1 |
#include <iostream> |
2 |
#include <cstdlib> |
3 |
#include <cmath> |
4 |
|
5 |
#ifdef IS_MPI |
6 |
#include "mpiSimulation.hpp" |
7 |
#include <unistd.h> |
8 |
#endif //is_mpi |
9 |
|
10 |
#include "Integrator.hpp" |
11 |
#include "simError.h" |
12 |
|
13 |
|
14 |
template<typename T> Integrator<T>::Integrator( SimInfo *theInfo, ForceFields* the_ff ) { |
15 |
|
16 |
info = theInfo; |
17 |
myFF = the_ff; |
18 |
isFirst = 1; |
19 |
|
20 |
molecules = info->molecules; |
21 |
nMols = info->n_mol; |
22 |
|
23 |
// give a little love back to the SimInfo object |
24 |
|
25 |
if( info->the_integrator != NULL ) delete info->the_integrator; |
26 |
info->the_integrator = this; |
27 |
|
28 |
nAtoms = info->n_atoms; |
29 |
|
30 |
// check for constraints |
31 |
|
32 |
constrainedA = NULL; |
33 |
constrainedB = NULL; |
34 |
constrainedDsqr = NULL; |
35 |
moving = NULL; |
36 |
moved = NULL; |
37 |
oldPos = NULL; |
38 |
|
39 |
nConstrained = 0; |
40 |
|
41 |
checkConstraints(); |
42 |
} |
43 |
|
44 |
template<typename T> Integrator<T>::~Integrator() { |
45 |
|
46 |
if( nConstrained ){ |
47 |
delete[] constrainedA; |
48 |
delete[] constrainedB; |
49 |
delete[] constrainedDsqr; |
50 |
delete[] moving; |
51 |
delete[] moved; |
52 |
delete[] oldPos; |
53 |
} |
54 |
|
55 |
} |
56 |
|
57 |
template<typename T> void Integrator<T>::checkConstraints( void ){ |
58 |
|
59 |
|
60 |
isConstrained = 0; |
61 |
|
62 |
Constraint *temp_con; |
63 |
Constraint *dummy_plug; |
64 |
temp_con = new Constraint[info->n_SRI]; |
65 |
nConstrained = 0; |
66 |
int constrained = 0; |
67 |
|
68 |
SRI** theArray; |
69 |
for(int i = 0; i < nMols; i++){ |
70 |
|
71 |
theArray = (SRI**) molecules[i].getMyBonds(); |
72 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 |
|
74 |
constrained = theArray[j]->is_constrained(); |
75 |
|
76 |
if(constrained){ |
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() ); |
81 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
82 |
|
83 |
nConstrained++; |
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constrained = 0; |
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} |
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} |
87 |
|
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theArray = (SRI**) molecules[i].getMyBends(); |
89 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
90 |
|
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constrained = theArray[j]->is_constrained(); |
92 |
|
93 |
if(constrained){ |
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|
95 |
dummy_plug = theArray[j]->get_constraint(); |
96 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
98 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
99 |
|
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nConstrained++; |
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constrained = 0; |
102 |
} |
103 |
} |
104 |
|
105 |
theArray = (SRI**) molecules[i].getMyTorsions(); |
106 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
107 |
|
108 |
constrained = theArray[j]->is_constrained(); |
109 |
|
110 |
if(constrained){ |
111 |
|
112 |
dummy_plug = theArray[j]->get_constraint(); |
113 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
114 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
115 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
116 |
|
117 |
nConstrained++; |
118 |
constrained = 0; |
119 |
} |
120 |
} |
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} |
122 |
|
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if(nConstrained > 0){ |
124 |
|
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isConstrained = 1; |
126 |
|
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if(constrainedA != NULL ) delete[] constrainedA; |
128 |
