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root/OpenMD/trunk/src/primitives/RigidBody.cpp

Comparing trunk/src/primitives/RigidBody.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1797 by gezelter, Mon Sep 10 20:58:00 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 "RigidBody.hpp"
45	<	#include "DirectionalAtom.hpp"
46	<	#include "simError.h"
47	<	#include "MatVec3.h"
48	<
49	<	RigidBody::RigidBody() : StuntDouble() {
50	<	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();
44	>	#include "primitives/RigidBody.hpp"
45	>	#include "utils/simError.h"
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();
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	<	}
53	>	void RigidBody::setPrevA(const RotMat3x3d& a) {
54	>	((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
55
56	<	euler[0] = ats->getEulerPhi();
57	<	euler[1] = ats->getEulerTheta();
58	<	euler[2] = ats->getEulerPsi();
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
57	–	doEulerToRotMat(euler, Atmp);
58	–
59	–	refOrients.push_back(Atmp);
60	–
62		}
63	<	}
63	>
64	>
65	>	void RigidBody::setA(const RotMat3x3d& a) {
66	>	((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
67
68	<	void RigidBody::getPos(double theP[3]){
69	<	for (int i = 0; i < 3 ; i++)
70	<	theP[i] = pos[i];
71	<	}
72	<
73	<	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 ){
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	<	A[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
76	<	A[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
107	<	A[0][2] = sin(theta) * sin(psi);
75	>	void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
76	>	((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
77
78	<	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);
78	>	//((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;
79
80	<	A[2][0] = sin(phi) * sin(theta);
81	<	A[2][1] = -cos(phi) * sin(theta);
82	<	A[2][2] = cos(theta);
83	<
84	<	}
85	<
86	<	void RigidBody::getQ( double q[4] ){
80	>	for (unsigned int i = 0 ; i < atoms_.size(); ++i){
81	>	if (atoms_[i]->isDirectional()) {
82	>	atoms_[i]->setA(refOrients_[i].transpose() * a, snapshotNo);
83	>	}
84	>	}
85	>
86	>	}
87
88	<	double t, s;
89	<	double ad1, ad2, ad3;
88	>	Mat3x3d RigidBody::getI() {
89	>	return inertiaTensor_;
90	>	}
91	>
92	>	std::vector<RealType> RigidBody::getGrad() {
93	>	std::vector<RealType> grad(6, 0.0);
94	>	Vector3d force;
95	>	Vector3d torque;
96	>	Vector3d myEuler;
97	>	RealType phi, theta;
98	>	// RealType psi;
99	>	RealType cphi, sphi, ctheta, stheta;
100	>	Vector3d ephi;
101	>	Vector3d etheta;
102	>	Vector3d epsi;
103
104	<	t = A[0][0] + A[1][1] + A[2][2] + 1.0;
105	<	if( t > 0.0 ){
104	>	force = getFrc();
105	>	torque =getTrq();
106	>	myEuler = getA().toEulerAngles();
107
108	<	s = 0.5 / sqrt( t );
109	<	q[0] = 0.25 / s;
110	<	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{
108	>	phi = myEuler[0];
109	>	theta = myEuler[1];
110	>	// psi = myEuler[2];
111
112	<	ad1 = fabs( A[0][0] );
113	<	ad2 = fabs( A[1][1] );
114	<	ad3 = fabs( A[2][2] );
112	>	cphi = cos(phi);
