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root/OpenMD/branches/development/src/primitives/RigidBody.cpp

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trunk/src/primitives/RigidBody.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/primitives/RigidBody.cpp (file contents), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

#	Line 1 | Line 1
1	+	/*
2	+	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	+	*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
12	+	* 2. Redistributions in binary form must reproduce the above copyright
13	+	*    notice, this list of conditions and the following disclaimer in the
14	+	*    documentation and/or other materials provided with the
15	+	*    distribution.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
28	+	* arising out of the use of or inability to use software, even if the
29	+	* University of Notre Dame has been advised of the possibility of
30	+	* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	+	*/
42	+	#include <algorithm>
43		#include <math.h>
44		#include "primitives/RigidBody.hpp"
3	–	#include "primitives/DirectionalAtom.hpp"
45		#include "utils/simError.h"
46	<	#include "math/MatVec3.h"
47	<
48	<	RigidBody::RigidBody() : StuntDouble() {
49	<	objType = OT_RIGIDBODY;
50	<	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();
46	>	#include "utils/NumericConstant.hpp"
47	>	namespace OpenMD {
48	>
49	>	RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData),
50	>	inertiaTensor_(0.0){
51		}
52
53	<	coords[0] = ats->getPosX();
54	<	coords[1] = ats->getPosY();
55	<	coords[2] = ats->getPosZ();
56	<
57	<	refCoords.push_back(coords);
53	>	void RigidBody::setPrevA(const RotMat3x3d& a) {
54	>	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
55	>
56	>	for (unsigned int i = 0 ; i < atoms_.size(); ++i){
57	>	if (atoms_[i]->isDirectional()) {
58	>	atoms_[i]->setPrevA(refOrients_[i].transpose() * a);
59	>	}
60	>	}
61	>
62	>	}
63
64	<	if (at->isDirectional()) {
64	>
65	>	void RigidBody::setA(const RotMat3x3d& a) {
66	>	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
67
68	<	if( !ats->haveOrientation() ){
69	<	sprintf( painCave.errMsg,
70	<	"RigidBody error.\n"
71	<	"\tAtom %s does not have an orientation specified.\n"
72	<	"\tThis means RigidBody cannot set up reference orientations.\n",
73	<	ats->getType() );
74	<	painCave.isFatal = 1;
75	<	simError();
76	<	}
68	>	for (unsigned int i = 0 ; i < atoms_.size(); ++i){
69	>	if (atoms_[i]->isDirectional()) {
70	>	atoms_[i]->setA(refOrients_[i].transpose() * a);
71	>	}
72	>	}
73	>	}
74	>
75	>	void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
76	>	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
77	>
78	>	for (unsigned int i = 0 ; i < atoms_.size(); ++i){
79	>	if (atoms_[i]->isDirectional()) {
80	>	atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
81	>	}
82	>	}
83
84	<	euler[0] = ats->getEulerPhi();
85	<	euler[1] = ats->getEulerTheta();
86	<	euler[2] = ats->getEulerPsi();
84	>	}
85	>
86	>	Mat3x3d RigidBody::getI() {
87	>	return inertiaTensor_;
88	>	}
89	>
90	>	std::vector<RealType> RigidBody::getGrad() {
91	>	std::vector<RealType> grad(6, 0.0);
92	>	Vector3d force;
93	>	Vector3d torque;
94	>	Vector3d myEuler;
95	>	RealType phi, theta, psi;
96	>	RealType cphi, sphi, ctheta, stheta;
97	>	Vector3d ephi;
98	>	Vector3d etheta;
