27 |
|
|
28 |
|
nAtoms = info->n_atoms; |
29 |
|
|
30 |
+ |
std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
31 |
+ |
|
32 |
|
// check for constraints |
33 |
|
|
34 |
|
constrainedA = NULL; |
74 |
|
for(int j=0; j<molecules[i].getNBonds(); j++){ |
75 |
|
|
76 |
|
constrained = theArray[j]->is_constrained(); |
77 |
+ |
|
78 |
+ |
std::cerr << "Is the folowing bond constrained \n"; |
79 |
+ |
theArray[j]->printMe(); |
80 |
|
|
81 |
|
if(constrained){ |
82 |
|
|
83 |
+ |
std::cerr << "Yes\n"; |
84 |
+ |
|
85 |
|
dummy_plug = theArray[j]->get_constraint(); |
86 |
|
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
87 |
|
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
89 |
|
|
90 |
|
nConstrained++; |
91 |
|
constrained = 0; |
92 |
< |
} |
92 |
> |
} |
93 |
> |
else std::cerr << "No.\n"; |
94 |
|
} |
95 |
|
|
96 |
|
theArray = (SRI**) molecules[i].getMyBends(); |
146 |
|
constrainedB[i] = temp_con[i].get_b(); |
147 |
|
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
148 |
|
|
141 |
– |
cerr << "constraint " << constrainedA[i] << " <-> " << constrainedB[i] |
142 |
– |
<< " => " << constrainedDsqr[i] << "\n"; |
149 |
|
} |
150 |
|
|
151 |
|
|
234 |
|
calcStress = 1; |
235 |
|
} |
236 |
|
|
237 |
+ |
std::cerr << "calcPot = " << calcPot << "; calcStress = " |
238 |
+ |
<< calcStress << "\n"; |
239 |
+ |
|
240 |
|
integrateStep( calcPot, calcStress ); |
241 |
|
|
242 |
|
currTime += dt; |
268 |
|
|
269 |
|
} |
270 |
|
|
271 |
< |
dumpOut->writeFinal(); |
271 |
> |
dumpOut->writeFinal(currTime); |
272 |
|
|
273 |
|
delete dumpOut; |
274 |
|
delete statOut; |
304 |
|
double Tb[3]; |
305 |
|
double ji[3]; |
306 |
|
double angle; |
307 |
+ |
double A[3][3]; |
308 |
|
|
309 |
+ |
|
310 |
|
for( i=0; i<nAtoms; i++ ){ |
311 |
|
atomIndex = i * 3; |
312 |
|
aMatIndex = i * 9; |
313 |
< |
|
313 |
> |
|
314 |
|
// velocity half step |
315 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
316 |
|
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
317 |
|
|
318 |
+ |
std::cerr<< "MoveA vel[" << i << "] = " |
319 |
+ |
<< vel[atomIndex] << "\t" |
320 |
+ |
<< vel[atomIndex+1]<< "\t" |
321 |
+ |
<< vel[atomIndex+2]<< "\n"; |
322 |
+ |
|
323 |
|
// position whole step |
324 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
325 |
< |
pos[j] += dt * vel[j]; |
324 |
> |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
325 |
> |
|
326 |
|
|
327 |
< |
|
327 |
> |
std::cerr<< "MoveA pos[" << i << "] = " |
328 |
> |
<< pos[atomIndex] << "\t" |
329 |
> |
<< pos[atomIndex+1]<< "\t" |
330 |
> |
<< pos[atomIndex+2]<< "\n"; |
331 |
> |
|
332 |
|
if( atoms[i]->isDirectional() ){ |
333 |
|
|
334 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
350 |
|
// use the angular velocities to propagate the rotation matrix a |
351 |
|
// full time step |
352 |
|
|
353 |
+ |
// get the atom's rotation matrix |
354 |
+ |
|
355 |
+ |
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 |
+ |
|
367 |
|
// rotate about the x-axis |
368 |
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
369 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
369 |
> |
this->rotate( 1, 2, angle, ji, A ); |
370 |
|
|
371 |
|
// rotate about the y-axis |
372 |
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
373 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
373 |
> |
this->rotate( 2, 0, angle, ji, A ); |
374 |
|
|
375 |
|
// rotate about the z-axis |
376 |
|
angle = dt * ji[2] / dAtom->getIzz(); |
377 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
377 |
> |
this->rotate( 0, 1, angle, ji, A ); |
378 |
|
|
379 |
|
// rotate about the y-axis |
380 |
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
