72 |
|
for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 |
|
|
74 |
|
constrained = theArray[j]->is_constrained(); |
75 |
< |
|
75 |
> |
|
76 |
|
if(constrained){ |
77 |
< |
|
77 |
> |
|
78 |
|
dummy_plug = theArray[j]->get_constraint(); |
79 |
|
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
80 |
|
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
82 |
|
|
83 |
|
nConstrained++; |
84 |
|
constrained = 0; |
85 |
< |
} |
85 |
> |
} |
86 |
|
} |
87 |
|
|
88 |
|
theArray = (SRI**) molecules[i].getMyBends(); |
137 |
|
constrainedA[i] = temp_con[i].get_a(); |
138 |
|
constrainedB[i] = temp_con[i].get_b(); |
139 |
|
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
140 |
+ |
|
141 |
|
} |
142 |
|
|
143 |
|
|
167 |
|
double currSample; |
168 |
|
double currThermal; |
169 |
|
double currStatus; |
169 |
– |
double currTime; |
170 |
|
|
171 |
|
int calcPot, calcStress; |
172 |
|
int isError; |
173 |
|
|
174 |
– |
|
175 |
– |
|
174 |
|
tStats = new Thermo( info ); |
175 |
|
statOut = new StatWriter( info ); |
176 |
|
dumpOut = new DumpWriter( info ); |
190 |
|
tStats->velocitize(); |
191 |
|
} |
192 |
|
|
195 |
– |
dumpOut->writeDump( 0.0 ); |
196 |
– |
statOut->writeStat( 0.0 ); |
197 |
– |
|
193 |
|
calcPot = 0; |
194 |
|
calcStress = 0; |
195 |
|
currSample = sampleTime; |
196 |
|
currThermal = thermalTime; |
197 |
|
currStatus = statusTime; |
203 |
– |
currTime = 0.0;; |
198 |
|
|
199 |
+ |
dumpOut->writeDump( info->getTime() ); |
200 |
+ |
statOut->writeStat( info->getTime() ); |
201 |
|
|
202 |
|
readyCheck(); |
203 |
|
|
207 |
|
MPIcheckPoint(); |
208 |
|
#endif // is_mpi |
209 |
|
|
210 |
+ |
while( info->getTime() < runTime ){ |
211 |
|
|
212 |
< |
pos = Atom::getPosArray(); |
216 |
< |
vel = Atom::getVelArray(); |
217 |
< |
frc = Atom::getFrcArray(); |
218 |
< |
trq = Atom::getTrqArray(); |
219 |
< |
Amat = Atom::getAmatArray(); |
220 |
< |
|
221 |
< |
while( currTime < runTime ){ |
222 |
< |
|
223 |
< |
if( (currTime+dt) >= currStatus ){ |
212 |
> |
if( (info->getTime()+dt) >= currStatus ){ |
213 |
|
calcPot = 1; |
214 |
|
calcStress = 1; |
215 |
|
} |
216 |
|
|
217 |
|
integrateStep( calcPot, calcStress ); |
218 |
|
|
219 |
< |
currTime += dt; |
219 |
> |
info->incrTime(dt); |
220 |
|
|
221 |
|
if( info->setTemp ){ |
222 |
< |
if( currTime >= currThermal ){ |
222 |
> |
if( info->getTime() >= currThermal ){ |
223 |
|
tStats->velocitize(); |
224 |
|
currThermal += thermalTime; |
225 |
|
} |
226 |
|
} |
227 |
|
|
228 |
< |
if( currTime >= currSample ){ |
229 |
< |
dumpOut->writeDump( currTime ); |
228 |
> |
if( info->getTime() >= currSample ){ |
229 |
> |
dumpOut->writeDump( info->getTime() ); |
230 |
|
currSample += sampleTime; |
231 |
|
} |
232 |
|
|
233 |
< |
if( currTime >= currStatus ){ |
234 |
< |
statOut->writeStat( currTime ); |
233 |
> |
if( info->getTime() >= currStatus ){ |
234 |
> |
statOut->writeStat( info->getTime() ); |