99	>	Vector3d epsi;
100
101	<	doEulerToRotMat(euler, Atmp);
101	>	force = getFrc();
102	>	torque =getTrq();
103	>	myEuler = getA().toEulerAngles();
104
105	<	refOrients.push_back(Atmp);
105	>	phi = myEuler[0];
106	>	theta = myEuler[1];
107	>	psi = myEuler[2];
108
109	<	}
110	<	}
111	<
112	<	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);
109	>	cphi = cos(phi);
110	>	sphi = sin(phi);
111	>	ctheta = cos(theta);
112	>	stheta = sin(theta);
113
114	<	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);
114	>	// get unit vectors along the phi, theta and psi rotation axes
115
116	<	A[2][0] = sin(phi) * sin(theta);
117	<	A[2][1] = -cos(phi) * sin(theta);
118	<	A[2][2] = cos(theta);
116	<
117	<	}
118	<
119	<	void RigidBody::getQ( double q[4] ){
120	<
121	<	double t, s;
122	<	double ad1, ad2, ad3;
116	>	ephi[0] = 0.0;
117	>	ephi[1] = 0.0;
118	>	ephi[2] = 1.0;
119
120	<	t = A[0][0] + A[1][1] + A[2][2] + 1.0;
121	<	if( t > 0.0 ){
120	>	//etheta[0] = -sphi;
121	>	//etheta[1] =  cphi;
122	>	//etheta[2] =  0.0;
123
124	<	s = 0.5 / sqrt( t );
125	<	q[0] = 0.25 / s;
126	<	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{
124	>	etheta[0] = cphi;
125	>	etheta[1] = sphi;
126	>	etheta[2] =  0.0;
127
128	<	ad1 = fabs( A[0][0] );
129	<	ad2 = fabs( A[1][1] );
130	<	ad3 = fabs( A[2][2] );
128	>	epsi[0] = stheta * cphi;
129	>	epsi[1] = stheta * sphi;
130	>	epsi[2] = ctheta;
131
132	<	if( ad1 >= ad2 && ad1 >= ad3 ){
132	>	//gradient is equal to -force
133	>	for (int j = 0 ; j<3; j++)
134	>	grad[j] = -force[j];
135	>
136	>	for (int j = 0; j < 3; j++ ) {
137
138	<	s = 2.0 * sqrt( 1.0 + A[0][0] - A[1][1] - A[2][2] );
139	<	q[0] = (A[1][2] + A[2][1]) / s;
140	<	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 ){
138	>	grad[3] += torque[j]*ephi[j];
139	>	grad[4] += torque[j]*etheta[j];
140	>	grad[5] += torque[j]*epsi[j];
141
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;
142		}
143	<	else{
143	>
144	>	return grad;
145	>	}
146	>
147	>	void RigidBody::accept(BaseVisitor* v) {
148	>	v->visit(this);
149	>	}
150	>
151	>	/**@todo need modification */
152	>	void  RigidBody::calcRefCoords() {
153	>	RealType mtmp;
154	>	Vector3d refCOM(0.0);
155	>	mass_ = 0.0;
156	>	for (std::size_t i = 0; i < atoms_.size(); ++i) {
157	>	mtmp = atoms_[i]->getMass();
158	>	mass_ += mtmp;
159	>	refCOM += refCoords_[i]*mtmp;
160	>	}
161	>	refCOM /= mass_;
162	>
163	>	// Next, move the origin of the reference coordinate system to the COM:
164	>	for (std::size_t i = 0; i < atoms_.size(); ++i) {
165	>	refCoords_[i] -= refCOM;
166	>	}
167	>
168	>	// Moment of Inertia calculation
169	>	Mat3x3d Itmp(0.0);
170	>	for (std::size_t i = 0; i < atoms_.size(); i++) {
171	>	Mat3x3d IAtom(0.0);
172	>	mtmp = atoms_[i]->getMass();
173	>	IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
174	>	RealType r2 = refCoords_[i].lengthSquare();
175	>	IAtom(0, 0) += mtmp * r2;
176	>	IAtom(1, 1) += mtmp * r2;
177	>	IAtom(2, 2) += mtmp * r2;
178	>	Itmp += IAtom;
179
180	<	s = sqrt( 1.0 + A[2][2] - A[0][0] - A[1][1] ) * 2.0;
181	<	q[0] = (A[0][1] + A[1][0]) / s;
182	<	q[1] = (A[0][2] + A[2][0]) / s;
183	<	q[2] = (A[1][2] + A[2][1]) / s;
161	<	q[3] = 0.5 / s;
180	>	//project the inertial moment of directional atoms into this rigid body
181	>	if (atoms_[i]->isDirectional()) {
182	>	Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
