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(); |
234 |
|
calcStress = 1; |
235 |
|
} |
236 |
|
|
237 |
+ |
std::cerr << "calcPot = " << calcPot << "; calcStress = " |
238 |
+ |
<< calcStress << "\n"; |
239 |
+ |
|
240 |
|
integrateStep( calcPot, calcStress ); |
241 |
|
|
242 |
|
currTime += dt; |
304 |
|
double Tb[3]; |
305 |
|
double ji[3]; |
306 |
|
double angle; |
307 |
+ |
double A[3][3]; |
308 |
|
|
309 |
|
|
298 |
– |
|
310 |
|
for( i=0; i<nAtoms; i++ ){ |
311 |
|
atomIndex = i * 3; |
312 |
|
aMatIndex = i * 9; |
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++ ) pos[j] += dt * vel[j]; |
325 |
|
|
326 |
+ |
|
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]; |
349 |
|
|
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]; |
464 |
|
double gab; |
465 |
|
int iteration; |
466 |
|
|
425 |
– |
|
426 |
– |
|
467 |
|
for( i=0; i<nAtoms; i++){ |
468 |
|
|
469 |
|
moving[i] = 0; |
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 |
|
} |