1 |
#include <math.h> |
2 |
#include "primitives/RigidBody.hpp" |
3 |
#include "primitives/DirectionalAtom.hpp" |
4 |
#include "utils/simError.h" |
5 |
#include "math/MatVec3.h" |
6 |
|
7 |
RigidBody::RigidBody() : StuntDouble() { |
8 |
objType = OT_RIGIDBODY; |
9 |
is_linear = false; |
10 |
linear_axis = -1; |
11 |
momIntTol = 1e-6; |
12 |
} |
13 |
|
14 |
RigidBody::~RigidBody() { |
15 |
} |
16 |
|
17 |
void RigidBody::addAtom(Atom* at, AtomStamp* ats) { |
18 |
|
19 |
vec3 coords; |
20 |
vec3 euler; |
21 |
mat3x3 Atmp; |
22 |
|
23 |
myAtoms.push_back(at); |
24 |
|
25 |
if( !ats->havePosition() ){ |
26 |
sprintf( painCave.errMsg, |
27 |
"RigidBody error.\n" |
28 |
"\tAtom %s does not have a position specified.\n" |
29 |
"\tThis means RigidBody cannot set up reference coordinates.\n", |
30 |
ats->getType() ); |
31 |
painCave.isFatal = 1; |
32 |
simError(); |
33 |
} |
34 |
|
35 |
coords[0] = ats->getPosX(); |
36 |
coords[1] = ats->getPosY(); |
37 |
coords[2] = ats->getPosZ(); |
38 |
|
39 |
refCoords.push_back(coords); |
40 |
|
41 |
if (at->isDirectional()) { |
42 |
|
43 |
if( !ats->haveOrientation() ){ |
44 |
sprintf( painCave.errMsg, |
45 |
"RigidBody error.\n" |
46 |
"\tAtom %s does not have an orientation specified.\n" |
47 |
"\tThis means RigidBody cannot set up reference orientations.\n", |
48 |
ats->getType() ); |
49 |
painCave.isFatal = 1; |
50 |
simError(); |
51 |
} |
52 |
|
53 |
euler[0] = ats->getEulerPhi(); |
54 |
euler[1] = ats->getEulerTheta(); |
55 |
euler[2] = ats->getEulerPsi(); |
56 |
|
57 |
doEulerToRotMat(euler, Atmp); |
58 |
|
59 |
refOrients.push_back(Atmp); |
60 |
|
61 |
} |
62 |
} |
63 |
|
64 |
void RigidBody::getPos(double theP[3]){ |
65 |
for (int i = 0; i < 3 ; i++) |
66 |
theP[i] = pos[i]; |
67 |
} |
68 |
|
69 |
void RigidBody::setPos(double theP[3]){ |
70 |
for (int i = 0; i < 3 ; i++) |
71 |
pos[i] = theP[i]; |
72 |
} |
73 |
|
74 |
void RigidBody::getVel(double theV[3]){ |
75 |
for (int i = 0; i < 3 ; i++) |
76 |
theV[i] = vel[i]; |
77 |
} |
78 |
|
79 |
void RigidBody::setVel(double theV[3]){ |
80 |
for (int i = 0; i < 3 ; i++) |
81 |
vel[i] = theV[i]; |
82 |
} |
83 |
|
84 |
void RigidBody::getFrc(double theF[3]){ |
85 |
for (int i = 0; i < 3 ; i++) |
86 |
theF[i] = frc[i]; |
87 |
} |
88 |
|
89 |
void RigidBody::addFrc(double theF[3]){ |
90 |
for (int i = 0; i < 3 ; i++) |
91 |
frc[i] += theF[i]; |
92 |
} |
93 |
|
94 |
void RigidBody::zeroForces() { |
95 |
|
96 |
for (int i = 0; i < 3; i++) { |
97 |
frc[i] = 0.0; |
98 |
trq[i] = 0.0; |
99 |
} |
100 |
|
101 |
} |
102 |
|
103 |
void RigidBody::setEuler( double phi, double theta, double psi ){ |
104 |
|
105 |
A[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
106 |
A[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
107 |
A[0][2] = sin(theta) * sin(psi); |