183	>	}
184		}
163	–	}
164	–	}
185
186	<	void RigidBody::setQ( double the_q[4] ){
186	>	//    std::cout << Itmp << std::endl;
187
188	<	double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
189	<
190	<	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;
188	>	//diagonalize
189	>	Vector3d evals;
190	>	Mat3x3d::diagonalize(Itmp, evals, sU_);
191
192	<	}
192	>	// zero out I and then fill the diagonals with the moments of inertia:
193	>	inertiaTensor_(0, 0) = evals[0];
194	>	inertiaTensor_(1, 1) = evals[1];
195	>	inertiaTensor_(2, 2) = evals[2];
196	>
197	>	int nLinearAxis = 0;
198	>	for (int i = 0; i < 3; i++) {
199	>	if (fabs(evals[i]) < OpenMD::epsilon) {
200	>	linear_ = true;
201	>	linearAxis_ = i;
202	>	++ nLinearAxis;
203	>	}
204	>	}
205
206	<	void RigidBody::getA( double the_A[3][3] ){
206	>	if (nLinearAxis > 1) {
207	>	sprintf( painCave.errMsg,
208	>	"RigidBody error.\n"
209	>	"\tOpenMD found more than one axis in this rigid body with a vanishing \n"
210	>	"\tmoment of inertia.  This can happen in one of three ways:\n"
211	>	"\t 1) Only one atom was specified, or \n"
212	>	"\t 2) All atoms were specified at the same location, or\n"
213	>	"\t 3) The programmers did something stupid.\n"
214	>	"\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
215	>	);
216	>	painCave.isFatal = 1;
217	>	simError();
218	>	}
219
220	<	for (int i = 0; i < 3; i++)
192	<	for (int j = 0; j < 3; j++)
193	<	the_A[i][j] = A[i][j];
220	>	}
221
222	<	}
222	>	void  RigidBody::calcForcesAndTorques() {
223	>	Vector3d afrc;
224	>	Vector3d atrq;
225	>	Vector3d apos;
226	>	Vector3d rpos;
227	>	Vector3d frc(0.0);
228	>	Vector3d trq(0.0);
229	>	Vector3d pos = this->getPos();
230	>	for (unsigned int i = 0; i < atoms_.size(); i++) {
231
232	<	void RigidBody::setA( double the_A[3][3] ){
232	>	afrc = atoms_[i]->getFrc();
233	>	apos = atoms_[i]->getPos();
234	>	rpos = apos - pos;
235	>
236	>	frc += afrc;
237
238	<	for (int i = 0; i < 3; i++)
239	<	for (int j = 0; j < 3; j++)
240	<	A[i][j] = the_A[i][j];
202	<
203	<	}
238	>	trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
239	>	trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
240	>	trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];
241
242	<	void RigidBody::getJ( double theJ[3] ){
243	<
207	<	for (int i = 0; i < 3; i++)
208	<	theJ[i] = ji[i];
242	>	// If the atom has a torque associated with it, then we also need to
243	>	// migrate the torques onto the center of mass:
244
245	<	}
245	>	if (atoms_[i]->isDirectional()) {
246	>	atrq = atoms_[i]->getTrq();
247	>	trq += atrq;
248	>	}
249	>	}
250	>	addFrc(frc);
251	>	addTrq(trq);
252	>	}
253
254	<	void RigidBody::setJ( double theJ[3] ){
255	<
256	<	for (int i = 0; i < 3; i++)
257	<	ji[i] = theJ[i];
254	>	Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() {
255	>	Vector3d afrc;
256	>	Vector3d atrq;
257	>	Vector3d apos;
258	>	Vector3d rpos;
259	>	Vector3d dfrc;
260	>	Vector3d frc(0.0);
261	>	Vector3d trq(0.0);
262	>	Vector3d pos = this->getPos();
263	>	Mat3x3d tau_(0.0);
264
265	<	}
265	>	for (unsigned int i = 0; i < atoms_.size(); i++) {
266	>
267	>	afrc = atoms_[i]->getFrc();
268	>	apos = atoms_[i]->getPos();
269	>	rpos = apos - pos;
270	>
271	>	frc += afrc;
272
273	<	void RigidBody::getTrq(double theT[3]){
274	<	for (int i = 0; i < 3 ; i++)
275	<	theT[i] = trq[i];
222	<	}
