224 |
|
pos = Atom::getPosArray(); |
225 |
|
vel = Atom::getVelArray(); |
226 |
|
frc = Atom::getFrcArray(); |
227 |
– |
trq = Atom::getTrqArray(); |
228 |
– |
Amat = Atom::getAmatArray(); |
227 |
|
|
228 |
|
while( currTime < runTime ){ |
229 |
|
|
232 |
|
calcStress = 1; |
233 |
|
} |
234 |
|
|
235 |
< |
std::cerr << "calcPot = " << calcPot << "; calcStress = " |
238 |
< |
<< calcStress << "\n"; |
235 |
> |
std::cerr << currTime << "\n"; |
236 |
|
|
237 |
|
integrateStep( calcPot, calcStress ); |
238 |
|
|
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]; |
304 |
> |
double A[3][3], At[3][3]; |
305 |
|
|
306 |
|
|
307 |
|
for( i=0; i<nAtoms; i++ ){ |
312 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) |
313 |
|
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
314 |
|
|
318 |
– |
std::cerr<< "MoveA vel[" << i << "] = " |
319 |
– |
<< vel[atomIndex] << "\t" |
320 |
– |
<< vel[atomIndex+1]<< "\t" |
321 |
– |
<< vel[atomIndex+2]<< "\n"; |
315 |
|
|
316 |
|
// position whole step |
317 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
318 |
|
|
319 |
|
|
327 |
– |
std::cerr<< "MoveA pos[" << i << "] = " |
328 |
– |
<< pos[atomIndex] << "\t" |
329 |
– |
<< pos[atomIndex+1]<< "\t" |
330 |
– |
<< pos[atomIndex+2]<< "\n"; |
331 |
– |
|
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; |
337 |
|
|
338 |
|
// use the angular velocities to propagate the rotation matrix a |
339 |
|
// 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(); |
340 |
|
|
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 |
– |
|
341 |
|
// rotate about the x-axis |
342 |
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
343 |
< |
this->rotate( 1, 2, angle, ji, A ); |
344 |
< |
|
343 |
> |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
344 |
> |
|
345 |
|
// rotate about the y-axis |
346 |
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
347 |
< |
this->rotate( 2, 0, angle, ji, A ); |
347 |
> |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
348 |
|
|
349 |
|
// rotate about the z-axis |
350 |
|
angle = dt * ji[2] / dAtom->getIzz(); |
351 |
< |
this->rotate( 0, 1, angle, ji, A ); |
351 |
> |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
352 |
|
|
353 |
|
// rotate about the y-axis |
354 |
|
angle = dt2 * ji[1] / dAtom->getIyy(); |
355 |
< |
this->rotate( 2, 0, angle, ji, A ); |
355 |
> |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
356 |
|
|
357 |
|
// rotate about the x-axis |
358 |
|
angle = dt2 * ji[0] / dAtom->getIxx(); |
359 |
< |
this->rotate( 1, 2, angle, ji, A ); |
359 |
> |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
360 |
|
|
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 |
< |
std::cerr<< "MoveB vel[" << i << "] = " |
411 |
< |
<< vel[atomIndex] << "\t" |
412 |
< |
<< vel[atomIndex+1]<< "\t" |
413 |
< |
<< vel[atomIndex+2]<< "\n"; |
414 |
< |
|
415 |
< |
|
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 |
|
|
683 |
|
|
684 |
|
|
685 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
686 |
< |
double A[3][3] ){ |
686 |
> |
double A[9] ){ |
687 |
|
|
688 |
|
int i,j,k; |
689 |
|
double sinAngle; |
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[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[j][i] = 0.0; |
760 |
> |
A[3*j+i] = 0.0; |
761 |
|
for(k=0; k<3; k++){ |
762 |
< |
A[j][i] += tempA[i][k] * rot[j][k]; |
762 |
> |
A[3*j+i] += tempA[i][k] * rot[j][k]; |
763 |
|
} |
764 |
|
} |
765 |
|
} |