108 |
|
109 |
A[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
110 |
A[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
111 |
A[1][2] = sin(theta) * cos(psi); |
112 |
|
113 |
A[2][0] = sin(phi) * sin(theta); |
114 |
A[2][1] = -cos(phi) * sin(theta); |
115 |
A[2][2] = cos(theta); |
116 |
|
117 |
} |
118 |
|
119 |
void RigidBody::getQ( double q[4] ){ |
120 |
|
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double t, s; |
122 |
double ad1, ad2, ad3; |
123 |
|
124 |
t = A[0][0] + A[1][1] + A[2][2] + 1.0; |
125 |
if( t > 0.0 ){ |
126 |
|
127 |
s = 0.5 / sqrt( t ); |
128 |
q[0] = 0.25 / s; |
129 |
q[1] = (A[1][2] - A[2][1]) * s; |
130 |
q[2] = (A[2][0] - A[0][2]) * s; |
131 |
q[3] = (A[0][1] - A[1][0]) * s; |
132 |
} |
133 |
else{ |
134 |
|
135 |
ad1 = fabs( A[0][0] ); |
136 |
ad2 = fabs( A[1][1] ); |
137 |
ad3 = fabs( A[2][2] ); |
138 |
|
139 |
if( ad1 >= ad2 && ad1 >= ad3 ){ |
140 |
|
141 |
s = 2.0 * sqrt( 1.0 + A[0][0] - A[1][1] - A[2][2] ); |
142 |
q[0] = (A[1][2] + A[2][1]) / s; |
143 |
q[1] = 0.5 / s; |
144 |
q[2] = (A[0][1] + A[1][0]) / s; |
145 |
q[3] = (A[0][2] + A[2][0]) / s; |
146 |
} |
147 |
else if( ad2 >= ad1 && ad2 >= ad3 ){ |
148 |
|
149 |
s = sqrt( 1.0 + A[1][1] - A[0][0] - A[2][2] ) * 2.0; |
150 |
q[0] = (A[0][2] + A[2][0]) / s; |
151 |
q[1] = (A[0][1] + A[1][0]) / s; |
152 |
q[2] = 0.5 / s; |
153 |
q[3] = (A[1][2] + A[2][1]) / s; |
154 |
} |
155 |
else{ |
156 |
|
157 |
s = sqrt( 1.0 + A[2][2] - A[0][0] - A[1][1] ) * 2.0; |
158 |
q[0] = (A[0][1] + A[1][0]) / s; |
159 |
q[1] = (A[0][2] + A[2][0]) / s; |
160 |
q[2] = (A[1][2] + A[2][1]) / s; |
161 |
q[3] = 0.5 / s; |
162 |
} |
163 |
} |
164 |
} |
165 |
|
166 |
void RigidBody::setQ( double the_q[4] ){ |
167 |
|
168 |
double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
169 |
|
170 |
q0Sqr = the_q[0] * the_q[0]; |
171 |
q1Sqr = the_q[1] * the_q[1]; |
172 |
q2Sqr = the_q[2] * the_q[2]; |
173 |
q3Sqr = the_q[3] * the_q[3]; |
174 |
|
175 |
A[0][0] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
176 |
A[0][1] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
177 |
A[0][2] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
178 |
|
179 |
A[1][0] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
180 |
A[1][1] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
181 |
A[1][2] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
182 |
|
183 |
A[2][0] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
184 |
A[2][1] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
185 |
A[2][2] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
186 |
|
187 |
} |
188 |
|
189 |
void RigidBody::getA( double the_A[3][3] ){ |
190 |
|
191 |
for (int i = 0; i < 3; i++) |
192 |
for (int j = 0; j < 3; j++) |
193 |
the_A[i][j] = A[i][j]; |
194 |
|
195 |
} |
196 |
|
197 |
