27 |
|
|
28 |
|
nAtoms = info->n_atoms; |
29 |
|
|
30 |
– |
std::cerr << "integ nAtoms = " << nAtoms << "\n"; |
31 |
– |
|
30 |
|
// check for constraints |
31 |
|
|
32 |
|
constrainedA = NULL; |
73 |
|
|
74 |
|
constrained = theArray[j]->is_constrained(); |
75 |
|
|
78 |
– |
std::cerr << "Is the folowing bond constrained \n"; |
79 |
– |
theArray[j]->printMe(); |
80 |
– |
|
76 |
|
if(constrained){ |
82 |
– |
|
83 |
– |
std::cerr << "Yes\n"; |
77 |
|
|
78 |
|
dummy_plug = theArray[j]->get_constraint(); |
79 |
|
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
83 |
|
nConstrained++; |
84 |
|
constrained = 0; |
85 |
|
} |
93 |
– |
else std::cerr << "No.\n"; |
86 |
|
} |
87 |
|
|
88 |
|
theArray = (SRI**) molecules[i].getMyBends(); |
172 |
|
int calcPot, calcStress; |
173 |
|
int isError; |
174 |
|
|
183 |
– |
|
184 |
– |
|
175 |
|
tStats = new Thermo( info ); |
176 |
|
statOut = new StatWriter( info ); |
177 |
|
dumpOut = new DumpWriter( info ); |
209 |
|
"The integrator is ready to go." ); |
210 |
|
MPIcheckPoint(); |
211 |
|
#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(); |
212 |
|
|
213 |
|
while( currTime < runTime ){ |
214 |
|
|
217 |
|
calcStress = 1; |
218 |
|
} |
219 |
|
|
237 |
– |
std::cerr << "calcPot = " << calcPot << "; calcStress = " |
238 |
– |
<< calcStress << "\n"; |
239 |
– |
|
220 |
|
integrateStep( calcPot, calcStress ); |
221 |
|
|
222 |
|
currTime += dt; |
264 |
|
moveA(); |
265 |
|
if( nConstrained ) constrainA(); |
266 |
|
|
267 |
+ |
|
268 |
+ |
#ifdef IS_MPI |
269 |
+ |
strcpy( checkPointMsg, "Succesful moveA\n" ); |
270 |
+ |
MPIcheckPoint(); |
271 |
+ |
#endif // is_mpi |
272 |
+ |
|
273 |
+ |
|
274 |
|
// calc forces |
275 |
|
|
276 |
|
myFF->doForces(calcPot,calcStress); |
277 |
|
|
278 |
+ |
#ifdef IS_MPI |
279 |
+ |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
280 |
+ |
MPIcheckPoint(); |
281 |
+ |
#endif // is_mpi |
282 |
+ |
|
283 |
+ |
|
284 |
|
// finish the velocity half step |
285 |
|
|
286 |
|
moveB(); |
287 |
|
if( nConstrained ) constrainB(); |
288 |
< |
|
288 |
> |
|
289 |
> |
#ifdef IS_MPI |
290 |
> |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
291 |
> |
MPIcheckPoint(); |
292 |
> |
#endif // is_mpi |
293 |
> |
|
294 |
> |
|
295 |
|
} |
296 |
|
|
297 |
|
|
298 |
|
void Integrator::moveA( void ){ |
299 |
|
|
300 |
< |
int i,j,k; |
302 |
< |
int atomIndex, aMatIndex; |
300 |
> |
int i, j; |
301 |
|
DirectionalAtom* dAtom; |
302 |
< |
double Tb[3]; |
303 |
< |
double ji[3]; |
304 |
< |
double angle; |
305 |
< |
double A[3][3]; |
306 |
< |
|
302 |
> |
double Tb[3], ji[3]; |
303 |
> |
double A[3][3], I[3][3]; |
304 |
> |
double angle; |
305 |
> |
double vel[3], pos[3], frc[3]; |
306 |
> |
double mass; |
307 |
|
|
308 |
|
for( i=0; i<nAtoms; i++ ){ |
311 |
– |
atomIndex = i * 3; |
312 |
– |
aMatIndex = i * 9; |
309 |
|
|
310 |
< |
// velocity half step |
311 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
312 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
310 |
> |
atoms[i]->getVel( vel ); |
311 |
> |
atoms[i]->getPos( pos ); |
312 |
> |
atoms[i]->getFrc( frc ); |
313 |
|
|
314 |
< |
std::cerr<< "MoveA vel[" << i << "] = " |
319 |
< |
<< vel[atomIndex] << "\t" |
320 |
< |
<< vel[atomIndex+1]<< "\t" |
321 |
< |
<< vel[atomIndex+2]<< "\n"; |
314 |