113	>	sphi = sin(phi);
114	>	ctheta = cos(theta);
115	>	stheta = sin(theta);
116
117	<	if( ad1 >= ad2 && ad1 >= ad3 ){
117	>	// get unit vectors along the phi, theta and psi rotation axes
118	>
119	>	ephi[0] = 0.0;
120	>	ephi[1] = 0.0;
121	>	ephi[2] = 1.0;
122	>
123	>	//etheta[0] = -sphi;
124	>	//etheta[1] =  cphi;
125	>	//etheta[2] =  0.0;
126	>
127	>	etheta[0] = cphi;
128	>	etheta[1] = sphi;
129	>	etheta[2] =  0.0;
130	>
131	>	epsi[0] = stheta * cphi;
132	>	epsi[1] = stheta * sphi;
133	>	epsi[2] = ctheta;
134	>
135	>	//gradient is equal to -force
136	>	for (int j = 0 ; j<3; j++)
137	>	grad[j] = -force[j];
138	>
139	>	for (int j = 0; j < 3; j++ ) {
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 ){
141	>	grad[3] += torque[j]*ephi[j];
142	>	grad[4] += torque[j]*etheta[j];
143	>	grad[5] += torque[j]*epsi[j];
144
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;
145		}
146	<	else{
146	>
147	>	return grad;
148	>	}
149	>
150	>	void RigidBody::accept(BaseVisitor* v) {
151	>	v->visit(this);
152	>	}
153	>
154	>	/**@todo need modification */
155	>	void  RigidBody::calcRefCoords() {
156	>	RealType mtmp;
157	>	Vector3d refCOM(0.0);
158	>	mass_ = 0.0;
159	>	for (std::size_t i = 0; i < atoms_.size(); ++i) {
160	>	mtmp = atoms_[i]->getMass();
161	>	mass_ += mtmp;
162	>	refCOM += refCoords_[i]*mtmp;
163	>	}
164	>	refCOM /= mass_;
165	>
166	>	// Next, move the origin of the reference coordinate system to the COM:
167	>	for (std::size_t i = 0; i < atoms_.size(); ++i) {
168	>	refCoords_[i] -= refCOM;
169	>	}
170	>
171	>	// Moment of Inertia calculation
172	>	Mat3x3d Itmp(0.0);
173	>	for (std::size_t i = 0; i < atoms_.size(); i++) {
174	>	Mat3x3d IAtom(0.0);
175	>	mtmp = atoms_[i]->getMass();
176	>	IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
177	>	RealType r2 = refCoords_[i].lengthSquare();
178	>	IAtom(0, 0) += mtmp * r2;
179	>	IAtom(1, 1) += mtmp * r2;
180	>	IAtom(2, 2) += mtmp * r2;
181	>	Itmp += IAtom;
182
183	<	s = sqrt( 1.0 + A[2][2] - A[0][0] - A[1][1] ) * 2.0;
184	<	q[0] = (A[0][1] + A[1][0]) / s;
185	<	q[1] = (A[0][2] + A[2][0]) / s;
186	<	q[2] = (A[1][2] + A[2][1]) / s;
161	<	q[3] = 0.5 / s;
183	>	//project the inertial moment of directional atoms into this rigid body
184	>	if (atoms_[i]->isDirectional()) {
185	>	Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
186	>	}
187		}
163	–	}
164	–	}
188
189	<	void RigidBody::setQ( double the_q[4] ){
189	>	//    std::cout << Itmp << std::endl;
190
191	<	double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
192	<
193	<	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;
191	>	//diagonalize
192	>	Vector3d evals;
193	>	Mat3x3d::diagonalize(Itmp, evals, sU_);
194
195	<	}
195	>	// zero out I and then fill the diagonals with the moments of inertia:
196	>	inertiaTensor_(0, 0) = evals[0];
197	>	inertiaTensor_(1, 1) = evals[1];
198	>	inertiaTensor_(2, 2) = evals[2];
199	>
200	>	int nLinearAxis = 0;
201	>	for (int i = 0; i < 3; i++) {
202	>	if (fabs(evals[i]) < OpenMD::epsilon) {
203	>	linear_ = true;
204	>	linearAxis_ = i;
205	>	++ nLinearAxis;
206	>	}
207	>	}
208
