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 |
|
|
224 |
|
pos = Atom::getPosArray(); |
225 |
|
vel = Atom::getVelArray(); |
226 |
|
frc = Atom::getFrcArray(); |
221 |
– |
trq = Atom::getTrqArray(); |
222 |
– |
Amat = Atom::getAmatArray(); |
227 |
|
|
228 |
|
while( currTime < runTime ){ |
229 |
|
|
232 |
|
calcStress = 1; |
233 |
|
} |
234 |
|
|
235 |
+ |
std::cerr << currTime << "\n"; |
236 |
+ |
|
237 |
|
integrateStep( calcPot, calcStress ); |
238 |
|
|
239 |
|
currTime += dt; |
265 |
|
|
266 |
|
} |
267 |
|
|
268 |
< |
dumpOut->writeFinal(); |
268 |
> |
dumpOut->writeFinal(currTime); |
269 |
|
|
270 |
|
delete dumpOut; |
271 |
|
delete statOut; |
279 |
|
|
280 |
|
preMove(); |
281 |
|
moveA(); |
282 |
< |
if( nConstrained ) constrainA(); |
282 |
> |
//if( nConstrained ) constrainA(); |
283 |
|
|
284 |
|
// calc forces |
285 |
|
|
301 |
|
double Tb[3]; |
302 |
|
double ji[3]; |
303 |
|
double angle; |
304 |
+ |
double A[3][3], At[3][3]; |
305 |
|
|
306 |
+ |
|
307 |
|
for( i=0; i<nAtoms; i++ ){ |
308 |
|
atomIndex = i * 3; |
309 |
|
aMatIndex = i * 9; |
310 |
< |
|
310 |
> |
|
311 |
|
// velocity half step |
312 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
313 |
|
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
314 |
|
|
315 |
+ |
|
316 |
|
// position whole step |
317 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
318 |
< |
pos[j] += dt * vel[j]; |
317 |
> |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
318 |
> |
|
319 |
|
|
311 |
– |
|
320 |
|
if( atoms[i]->isDirectional() ){ |
321 |
|
|
322 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
326 |
|
Tb[0] = dAtom->getTx(); |
327 |
|
Tb[1] = dAtom->getTy(); |
328 |
|
Tb[2] = dAtom->getTz(); |
329 |
< |
|
329 |
> |
|
330 |
|
dAtom->lab2Body( Tb ); |
331 |
< |
|
331 |
> |
|
332 |
|
// get the angular momentum, and propagate a half step |
333 |
|
|
334 |
|
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
341 |
|
// rotate about the x-axis |
342 |
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
343 |
|
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
344 |
< |
|
344 |
> |
|
345 |
|
// rotate about the y-axis |
346 |
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
347 |
|
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
361 |
|
dAtom->setJx( ji[0] ); |
362 |
|
dAtom->setJy( ji[1] ); |
363 |
|
dAtom->setJz( ji[2] ); |
364 |
+ |
|
365 |
+ |
std::cerr << "Amat[" << i << "]\n"; |
366 |
+ |
info->printMat9( &Amat[aMatIndex] ); |
367 |
+ |
|
368 |
+ |
std::cerr << "ji[" << i << "]\t" |
369 |
+ |
<< ji[0] << "\t" |
370 |
+ |
<< ji[1] << "\t" |
371 |
+ |
<< ji[2] << "\n"; |
372 |
+ |
|
373 |
|
} |
374 |
|
|
375 |
|
} |
378 |
|
|
379 |
|
void Integrator::moveB( void ){ |
380 |
|
int i,j,k; |
381 |
< |
int atomIndex; |
381 |
> |
int atomIndex, aMatIndex; |
382 |
|
DirectionalAtom* dAtom; |
383 |
|
double Tb[3]; |
384 |
|
double ji[3]; |
385 |
|
|
386 |
|
for( i=0; i<nAtoms; i++ ){ |
387 |
|
atomIndex = i * 3; |
388 |
+ |
aMatIndex = i * 9; |
389 |
|
|
390 |
|
// velocity half step |
391 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
392 |
|
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
393 |
|
|
394 |
+ |
|
395 |
|