if(constrainedB != NULL ) delete[] constrainedB; |
129 |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
130 |
|
131 |
constrainedA = new int[nConstrained]; |
132 |
constrainedB = new int[nConstrained]; |
133 |
constrainedDsqr = new double[nConstrained]; |
134 |
|
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for( int i = 0; i < nConstrained; i++){ |
136 |
|
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constrainedA[i] = temp_con[i].get_a(); |
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constrainedB[i] = temp_con[i].get_b(); |
139 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
140 |
|
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} |
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|
143 |
|
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// save oldAtoms to check for lode balanceing later on. |
145 |
|
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oldAtoms = nAtoms; |
147 |
|
148 |
moving = new int[nAtoms]; |
149 |
moved = new int[nAtoms]; |
150 |
|
151 |
oldPos = new double[nAtoms*3]; |
152 |
} |
153 |
|
154 |
delete[] temp_con; |
155 |
} |
156 |
|
157 |
|
158 |
template<typename T> void Integrator<T>::integrate( void ){ |
159 |
|
160 |
int i, j; // loop counters |
161 |
|
162 |
double runTime = info->run_time; |
163 |
double sampleTime = info->sampleTime; |
164 |
double statusTime = info->statusTime; |
165 |
double thermalTime = info->thermalTime; |
166 |
|
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double currSample; |
168 |
double currThermal; |
169 |
double currStatus; |
170 |
|
171 |
int calcPot, calcStress; |
172 |
int isError; |
173 |
|
174 |
tStats = new Thermo( info ); |
175 |
statOut = new StatWriter( info ); |
176 |
dumpOut = new DumpWriter( info ); |
177 |
|
178 |
atoms = info->atoms; |
179 |
DirectionalAtom* dAtom; |
180 |
|
181 |
dt = info->dt; |
182 |
dt2 = 0.5 * dt; |
183 |
|
184 |
// initialize the forces before the first step |
185 |
|
186 |
calcForce(1, 1); |
187 |
|
188 |
if( info->setTemp ){ |
189 |
|
190 |
thermalize(); |
191 |
} |
192 |
|
193 |
calcPot = 0; |
194 |
calcStress = 0; |
195 |
currSample = sampleTime; |
196 |
currThermal = thermalTime; |
197 |
currStatus = statusTime; |
198 |
|
199 |
dumpOut->writeDump( info->getTime() ); |
200 |
statOut->writeStat( info->getTime() ); |
201 |
|
202 |
readyCheck(); |
203 |
|
204 |
#ifdef IS_MPI |
205 |
strcpy( checkPointMsg, |
206 |
"The integrator is ready to go." ); |
207 |
MPIcheckPoint(); |
208 |
#endif // is_mpi |
209 |
|
210 |
while( info->getTime() < runTime ){ |
211 |
|
212 |
if( (info->getTime()+dt) >= currStatus ){ |
213 |
calcPot = 1; |
214 |
calcStress = 1; |
215 |
} |
216 |
|
217 |
integrateStep( calcPot, calcStress ); |
218 |
|
219 |
info->incrTime(dt); |
220 |
|
221 |
if( info->setTemp ){ |
222 |
if( info->getTime() >= currThermal ){ |
223 |
thermalize(); |
224 |
currThermal += thermalTime; |
225 |
} |
226 |
} |
227 |
|
228 |
if( info->getTime() >= currSample ){ |
229 |
dumpOut->writeDump( info->getTime() ); |
230 |
currSample += sampleTime; |
231 |
} |
232 |
|
233 |
if( info->getTime() >= currStatus ){ |
234 |
statOut->writeStat( info->getTime() ); |
235 |
calcPot = 0; |
236 |
calcStress = 0; |
237 |
currStatus += statusTime; |
238 |
} |
239 |
|
240 |
#ifdef IS_MPI |
241 |
strcpy( checkPointMsg, |
242 |
"successfully took a time step." ); |
243 |
MPIcheckPoint(); |
244 |
#endif // is_mpi |
245 |
|
246 |
} |
247 |
|
248 |
dumpOut->writeFinal(info->getTime()); |
249 |
|
250 |
delete dumpOut; |
251 |
delete statOut; |
252 |
} |
253 |
|
254 |
template<typename T> void Integrator<T>::integrateStep( int calcPot, int calcStress ){ |
255 |
|
256 |
|
257 |
|
258 |
// Position full step, and velocity half step |
259 |
|
260 |
preMove(); |