209	<	void RigidBody::getA( double the_A[3][3] ){
209	>	if (nLinearAxis > 1) {
210	>	sprintf( painCave.errMsg,
211	>	"RigidBody error.\n"
212	>	"\tOpenMD found more than one axis in this rigid body with a vanishing \n"
213	>	"\tmoment of inertia.  This can happen in one of three ways:\n"
214	>	"\t 1) Only one atom was specified, or \n"
215	>	"\t 2) All atoms were specified at the same location, or\n"
216	>	"\t 3) The programmers did something stupid.\n"
217	>	"\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
218	>	);
219	>	painCave.isFatal = 1;
220	>	simError();
221	>	}
222
223	<	for (int i = 0; i < 3; i++)
192	<	for (int j = 0; j < 3; j++)
193	<	the_A[i][j] = A[i][j];
223	>	}
224
225	<	}
225	>	void  RigidBody::calcForcesAndTorques() {
226	>	Vector3d afrc;
227	>	Vector3d atrq;
228	>	Vector3d apos;
229	>	Vector3d rpos;
230	>	Vector3d frc(0.0);
231	>	Vector3d trq(0.0);
232	>	Vector3d pos = this->getPos();
233	>	for (unsigned int i = 0; i < atoms_.size(); i++) {
234
235	<	void RigidBody::setA( double the_A[3][3] ){
235	>	afrc = atoms_[i]->getFrc();
236	>	apos = atoms_[i]->getPos();
237	>	rpos = apos - pos;
238	>
239	>	frc += afrc;
240
241	<	for (int i = 0; i < 3; i++)
242	<	for (int j = 0; j < 3; j++)
243	<	A[i][j] = the_A[i][j];
202	<
203	<	}
241	>	trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
242	>	trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
243	>	trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];
244
245	<	void RigidBody::getJ( double theJ[3] ){
246	<
207	<	for (int i = 0; i < 3; i++)
208	<	theJ[i] = ji[i];
245	>	// If the atom has a torque associated with it, then we also need to
246	>	// migrate the torques onto the center of mass:
247
248	<	}
248	>	if (atoms_[i]->isDirectional()) {
249	>	atrq = atoms_[i]->getTrq();
250	>	trq += atrq;
251	>	}
252	>	}
253	>	addFrc(frc);
254	>	addTrq(trq);
255	>	}
256
257	<	void RigidBody::setJ( double theJ[3] ){
258	<
259	<	for (int i = 0; i < 3; i++)
260	<	ji[i] = theJ[i];
257	>	Mat3x3d RigidBody::calcForcesAndTorquesAndVirial() {
258	>	Vector3d afrc;
259	>	Vector3d atrq;
260	>	Vector3d apos;
261	>	Vector3d rpos;
262	>	Vector3d dfrc;
263	>	Vector3d frc(0.0);
264	>	Vector3d trq(0.0);
265	>	Vector3d pos = this->getPos();
266	>	Mat3x3d tau_(0.0);
267
268	<	}
268	>	for (unsigned int i = 0; i < atoms_.size(); i++) {
269	>
270	>	afrc = atoms_[i]->getFrc();
271	>	apos = atoms_[i]->getPos();
272	>	rpos = apos - pos;
273	>
274	>	frc += afrc;
275
276	<	void RigidBody::getTrq(double theT[3]){
277	<	for (int i = 0; i < 3 ; i++)
278	<	theT[i] = trq[i];
222	<	}
276	>	trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
277	>	trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
278	>	trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];
279
280	<	void RigidBody::addTrq(double theT[3]){
281	<	for (int i = 0; i < 3 ; i++)
226	<	trq[i] += theT[i];
227	<	}
280	>	// If the atom has a torque associated with it, then we also need to
281	>	// migrate the torques onto the center of mass:
282
283	<	void RigidBody::getI( double the_I[3][3] ){
283	>	if (atoms_[i]->isDirectional()) {