273	>	trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
274	>	trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
275	>	trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];
276
277	<	void RigidBody::addTrq(double theT[3]){
278	<	for (int i = 0; i < 3 ; i++)
226	<	trq[i] += theT[i];
227	<	}
277	>	// If the atom has a torque associated with it, then we also need to
278	>	// migrate the torques onto the center of mass:
279
280	<	void RigidBody::getI( double the_I[3][3] ){
280	>	if (atoms_[i]->isDirectional()) {
281	>	atrq = atoms_[i]->getTrq();
282	>	trq += atrq;
283	>	}
284	>
285	>	tau_(0,0) -= rpos[0]*afrc[0];
286	>	tau_(0,1) -= rpos[0]*afrc[1];
287	>	tau_(0,2) -= rpos[0]*afrc[2];
288	>	tau_(1,0) -= rpos[1]*afrc[0];
289	>	tau_(1,1) -= rpos[1]*afrc[1];
290	>	tau_(1,2) -= rpos[1]*afrc[2];
291	>	tau_(2,0) -= rpos[2]*afrc[0];
292	>	tau_(2,1) -= rpos[2]*afrc[1];
293	>	tau_(2,2) -= rpos[2]*afrc[2];
294
295	<	for (int i = 0; i < 3; i++)
296	<	for (int j = 0; j < 3; j++)
297	<	the_I[i][j] = I[i][j];
295	>	}
296	>	addFrc(frc);
297	>	addTrq(trq);
298	>	return tau_;
299	>	}
300
301	<	}
301	>	void  RigidBody::updateAtoms() {
302	>	unsigned int i;
303	>	Vector3d ref;
304	>	Vector3d apos;
305	>	DirectionalAtom* dAtom;
306	>	Vector3d pos = getPos();
307	>	RotMat3x3d a = getA();
308	>
309	>	for (i = 0; i < atoms_.size(); i++) {
310	>
311	>	ref = body2Lab(refCoords_[i]);
312
313	<	void RigidBody::lab2Body( double r[3] ){
313	>	apos = pos + ref;
314
315	<	double rl[3]; // the lab frame vector
315	>	atoms_[i]->setPos(apos);
316	>
317	>	if (atoms_[i]->isDirectional()) {
318	>
319	>	dAtom = (DirectionalAtom *) atoms_[i];
320	>	dAtom->setA(refOrients_[i].transpose() * a);
321	>	}
322	>
323	>	}
324
325	<	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]);
325	>	}
326
249	–	}
327
328	<	void RigidBody::body2Lab( double r[3] ){
328	>	void  RigidBody::updateAtoms(int frame) {
329	>	unsigned int i;
330	>	Vector3d ref;
331	>	Vector3d apos;
332	>	DirectionalAtom* dAtom;
333	>	Vector3d pos = getPos(frame);
334	>	RotMat3x3d a = getA(frame);
335	>
336	>	for (i = 0; i < atoms_.size(); i++) {
337	>
338	>	ref = body2Lab(refCoords_[i], frame);
339
340	<	double rb[3]; // the body frame vector
340	>	apos = pos + ref;
341	>
342	>	atoms_[i]->setPos(apos, frame);
343	>
344	>	if (atoms_[i]->isDirectional()) {
345	>
346	>	dAtom = (DirectionalAtom *) atoms_[i];
347	>	dAtom->setA(refOrients_[i].transpose() * a, frame);
348	>	}
349	>
350	>	}
351
352	<	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]);
352	>	}
353
354	<	}
354	>	void RigidBody::updateAtomVel() {
355	>	Mat3x3d skewMat;;
356
357	<	double RigidBody::getZangle( ){
358	<	return zAngle;
267	<	}
357	>	Vector3d ji = getJ();
358	>	Mat3x3d I =  getI();
359
360	<	void RigidBody::setZangle( double zAng ){
361	<	zAngle = zAng;
362	<	}
360	>	skewMat(0, 0) =0;
361	>	skewMat(0, 1) = ji[2] /I(2, 2);
362	>	skewMat(0, 2) = -ji[1] /I(1, 1);
363
364	<	void RigidBody::addZangle( double zAng ){
365	<	zAngle += zAng;
366	<	}
364	>	skewMat(1, 0) = -ji[2] /I(2, 2);
365	>	skewMat(1, 1) = 0;
366	>	skewMat(1, 2) = ji[0]/I(0, 0);
367
368	<	void RigidBody::calcRefCoords( ) {
368	>	skewMat(2, 0) =ji[1] /I(1, 1);
369	>	skewMat(2, 1) = -ji[0]/I(0, 0);
370	>	skewMat(2, 2) = 0;
371
372	<	int i,j,k, it, n_linear_coords;
373	<	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;