235 |
|
calcPot = 0; |
236 |
|
calcStress = 0; |
237 |
|
currStatus += statusTime; |
245 |
|
|
246 |
|
} |
247 |
|
|
248 |
< |
dumpOut->writeFinal(); |
248 |
> |
dumpOut->writeFinal(info->getTime()); |
249 |
|
|
250 |
|
delete dumpOut; |
251 |
|
delete statOut; |
261 |
|
moveA(); |
262 |
|
if( nConstrained ) constrainA(); |
263 |
|
|
264 |
+ |
|
265 |
+ |
#ifdef IS_MPI |
266 |
+ |
strcpy( checkPointMsg, "Succesful moveA\n" ); |
267 |
+ |
MPIcheckPoint(); |
268 |
+ |
#endif // is_mpi |
269 |
+ |
|
270 |
+ |
|
271 |
|
// calc forces |
272 |
|
|
273 |
|
myFF->doForces(calcPot,calcStress); |
274 |
|
|
275 |
+ |
#ifdef IS_MPI |
276 |
+ |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
277 |
+ |
MPIcheckPoint(); |
278 |
+ |
#endif // is_mpi |
279 |
+ |
|
280 |
+ |
|
281 |
|
// finish the velocity half step |
282 |
|
|
283 |
|
moveB(); |
284 |
|
if( nConstrained ) constrainB(); |
285 |
< |
|
285 |
> |
|
286 |
> |
#ifdef IS_MPI |
287 |
> |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
288 |
> |
MPIcheckPoint(); |
289 |
> |
#endif // is_mpi |
290 |
> |
|
291 |
> |
|
292 |
|
} |
293 |
|
|
294 |
|
|
295 |
|
void Integrator::moveA( void ){ |
296 |
|
|
297 |
< |
int i,j,k; |
290 |
< |
int atomIndex, aMatIndex; |
297 |
> |
int i, j; |
298 |
|
DirectionalAtom* dAtom; |
299 |
< |
double Tb[3]; |
300 |
< |
double ji[3]; |
299 |
> |
double Tb[3], ji[3]; |
300 |
> |
double A[3][3], I[3][3]; |
301 |
|
double angle; |
302 |
+ |
double vel[3], pos[3], frc[3]; |
303 |
+ |
double mass; |
304 |
|
|
305 |
|
for( i=0; i<nAtoms; i++ ){ |
297 |
– |
atomIndex = i * 3; |
298 |
– |
aMatIndex = i * 9; |
299 |
– |
|
300 |
– |
// velocity half step |
301 |
– |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
302 |
– |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
306 |
|
|
307 |
< |
// position whole step |
308 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
307 |
> |
atoms[i]->getVel( vel ); |
308 |
> |
atoms[i]->getPos( pos ); |
309 |
> |
atoms[i]->getFrc( frc ); |
310 |
> |
|
311 |
> |
mass = atoms[i]->getMass(); |
312 |
> |
|
313 |
> |
for (j=0; j < 3; j++) { |
314 |
> |
// velocity half step |
315 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
316 |
> |
// position whole step |
317 |
|
pos[j] += dt * vel[j]; |
318 |
+ |
} |
319 |
|
|
320 |
< |
|
320 |
> |
atoms[i]->setVel( vel ); |
321 |
> |
atoms[i]->setPos( pos ); |
322 |
> |
|
323 |
|
if( atoms[i]->isDirectional() ){ |
324 |
|
|
325 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
326 |
|
|
327 |
|
// get and convert the torque to body frame |
328 |
|
|
329 |
< |
Tb[0] = dAtom->getTx(); |
316 |
< |
Tb[1] = dAtom->getTy(); |
317 |
< |
Tb[2] = dAtom->getTz(); |
318 |
< |
|
329 |
> |
dAtom->getTrq( Tb ); |
330 |
|
dAtom->lab2Body( Tb ); |
331 |
< |
|
331 |
> |
|
332 |
|
// get the angular momentum, and propagate a half step |
333 |
+ |
|
334 |
+ |
dAtom->getJ( ji ); |