void RigidBody::setA( double the_A[3][3] ){ |
198 |
|
199 |
for (int i = 0; i < 3; i++) |
200 |
for (int j = 0; j < 3; j++) |
201 |
A[i][j] = the_A[i][j]; |
202 |
|
203 |
} |
204 |
|
205 |
void RigidBody::getJ( double theJ[3] ){ |
206 |
|
207 |
for (int i = 0; i < 3; i++) |
208 |
theJ[i] = ji[i]; |
209 |
|
210 |
} |
211 |
|
212 |
void RigidBody::setJ( double theJ[3] ){ |
213 |
|
214 |
for (int i = 0; i < 3; i++) |
215 |
ji[i] = theJ[i]; |
216 |
|
217 |
} |
218 |
|
219 |
void RigidBody::getTrq(double theT[3]){ |
220 |
for (int i = 0; i < 3 ; i++) |
221 |
theT[i] = trq[i]; |
222 |
} |
223 |
|
224 |
void RigidBody::addTrq(double theT[3]){ |
225 |
for (int i = 0; i < 3 ; i++) |
226 |
trq[i] += theT[i]; |
227 |
} |
228 |
|
229 |
void RigidBody::getI( double the_I[3][3] ){ |
230 |
|
231 |
for (int i = 0; i < 3; i++) |
232 |
for (int j = 0; j < 3; j++) |
233 |
the_I[i][j] = I[i][j]; |
234 |
|
235 |
} |
236 |
|
237 |
void RigidBody::lab2Body( double r[3] ){ |
238 |
|
239 |
double rl[3]; // the lab frame vector |
240 |
|
241 |
rl[0] = r[0]; |
242 |
rl[1] = r[1]; |
243 |
rl[2] = r[2]; |
244 |
|
245 |
r[0] = (A[0][0] * rl[0]) + (A[0][1] * rl[1]) + (A[0][2] * rl[2]); |
246 |
r[1] = (A[1][0] * rl[0]) + (A[1][1] * rl[1]) + (A[1][2] * rl[2]); |
247 |
r[2] = (A[2][0] * rl[0]) + (A[2][1] * rl[1]) + (A[2][2] * rl[2]); |
248 |
|
249 |
} |
250 |
|
251 |
void RigidBody::body2Lab( double r[3] ){ |
252 |
|
253 |
double rb[3]; // the body frame vector |
254 |
|
255 |
rb[0] = r[0]; |
256 |
rb[1] = r[1]; |
257 |
rb[2] = r[2]; |
258 |
|
259 |
r[0] = (A[0][0] * rb[0]) + (A[1][0] * rb[1]) + (A[2][0] * rb[2]); |
260 |
r[1] = (A[0][1] * rb[0]) + (A[1][1] * rb[1]) + (A[2][1] * rb[2]); |
261 |
r[2] = (A[0][2] * rb[0]) + (A[1][2] * rb[1]) + (A[2][2] * rb[2]); |
262 |
|
263 |
} |
264 |
|
265 |
double RigidBody::getZangle( ){ |
266 |
return zAngle; |
267 |
} |
268 |
|
269 |
void RigidBody::setZangle( double zAng ){ |
270 |
zAngle = zAng; |
271 |
} |
272 |
|
273 |
void RigidBody::addZangle( double zAng ){ |
274 |
zAngle += zAng; |
275 |
} |
276 |
|
277 |
void RigidBody::calcRefCoords( ) { |
278 |
|
279 |
int i,j,k, it, n_linear_coords; |
280 |
double mtmp; |
281 |
vec3 apos; |
282 |
double refCOM[3]; |
283 |
vec3 ptmp; |
284 |
double Itmp[3][3]; |
285 |
double evals[3]; |
286 |
double evects[3][3]; |
287 |
double r, r2, len; |
288 |
|
289 |
// First, find the center of mass: |
290 |
|
291 |
mass = 0.0; |
292 |
for (j=0; j<3; j++) |
293 |
refCOM[j] = 0.0; |
294 |
|
295 |
for (i = 0; i < myAtoms.size(); i++) { |
296 |
mtmp = myAtoms[i]->getMass(); |
297 |
mass += mtmp; |
298 |
|
299 |
apos = refCoords[i]; |
300 |
|
301 |
for(j = 0; j < 3; j++) { |
302 |
refCOM[j] += apos[j]*mtmp; |
303 |
} |
304 |
} |
305 |
|
306 |
for(j = 0; j < 3; j++) |
307 |
refCOM[j] /= mass; |
308 |