381 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
381 |
> |
this->rotate( 2, 0, angle, ji, A ); |
382 |
|
|
383 |
|
// rotate about the x-axis |
384 |
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
385 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
385 |
> |
this->rotate( 1, 2, angle, ji, A ); |
386 |
|
|
387 |
|
dAtom->setJx( ji[0] ); |
388 |
|
dAtom->setJy( ji[1] ); |
407 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
408 |
|
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
409 |
|
|
410 |
+ |
std::cerr<< "MoveB vel[" << i << "] = " |
411 |
+ |
<< vel[atomIndex] << "\t" |
412 |
+ |
<< vel[atomIndex+1]<< "\t" |
413 |
+ |
<< vel[atomIndex+2]<< "\n"; |
414 |
+ |
|
415 |
+ |
|
416 |
|
if( atoms[i]->isDirectional() ){ |
417 |
|
|
418 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
453 |
|
|
454 |
|
int i,j,k; |
455 |
|
int done; |
456 |
< |
double pxab, pyab, pzab; |
457 |
< |
double rxab, ryab, rzab; |
456 |
> |
double pab[3]; |
457 |
> |
double rab[3]; |
458 |
|
int a, b, ax, ay, az, bx, by, bz; |
459 |
|
double rma, rmb; |
460 |
|
double dx, dy, dz; |
464 |
|
double gab; |
465 |
|
int iteration; |
466 |
|
|
427 |
– |
|
428 |
– |
|
467 |
|
for( i=0; i<nAtoms; i++){ |
468 |
|
|
469 |
|
moving[i] = 0; |
470 |
|
moved[i] = 1; |
471 |
|
} |
472 |
< |
|
435 |
< |
|
472 |
> |
|
473 |
|
iteration = 0; |
474 |
|
done = 0; |
475 |
|
while( !done && (iteration < maxIteration )){ |
488 |
|
by = (b*3) + 1; |
489 |
|
bz = (b*3) + 2; |
490 |
|
|
454 |
– |
|
491 |
|
if( moved[a] || moved[b] ){ |
492 |
|
|
493 |
< |
pxab = pos[ax] - pos[bx]; |
494 |
< |
pyab = pos[ay] - pos[by]; |
495 |
< |
pzab = pos[az] - pos[bz]; |
493 |
> |
pab[0] = pos[ax] - pos[bx]; |
494 |
> |
pab[1] = pos[ay] - pos[by]; |
495 |
> |
pab[2] = pos[az] - pos[bz]; |
496 |
|
|
497 |
< |
//periodic boundary condition |
498 |
< |
pxab = pxab - info->box_x * copysign(1, pxab) |
499 |
< |
* (int)( fabs(pxab / info->box_x) + 0.5); |
500 |
< |
pyab = pyab - info->box_y * copysign(1, pyab) |
501 |
< |
* (int)( fabs(pyab / info->box_y) + 0.5); |
502 |
< |
pzab = pzab - info->box_z * copysign(1, pzab) |
467 |
< |
* (int)( fabs(pzab / info->box_z) + 0.5); |
468 |
< |
|
469 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
497 |
> |
//periodic boundary condition |
498 |
> |
|
499 |
> |
info->wrapVector( pab ); |
500 |
> |
|
501 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
502 |
> |
|
503 |
|
rabsq = constrainedDsqr[i]; |
504 |
< |
diffsq = pabsq - rabsq; |
504 |
> |
diffsq = rabsq - pabsq; |
505 |
|
|
506 |
|
// the original rattle code from alan tidesley |
507 |
|
if (fabs(diffsq) > (tol*rabsq*2)) { |
508 |
< |
rxab = oldPos[ax] - oldPos[bx]; |
509 |
< |
ryab = oldPos[ay] - oldPos[by]; |
510 |
< |
rzab = oldPos[az] - oldPos[bz]; |
478 |
< |
|
479 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
480 |
< |
* (int)( fabs(rxab / info->box_x) + 0.5); |
481 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
482 |
< |
* (int)( fabs(ryab / info->box_y) + 0.5); |
483 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
484 |
< |
* (int)( fabs(rzab / info->box_z) + 0.5); |
508 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
509 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
510 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
511 |
|
|
512 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
512 |
> |
info->wrapVector( rab ); |
513 |
> |
|
514 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
515 |
> |
|
516 |
|
rpabsq = rpab * rpab; |
517 |
|
|
518 |
|
|
519 |
|
if (rpabsq < (rabsq * -diffsq)){ |
520 |
|
|
492 |
– |
cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq |
493 |
– |
<< ", -diffsq = " << -diffsq << "\n"; |
494 |
– |
|
521 |
|
#ifdef IS_MPI |
522 |
|
a = atoms[a]->getGlobalIndex(); |
523 |
|
b = atoms[b]->getGlobalIndex(); |
531 |
|
|
532 |
|
rma = 1.0 / atoms[a]->getMass(); |
533 |
|
rmb = 1.0 / atoms[b]->getMass(); |
534 |
< |
|
534 |
> |
|
535 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
510 |
– |
dx = rxab * gab; |
511 |
– |
dy = ryab * gab; |
512 |
– |
dz = rzab * gab; |
536 |
|
|
537 |
+ |
dx = rab[0] * gab; |
538 |
+ |
dy = rab[1] * gab; |
539 |
+ |
dz = rab[2] * gab; |
540 |
+ |
|
541 |
|
pos[ax] += rma * dx; |
542 |
|
pos[ay] += rma * dy; |
543 |
|
pos[az] += rma * dz; |
572 |
|
} |
573 |
|
|
574 |
|
iteration++; |
548 |
– |
cerr << "iterainA = " << iteration << "\n"; |
575 |
|
} |
576 |
|
|
577 |
|
if( !done ){ |
590 |
|
int i,j,k; |
591 |
|
int done; |
592 |
|
double vxab, vyab, vzab; |
593 |
< |
double rxab, ryab, rzab; |
593 |
> |
double rab[3]; |
594 |
|
int a, b, ax, ay, az, bx, by, bz; |
595 |
|
double rma, rmb; |
596 |
|
double dx, dy, dz; |
608 |
|
iteration = 0; |
609 |
|
while( !done && (iteration < maxIteration ) ){ |
610 |
|
|
611 |
+ |
done = 1; |
612 |
+ |
|
613 |
|
for(i=0; i<nConstrained; i++){ |
614 |
|
|
615 |
|
a = constrainedA[i]; |
616 |
|
b = constrainedB[i]; |
617 |
|
|
618 |
< |
ax = 3*a +0; |
619 |
< |
ay = 3*a +1; |
620 |
< |
az = 3*a +2; |
618 |
> |
ax = (a*3) + 0; |
619 |
> |
ay = (a*3) + 1; |
620 |
> |
az = (a*3) + 2; |
621 |
|
|
622 |
< |
bx = 3*b +0; |
623 |
< |
by = 3*b +1; |
624 |
< |
bz = 3*b +2; |
622 |
> |
bx = (b*3) + 0; |
623 |
> |
by = (b*3) + 1; |
624 |
> |
bz = (b*3) + 2; |
625 |
|
|
626 |
|
if( moved[a] || moved[b] ){ |
627 |
|
|
629 |
|
vyab = vel[ay] - vel[by]; |
630 |
|
vzab = vel[az] - vel[bz]; |
631 |
|
|
632 |
< |
rxab = pos[ax] - pos[bx]; |
633 |
< |
ryab = pos[ay] - pos[by]; |
634 |
< |
rzab = pos[az] - pos[bz]; |
632 |
> |
rab[0] = pos[ax] - pos[bx]; |
633 |
> |
rab[1] = pos[ay] - pos[by]; |
634 |
> |
rab[2] = pos[az] - pos[bz]; |
635 |
|
|
636 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
637 |
< |
* (int)( fabs(rxab / info->box_x) + 0.5); |
610 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
611 |
< |
* (int)( fabs(ryab / info->box_y) + 0.5); |
612 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
613 |
< |
* (int)( fabs(rzab / info->box_z) + 0.5); |
614 |
< |
|
636 |
> |
info->wrapVector( rab ); |
637 |
> |
|
638 |
|
rma = 1.0 / atoms[a]->getMass(); |
639 |
|
rmb = 1.0 / atoms[b]->getMass(); |
640 |
|
|
641 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
641 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
642 |
|
|
643 |
|
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
644 |
|
|
645 |
|
if (fabs(gab) > tol) { |
646 |
|
|
647 |
< |
dx = rxab * gab; |
648 |
< |
dy = ryab * gab; |
649 |
< |
dz = rzab * gab; |
647 |
> |
dx = rab[0] * gab; |
648 |
> |
dy = rab[1] * gab; |
649 |
> |
dz = rab[2] * gab; |
650 |
|
|
651 |
|
vel[ax] += rma * dx; |
652 |
|
vel[ay] += rma * dy; |
690 |
|
|
691 |
|
|
692 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
693 |
< |
double A[9] ){ |
693 |
> |
double A[3][3] ){ |
694 |
|
|
695 |
|
int i,j,k; |
696 |
|
double sinAngle; |
706 |
|
|
707 |
|
for(i=0; i<3; i++){ |
708 |
|
for(j=0; j<3; j++){ |
709 |
< |
tempA[j][i] = A[3*i + j]; |
709 |
> |
tempA[j][i] = A[i][j]; |
710 |
|
} |
711 |
|
} |
712 |
|
|
763 |
|
|
764 |
|
for(i=0; i<3; i++){ |
765 |
|
for(j=0; j<3; j++){ |
766 |
< |
A[3*j + i] = 0.0; |
766 |
> |
A[j][i] = 0.0; |
767 |
|
for(k=0; k<3; k++){ |
768 |
< |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
768 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
769 |
|
} |
770 |
|
} |
771 |
|
} |