getAyx(); |
360 |
< |
A[1][1] = dAtom->getAyy(); |
361 |
< |
A[1][2] = dAtom->getAyz(); |
362 |
< |
|
363 |
< |
A[2][0] = dAtom->getAzx(); |
364 |
< |
A[2][1] = dAtom->getAzy(); |
365 |
< |
A[2][2] = dAtom->getAzz(); |
366 |
< |
|
335 |
> |
|
336 |
> |
dAtom->getA(A); |
337 |
> |
dAtom->getI(I); |
338 |
> |
|
339 |
|
// rotate about the x-axis |
340 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
340 |
> |
angle = dt2 * ji[0] / I[0][0]; |
341 |
|
this->rotate( 1, 2, angle, ji, A ); |
342 |
< |
|
342 |
> |
|
343 |
|
// rotate about the y-axis |
344 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
344 |
> |
angle = dt2 * ji[1] / I[1][1]; |
345 |
|
this->rotate( 2, 0, angle, ji, A ); |
346 |
|
|
347 |
|
// rotate about the z-axis |
348 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
349 |
< |
this->rotate( 0, 1, angle, ji, A ); |
348 |
> |
angle = dt * ji[2] / I[2][2]; |
349 |
> |
this->rotate( 0, 1, angle, ji, A); |
350 |
|
|
351 |
|
// rotate about the y-axis |
352 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
352 |
> |
angle = dt2 * ji[1] / I[1][1]; |
353 |
|
this->rotate( 2, 0, angle, ji, A ); |
354 |
|
|
355 |
|
// rotate about the x-axis |
356 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
356 |
> |
angle = dt2 * ji[0] / I[0][0]; |
357 |
|
this->rotate( 1, 2, angle, ji, A ); |
358 |
|
|
359 |
< |
dAtom->setJx( ji[0] ); |
360 |
< |
dAtom->setJy( ji[1] ); |
361 |
< |
dAtom->setJz( ji[2] ); |
362 |
< |
} |
363 |
< |
|
359 |
> |
|
360 |
> |
dAtom->setJ( ji ); |
361 |
> |
dAtom->setA( A ); |
362 |
> |
|
363 |
> |
} |
364 |
|
} |
365 |
|
} |
366 |
|
|
367 |
|
|
368 |
|
void Integrator::moveB( void ){ |
369 |
< |
int i,j,k; |
398 |
< |
int atomIndex; |
369 |
> |
int i, j; |
370 |
|
DirectionalAtom* dAtom; |
371 |
< |
double Tb[3]; |
372 |
< |
double ji[3]; |
371 |
> |
double Tb[3], ji[3]; |
372 |
> |
double vel[3], frc[3]; |
373 |
> |
double mass; |
374 |
|
|
375 |
|
for( i=0; i<nAtoms; i++ ){ |
376 |
< |
atomIndex = i * 3; |
376 |
> |
|
377 |
> |
atoms[i]->getVel( vel ); |
378 |
> |
atoms[i]->getFrc( frc ); |
379 |
|
|
380 |
+ |
mass = atoms[i]->getMass(); |
381 |
+ |
|
382 |
|
// velocity half step |
383 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
384 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
383 |
> |
for (j=0; j < 3; j++) |
384 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
385 |
> |
|
386 |
> |
atoms[i]->setVel( vel ); |
387 |
> |
|
388 |
> |
if( atoms[i]->isDirectional() ){ |
389 |
|
|
390 |
< |
std::cerr<< "MoveB vel[" << i << "] = " |
411 |
< |
<< vel[atomIndex] << "\t" |
412 |
< |
<< vel[atomIndex+1]<< "\t" |
413 |
< |
<< vel[atomIndex+2]<< "\n"; |
390 |
> |
dAtom = (DirectionalAtom *)atoms[i]; |
391 |
|
|
392 |
+ |
// get and convert the torque to body frame |
393 |
|
|
394 |
< |
if( atoms[i]->isDirectional() ){ |
417 |
< |
|
418 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
419 |
< |
|
420 |