372	>	Mat3x3d mat = (getA() * skewMat).transpose();
373	>	Vector3d rbVel = getVel();
374
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;
375
376	<	apos = refCoords[i];
377	<
378	<	for(j = 0; j < 3; j++) {
379	<	refCOM[j] += apos[j]*mtmp;
380	<	}
376	>	Vector3d velRot;
377	>	for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
378	>	atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
379	>	}
380	>
381		}
305	–
306	–	for(j = 0; j < 3; j++)
307	–	refCOM[j] /= mass;
382
383	<	// Next, move the origin of the reference coordinate system to the COM:
383	>	void RigidBody::updateAtomVel(int frame) {
384	>	Mat3x3d skewMat;;
385
386	<	for (i = 0; i < myAtoms.size(); i++) {
387	<	apos = refCoords[i];
313	<	for (j=0; j < 3; j++) {
314	<	apos[j] = apos[j] - refCOM[j];
315	<	}
316	<	refCoords[i] = apos;
317	<	}
386	>	Vector3d ji = getJ(frame);
387	>	Mat3x3d I =  getI();
388
389	<	// Moment of Inertia calculation
389	>	skewMat(0, 0) =0;
390	>	skewMat(0, 1) = ji[2] /I(2, 2);
391	>	skewMat(0, 2) = -ji[1] /I(1, 1);
392
393	<	for (i = 0; i < 3; i++)
394	<	for (j = 0; j < 3; j++)
395	<	Itmp[i][j] = 0.0;
324	<
325	<	for (it = 0; it < myAtoms.size(); it++) {
393	>	skewMat(1, 0) = -ji[2] /I(2, 2);
394	>	skewMat(1, 1) = 0;
395	>	skewMat(1, 2) = ji[0]/I(0, 0);
396
397	<	mtmp = myAtoms[it]->getMass();
398	<	ptmp = refCoords[it];
399	<	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;
397	>	skewMat(2, 0) =ji[1] /I(1, 1);
398	>	skewMat(2, 1) = -ji[0]/I(0, 0);
399	>	skewMat(2, 2) = 0;
400
401	<	Itmp[i][j] -= mtmp * ptmp.vec[i]*ptmp.vec[j];
402	<	}
339	<	}
340	<	}
341	<
342	<	diagonalize3x3(Itmp, evals, sU);
343	<
344	<	// zero out I and then fill the diagonals with the moments of inertia:
401	>	Mat3x3d mat = (getA(frame) * skewMat).transpose();
402	>	Vector3d rbVel = getVel(frame);
403
346	–	n_linear_coords = 0;
404
405	<	for (i = 0; i < 3; i++) {
406	<	for (j = 0; j < 3; j++) {
407	<	I[i][j] = 0.0;
405	>	Vector3d velRot;
406	>	for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
407	>	atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
408		}
352	–	I[i][i] = evals[i];
409
354	–	if (fabs(evals[i]) < momIntTol) {
355	–	is_linear = true;
356	–	n_linear_coords++;
357	–	linear_axis = i;
358	–	}
410		}
411
412	<	if (n_linear_coords > 1) {
413	<	sprintf( painCave.errMsg,
414	<	"RigidBody error.\n"
415	<	"\tOOPSE found more than one axis in this rigid body with a vanishing \n"
416	<	"\tmoment of inertia.  This can happen in one of three ways:\n"
417	<	"\t 1) Only one atom was specified, or \n"
418	<	"\t 2) All atoms were specified at the same location, or\n"
419	<	"\t 3) The programmers did something stupid.\n"
420	<	"\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
421	<	);
422	<	painCave.isFatal = 1;
423	<	simError();
412	>
413	>
414	>	bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
415	>	if (index < atoms_.size()) {
416	>
417	>	Vector3d ref = body2Lab(refCoords_[index]);
418	>	pos = getPos() + ref;
419	>	return true;
420	>	} else {
421	>	std::cerr << index << " is an invalid index, current rigid body contains "
422	>	<< atoms_.size() << "atoms" << std::endl;
423	>	return false;
424	>	}
425		}
426	<
427	<	// renormalize column vectors:
428	<
429	<	for (i=0; i < 3; i++) {
430	<	len = 0.0;
431	<	for (j = 0; j < 3; j++) {
432	<	len += sU[i][j]*sU[i][j];
