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 ); |
210 |
|
MPIcheckPoint(); |
211 |
|
#endif // is_mpi |
212 |
|
|
223 |
– |
|
224 |
– |
pos = Atom::getPosArray(); |
225 |
– |
vel = Atom::getVelArray(); |
226 |
– |
frc = Atom::getFrcArray(); |
227 |
– |
|
213 |
|
while( currTime < runTime ){ |
214 |
|
|
215 |
|
if( (currTime+dt) >= currStatus ){ |
217 |
|
calcStress = 1; |
218 |
|
} |
219 |
|
|
235 |
– |
std::cerr << currTime << "\n"; |
236 |
– |
|
220 |
|
integrateStep( calcPot, calcStress ); |
221 |
|
|
222 |
|
currTime += dt; |
223 |
+ |
info->setTime(currTime); |
224 |
|
|
225 |
|
if( info->setTemp ){ |
226 |
|
if( currTime >= currThermal ){ |
263 |
|
|
264 |
|
preMove(); |
265 |
|
moveA(); |
266 |
< |
//if( nConstrained ) constrainA(); |
266 |
> |
if( nConstrained ) constrainA(); |
267 |
|
|
268 |
+ |
|
269 |
+ |
#ifdef IS_MPI |
270 |
+ |
strcpy( checkPointMsg, "Succesful moveA\n" ); |
271 |
+ |
MPIcheckPoint(); |
272 |
+ |
#endif // is_mpi |
273 |
+ |
|
274 |
+ |
|
275 |
|
// calc forces |
276 |
|
|
277 |
|
myFF->doForces(calcPot,calcStress); |
278 |
+ |
|
279 |
+ |
#ifdef IS_MPI |
280 |
+ |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
281 |
+ |
MPIcheckPoint(); |
282 |
+ |
#endif // is_mpi |
283 |
+ |
|
284 |
|
|
285 |
|
// finish the velocity half step |
286 |
|
|
287 |
|
moveB(); |
288 |
|
if( nConstrained ) constrainB(); |
289 |
< |
|
289 |
> |
|
290 |
> |
#ifdef IS_MPI |
291 |
> |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
292 |
> |
MPIcheckPoint(); |
293 |
> |
#endif // is_mpi |
294 |
> |
|
295 |
> |
|
296 |
|
} |
297 |
|
|
298 |
|
|
299 |
|
void Integrator::moveA( void ){ |
300 |
|
|
301 |
< |
int i,j,k; |
299 |
< |
int atomIndex, aMatIndex; |
301 |
> |
int i, j; |
302 |
|
DirectionalAtom* dAtom; |
303 |
< |
double Tb[3]; |
304 |
< |
double ji[3]; |
303 |
> |
double Tb[3], ji[3]; |
304 |
> |
double A[3][3], I[3][3]; |
305 |
|
double angle; |
306 |
< |
double A[3][3], At[3][3]; |
306 |
> |
double vel[3], pos[3], frc[3]; |
307 |
> |
double mass; |
308 |
|
|
306 |
– |
|
309 |
|
for( i=0; i<nAtoms; i++ ){ |
308 |
– |
atomIndex = i * 3; |
309 |
– |
aMatIndex = i * 9; |
310 |
|
|
311 |
< |
// velocity half step |
312 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
313 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
311 |
> |
atoms[i]->getVel( vel ); |
312 |
> |
atoms[i]->getPos( pos ); |
313 |
> |
atoms[i]->getFrc( frc ); |
314 |
|
|
315 |
+ |
mass = atoms[i]->getMass(); |
316 |
|
|
317 |
< |
// position whole step |
318 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
319 |
< |
|
317 |
> |
for (j=0; j < 3; j++) { |
318 |
> |
// velocity half step |
319 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
320 |
> |
// position whole step |
321 |
> |
pos[j] += dt * vel[j]; |
322 |
> |
} |
323 |
|
|
324 |
+ |
atoms[i]->setVel( vel ); |
325 |
+ |
atoms[i]->setPos( pos ); |
326 |
+ |
|
327 |
|
if( atoms[i]->isDirectional() ){ |
328 |
|
|
329 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
330 |
|
|
331 |
|
// get and convert the torque to body frame |
332 |
|
|
333 |
< |
Tb[0] = dAtom->getTx(); |
327 |
< |
Tb[1] = dAtom->getTy(); |
328 |
< |
Tb[2] = dAtom->getTz(); |
329 |
< |
|
333 |
> |
dAtom->getTrq( Tb ); |