> |
mass = atoms[i]->getMass(); |
315 |
|
|
316 |
< |
// position whole step |
317 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
318 |
< |
|
316 |
> |
for (j=0; j < 3; j++) { |
317 |
> |
// velocity half step |
318 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
319 |
> |
// position whole step |
320 |
> |
pos[j] += dt * vel[j]; |
321 |
> |
} |
322 |
|
|
323 |
< |
std::cerr<< "MoveA pos[" << i << "] = " |
324 |
< |
<< pos[atomIndex] << "\t" |
329 |
< |
<< pos[atomIndex+1]<< "\t" |
330 |
< |
<< pos[atomIndex+2]<< "\n"; |
323 |
> |
atoms[i]->setVel( vel ); |
324 |
> |
atoms[i]->setPos( pos ); |
325 |
|
|
326 |
|
if( atoms[i]->isDirectional() ){ |
327 |
|
|
329 |
|
|
330 |
|
// get and convert the torque to body frame |
331 |
|
|
332 |
< |
Tb[0] = dAtom->getTx(); |
339 |
< |
Tb[1] = dAtom->getTy(); |
340 |
< |
Tb[2] = dAtom->getTz(); |
341 |
< |
|
332 |
> |
dAtom->getTrq( Tb ); |
333 |
|
dAtom->lab2Body( Tb ); |
334 |
< |
|
334 |
> |
|
335 |
|
// get the angular momentum, and propagate a half step |
336 |
< |
|
337 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
338 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
339 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
336 |
> |
|
337 |
> |
dAtom->getJ( ji ); |
338 |
> |
|
339 |
> |
for (j=0; j < 3; j++) |
340 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
341 |
|
|
342 |
|
// use the angular velocities to propagate the rotation matrix a |
343 |
|
// full time step |
344 |
< |
|
345 |
< |
// get the atom's rotation matrix |
346 |
< |
|
347 |
< |
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 |
< |
|
344 |
> |
|
345 |
> |
dAtom->getA(A); |
346 |
> |
dAtom->getI(I); |
347 |
> |
|
348 |
|
// rotate about the x-axis |
349 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
349 |
> |
angle = dt2 * ji[0] / I[0][0]; |
350 |
|
this->rotate( 1, 2, angle, ji, A ); |
351 |
< |
|
351 |
> |
|
352 |
|
// rotate about the y-axis |
353 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
353 |
> |
angle = dt2 * ji[1] / I[1][1]; |
354 |
|
this->rotate( 2, 0, angle, ji, A ); |
355 |
|
|
356 |
|
// rotate about the z-axis |
357 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
358 |
< |
this->rotate( 0, 1, angle, ji, A ); |
357 |
> |
angle = dt * ji[2] / I[2][2]; |
358 |
> |
this->rotate( 0, 1, angle, ji, A); |
359 |
|
|
360 |
|
// rotate about the y-axis |
361 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
361 |
> |
angle = dt2 * ji[1] / I[1][1]; |
362 |
|
this->rotate( 2, 0, angle, ji, A ); |
363 |
|
|
364 |
|
// rotate about the x-axis |
365 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
365 |
> |
angle = dt2 * ji[0] / I[0][0]; |
366 |
|
this->rotate( 1, 2, angle, ji, A ); |
367 |
|
|
368 |
< |
dAtom->setJx( ji[0] ); |
369 |
< |
dAtom->setJy( ji[1] ); |
370 |
< |
dAtom->setJz( ji[2] ); |
371 |
< |
} |
372 |
< |
|
368 |
> |
|
369 |
> |
dAtom->setJ( ji ); |
370 |
> |
dAtom->setA( A ); |
371 |
> |
|
372 |
> |
} |
373 |
|
} |
374 |
|
} |
375 |
|
|
376 |
|
|
377 |
|
void Integrator::moveB( void ){ |
378 |
< |
int i,j,k; |
398 |
< |
int atomIndex; |
378 |
> |
int i, j; |
379 |
|
DirectionalAtom* dAtom; |
380 |
< |
double Tb[3]; |
381 |
< |
double ji[3]; |
380 |
> |
double Tb[3], ji[3]; |
381 |
> |
double vel[3], frc[3]; |
382 |
> |