426	>
427	>	bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
428	>	std::vector<Atom*>::iterator i;
429	>	i = std::find(atoms_.begin(), atoms_.end(), atom);
430	>	if (i != atoms_.end()) {
431	>	//RigidBody class makes sure refCoords_ and atoms_ match each other
432	>	Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
433	>	pos = getPos() + ref;
434	>	return true;
435	>	} else {
436	>	std::cerr << "Atom " << atom->getGlobalIndex()
437	>	<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
438	>	return false;
439		}
382	–	len = sqrt(len);
383	–	for (j = 0; j < 3; j++) {
384	–	sU[i][j] /= len;
385	–	}
440		}
441	<	}
441	>	bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
442
443	<	void RigidBody::doEulerToRotMat(vec3 &euler, mat3x3 &myA ){
443	>	//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
444
445	<	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);
445	>	if (index < atoms_.size()) {
446
447	<	}
447	>	Vector3d velRot;
448	>	Mat3x3d skewMat;;
449	>	Vector3d ref = refCoords_[index];
450	>	Vector3d ji = getJ();
451	>	Mat3x3d I =  getI();
452
453	<	void RigidBody::calcForcesAndTorques() {
453	>	skewMat(0, 0) =0;
454	>	skewMat(0, 1) = ji[2] /I(2, 2);
455	>	skewMat(0, 2) = -ji[1] /I(1, 1);
456
457	<	// Convert Atomic forces and torques to total forces and torques:
458	<	int i, j;
459	<	double apos[3];
416	<	double afrc[3];
417	<	double atrq[3];
418	<	double rpos[3];
457	>	skewMat(1, 0) = -ji[2] /I(2, 2);
458	>	skewMat(1, 1) = 0;
459	>	skewMat(1, 2) = ji[0]/I(0, 0);
460
461	<	zeroForces();
462	<
463	<	for (i = 0; i < myAtoms.size(); i++) {
461	>	skewMat(2, 0) =ji[1] /I(1, 1);
462	>	skewMat(2, 1) = -ji[0]/I(0, 0);
463	>	skewMat(2, 2) = 0;
464
465	<	myAtoms[i]->getPos(apos);
425	<	myAtoms[i]->getFrc(afrc);
465	>	velRot = (getA() * skewMat).transpose() * ref;
466
467	<	for (j=0; j<3; j++) {
468	<	rpos[j] = apos[j] - pos[j];
469	<	frc[j] += afrc[j];
467	>	vel =getVel() + velRot;
468	>	return true;
469	>
470	>	} else {
471	>	std::cerr << index << " is an invalid index, current rigid body contains "
472	>	<< atoms_.size() << "atoms" << std::endl;
473	>	return false;
474		}
475	<
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];
475	>	}
476
477	<	// If the atom has a torque associated with it, then we also need to
437	<	// migrate the torques onto the center of mass:
477	>	bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
478
479	<	if (myAtoms[i]->isDirectional()) {
479	>	std::vector<Atom*>::iterator i;
480	>	i = std::find(atoms_.begin(), atoms_.end(), atom);
481	>	if (i != atoms_.end()) {
482	>	return getAtomVel(vel, i - atoms_.begin());
483	>	} else {
484	>	std::cerr << "Atom " << atom->getGlobalIndex()
485	>	<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
486	>	return false;
487	>	}
488	>	}
489
490	<	myAtoms[i]->getTrq(atrq);
491	<
492	<	for (j=0; j<3; j++)
493	<	trq[j] += atrq[j];
490	>	bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
491	>	if (index < atoms_.size()) {
492	>
493	>	coor = refCoords_[index];
494	>	return true;
495	>	} else {
496	>	std::cerr << index << " is an invalid index, current rigid body contains "
497	>	<< atoms_.size() << "atoms" << std::endl;
498	>	return false;
499		}
500	+
501		}
502
503	<	// Convert Torque to Body-fixed coordinates:
504	<	// (Actually, on second thought, don't.  Integrator does this now.)