334 |
|
dAtom->lab2Body( Tb ); |
335 |
|
|
336 |
|
// get the angular momentum, and propagate a half step |
337 |
+ |
|
338 |
+ |
dAtom->getJ( ji ); |
339 |
+ |
|
340 |
+ |
for (j=0; j < 3; j++) |
341 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
342 |
|
|
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 |
– |
|
343 |
|
// use the angular velocities to propagate the rotation matrix a |
344 |
|
// full time step |
345 |
< |
|
345 |
> |
|
346 |
> |
dAtom->getA(A); |
347 |
> |
dAtom->getI(I); |
348 |
> |
|
349 |
|
// rotate about the x-axis |
350 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
351 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
350 |
> |
angle = dt2 * ji[0] / I[0][0]; |
351 |
> |
this->rotate( 1, 2, angle, ji, A ); |
352 |
|
|
353 |
|
// rotate about the y-axis |
354 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
355 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
354 |
> |
angle = dt2 * ji[1] / I[1][1]; |
355 |
> |
this->rotate( 2, 0, angle, ji, A ); |
356 |
|
|
357 |
|
// rotate about the z-axis |
358 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
359 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
358 |
> |
angle = dt * ji[2] / I[2][2]; |
359 |
> |
this->rotate( 0, 1, angle, ji, A); |
360 |
|
|
361 |
|
// rotate about the y-axis |
362 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
363 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
362 |
> |
angle = dt2 * ji[1] / I[1][1]; |
363 |
> |
this->rotate( 2, 0, angle, ji, A ); |
364 |
|
|
365 |
|
// rotate about the x-axis |
366 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
367 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
366 |
> |
angle = dt2 * ji[0] / I[0][0]; |
367 |
> |
this->rotate( 1, 2, angle, ji, A ); |
368 |
|
|
361 |
– |
dAtom->setJx( ji[0] ); |
362 |
– |
dAtom->setJy( ji[1] ); |
363 |
– |
dAtom->setJz( ji[2] ); |
369 |
|
|
370 |
< |
std::cerr << "Amat[" << i << "]\n"; |
371 |
< |
info->printMat9( &Amat[aMatIndex] ); |
370 |
> |
dAtom->setJ( ji ); |
371 |
> |
dAtom->setA( A ); |
372 |
|
|
373 |
< |
std::cerr << "ji[" << i << "]\t" |
369 |
< |
<< ji[0] << "\t" |
370 |
< |
<< ji[1] << "\t" |
371 |
< |
<< ji[2] << "\n"; |
372 |
< |
|
373 |
< |
} |
374 |
< |
|
373 |
> |
} |
374 |
|
} |
375 |
|
} |
376 |
|
|
377 |
|
|
378 |
|
void Integrator::moveB( void ){ |
379 |
< |
int i,j,k; |
381 |
< |
int atomIndex, aMatIndex; |
379 |
> |
int i, j; |
380 |
|
DirectionalAtom* dAtom; |
381 |
< |
double Tb[3]; |
382 |
< |
double ji[3]; |
381 |
> |
double Tb[3], ji[3]; |
382 |
> |
double vel[3], frc[3]; |
383 |
> |
double mass; |
384 |
|
|
385 |
|
for( i=0; i<nAtoms; i++ ){ |
386 |
< |
atomIndex = i * 3; |
387 |
< |
aMatIndex = i * 9; |
386 |
> |
|
387 |
> |
atoms[i]->getVel( vel ); |
388 |
> |
atoms[i]->getFrc( frc ); |
389 |
|
|
390 |
< |
// velocity half step |
391 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
392 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
390 |
> |
mass = atoms[i]->getMass(); |
391 |
|
|
392 |
+ |
// velocity half step |
393 |
+ |
for (j=0; j < 3; j++) |
394 |
+ |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
395 |
+ |
|
396 |
+ |
atoms[i]->setVel( vel ); |
397 |
|
|
398 |
|