335 |
+ |
|
336 |
+ |
for (j=0; j < 3; j++) |
337 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
338 |
|
|
323 |
– |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
324 |
– |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
325 |
– |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
326 |
– |
|
339 |
|
// use the angular velocities to propagate the rotation matrix a |
340 |
|
// full time step |
341 |
< |
|
341 |
> |
|
342 |
> |
dAtom->getA(A); |
343 |
> |
dAtom->getI(I); |
344 |
> |
|
345 |
|
// rotate about the x-axis |
346 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
347 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
348 |
< |
|
346 |
> |
angle = dt2 * ji[0] / I[0][0]; |
347 |
> |
this->rotate( 1, 2, angle, ji, A ); |
348 |
> |
|
349 |
|
// rotate about the y-axis |
350 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
351 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
350 |
> |
angle = dt2 * ji[1] / I[1][1]; |
351 |
> |
this->rotate( 2, 0, angle, ji, A ); |
352 |
|
|
353 |
|
// rotate about the z-axis |
354 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
355 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
354 |
> |
angle = dt * ji[2] / I[2][2]; |
355 |
> |
this->rotate( 0, 1, angle, ji, A); |
356 |
|
|
357 |
|
// rotate about the y-axis |
358 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
359 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
358 |
> |
angle = dt2 * ji[1] / I[1][1]; |
359 |
> |
this->rotate( 2, 0, angle, ji, A ); |
360 |
|
|
361 |
|
// rotate about the x-axis |
362 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
363 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
362 |
> |
angle = dt2 * ji[0] / I[0][0]; |
363 |
> |
this->rotate( 1, 2, angle, ji, A ); |
364 |
|
|
365 |
< |
dAtom->setJx( ji[0] ); |
366 |
< |
dAtom->setJy( ji[1] ); |
367 |
< |
dAtom->setJz( ji[2] ); |
368 |
< |
} |
369 |
< |
|
365 |
> |
|
366 |
> |
dAtom->setJ( ji ); |
367 |
> |
dAtom->setA( A ); |
368 |
> |
|
369 |
> |
} |
370 |
|
} |
371 |
|
} |
372 |
|
|
373 |
|
|
374 |
|
void Integrator::moveB( void ){ |
375 |
< |
int i,j,k; |
361 |
< |
int atomIndex; |
375 |
> |
int i, j; |
376 |
|
DirectionalAtom* dAtom; |
377 |
< |
double Tb[3]; |
378 |
< |
double ji[3]; |
377 |
> |
double Tb[3], ji[3]; |
378 |
> |
double vel[3], frc[3]; |
379 |
> |
double mass; |
380 |
|
|
381 |
|
for( i=0; i<nAtoms; i++ ){ |
382 |
< |
atomIndex = i * 3; |
382 |
> |
|
383 |
> |
atoms[i]->getVel( vel ); |
384 |
> |
atoms[i]->getFrc( frc ); |
385 |
|
|
386 |
< |
// velocity half step |
370 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
371 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
386 |
> |
mass = atoms[i]->getMass(); |
387 |
|
|
388 |
+ |
// velocity half step |
389 |
+ |
for (j=0; j < 3; j++) |
390 |
+ |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
391 |
+ |
|
392 |
+ |