505	<	// lab2Body(trq);
503	>	bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
504	>	std::vector<Atom*>::iterator i;
505	>	i = std::find(atoms_.begin(), atoms_.end(), atom);
506	>	if (i != atoms_.end()) {
507	>	//RigidBody class makes sure refCoords_ and atoms_ match each other
508	>	coor = refCoords_[i - atoms_.begin()];
509	>	return true;
510	>	} else {
511	>	std::cerr << "Atom " << atom->getGlobalIndex()
512	>	<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
513	>	return false;
514	>	}
515
516	<	}
516	>	}
517
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];
518
519	<	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	<	}
519	>	void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
520
521	<	void RigidBody::getGrad( double grad[6] ) {
521	>	Vector3d coords;
522	>	Vector3d euler;
523	>
524
525	<	double myEuler[3];
526	<	double phi, theta, psi;
527	<	double cphi, sphi, ctheta, stheta;
528	<	double ephi[3];
529	<	double etheta[3];
530	<	double epsi[3];
525	>	atoms_.push_back(at);
526	>
527	>	if( !ats->havePosition() ){
528	>	sprintf( painCave.errMsg,
529	>	"RigidBody error.\n"
530	>	"\tAtom %s does not have a position specified.\n"
531	>	"\tThis means RigidBody cannot set up reference coordinates.\n",
532	>	ats->getType().c_str() );
533	>	painCave.isFatal = 1;
534	>	simError();
535	>	}
536
537	<	this->getEulerAngles(myEuler);
537	>	coords[0] = ats->getPosX();
538	>	coords[1] = ats->getPosY();
539	>	coords[2] = ats->getPosZ();
540
541	<	phi = myEuler[0];
492	<	theta = myEuler[1];
493	<	psi = myEuler[2];
541	>	refCoords_.push_back(coords);
542
543	<	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;
543	>	RotMat3x3d identMat = RotMat3x3d::identity();
544
545	<	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];
545	>	if (at->isDirectional()) {
546
547	<	grad[3] = 0.0;
548	<	grad[4] = 0.0;
549	<	grad[5] = 0.0;
550	<
551	<	for (int j = 0; j < 3; j++ ) {
547	>	if( !ats->haveOrientation() ){
548	>	sprintf( painCave.errMsg,
549	>	"RigidBody error.\n"
550	>	"\tAtom %s does not have an orientation specified.\n"
551	>	"\tThis means RigidBody cannot set up reference orientations.\n",
552	>	ats->getType().c_str() );
553	>	painCave.isFatal = 1;
554	>	simError();
555	>	}
556
557	<	grad[3] += trq[j]*ephi[j];
558	<	grad[4] += trq[j]*etheta[j];
559	<	grad[5] += trq[j]*epsi[j];
526	<
527	<	}
528	<
529	<	}
557	>	euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
558	>	euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
559	>	euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;
560
561	<	/**
562	<	* 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++) {
561	>	RotMat3x3d Atmp(euler);
562	>	refOrients_.push_back(Atmp);
563
564	<	mtmp = myAtoms[i]->getMass();
565	<	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;
564	>	}else {
565	>	refOrients_.push_back(identMat);
566		}
632	–
633	–	}
567
568	<	for(j = 0; j < 3; j++) {
636	<	pos[j] /= mass;
637	<	vel[j] /= mass;
568	>
569		}
570
571		}
572
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	–

Comparing:
trunk/src/primitives/RigidBody.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/primitives/RigidBody.cpp (property svn:keywords), Revision 1794 by gezelter, Thu Sep 6 19:44:06 2012 UTC

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