if( atoms[i]->isDirectional() ){ |
399 |
< |
|
399 |
> |
|
400 |
|
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"; |
401 |
|
|
402 |
+ |
// get and convert the torque to body frame |
403 |
+ |
|
404 |
+ |
dAtom->getTrq( Tb ); |
405 |
|
dAtom->lab2Body( Tb ); |
406 |
< |
|
407 |
< |
// 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] ); |
406 |
> |
|
407 |
> |
// get the angular momentum, and propagate a half step |
408 |
|
|
409 |
+ |
dAtom->getJ( ji ); |
410 |
|
|
411 |
< |
std::cerr << "Amat[" << i << "]\n"; |
412 |
< |
info->printMat9( &Amat[aMatIndex] ); |
413 |
< |
|
414 |
< |
std::cerr << "ji[" << i << "]\t" |
415 |
< |
<< ji[0] << "\t" |
429 |
< |
<< ji[1] << "\t" |
430 |
< |
<< ji[2] << "\n"; |
411 |
> |
for (j=0; j < 3; j++) |
412 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
413 |
> |
|
414 |
> |
|
415 |
> |
dAtom->setJ( ji ); |
416 |
|
} |
417 |
|
} |
433 |
– |
|
418 |
|
} |
419 |
|
|
420 |
|
void Integrator::preMove( void ){ |
421 |
< |
int i; |
421 |
> |
int i, j; |
422 |
> |
double pos[3]; |
423 |
|
|
424 |
|
if( nConstrained ){ |
425 |
|
|
426 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
427 |
< |
} |
428 |
< |
} |
426 |
> |
for(i=0; i < nAtoms; i++) { |
427 |
> |
|
428 |
> |
atoms[i]->getPos( pos ); |
429 |
|
|
430 |
+ |
for (j = 0; j < 3; j++) { |
431 |
+ |
oldPos[3*i + j] = pos[j]; |
432 |
+ |
} |
433 |
+ |
|
434 |
+ |
} |
435 |
+ |
} |
436 |
+ |
} |
437 |
+ |
|
438 |
|
void Integrator::constrainA(){ |
439 |
|
|
440 |
|
int i,j,k; |
441 |
|
int done; |
442 |
+ |
double posA[3], posB[3]; |
443 |
+ |
double velA[3], velB[3]; |
444 |
|
double pab[3]; |
445 |
|
double rab[3]; |
446 |
|
int a, b, ax, ay, az, bx, by, bz; |
452 |
|
double gab; |
453 |
|
int iteration; |
454 |
|
|
455 |
< |
for( i=0; i<nAtoms; i++){ |
461 |
< |
|
455 |
> |
for( i=0; i<nAtoms; i++){ |
456 |
|
moving[i] = 0; |
457 |
|
moved[i] = 1; |
458 |
|
} |
476 |
|
bz = (b*3) + 2; |
477 |
|
|
478 |
|
if( moved[a] || moved[b] ){ |
479 |
< |
|
480 |
< |
pab[0] = pos[ax] - pos[bx]; |
481 |
< |
pab[1] = pos[ay] - pos[by]; |
482 |
< |
pab[2] = pos[az] - pos[bz]; |
483 |
< |
|
479 |
> |
|
480 |
> |
atoms[a]->getPos( posA ); |
481 |
> |
atoms[b]->getPos( posB ); |
482 |
> |
|
483 |
> |
for (j = 0; j < 3; j++ ) |
484 |
> |
pab[j] = posA[j] - posB[j]; |
485 |
> |
|
486 |
|
//periodic boundary condition |
487 |
|
|
488 |
|
info->wrapVector( pab ); |
527 |
|
dy = rab[1] * gab; |
528 |
|
dz = rab[2] * gab; |
529 |
|
|
530 |
< |
pos[ax] += rma * dx; |
531 |
< |
pos[ay] += rma * dy; |
532 |
< |
pos[az] += rma * dz; |
530 |
> |
posA[0] += rma * dx; |
531 |
> |
posA[1] += rma * dy; |
532 |
> |
posA[2] += rma * dz; |
533 |
|
|
534 |
< |
pos[bx] -= rmb * dx; |
539 |
< |
pos[by] -= rmb * dy; |
540 |
< |
pos[bz] -= rmb * dz; |
534 |
> |
atoms[a]->setPos( posA ); |
535 |
|
|
536 |
+ |
posB[0] -= rmb * dx; |
537 |
+ |
posB[1] -= rmb * dy; |
538 |
+ |
posB[2] -= rmb * dz; |
539 |
+ |
|
540 |
+ |
atoms[b]->setPos( posB ); |
541 |
+ |
|
542 |
|
dx = dx / dt; |
543 |
|
dy = dy / dt; |
544 |
|
dz = dz / dt; |
545 |
|
|
546 |
< |
vel[ax] += rma * dx; |
547 |
< |
vel[ay] += rma * dy; |
548 |
< |
vel[az] += rma * dz; |
546 |
> |
atoms[a]->getVel( velA ); |
547 |
|
|
548 |
< |
