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(); |
224 |
|
pos = Atom::getPosArray(); |
225 |
|
vel = Atom::getVelArray(); |
226 |
|
frc = Atom::getFrcArray(); |
219 |
– |
trq = Atom::getTrqArray(); |
220 |
– |
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; |
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 |
< |
|
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 |
|
|
315 |
+ |
|
316 |
|
// position whole step |
317 |
|
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
318 |
|
|
319 |
+ |
|
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 |
|
|
457 |
|
double gab; |
458 |
|
int iteration; |
459 |
|
|
425 |
– |
|
426 |
– |
|
460 |
|
for( i=0; i<nAtoms; i++){ |
461 |
|
|
462 |
|
moving[i] = 0; |
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 |
|
} |