if( atoms[i]->isDirectional() ){ |
396 |
|
|
397 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
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"; |
409 |
+ |
|
410 |
|
dAtom->lab2Body( Tb ); |
411 |
|
|
412 |
|
// get the angular momentum, and complete the angular momentum |
419 |
|
dAtom->setJx( ji[0] ); |
420 |
|
dAtom->setJy( ji[1] ); |
421 |
|
dAtom->setJz( ji[2] ); |
422 |
+ |
|
423 |
+ |
|
424 |
+ |
std::cerr << "Amat[" << i << "]\n"; |
425 |
+ |
info->printMat9( &Amat[aMatIndex] ); |
426 |
+ |
|
427 |
+ |
std::cerr << "ji[" << i << "]\t" |
428 |
+ |
<< ji[0] << "\t" |
429 |
+ |
<< ji[1] << "\t" |
430 |
+ |
<< ji[2] << "\n"; |
431 |
|
} |
432 |
|
} |
433 |
|
|
446 |
|
|
447 |
|
int i,j,k; |
448 |
|
int done; |
449 |
< |
double pxab, pyab, pzab; |
450 |
< |
double rxab, ryab, rzab; |
449 |
> |
double pab[3]; |
450 |
> |
double rab[3]; |
451 |
|
int a, b, ax, ay, az, bx, by, bz; |
452 |
|
double rma, rmb; |
453 |
|
double dx, dy, dz; |
457 |
|
double gab; |
458 |
|
int iteration; |
459 |
|
|
427 |
– |
|
428 |
– |
|
460 |
|
for( i=0; i<nAtoms; i++){ |
461 |
|
|
462 |
|
moving[i] = 0; |
463 |
|
moved[i] = 1; |
464 |
|
} |
465 |
< |
|
435 |
< |
|
465 |
> |
|
466 |
|
iteration = 0; |
467 |
|
done = 0; |
468 |
|
while( !done && (iteration < maxIteration )){ |
481 |
|
by = (b*3) + 1; |
482 |
|
bz = (b*3) + 2; |
483 |
|
|
454 |
– |
|
484 |
|
if( moved[a] || moved[b] ){ |
485 |
|
|
486 |
< |
pxab = pos[ax] - pos[bx]; |
487 |
< |
pyab = pos[ay] - pos[by]; |
488 |
< |
pzab = pos[az] - pos[bz]; |
486 |
> |
pab[0] = pos[ax] - pos[bx]; |
487 |
> |
pab[1] = pos[ay] - pos[by]; |
488 |
> |
pab[2] = pos[az] - pos[bz]; |
489 |
|
|
490 |
< |
//periodic boundary condition |
491 |
< |
pxab = pxab - info->box_x * copysign(1, pxab) |
492 |
< |
* (int)( fabs(pxab / info->box_x) + 0.5); |
493 |
< |
pyab = pyab - info->box_y * copysign(1, pyab) |
494 |
< |
* (int)( fabs(pyab / info->box_y) + 0.5); |
495 |
< |
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; |
490 |
> |
//periodic boundary condition |
491 |
> |
|
492 |
> |
info->wrapVector( pab ); |
493 |
> |
|
494 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
495 |
> |
|
496 |
|
rabsq = constrainedDsqr[i]; |
497 |
< |
diffsq = pabsq - rabsq; |
497 |
> |
diffsq = rabsq - pabsq; |
498 |
|
|
499 |
|
// the original rattle code from alan tidesley |
500 |
|
if (fabs(diffsq) > (tol*rabsq*2)) { |
501 |
< |
rxab = oldPos[ax] - oldPos[bx]; |
502 |
< |
ryab = oldPos[ay] - oldPos[by]; |
503 |
< |
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); |
501 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
502 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
503 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
504 |
|
|
505 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
505 |
> |
info->wrapVector( rab ); |
506 |
> |
|
507 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
508 |
> |
|
509 |
|
rpabsq = rpab * rpab; |
510 |
|
|
511 |
|
|
512 |
|
if (rpabsq < (rabsq * -diffsq)){ |
513 |
|
|
492 |
– |
cerr << "rpabsq = " << rpabsq << ", rabsq = " << rabsq |
493 |
– |
<< ", -diffsq = " << -diffsq << "\n"; |
494 |
– |
|
514 |
|
#ifdef IS_MPI |
515 |
|
a = atoms[a]->getGlobalIndex(); |
516 |
|