atoms[i]->setVel( vel ); |
393 |
+ |
|
394 |
|
if( atoms[i]->isDirectional() ){ |
395 |
< |
|
395 |
> |
|
396 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
397 |
< |
|
398 |
< |
// get and convert the torque to body frame |
399 |
< |
|
400 |
< |
Tb[0] = dAtom->getTx(); |
380 |
< |
Tb[1] = dAtom->getTy(); |
381 |
< |
Tb[2] = dAtom->getTz(); |
382 |
< |
|
397 |
> |
|
398 |
> |
// get and convert the torque to body frame |
399 |
> |
|
400 |
> |
dAtom->getTrq( Tb ); |
401 |
|
dAtom->lab2Body( Tb ); |
402 |
+ |
|
403 |
+ |
// get the angular momentum, and propagate a half step |
404 |
+ |
|
405 |
+ |
dAtom->getJ( ji ); |
406 |
+ |
|
407 |
+ |
for (j=0; j < 3; j++) |
408 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
409 |
|
|
410 |
< |
// get the angular momentum, and complete the angular momentum |
411 |
< |
// half step |
387 |
< |
|
388 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
389 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
390 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
391 |
< |
|
392 |
< |
dAtom->setJx( ji[0] ); |
393 |
< |
dAtom->setJy( ji[1] ); |
394 |
< |
dAtom->setJz( ji[2] ); |
410 |
> |
|
411 |
> |
dAtom->setJ( ji ); |
412 |
|
} |
413 |
|
} |
397 |
– |
|
414 |
|
} |
415 |
|
|
416 |
|
void Integrator::preMove( void ){ |
417 |
< |
int i; |
417 |
> |
int i, j; |
418 |
> |
double pos[3]; |
419 |
|
|
420 |
|
if( nConstrained ){ |
421 |
|
|
422 |
< |
// if( oldAtoms != nAtoms ){ |
423 |
< |
|
424 |
< |
// // save oldAtoms to check for lode balanceing later on. |
425 |
< |
|
426 |
< |
// oldAtoms = nAtoms; |
427 |
< |
|
428 |
< |
// delete[] moving; |
429 |
< |
// delete[] moved; |
430 |
< |
// delete[] oldPos; |
431 |
< |
|
432 |
< |
// moving = new int[nAtoms]; |
416 |
< |
// moved = new int[nAtoms]; |
417 |
< |
|
418 |
< |
// oldPos = new double[nAtoms*3]; |
419 |
< |
// } |
420 |
< |
|
421 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
422 |
< |
} |
423 |
< |
} |
422 |
> |
for(i=0; i < nAtoms; i++) { |
423 |
> |
|
424 |
> |
atoms[i]->getPos( pos ); |
425 |
> |
|
426 |
> |
for (j = 0; j < 3; j++) { |
427 |
> |
oldPos[3*i + j] = pos[j]; |
428 |
> |
} |
429 |
> |
|
430 |
> |
} |
431 |
> |
} |
432 |
> |
} |
433 |
|
|
434 |
|
void Integrator::constrainA(){ |
435 |
|
|
436 |
|
int i,j,k; |
437 |
|
int done; |
438 |
< |
double pxab, pyab, pzab; |
439 |
< |
double rxab, ryab, rzab; |
440 |
< |
int a, b; |
438 |
> |
double posA[3], posB[3]; |
439 |
> |
double velA[3], velB[3]; |
440 |
> |
double pab[3]; |
441 |
> |
double rab[3]; |
442 |
> |
int a, b, ax, ay, az, bx, by, bz; |
443 |
|
double rma, rmb; |
444 |
|
double dx, dy, dz; |
445 |
|
double rpab; |
448 |
|
double gab; |
449 |
|
int iteration; |
450 |
|
|
451 |
< |
|
441 |
< |
|
442 |
< |
for( i=0; i<nAtoms; i++){ |
443 |
< |
|
451 |
> |
for( i=0; i<nAtoms; i++){ |
452 |
|
moving[i] = 0; |
453 |
|
moved[i] = 1; |
454 |
|
} |
455 |
< |
|
448 |