< |
// get and convert the torque to body frame |
421 |
< |
|
422 |
< |
Tb[0] = dAtom->getTx(); |
423 |
< |
Tb[1] = dAtom->getTy(); |
424 |
< |
Tb[2] = dAtom->getTz(); |
425 |
< |
|
394 |
> |
dAtom->getTrq( Tb ); |
395 |
|
dAtom->lab2Body( Tb ); |
396 |
+ |
|
397 |
+ |
// get the angular momentum, and propagate a half step |
398 |
+ |
|
399 |
+ |
dAtom->getJ( ji ); |
400 |
+ |
|
401 |
+ |
for (j=0; j < 3; j++) |
402 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
403 |
|
|
404 |
< |
// get the angular momentum, and complete the angular momentum |
405 |
< |
// half step |
430 |
< |
|
431 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
432 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
433 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
434 |
< |
|
435 |
< |
dAtom->setJx( ji[0] ); |
436 |
< |
dAtom->setJy( ji[1] ); |
437 |
< |
dAtom->setJz( ji[2] ); |
404 |
> |
|
405 |
> |
dAtom->setJ( ji ); |
406 |
|
} |
407 |
|
} |
440 |
– |
|
408 |
|
} |
409 |
|
|
410 |
|
void Integrator::preMove( void ){ |
411 |
< |
int i; |
411 |
> |
int i, j; |
412 |
> |
double pos[3]; |
413 |
|
|
414 |
|
if( nConstrained ){ |
415 |
|
|
416 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
417 |
< |
} |
418 |
< |
} |
416 |
> |
for(i=0; i < nAtoms; i++) { |
417 |
> |
|
418 |
> |
atoms[i]->getPos( pos ); |
419 |
|
|
420 |
+ |
for (j = 0; j < 3; j++) { |
421 |
+ |
oldPos[3*i + j] = pos[j]; |
422 |
+ |
} |
423 |
+ |
|
424 |
+ |
} |
425 |
+ |
} |
426 |
+ |
} |
427 |
+ |
|
428 |
|
void Integrator::constrainA(){ |
429 |
|
|
430 |
|
int i,j,k; |
431 |
|
int done; |
432 |
+ |
double posA[3], posB[3]; |
433 |
+ |
double velA[3], velB[3]; |
434 |
|
double pab[3]; |
435 |
|
double rab[3]; |
436 |
|
int a, b, ax, ay, az, bx, by, bz; |
442 |
|
double gab; |
443 |
|
int iteration; |
444 |
|
|
445 |
< |
for( i=0; i<nAtoms; i++){ |
468 |
< |
|
445 |
> |
for( i=0; i<nAtoms; i++){ |
446 |
|
moving[i] = 0; |
447 |
|
moved[i] = 1; |
448 |
|
} |
466 |
|
bz = (b*3) + 2; |
467 |
|
|
468 |
|
if( moved[a] || moved[b] ){ |
469 |
< |
|
470 |
< |
pab[0] = pos[ax] - pos[bx]; |
471 |
< |
pab[1] = pos[ay] - pos[by]; |
472 |
< |
pab[2] = pos[az] - pos[bz]; |
473 |
< |
|
469 |
> |
|
470 |
> |
atoms[a]->getPos( posA ); |
471 |
> |
atoms[b]->getPos( posB ); |
472 |
> |
|
473 |
> |
for (j = 0; j < 3; j++ ) |
474 |
> |
pab[j] = posA[j] - posB[j]; |
475 |
> |
|
476 |
|
//periodic boundary condition |
477 |
|
|
478 |
|
info->wrapVector( pab ); |
517 |
|
dy = rab[1] * gab; |
518 |
|
dz = rab[2] * gab; |
519 |
|
|
520 |
< |
pos[ax] += rma * dx; |
521 |
< |
pos[ay] += rma * dy; |
522 |
< |
pos[az] += rma * dz; |
520 |
> |
posA[0] += rma * dx; |
521 |
> |
posA[1] += rma * dy; |
522 |
> |
posA[2] += rma * dz; |
523 |
|
|
524 |
< |
pos[bx] -= rmb * dx; |
546 |
< |
pos[by] -= rmb * dy; |
547 |
< |
pos[bz] -= rmb * dz; |
524 |
> |
atoms[a]->setPos( posA ); |
525 |
|
|
526 |
+ |
posB[0] -= rmb * dx; |
527 |
+ |