vel[bx] -= rmb * dx; |
549 |
< |
vel[by] -= rmb * dy; |
550 |
< |
vel[bz] -= rmb * dz; |
548 |
> |
velA[0] += rma * dx; |
549 |
> |
velA[1] += rma * dy; |
550 |
> |
velA[2] += rma * dz; |
551 |
|
|
552 |
+ |
atoms[a]->setVel( velA ); |
553 |
+ |
|
554 |
+ |
atoms[b]->getVel( velB ); |
555 |
+ |
|
556 |
+ |
velB[0] -= rmb * dx; |
557 |
+ |
velB[1] -= rmb * dy; |
558 |
+ |
velB[2] -= rmb * dz; |
559 |
+ |
|
560 |
+ |
atoms[b]->setVel( velB ); |
561 |
+ |
|
562 |
|
moving[a] = 1; |
563 |
|
moving[b] = 1; |
564 |
|
done = 0; |
590 |
|
|
591 |
|
int i,j,k; |
592 |
|
int done; |
593 |
+ |
double posA[3], posB[3]; |
594 |
+ |
double velA[3], velB[3]; |
595 |
|
double vxab, vyab, vzab; |
596 |
|
double rab[3]; |
597 |
|
int a, b, ax, ay, az, bx, by, bz; |
627 |
|
bz = (b*3) + 2; |
628 |
|
|
629 |
|
if( moved[a] || moved[b] ){ |
620 |
– |
|
621 |
– |
vxab = vel[ax] - vel[bx]; |
622 |
– |
vyab = vel[ay] - vel[by]; |
623 |
– |
vzab = vel[az] - vel[bz]; |
630 |
|
|
631 |
< |
rab[0] = pos[ax] - pos[bx]; |
632 |
< |
rab[1] = pos[ay] - pos[by]; |
633 |
< |
rab[2] = pos[az] - pos[bz]; |
634 |
< |
|
631 |
> |
atoms[a]->getVel( velA ); |
632 |
> |
atoms[b]->getVel( velB ); |
633 |
> |
|
634 |
> |
vxab = velA[0] - velB[0]; |
635 |
> |
vyab = velA[1] - velB[1]; |
636 |
> |
vzab = velA[2] - velB[2]; |
637 |
> |
|
638 |
> |
atoms[a]->getPos( posA ); |
639 |
> |
atoms[b]->getPos( posB ); |
640 |
> |
|
641 |
> |
for (j = 0; j < 3; j++) |
642 |
> |
rab[j] = posA[j] - posB[j]; |
643 |
> |
|
644 |
|
info->wrapVector( rab ); |
645 |
|
|
646 |
|
rma = 1.0 / atoms[a]->getMass(); |
655 |
|
dx = rab[0] * gab; |
656 |
|
dy = rab[1] * gab; |
657 |
|
dz = rab[2] * gab; |
658 |
< |
|
659 |
< |
vel[ax] += rma * dx; |
660 |
< |
vel[ay] += rma * dy; |
661 |
< |
vel[az] += rma * dz; |
658 |
> |
|
659 |
> |
velA[0] += rma * dx; |
660 |
> |
velA[1] += rma * dy; |
661 |
> |
velA[2] += rma * dz; |
662 |
|
|
663 |
< |
vel[bx] -= rmb * dx; |
664 |
< |
vel[by] -= rmb * dy; |
665 |
< |
vel[bz] -= rmb * dz; |
663 |
> |
atoms[a]->setVel( velA ); |
664 |
> |
|
665 |
> |
velB[0] -= rmb * dx; |
666 |
> |
velB[1] -= rmb * dy; |
667 |
> |
velB[2] -= rmb * dz; |
668 |
> |
|
669 |
> |
atoms[b]->setVel( velB ); |
670 |
|
|
671 |
|
moving[a] = 1; |
672 |
|
moving[b] = 1; |
682 |
|
|
683 |
|
iteration++; |
684 |
|
} |
685 |
< |
|
685 |
> |
|
686 |
|
if( !done ){ |
687 |
|
|
688 |
|
|
695 |
|
|
696 |
|
} |
697 |
|
|
679 |
– |
|
680 |
– |
|
681 |
– |
|
682 |
– |
|
683 |
– |
|
684 |
– |
|
698 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
699 |
< |
double A[9] ){ |
699 |
> |
double A[3][3] ){ |
700 |
|
|
701 |
|
int i,j,k; |
702 |
|
double sinAngle; |
708 |
|
double tempA[3][3]; |
709 |
|
double tempJ[3]; |
710 |
|
|
698 |
– |
|
711 |
|
// initialize the tempA |
712 |
|
|
713 |
|
for(i=0; i<3; i++){ |
714 |
|
for(j=0; j<3; j++){ |
715 |
< |
tempA[j][i] = A[3*i+j]; |
715 |
> |
tempA[j][i] = A[i][j]; |
716 |
|
} |
717 |
|
} |
718 |
|
|
769 |
|
|
770 |
|
for(i=0; i<3; i++){ |
771 |
|
for(j=0; j<3; j++){ |
772 |
< |
A[3*j+i] = 0.0; |
772 |
> |
A[j][i] = 0.0; |
773 |
|
for(k=0; k<3; k++){ |
774 |
< |
A[3*j+i] += tempA[i][k] * rot[j][k]; |
774 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
775 |
|
} |
776 |
|
} |
777 |
|
} |