< |
|
455 |
> |
|
456 |
|
iteration = 0; |
457 |
|
done = 0; |
458 |
|
while( !done && (iteration < maxIteration )){ |
462 |
|
|
463 |
|
a = constrainedA[i]; |
464 |
|
b = constrainedB[i]; |
465 |
< |
|
465 |
> |
|
466 |
> |
ax = (a*3) + 0; |
467 |
> |
ay = (a*3) + 1; |
468 |
> |
az = (a*3) + 2; |
469 |
> |
|
470 |
> |
bx = (b*3) + 0; |
471 |
> |
by = (b*3) + 1; |
472 |
> |
bz = (b*3) + 2; |
473 |
> |
|
474 |
|
if( moved[a] || moved[b] ){ |
475 |
< |
|
476 |
< |
pxab = pos[3*a+0] - pos[3*b+0]; |
477 |
< |
pyab = pos[3*a+1] - pos[3*b+1]; |
478 |
< |
pzab = pos[3*a+2] - pos[3*b+2]; |
475 |
> |
|
476 |
> |
atoms[a]->getPos( posA ); |
477 |
> |
atoms[b]->getPos( posB ); |
478 |
> |
|
479 |
> |
for (j = 0; j < 3; j++ ) |
480 |
> |
pab[j] = posA[j] - posB[j]; |
481 |
> |
|
482 |
> |
//periodic boundary condition |
483 |
|
|
484 |
< |
//periodic boundary condition |
485 |
< |
pxab = pxab - info->box_x * copysign(1, pxab) |
486 |
< |
* int( fabs(pxab) / info->box_x + 0.5); |
487 |
< |
pyab = pyab - info->box_y * copysign(1, pyab) |
469 |
< |
* int( fabs(pyab) / info->box_y + 0.5); |
470 |
< |
pzab = pzab - info->box_z * copysign(1, pzab) |
471 |
< |
* int( fabs(pzab) / info->box_z + 0.5); |
472 |
< |
|
473 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
484 |
> |
info->wrapVector( pab ); |
485 |
> |
|
486 |
> |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
487 |
> |
|
488 |
|
rabsq = constrainedDsqr[i]; |
489 |
< |
diffsq = pabsq - rabsq; |
489 |
> |
diffsq = rabsq - pabsq; |
490 |
|
|
491 |
|
// the original rattle code from alan tidesley |
492 |
< |
if (fabs(diffsq) > tol*rabsq*2) { |
493 |
< |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
494 |
< |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
495 |
< |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
482 |
< |
|
483 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
484 |
< |
* int( fabs(rxab) / info->box_x + 0.5); |
485 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
486 |
< |
* int( fabs(ryab) / info->box_y + 0.5); |
487 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
488 |
< |
* int( fabs(rzab) / info->box_z + 0.5); |
492 |
> |
if (fabs(diffsq) > (tol*rabsq*2)) { |
493 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
494 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
495 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
496 |
|
|
497 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
497 |
> |
info->wrapVector( rab ); |
498 |
> |
|
499 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
500 |
> |
|
501 |
|
rpabsq = rpab * rpab; |
502 |
|
|
503 |
|
|
504 |
|
if (rpabsq < (rabsq * -diffsq)){ |
505 |
+ |
|
506 |
|
#ifdef IS_MPI |
507 |
|
a = atoms[a]->getGlobalIndex(); |
508 |
|
b = atoms[b]->getGlobalIndex(); |
509 |
|
#endif //is_mpi |
510 |
|
sprintf( painCave.errMsg, |
511 |
< |
"Constraint failure in constrainA at atom %d and %d\n.", |