posB[1] -= rmb * dy; |
528 |
+ |
posB[2] -= rmb * dz; |
529 |
+ |
|
530 |
+ |
atoms[b]->setPos( posB ); |
531 |
+ |
|
532 |
|
dx = dx / dt; |
533 |
|
dy = dy / dt; |
534 |
|
dz = dz / dt; |
535 |
|
|
536 |
< |
vel[ax] += rma * dx; |
554 |
< |
vel[ay] += rma * dy; |
555 |
< |
vel[az] += rma * dz; |
536 |
> |
atoms[a]->getVel( velA ); |
537 |
|
|
538 |
< |
vel[bx] -= rmb * dx; |
539 |
< |
vel[by] -= rmb * dy; |
540 |
< |
vel[bz] -= rmb * dz; |
538 |
> |
velA[0] += rma * dx; |
539 |
> |
velA[1] += rma * dy; |
540 |
> |
velA[2] += rma * dz; |
541 |
|
|
542 |
+ |
atoms[a]->setVel( velA ); |
543 |
+ |
|
544 |
+ |
atoms[b]->getVel( velB ); |
545 |
+ |
|
546 |
+ |
velB[0] -= rmb * dx; |
547 |
+ |
velB[1] -= rmb * dy; |
548 |
+ |
velB[2] -= rmb * dz; |
549 |
+ |
|
550 |
+ |
atoms[b]->setVel( velB ); |
551 |
+ |
|
552 |
|
moving[a] = 1; |
553 |
|
moving[b] = 1; |
554 |
|
done = 0; |
580 |
|
|
581 |
|
int i,j,k; |
582 |
|
int done; |
583 |
+ |
double posA[3], posB[3]; |
584 |
+ |
double velA[3], velB[3]; |
585 |
|
double vxab, vyab, vzab; |
586 |
|
double rab[3]; |
587 |
|
int a, b, ax, ay, az, bx, by, bz; |
617 |
|
bz = (b*3) + 2; |
618 |
|
|
619 |
|
if( moved[a] || moved[b] ){ |
627 |
– |
|
628 |
– |
vxab = vel[ax] - vel[bx]; |
629 |
– |
vyab = vel[ay] - vel[by]; |
630 |
– |
vzab = vel[az] - vel[bz]; |
620 |
|
|
621 |
< |
rab[0] = pos[ax] - pos[bx]; |
622 |
< |
rab[1] = pos[ay] - pos[by]; |
623 |
< |
rab[2] = pos[az] - pos[bz]; |
624 |
< |
|
621 |
> |
atoms[a]->getVel( velA ); |
622 |
> |
atoms[b]->getVel( velB ); |
623 |
> |
|
624 |
> |
vxab = velA[0] - velB[0]; |
625 |
> |
vyab = velA[1] - velB[1]; |
626 |
> |
vzab = velA[2] - velB[2]; |
627 |
> |
|
628 |
> |
atoms[a]->getPos( posA ); |
629 |
> |
atoms[b]->getPos( posB ); |
630 |
> |
|
631 |
> |
for (j = 0; j < 3; j++) |
632 |
> |
rab[j] = posA[j] - posB[j]; |
633 |
> |
|
634 |
|
info->wrapVector( rab ); |
635 |
|
|
636 |
|
rma = 1.0 / atoms[a]->getMass(); |
645 |
|
dx = rab[0] * gab; |
646 |
|
dy = rab[1] * gab; |
647 |
|
dz = rab[2] * gab; |
648 |
< |
|
649 |
< |
vel[ax] += rma * dx; |
650 |
< |
vel[ay] += rma * dy; |
651 |
< |
vel[az] += rma * dz; |
648 |
> |
|
649 |
> |
velA[0] += rma * dx; |
650 |
> |
velA[1] += rma * dy; |
651 |
> |
velA[2] += rma * dz; |
652 |
|
|
653 |
< |
vel[bx] -= rmb * dx; |
654 |
< |
vel[by] -= rmb * dy; |
655 |
< |
vel[bz] -= rmb * dz; |
653 |
> |
atoms[a]->setVel( velA ); |
654 |
> |
|
655 |
> |
velB[0] -= rmb * dx; |
656 |
> |
velB[1] -= rmb * dy; |
657 |
> |
velB[2] -= rmb * dz; |
658 |
> |
|
659 |
> |
atoms[b]->setVel( velB ); |
660 |
|
|
661 |
|
moving[a] = 1; |
662 |
|
moving[b] = 1; |
672 |
|
|
673 |
|
iteration++; |
674 |
|
} |
675 |
< |
|
675 |
> |
|
676 |
|
if( !done ){ |
677 |
|
|
678 |
|
|
685 |
|
|
686 |
|
} |
687 |
|
|
686 |
– |
|
687 |
– |
|
688 |
– |
|
689 |
– |
|
690 |
– |
|
691 |
– |
|
688 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
689 |
|
double A[3][3] ){ |
690 |
|
|