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 |
calcForce(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 |
|
286 |
#ifdef IS_MPI |
287 |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
288 |
MPIcheckPoint(); |
289 |
#endif // is_mpi |
290 |
|
291 |
|
292 |
} |
293 |
|
294 |
|
295 |
template<typename T> void Integrator<T>::moveA( void ){ |
296 |
|
297 |
int i, j; |
298 |
DirectionalAtom* dAtom; |
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++ ){ |
306 |
|
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 |
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 |
dAtom->getTrq( Tb ); |
330 |
dAtom->lab2Body( Tb ); |
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 |
|
339 |
// use the angular velocities to propagate the rotation matrix a |
340 |
// full time step |
341 |
|
342 |
dAtom->getA(A); |
343 |
dAtom->getI(I); |
344 |
|
345 |
// rotate about the x-axis |
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] / I[1][1]; |
351 |
this->rotate( 2, 0, angle, ji, A ); |
352 |
|
353 |
// rotate about the z-axis |
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] / I[1][1]; |
359 |
this->rotate( 2, 0, angle, ji, A ); |
360 |
|
361 |
// rotate about the x-axis |
362 |
angle = dt2 * ji[0] / I[0][0]; |
363 |
this->rotate( 1, 2, angle, ji, A ); |
364 |
|
365 |
|
366 |
dAtom->setJ( ji ); |
367 |
dAtom->setA( A ); |
368 |
|
369 |
} |
370 |
} |
371 |
} |
372 |
|
373 |
|
374 |
template<typename T> void Integrator<T>::moveB( void ){ |
375 |
int i, j; |
376 |
DirectionalAtom* dAtom; |
377 |
double Tb[3], ji[3]; |
378 |
double vel[3], frc[3]; |
379 |
double mass; |
380 |
|
381 |
for( i=0; i<nAtoms; i++ ){ |
382 |
|
383 |
atoms[i]->getVel( vel ); |
384 |
atoms[i]->getFrc( frc ); |
385 |
|
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 |
|
396 |
dAtom = (DirectionalAtom *)atoms[i]; |
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 |
|
411 |
dAtom->setJ( ji ); |
412 |
} |
413 |
} |
414 |
} |
415 |
|
416 |
template<typename T> void Integrator<T>::preMove( void ){ |
417 |
int i, j; |
418 |
double pos[3]; |
419 |
|
420 |
if( nConstrained ){ |
421 |
|
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 |
template<typename T> void Integrator<T>::constrainA(){ |
435 |
|
436 |
int i,j,k; |
437 |
int done; |
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; |
446 |
double rabsq, pabsq, rpabsq; |
447 |
double diffsq; |
448 |
double gab; |
449 |
int iteration; |
450 |
|
451 |
for( i=0; i<nAtoms; i++){ |
452 |
moving[i] = 0; |
453 |
moved[i] = 1; |
454 |
} |
455 |
|
456 |
iteration = 0; |
457 |
done = 0; |
458 |
while( !done && (iteration < maxIteration )){ |
459 |
|
460 |
done = 1; |
461 |
for(i=0; i<nConstrained; i++){ |
462 |
|
463 |
a = constrainedA[i]; |
464 |
b = constrainedB[i]; |
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 |
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 |
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 = rabsq - pabsq; |
490 |
|
491 |
// the original rattle code from alan tidesley |
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 |
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", |
512 |
a, b ); |
513 |
painCave.isFatal = 1; |
514 |
simError(); |
515 |
} |
516 |
|
517 |
rma = 1.0 / atoms[a]->getMass(); |
518 |
rmb = 1.0 / atoms[b]->getMass(); |
519 |
|
520 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
521 |
|
522 |
dx = rab[0] * gab; |
523 |
dy = rab[1] * gab; |
524 |
dz = rab[2] * gab; |
525 |
|
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 |
atoms[a]->getVel( velA ); |
543 |
|
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; |
561 |
} |
562 |
} |
563 |
} |
564 |
|
565 |
for(i=0; i<nAtoms; i++){ |
566 |
|
567 |
moved[i] = moving[i]; |
568 |
moving[i] = 0; |
569 |
} |