511 |
> |
"Constraint failure in constrainA at atom %d and %d.\n", |
512 |
|
a, b ); |
513 |
|
painCave.isFatal = 1; |
514 |
|
simError(); |
516 |
|
|
517 |
|
rma = 1.0 / atoms[a]->getMass(); |
518 |
|
rmb = 1.0 / atoms[b]->getMass(); |
519 |
< |
|
519 |
> |
|
520 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
510 |
– |
dx = rxab * gab; |
511 |
– |
dy = ryab * gab; |
512 |
– |
dz = rzab * gab; |
521 |
|
|
522 |
< |
pos[3*a+0] += rma * dx; |
523 |
< |
pos[3*a+1] += rma * dy; |
524 |
< |
pos[3*a+2] += rma * dz; |
522 |
> |
dx = rab[0] * gab; |
523 |
> |
dy = rab[1] * gab; |
524 |
> |
dz = rab[2] * gab; |
525 |
|
|
526 |
< |
pos[3*b+0] -= rmb * dx; |
527 |
< |
pos[3*b+1] -= rmb * dy; |
528 |
< |
pos[3*b+2] -= rmb * dz; |
526 |
> |
posA[0] += rma * dx; |
527 |
> |
posA[1] += rma * dy; |
528 |
> |
posA[2] += rma * dz; |
529 |
|
|
530 |
+ |
atoms[a]->setPos( posA ); |
531 |
+ |
|
532 |
+ |
posB[0] -= rmb * dx; |
533 |
+ |
posB[1] -= rmb * dy; |
534 |
+ |
posB[2] -= rmb * dz; |
535 |
+ |
|
536 |
+ |
atoms[b]->setPos( posB ); |
537 |
+ |
|
538 |
|
dx = dx / dt; |
539 |
|
dy = dy / dt; |
540 |
|
dz = dz / dt; |
541 |
|
|
542 |
< |
vel[3*a+0] += rma * dx; |
527 |
< |
vel[3*a+1] += rma * dy; |
528 |
< |
vel[3*a+2] += rma * dz; |
542 |
> |
atoms[a]->getVel( velA ); |
543 |
|
|
544 |
< |
vel[3*b+0] -= rmb * dx; |
545 |
< |
vel[3*b+1] -= rmb * dy; |
546 |
< |
vel[3*b+2] -= rmb * dz; |
544 |
> |
velA[0] += rma * dx; |
545 |
> |
velA[1] += rma * dy; |
546 |
> |
velA[2] += rma * dz; |
547 |
|
|
548 |
+ |
atoms[a]->setVel( velA ); |
549 |
+ |
|
550 |
+ |
atoms[b]->getVel( velB ); |
551 |
+ |
|
552 |
+ |
velB[0] -= rmb * dx; |
553 |
+ |
velB[1] -= rmb * dy; |
554 |
+ |
velB[2] -= rmb * dz; |
555 |
+ |
|
556 |
+ |
atoms[b]->setVel( velB ); |
557 |
+ |
|
558 |
|
moving[a] = 1; |
559 |
|
moving[b] = 1; |
560 |
|
done = 0; |
586 |
|
|
587 |
|
int i,j,k; |
588 |
|
int done; |
589 |
+ |
double posA[3], posB[3]; |
590 |
+ |
double velA[3], velB[3]; |
591 |
|
double vxab, vyab, vzab; |
592 |
< |
double rxab, ryab, rzab; |
593 |
< |
int a, b; |
592 |
> |
double rab[3]; |
593 |
> |
int a, b, ax, ay, az, bx, by, bz; |
594 |
|
double rma, rmb; |
595 |
|
double dx, dy, dz; |
596 |
|
double rabsq, pabsq, rvab; |
607 |
|
iteration = 0; |
608 |
|
while( !done && (iteration < maxIteration ) ){ |
609 |
|
|
610 |
+ |
done = 1; |
611 |
+ |
|
612 |
|
for(i=0; i<nConstrained; i++){ |
613 |
|
|
614 |
|
a = constrainedA[i]; |
615 |
|
b = constrainedB[i]; |
616 |
|
|
617 |
+ |
ax = (a*3) + 0; |
618 |
+ |
ay = (a*3) + 1; |
619 |
+ |
az = (a*3) + 2; |
620 |
+ |
|
621 |
+ |
bx = (b*3) + 0; |
622 |
+ |
by = (b*3) + 1; |
623 |
+ |
bz = (b*3) + 2; |
624 |
+ |
|
625 |
|
if( moved[a] || moved[b] ){ |
590 |
– |
|
591 |
– |
vxab = vel[3*a+0] - vel[3*b+0]; |
592 |
– |
vyab = vel[3*a+1] - vel[3*b+1]; |
593 |
– |
vzab = vel[3*a+2] - vel[3*b+2]; |
626 |
|
|
627 |
< |