double mass; |
383 |
|
|
384 |
|
for( i=0; i<nAtoms; i++ ){ |
385 |
< |
atomIndex = i * 3; |
385 |
> |
|
386 |
> |
atoms[i]->getVel( vel ); |
387 |
> |
atoms[i]->getFrc( frc ); |
388 |
|
|
389 |
< |
// velocity half step |
407 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
408 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
389 |
> |
mass = atoms[i]->getMass(); |
390 |
|
|
391 |
< |
std::cerr<< "MoveB vel[" << i << "] = " |
392 |
< |
<< vel[atomIndex] << "\t" |
393 |
< |
<< vel[atomIndex+1]<< "\t" |
394 |
< |
<< vel[atomIndex+2]<< "\n"; |
395 |
< |
|
396 |
< |
|
391 |
> |
// velocity half step |
392 |
> |
for (j=0; j < 3; j++) |
393 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
394 |
> |
|
395 |
> |
atoms[i]->setVel( vel ); |
396 |
> |
|
397 |
|
if( atoms[i]->isDirectional() ){ |
398 |
< |
|
398 |
> |
|
399 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
400 |
< |
|
401 |
< |
// get and convert the torque to body frame |
402 |
< |
|
403 |
< |
Tb[0] = dAtom->getTx(); |
423 |
< |
Tb[1] = dAtom->getTy(); |
424 |
< |
Tb[2] = dAtom->getTz(); |
425 |
< |
|
400 |
> |
|
401 |
> |
// get and convert the torque to body frame |
402 |
> |
|
403 |
> |
dAtom->getTrq( Tb ); |
404 |
|
dAtom->lab2Body( Tb ); |
405 |
+ |
|
406 |
+ |
// get the angular momentum, and propagate a half step |
407 |
+ |
|
408 |
+ |
dAtom->getJ( ji ); |
409 |
+ |
|
410 |
+ |
for (j=0; j < 3; j++) |
411 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
412 |
|
|
413 |
< |
// get the angular momentum, and complete the angular momentum |
414 |
< |
// 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] ); |
413 |
> |
|
414 |
> |
dAtom->setJ( ji ); |
415 |
|
} |
416 |
|
} |
440 |
– |
|
417 |
|
} |
418 |
|
|
419 |
|
void Integrator::preMove( void ){ |
420 |
< |
int i; |
420 |
> |
int i, j; |
421 |
> |
double pos[3]; |
422 |
|
|
423 |
|
if( nConstrained ){ |
424 |
|
|
425 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
426 |
< |
} |
427 |
< |
} |
425 |
> |
for(i=0; i < nAtoms; i++) { |
426 |
> |
|
427 |
> |
atoms[i]->getPos( pos ); |
428 |
|
|
429 |
+ |
for (j = 0; j < 3; j++) { |
430 |
+ |
oldPos[3*i + j] = pos[j]; |
431 |
+ |
} |
432 |
+ |
|
433 |
+ |
} |
434 |
+ |
} |
435 |
+ |
} |
436 |
+ |
|
437 |
|
void Integrator::constrainA(){ |
438 |
|
|
439 |
|
int i,j,k; |
440 |
|
int done; |
441 |
+ |
double posA[3], posB[3]; |
442 |
+ |
double velA[3], velB[3]; |
443 |
|
double pab[3]; |
444 |
|
double rab[3]; |
445 |
|
int a, b, ax, ay, az, bx, by, bz; |
451 |
|
double gab; |
452 |
|
int iteration; |
453 |
|
|
454 |
< |
for( i=0; i<nAtoms; i++){ |
468 |
< |
|
454 |
> |
for( i=0; i<nAtoms; i++){ |
455 |
|
moving[i] = 0; |
456 |
|
moved[i] = 1; |
457 |
|
} |
475 |
|
bz = (b*3) + 2; |
476 |
|
|
477 |
|
if( moved[a] || moved[b] ){ |
478 |
< |
|
479 |
< |
pab[0] = pos[ax] - pos[bx]; |
480 |
< |
pab[1] = pos[ay] - pos[by]; |
481 |
< |
pab[2] = pos[az] - pos[bz]; |
482 |
< |
|
478 |
> |
|
479 |
> |
atoms[a]->getPos( posA ); |
480 |
> |
atoms[b]->getPos( posB ); |
481 |
> |
|
482 |
> |
for (j = 0; j < 3; j++ ) |
483 |
> |
pab[j] = posA[j] - posB[j]; |
484 |
> |
|
485 |
|
//periodic boundary condition |
486 |
|
|
487 |
|
info->wrapVector( pab ); |
526 |
|
dy = rab[1] * gab; |
527 |
|
dz = rab[2] * gab; |
528 |
|
|
529 |
< |
pos[ax] += rma * dx; |
530 |