|
309 |
// Next, move the origin of the reference coordinate system to the COM: |
310 |
|
311 |
for (i = 0; i < myAtoms.size(); i++) { |
312 |
apos = refCoords[i]; |
313 |
for (j=0; j < 3; j++) { |
314 |
apos[j] = apos[j] - refCOM[j]; |
315 |
} |
316 |
refCoords[i] = apos; |
317 |
} |
318 |
|
319 |
// Moment of Inertia calculation |
320 |
|
321 |
for (i = 0; i < 3; i++) |
322 |
for (j = 0; j < 3; j++) |
323 |
Itmp[i][j] = 0.0; |
324 |
|
325 |
for (it = 0; it < myAtoms.size(); it++) { |
326 |
|
327 |
mtmp = myAtoms[it]->getMass(); |
328 |
ptmp = refCoords[it]; |
329 |
r= norm3(ptmp.vec); |
330 |
r2 = r*r; |
331 |
|
332 |
for (i = 0; i < 3; i++) { |
333 |
for (j = 0; j < 3; j++) { |
334 |
|
335 |
if (i==j) Itmp[i][j] += mtmp * r2; |
336 |
|
337 |
Itmp[i][j] -= mtmp * ptmp.vec[i]*ptmp.vec[j]; |
338 |
} |
339 |
} |
340 |
} |
341 |
|
342 |
diagonalize3x3(Itmp, evals, sU); |
343 |
|
344 |
// zero out I and then fill the diagonals with the moments of inertia: |
345 |
|
346 |
n_linear_coords = 0; |
347 |
|
348 |
for (i = 0; i < 3; i++) { |
349 |
for (j = 0; j < 3; j++) { |
350 |
I[i][j] = 0.0; |
351 |
} |
352 |
I[i][i] = evals[i]; |
353 |
|
354 |
if (fabs(evals[i]) < momIntTol) { |
355 |
is_linear = true; |
356 |
n_linear_coords++; |
357 |
linear_axis = i; |
358 |
} |
359 |
} |
360 |
|
361 |
if (n_linear_coords > 1) { |
362 |
sprintf( painCave.errMsg, |
363 |
"RigidBody error.\n" |
364 |
"\tOOPSE found more than one axis in this rigid body with a vanishing \n" |
365 |
"\tmoment of inertia. This can happen in one of three ways:\n" |
366 |
"\t 1) Only one atom was specified, or \n" |
367 |
"\t 2) All atoms were specified at the same location, or\n" |
368 |
"\t 3) The programmers did something stupid.\n" |
369 |
"\tIt is silly to use a rigid body to describe this situation. Be smarter.\n" |
370 |
); |
371 |
painCave.isFatal = 1; |
372 |
simError(); |
373 |
} |
374 |
|
375 |
// renormalize column vectors: |
376 |
|
377 |
for (i=0; i < 3; i++) { |
378 |
len = 0.0; |
379 |
for (j = 0; j < 3; j++) { |
380 |
len += sU[i][j]*sU[i][j]; |
381 |
} |
382 |
len = sqrt(len); |
383 |
for (j = 0; j < 3; j++) { |
384 |
sU[i][j] /= len; |
385 |
} |
386 |
} |
387 |
} |
388 |
|
389 |
void RigidBody::doEulerToRotMat(vec3 &euler, mat3x3 &myA ){ |
390 |
|
391 |
double phi, theta, psi; |
392 |
|
393 |
phi = euler[0]; |
394 |
theta = euler[1]; |
395 |
psi = euler[2]; |
396 |
|
397 |
myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
398 |
myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
399 |
myA[0][2] = sin(theta) * sin(psi); |
400 |
|
401 |
myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
402 |
myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
403 |
myA[1][2] = sin(theta) * cos(psi); |
404 |
|
405 |
myA[2][0] = sin(phi) * sin(theta); |
406 |