rxab = pos[3*a+0] - pos[3*b+0]; |
628 |
< |
ryab = pos[3*a+1] - pos[3*b+1]; |
629 |
< |
rzab = pos[3*a+2] - pos[3*b+2]; |
630 |
< |
|
631 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
632 |
< |
* int( fabs(rxab) / info->box_x + 0.5); |
601 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
602 |
< |
* int( fabs(ryab) / info->box_y + 0.5); |
603 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
604 |
< |
* int( fabs(rzab) / info->box_z + 0.5); |
627 |
> |
atoms[a]->getVel( velA ); |
628 |
> |
atoms[b]->getVel( velB ); |
629 |
> |
|
630 |
> |
vxab = velA[0] - velB[0]; |
631 |
> |
vyab = velA[1] - velB[1]; |
632 |
> |
vzab = velA[2] - velB[2]; |
633 |
|
|
634 |
+ |
atoms[a]->getPos( posA ); |
635 |
+ |
atoms[b]->getPos( posB ); |
636 |
+ |
|
637 |
+ |
for (j = 0; j < 3; j++) |
638 |
+ |
rab[j] = posA[j] - posB[j]; |
639 |
+ |
|
640 |
+ |
info->wrapVector( rab ); |
641 |
+ |
|
642 |
|
rma = 1.0 / atoms[a]->getMass(); |
643 |
|
rmb = 1.0 / atoms[b]->getMass(); |
644 |
|
|
645 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
645 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
646 |
|
|
647 |
|
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
648 |
|
|
649 |
|
if (fabs(gab) > tol) { |
650 |
|
|
651 |
< |
dx = rxab * gab; |
652 |
< |
dy = ryab * gab; |
653 |
< |
dz = rzab * gab; |
654 |
< |
|
655 |
< |
vel[3*a+0] += rma * dx; |
656 |
< |
vel[3*a+1] += rma * dy; |
657 |
< |
vel[3*a+2] += rma * dz; |
651 |
> |
dx = rab[0] * gab; |
652 |
> |
dy = rab[1] * gab; |
653 |
> |
dz = rab[2] * gab; |
654 |
> |
|
655 |
> |
velA[0] += rma * dx; |
656 |
> |
velA[1] += rma * dy; |
657 |
> |
velA[2] += rma * dz; |
658 |
|
|
659 |
< |
vel[3*b+0] -= rmb * dx; |
660 |
< |
vel[3*b+1] -= rmb * dy; |
661 |
< |
vel[3*b+2] -= rmb * dz; |
659 |
> |
atoms[a]->setVel( velA ); |
660 |
> |
|
661 |
> |
velB[0] -= rmb * dx; |
662 |
> |
velB[1] -= rmb * dy; |
663 |
> |
velB[2] -= rmb * dz; |
664 |
> |
|
665 |
> |
atoms[b]->setVel( velB ); |
666 |
|
|
667 |
|
moving[a] = 1; |
668 |
|
moving[b] = 1; |
678 |
|
|
679 |
|
iteration++; |
680 |
|
} |
681 |
< |
|
681 |
> |
|
682 |
|
if( !done ){ |
683 |
|
|
684 |
|
|
691 |
|
|
692 |
|
} |
693 |
|
|
654 |
– |
|
655 |
– |
|
656 |
– |
|
657 |
– |
|
658 |
– |
|
659 |
– |
|
694 |
|
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
695 |
< |
double A[9] ){ |
695 |
> |
double A[3][3] ){ |
696 |
|
|
697 |
|
int i,j,k; |
698 |
|
double sinAngle; |
708 |
|
|
709 |
|
for(i=0; i<3; i++){ |
710 |
|
for(j=0; j<3; j++){ |
711 |
< |
tempA[j][i] = A[3*i + j]; |
711 |
> |
tempA[j][i] = A[i][j]; |
712 |
|
} |
713 |
|
} |
714 |
|
|
765 |
|
|
766 |
|
for(i=0; i<3; i++){ |
767 |
|
for(j=0; j<3; j++){ |
768 |
< |
A[3*j + i] = 0.0; |
768 |
> |
A[j][i] = 0.0; |
769 |
|
for(k=0; k<3; k++){ |
770 |
< |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
770 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
771 |
|
} |
772 |
|
} |
773 |
|
} |