570 |
|
571 |
iteration++; |
572 |
} |
573 |
|
574 |
if( !done ){ |
575 |
|
576 |
sprintf( painCave.errMsg, |
577 |
"Constraint failure in constrainA, too many iterations: %d\n", |
578 |
iteration ); |
579 |
painCave.isFatal = 1; |
580 |
simError(); |
581 |
} |
582 |
|
583 |
} |
584 |
|
585 |
template<typename T> void Integrator<T>::constrainB( void ){ |
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 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; |
597 |
double diffsq; |
598 |
double gab; |
599 |
int iteration; |
600 |
|
601 |
for(i=0; i<nAtoms; i++){ |
602 |
moving[i] = 0; |
603 |
moved[i] = 1; |
604 |
} |
605 |
|
606 |
done = 0; |
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] ){ |
626 |
|
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 = 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 = 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 |
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; |
669 |
done = 0; |
670 |
} |
671 |
} |
672 |
} |
673 |
|
674 |
for(i=0; i<nAtoms; i++){ |
675 |
moved[i] = moving[i]; |
676 |
moving[i] = 0; |
677 |
} |
678 |
|
679 |
iteration++; |
680 |
} |
681 |
|
682 |
if( !done ){ |
683 |
|
684 |
|
685 |
sprintf( painCave.errMsg, |
686 |
"Constraint failure in constrainB, too many iterations: %d\n", |
687 |
iteration ); |
688 |
painCave.isFatal = 1; |
689 |
simError(); |
690 |
} |
691 |
|
692 |
} |
693 |
|
694 |
template<typename T> void Integrator<T>::rotate( int axes1, int axes2, double angle, double ji[3], |
695 |
double A[3][3] ){ |
696 |
|
697 |
int i,j,k; |
698 |
double sinAngle; |
699 |
double cosAngle; |
700 |
double angleSqr; |
701 |
double angleSqrOver4; |
702 |
double top, bottom; |
703 |
double rot[3][3]; |
704 |
double tempA[3][3]; |
705 |
double tempJ[3]; |
706 |
|
707 |
// initialize the tempA |
708 |
|
709 |
for(i=0; i<3; i++){ |
710 |
for(j=0; j<3; j++){ |
711 |
tempA[j][i] = A[i][j]; |
712 |
} |
713 |
} |
714 |
|
715 |
// initialize the tempJ |
716 |
|
717 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
718 |
|
719 |
// initalize rot as a unit matrix |
720 |
|
721 |
rot[0][0] = 1.0; |
722 |
rot[0][1] = 0.0; |
723 |
rot[0][2] = 0.0; |
724 |
|
725 |
rot[1][0] = 0.0; |
726 |
rot[1][1] = 1.0; |
727 |
rot[1][2] = 0.0; |
728 |
|
729 |
rot[2][0] = 0.0; |
730 |
rot[2][1] = 0.0; |
731 |
rot[2][2] = 1.0; |
732 |
|
733 |
// use a small angle aproximation for sin and cosine |
734 |
|
735 |
angleSqr = angle * angle; |
736 |
angleSqrOver4 = angleSqr / 4.0; |
737 |
top = 1.0 - angleSqrOver4; |
738 |
bottom = 1.0 + angleSqrOver4; |
739 |
|
740 |
cosAngle = top / bottom; |
741 |
sinAngle = angle / bottom; |
742 |
|
743 |
rot[axes1][axes1] = cosAngle; |
744 |
rot[axes2][axes2] = cosAngle; |
745 |
|
746 |
rot[axes1][axes2] = sinAngle; |
747 |
rot[axes2][axes1] = -sinAngle; |
748 |
|
749 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
750 |
|
751 |
for(i=0; i<3; i++){ |
752 |
ji[i] = 0.0; |
753 |
for(k=0; k<3; k++){ |
754 |
ji[i] += rot[i][k] * tempJ[k]; |
755 |
} |
756 |
} |
757 |
|
758 |
// rotate the Rotation matrix acording to: |
759 |
// A[][] = A[][] * transpose(rot[][]) |
760 |
|
761 |
|
762 |
// NOte for as yet unknown reason, we are performing the |
763 |
// calculation as: |
764 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
765 |
|
766 |
for(i=0; i<3; i++){ |
767 |
for(j=0; j<3; j++){ |
768 |
A[j][i] = 0.0; |
769 |
for(k=0; k<3; k++){ |
770 |
A[j][i] += tempA[i][k] * rot[j][k]; |
771 |
} |
772 |
} |
773 |
} |
774 |
} |
775 |
|
776 |
template<typename T> void Integrator<T>::calcForce( int calcPot, int calcStress ){ |
777 |
myFF->doForces(calcPot,calcStress); |
778 |
|
779 |
} |
780 |
|
781 |
template<typename T> void Integrator<T>::thermalize(){ |
782 |
tStats->velocitize(); |
783 |
} |