b = atoms[b]->getGlobalIndex(); |
524 |
|
|
525 |
|
rma = 1.0 / atoms[a]->getMass(); |
526 |
|
rmb = 1.0 / atoms[b]->getMass(); |
527 |
< |
|
527 |
> |
|
528 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
510 |
– |
dx = rxab * gab; |
511 |
– |
dy = ryab * gab; |
512 |
– |
dz = rzab * gab; |
529 |
|
|
530 |
+ |
dx = rab[0] * gab; |
531 |
+ |
dy = rab[1] * gab; |
532 |
+ |
dz = rab[2] * gab; |
533 |
+ |
|
534 |
|
pos[ax] += rma * dx; |
535 |
|
pos[ay] += rma * dy; |
536 |
|
pos[az] += rma * dz; |
565 |
|
} |
566 |
|
|
567 |
|
iteration++; |
548 |
– |
cerr << "iterainA = " << iteration << "\n"; |
568 |
|
} |
569 |
|
|
570 |
|
if( !done ){ |
583 |
|
int i,j,k; |
584 |
|
int done; |
585 |
|
double vxab, vyab, vzab; |
586 |
< |
double rxab, ryab, rzab; |
586 |
> |
double rab[3]; |
587 |
|
int a, b, ax, ay, az, bx, by, bz; |
588 |
|
double rma, rmb; |
589 |
|
double dx, dy, dz; |
601 |
|
iteration = 0; |
602 |
|
while( !done && (iteration < maxIteration ) ){ |
603 |
|
|
604 |
+ |
done = 1; |
605 |
+ |
|
606 |
|
for(i=0; i<nConstrained; i++){ |
607 |
|
|
608 |
|
a = constrainedA[i]; |
609 |
|
b = constrainedB[i]; |
610 |
|
|
611 |
< |
ax = 3*a +0; |
612 |
< |
ay = 3*a +1; |
613 |
< |
az = 3*a +2; |
611 |
> |
ax = (a*3) + 0; |
612 |
> |
ay = (a*3) + 1; |
613 |
> |
az = (a*3) + 2; |
614 |
|
|
615 |
< |
bx = 3*b +0; |
616 |
< |
by = 3*b +1; |
617 |
< |
bz = 3*b +2; |
615 |
> |
bx = (b*3) + 0; |
616 |
> |
by = (b*3) + 1; |
617 |
> |
bz = (b*3) + 2; |
618 |
|
|
619 |
|
if( moved[a] || moved[b] ){ |
620 |
|
|
622 |
|
vyab = vel[ay] - vel[by]; |
623 |
|
vzab = vel[az] - vel[bz]; |
624 |
|
|
625 |
< |
rxab = pos[ax] - pos[bx]; |
626 |
< |
ryab = pos[ay] - pos[by]; |
627 |
< |
rzab = pos[az] - pos[bz]; |
625 |
> |
rab[0] = pos[ax] - pos[bx]; |
626 |
> |
rab[1] = pos[ay] - pos[by]; |
627 |
> |
rab[2] = pos[az] - pos[bz]; |
628 |
|
|
629 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
630 |
< |
* (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 |
< |
|
629 |
> |
info->wrapVector( rab ); |
630 |
> |
|
631 |
|
rma = 1.0 / atoms[a]->getMass(); |
632 |
|
rmb = 1.0 / atoms[b]->getMass(); |
633 |
|
|
634 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
634 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
635 |
|
|
636 |
|
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
637 |
|
|
638 |
|
if (fabs(gab) > tol) { |
639 |
|
|
640 |
< |
dx = rxab * gab; |
641 |
< |
dy = ryab * gab; |
642 |
< |
dz = rzab * gab; |
640 |
> |
dx = rab[0] * gab; |
641 |
> |
dy = rab[1] * gab; |
642 |
> |
dz = rab[2] * gab; |
643 |
|
|
644 |
|
vel[ax] += rma * dx; |
645 |
|
vel[ay] += rma * dy; |
695 |
|
double tempA[3][3]; |
696 |
|
double tempJ[3]; |
697 |
|
|
698 |
+ |
|
699 |
|
// initialize the tempA |
700 |
|
|
701 |
|
for(i=0; i<3; i++){ |
702 |
|
for(j=0; j<3; j++){ |
703 |
< |
tempA[j][i] = A[3*i + j]; |
703 |
> |
tempA[j][i] = A[3*i+j]; |
704 |
|
} |
705 |
|
} |
706 |
|
|
757 |
|
|
758 |
|
for(i=0; i<3; i++){ |
759 |
|
for(j=0; j<3; j++){ |
760 |
< |
A[3*j + i] = 0.0; |
760 |
> |
A[3*j+i] = 0.0; |
761 |
|
for(k=0; k<3; k++){ |
762 |
< |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
762 |
> |
A[3*j+i] += tempA[i][k] * rot[j][k]; |
763 |
|
} |
764 |
|
} |
765 |
|
} |