myA[2][1] = -cos(phi) * sin(theta); |
407 |
myA[2][2] = cos(theta); |
408 |
|
409 |
} |
410 |
|
411 |
void RigidBody::calcForcesAndTorques() { |
412 |
|
413 |
// Convert Atomic forces and torques to total forces and torques: |
414 |
int i, j; |
415 |
double apos[3]; |
416 |
double afrc[3]; |
417 |
double atrq[3]; |
418 |
double rpos[3]; |
419 |
|
420 |
zeroForces(); |
421 |
|
422 |
for (i = 0; i < myAtoms.size(); i++) { |
423 |
|
424 |
myAtoms[i]->getPos(apos); |
425 |
myAtoms[i]->getFrc(afrc); |
426 |
|
427 |
for (j=0; j<3; j++) { |
428 |
rpos[j] = apos[j] - pos[j]; |
429 |
frc[j] += afrc[j]; |
430 |
} |
431 |
|
432 |
trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1]; |
433 |
trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2]; |
434 |
trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0]; |
435 |
|
436 |
// If the atom has a torque associated with it, then we also need to |
437 |
// migrate the torques onto the center of mass: |
438 |
|
439 |
if (myAtoms[i]->isDirectional()) { |
440 |
|
441 |
myAtoms[i]->getTrq(atrq); |
442 |
|
443 |
for (j=0; j<3; j++) |
444 |
trq[j] += atrq[j]; |
445 |
} |
446 |
} |
447 |
|
448 |
// Convert Torque to Body-fixed coordinates: |
449 |
// (Actually, on second thought, don't. Integrator does this now.) |
450 |
// lab2Body(trq); |
451 |
|
452 |
} |
453 |
|
454 |
void RigidBody::updateAtoms() { |
455 |
int i, j; |
456 |
vec3 ref; |
457 |
double apos[3]; |
458 |
DirectionalAtom* dAtom; |
459 |
|
460 |
for (i = 0; i < myAtoms.size(); i++) { |
461 |
|
462 |
ref = refCoords[i]; |
463 |
|
464 |
body2Lab(ref.vec); |
465 |
|
466 |
for (j = 0; j<3; j++) |
467 |
apos[j] = pos[j] + ref.vec[j]; |
468 |
|
469 |
myAtoms[i]->setPos(apos); |
470 |
|
471 |
if (myAtoms[i]->isDirectional()) { |
472 |
|
473 |
dAtom = (DirectionalAtom *) myAtoms[i]; |
474 |
dAtom->rotateBy( A ); |
475 |
|
476 |
} |
477 |
} |
478 |
} |
479 |
|
480 |
void RigidBody::getGrad( double grad[6] ) { |
481 |
|
482 |
double myEuler[3]; |
483 |
double phi, theta, psi; |
484 |
double cphi, sphi, ctheta, stheta; |
485 |
double ephi[3]; |
486 |
double etheta[3]; |
487 |
double epsi[3]; |
488 |
|
489 |
this->getEulerAngles(myEuler); |
490 |
|
491 |
phi = myEuler[0]; |
492 |
theta = myEuler[1]; |
493 |
psi = myEuler[2]; |
494 |
|
495 |
cphi = cos(phi); |
496 |
sphi = sin(phi); |
497 |
ctheta = cos(theta); |
498 |
stheta = sin(theta); |
499 |
|
500 |
// get unit vectors along the phi, theta and psi rotation axes |
501 |
|
502 |
ephi[0] = 0.0; |
503 |
ephi[1] = 0.0; |
504 |
ephi[2] = 1.0; |
505 |
|
506 |
etheta[0] = cphi; |
507 |
etheta[1] = sphi; |
508 |
etheta[2] = 0.0; |
509 |
|
510 |
epsi[0] = stheta * cphi; |
511 |
epsi[1] = stheta * sphi; |
512 |
epsi[2] = ctheta; |
513 |
|
514 |
for (int j = 0 ; j<3; j++) |
515 |
grad[j] = frc[j]; |
516 |