< |
pos[ay] += rma * dy; |
531 |
< |
pos[az] += rma * dz; |
529 |
> |
posA[0] += rma * dx; |
530 |
> |
posA[1] += rma * dy; |
531 |
> |
posA[2] += rma * dz; |
532 |
|
|
533 |
< |
pos[bx] -= rmb * dx; |
534 |
< |
pos[by] -= rmb * dy; |
535 |
< |
pos[bz] -= rmb * dz; |
533 |
> |
atoms[a]->setPos( posA ); |
534 |
> |
|
535 |
> |
posB[0] -= rmb * dx; |
536 |
> |
posB[1] -= rmb * dy; |
537 |
> |
posB[2] -= rmb * dz; |
538 |
|
|
539 |
+ |
atoms[b]->setPos( posB ); |
540 |
+ |
|
541 |
|
dx = dx / dt; |
542 |
|
dy = dy / dt; |
543 |
|
dz = dz / dt; |
544 |
|
|
545 |
< |
vel[ax] += rma * dx; |
554 |
< |
vel[ay] += rma * dy; |
555 |
< |
vel[az] += rma * dz; |
545 |
> |
atoms[a]->getVel( velA ); |
546 |
|
|
547 |
< |
vel[bx] -= rmb * dx; |
548 |
< |
vel[by] -= rmb * dy; |
549 |
< |
vel[bz] -= rmb * dz; |
547 |
> |
velA[0] += rma * dx; |
548 |
> |
velA[1] += rma * dy; |
549 |
> |
velA[2] += rma * dz; |
550 |
|
|
551 |
+ |
atoms[a]->setVel( velA ); |
552 |
+ |
|
553 |
+ |
atoms[b]->getVel( velB ); |
554 |
+ |
|
555 |
+ |
velB[0] -= rmb * dx; |
556 |
+ |
velB[1] -= rmb * dy; |
557 |
+ |
velB[2] -= rmb * dz; |
558 |
+ |
|
559 |
+ |
atoms[b]->setVel( velB ); |
560 |
+ |
|
561 |
|
moving[a] = 1; |
562 |
|
moving[b] = 1; |
563 |
|
done = 0; |
589 |
|
|
590 |
|
int i,j,k; |
591 |
|
int done; |
592 |
+ |
double posA[3], posB[3]; |
593 |
+ |
double velA[3], velB[3]; |
594 |
|
double vxab, vyab, vzab; |
595 |
|
double rab[3]; |
596 |
|
int a, b, ax, ay, az, bx, by, bz; |
626 |
|
bz = (b*3) + 2; |
627 |
|
|
628 |
|
if( moved[a] || moved[b] ){ |
627 |
– |
|
628 |
– |
vxab = vel[ax] - vel[bx]; |
629 |
– |
vyab = vel[ay] - vel[by]; |
630 |
– |
vzab = vel[az] - vel[bz]; |
629 |
|
|
630 |
< |
rab[0] = pos[ax] - pos[bx]; |
631 |
< |
rab[1] = pos[ay] - pos[by]; |
632 |
< |
rab[2] = pos[az] - pos[bz]; |
633 |
< |
|
630 |
> |
atoms[a]->getVel( velA ); |
631 |
> |
atoms[b]->getVel( velB ); |
632 |
> |
|
633 |
> |
vxab = velA[0] - velB[0]; |
634 |
> |
vyab = velA[1] - velB[1]; |
635 |
> |
vzab = velA[2] - velB[2]; |
636 |
> |
|
637 |
> |
atoms[a]->getPos( posA ); |
638 |
> |
atoms[b]->getPos( posB ); |
639 |
> |
|
640 |
> |
for (j = 0; j < 3; j++) |
641 |
> |
rab[j] = posA[j] - posB[j]; |
642 |
> |
|
643 |
|
info->wrapVector( rab ); |
644 |
|
|
645 |
|
rma = 1.0 / atoms[a]->getMass(); |
654 |
|
dx = rab[0] * gab; |
655 |
|
dy = rab[1] * gab; |
656 |
|
dz = rab[2] * gab; |
657 |
< |
|
658 |
< |
vel[ax] += rma * dx; |
659 |
< |
vel[ay] += rma * dy; |
660 |
< |
vel[az] += rma * dz; |
657 |
> |
|
658 |
> |
velA[0] += rma * dx; |
659 |
> |
velA[1] += rma * dy; |
660 |
> |
velA[2] += rma * dz; |
661 |
|
|
662 |
< |
vel[bx] -= rmb * dx; |
663 |
< |
vel[by] -= rmb * dy; |
664 |
< |
vel[bz] -= rmb * dz; |
662 |
> |
atoms[a]->setVel( velA ); |
663 |
> |
|
664 |
> |
velB[0] -= rmb * dx; |
665 |
> |
velB[1] -= rmb * dy; |
666 |
> |
velB[2] -= rmb * dz; |
667 |
> |
|
668 |
> |
atoms[b]->setVel( velB ); |
669 |
|
|
670 |
|
moving[a] = 1; |
671 |
|
moving[b] = 1; |
681 |
|
|
682 |
|
iteration++; |
683 |
|
} |
684 |
< |
|
684 |
> |
|
685 |
|
if( !done ){ |
686 |
|
|
687 |
|
|
694 |
|
|
695 |
|
} |
696 |
|
|
686 |
– |
|
687 |
– |
|
688 |
– |
|
689 |
– |
|
690 |
– |
|
691 |
– |
|
697 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
698 |
|
double A[3][3] ){ |
699 |
|
|