|
517 |
grad[3] = 0.0; |
518 |
grad[4] = 0.0; |
519 |
grad[5] = 0.0; |
520 |
|
521 |
for (int j = 0; j < 3; j++ ) { |
522 |
|
523 |
grad[3] += trq[j]*ephi[j]; |
524 |
grad[4] += trq[j]*etheta[j]; |
525 |
grad[5] += trq[j]*epsi[j]; |
526 |
|
527 |
} |
528 |
|
529 |
} |
530 |
|
531 |
/** |
532 |
* getEulerAngles computes a set of Euler angle values consistent |
533 |
* with an input rotation matrix. They are returned in the following |
534 |
* order: |
535 |
* myEuler[0] = phi; |
536 |
* myEuler[1] = theta; |
537 |
* myEuler[2] = psi; |
538 |
*/ |
539 |
void RigidBody::getEulerAngles(double myEuler[3]) { |
540 |
|
541 |
// We use so-called "x-convention", which is the most common |
542 |
// definition. In this convention, the rotation given by Euler |
543 |
// angles (phi, theta, psi), where the first rotation is by an angle |
544 |
// phi about the z-axis, the second is by an angle theta (0 <= theta |
545 |
// <= 180) about the x-axis, and the third is by an angle psi about |
546 |
// the z-axis (again). |
547 |
|
548 |
|
549 |
double phi,theta,psi,eps; |
550 |
double pi; |
551 |
double cphi,ctheta,cpsi; |
552 |
double sphi,stheta,spsi; |
553 |
double b[3]; |
554 |
int flip[3]; |
555 |
|
556 |
// set the tolerance for Euler angles and rotation elements |
557 |
|
558 |
eps = 1.0e-8; |
559 |
|
560 |
theta = acos(min(1.0,max(-1.0,A[2][2]))); |
561 |
ctheta = A[2][2]; |
562 |
stheta = sqrt(1.0 - ctheta * ctheta); |
563 |
|
564 |
// when sin(theta) is close to 0, we need to consider the |
565 |
// possibility of a singularity. In this case, we can assign an |
566 |
// arbitary value to phi (or psi), and then determine the psi (or |
567 |
// phi) or vice-versa. We'll assume that phi always gets the |
568 |
// rotation, and psi is 0 in cases of singularity. we use atan2 |
569 |
// instead of atan, since atan2 will give us -Pi to Pi. Since 0 <= |
570 |
// theta <= 180, sin(theta) will be always non-negative. Therefore, |
571 |
// it never changes the sign of both of the parameters passed to |
572 |
// atan2. |
573 |
|
574 |
if (fabs(stheta) <= eps){ |
575 |
psi = 0.0; |
576 |
phi = atan2(-A[1][0], A[0][0]); |
577 |
} |
578 |
// we only have one unique solution |
579 |
else{ |
580 |
phi = atan2(A[2][0], -A[2][1]); |
581 |
psi = atan2(A[0][2], A[1][2]); |
582 |
} |
583 |
|
584 |
//wrap phi and psi, make sure they are in the range from 0 to 2*Pi |
585 |
//if (phi < 0) |
586 |
// phi += M_PI; |
587 |
|
588 |
//if (psi < 0) |
589 |
// psi += M_PI; |
590 |
|
591 |
myEuler[0] = phi; |
592 |
myEuler[1] = theta; |
593 |
myEuler[2] = psi; |
594 |
|
595 |
return; |
596 |
} |
597 |
|
598 |
double RigidBody::max(double x, double y) { |
599 |
return (x > y) ? x : y; |
600 |
} |
601 |
|
602 |
double RigidBody::min(double x, double y) { |
603 |
return (x > y) ? y : x; |
604 |
} |
605 |
|
606 |
void RigidBody::findCOM() { |
607 |
|
608 |
size_t i; |
609 |
int j; |
610 |
double mtmp; |
611 |
double ptmp[3]; |
612 |
double vtmp[3]; |
613 |
|
614 |
for(j = 0; j < 3; j++) { |
615 |
pos[j] = 0.0; |
616 |
vel[j] = 0.0; |
617 |
} |
618 |
mass = 0.0; |
619 |
|
620 |
for (i = 0; i < myAtoms.size(); i++) { |
621 |
|
622 |
mtmp = myAtoms[i]->getMass(); |
623 |
myAtoms[i]->getPos(ptmp); |
624 |
myAtoms[i]->getVel(vtmp); |
625 |
|
626 |
mass += mtmp; |
627 |
|
628 |
for(j = 0; j < 3; j++) { |
629 |
pos[j] += ptmp[j]*mtmp; |
630 |
vel[j] += vtmp[j]*mtmp; |
631 |
} |
632 |
|
633 |
} |
634 |
|
635 |
for(j = 0; j < 3; j++) { |
636 |
pos[j] /= mass; |
637 |
vel[j] /= mass; |
638 |
} |
639 |
|
640 |
} |
641 |
|
642 |
void RigidBody::accept(BaseVisitor* v){ |
643 |
vector<Atom*>::iterator atomIter; |
644 |
v->visit(this); |
645 |
|
646 |
//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter) |
647 |
// (*atomIter)->accept(v); |
648 |
} |
649 |
void RigidBody::getAtomRefCoor(double pos[3], int index){ |
650 |
vec3 ref; |
651 |
|
652 |
ref = refCoords[index]; |
653 |
pos[0] = ref[0]; |
654 |
pos[1] = ref[1]; |
655 |
pos[2] = ref[2]; |
656 |
|
657 |
} |
658 |
|
659 |
|
660 |
void RigidBody::getAtomPos(double theP[3], int index){ |
661 |
vec3 ref; |
662 |
|
663 |
if (index >= myAtoms.size()) |
664 |
cerr << index << " is an invalid index, current rigid body contains " << myAtoms.size() << "atoms" << endl; |
665 |
|
666 |
ref = refCoords[index]; |
667 |
body2Lab(ref.vec); |
668 |
|
669 |
theP[0] = pos[0] + ref[0]; |
670 |
theP[1] = pos[1] + ref[1]; |
671 |
theP[2] = pos[2] + ref[2]; |
672 |
} |
673 |
|
674 |
|
675 |
void RigidBody::getAtomVel(double theV[3], int index){ |
676 |
vec3 ref; |
677 |
double velRot[3]; |
678 |
double skewMat[3][3]; |
679 |
double aSkewMat[3][3]; |
680 |
double aSkewTransMat[3][3]; |
681 |
|
682 |
//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$ |
683 |
|
684 |
if (index >= myAtoms.size()) |
685 |
cerr << index << " is an invalid index, current rigid body contains " << myAtoms.size() << "atoms" << endl; |
686 |
|
687 |
ref = refCoords[index]; |
688 |
|
689 |
skewMat[0][0] =0; |
690 |
skewMat[0][1] = ji[2] /I[2][2]; |
691 |
skewMat[0][2] = -ji[1] /I[1][1]; |
692 |
|
693 |
skewMat[1][0] = -ji[2] /I[2][2]; |
694 |
skewMat[1][1] = 0; |
695 |
skewMat[1][2] = ji[0]/I[0][0]; |
696 |
|
697 |
skewMat[2][0] =ji[1] /I[1][1]; |
698 |
skewMat[2][1] = -ji[0]/I[0][0]; |
699 |
skewMat[2][2] = 0; |
700 |
|
701 |
matMul3(A, skewMat, aSkewMat); |
702 |
|
703 |
transposeMat3(aSkewMat, aSkewTransMat); |
704 |
|
705 |
matVecMul3(aSkewTransMat, ref.vec, velRot); |
706 |
theV[0] = vel[0] + velRot[0]; |
707 |
theV[1] = vel[1] + velRot[1]; |
708 |
theV[2] = vel[2] + velRot[2]; |
709 |
} |
710 |
|
711 |
|