284	>	atrq = atoms_[i]->getTrq();
285	>	trq += atrq;
286	>	}
287	>
288	>	tau_(0,0) -= rpos[0]*afrc[0];
289	>	tau_(0,1) -= rpos[0]*afrc[1];
290	>	tau_(0,2) -= rpos[0]*afrc[2];
291	>	tau_(1,0) -= rpos[1]*afrc[0];
292	>	tau_(1,1) -= rpos[1]*afrc[1];
293	>	tau_(1,2) -= rpos[1]*afrc[2];
294	>	tau_(2,0) -= rpos[2]*afrc[0];
295	>	tau_(2,1) -= rpos[2]*afrc[1];
296	>	tau_(2,2) -= rpos[2]*afrc[2];
297
298	<	for (int i = 0; i < 3; i++)
299	<	for (int j = 0; j < 3; j++)
300	<	the_I[i][j] = I[i][j];
298	>	}
299	>	addFrc(frc);
300	>	addTrq(trq);
301	>	return tau_;
302	>	}
303
304	<	}
304	>	void  RigidBody::updateAtoms() {
305	>	unsigned int i;
306	>	Vector3d ref;
307	>	Vector3d apos;
308	>	DirectionalAtom* dAtom;
309	>	Vector3d pos = getPos();
310	>	RotMat3x3d a = getA();
311	>
312	>	for (i = 0; i < atoms_.size(); i++) {
313	>
314	>	ref = body2Lab(refCoords_[i]);
315
316	<	void RigidBody::lab2Body( double r[3] ){
316	>	apos = pos + ref;
317
318	<	double rl[3]; // the lab frame vector
318	>	atoms_[i]->setPos(apos);
319	>
320	>	if (atoms_[i]->isDirectional()) {
321	>
322	>	dAtom = (DirectionalAtom *) atoms_[i];
323	>	dAtom->setA(refOrients_[i].transpose() * a);
324	>	}
325	>
326	>	}
327
328	<	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]);
328	>	}
329
249	–	}
330
331	<	void RigidBody::body2Lab( double r[3] ){
331	>	void  RigidBody::updateAtoms(int frame) {
332	>	unsigned int i;
333	>	Vector3d ref;
334	>	Vector3d apos;
335	>	DirectionalAtom* dAtom;
336	>	Vector3d pos = getPos(frame);
337	>	RotMat3x3d a = getA(frame);
338	>
339	>	for (i = 0; i < atoms_.size(); i++) {
340	>
341	>	ref = body2Lab(refCoords_[i], frame);
342
343	<	double rb[3]; // the body frame vector
343	>	apos = pos + ref;
344	>
345	>	atoms_[i]->setPos(apos, frame);
346	>
347	>	if (atoms_[i]->isDirectional()) {
348	>
349	>	dAtom = (DirectionalAtom *) atoms_[i];
350	>	dAtom->setA(refOrients_[i].transpose() * a, frame);
351	>	}
352	>
353	>	}
354
355	<	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]);
355	>	}
356
357	<	}
357	>	void RigidBody::updateAtomVel() {
358	>	Mat3x3d skewMat;;
359
360	<	double RigidBody::getZangle( ){
361	<	return zAngle;
267	<	}
360	>	Vector3d ji = getJ();
361	>	Mat3x3d I =  getI();
362
363	<	void RigidBody::setZangle( double zAng ){
364	<	zAngle = zAng;
365	<	}
363	>	skewMat(0, 0) =0;
364	>	skewMat(0, 1) = ji[2] /I(2, 2);
365	>	skewMat(0, 2) = -ji[1] /I(1, 1);
366
367	<	void RigidBody::addZangle( double zAng ){
368	<	zAngle += zAng;
369	<	}
367	>	skewMat(1, 0) = -ji[2] /I(2, 2);
368	>	skewMat(1, 1) = 0;
369	>	skewMat(1, 2) = ji[0]/I(0, 0);
370
371	<	void RigidBody::calcRefCoords( ) {
371	>	skewMat(2, 0) =ji[1] /I(1, 1);
372	>	skewMat(2, 1) = -ji[0]/I(0, 0);
373	>	skewMat(2, 2) = 0;
374
375	<	int i,j,k, it, n_linear_coords;
376	<	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;
375	>	Mat3x3d mat = (getA() * skewMat).transpose();
376	>	Vector3d rbVel = getVel();
377
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;
378
379	<	apos = refCoords[i];
380	<
381	<	for(j = 0; j < 3; j++) {
382	<	refCOM[j] += apos[j]*mtmp;
383	<	}
379	>	Vector3d velRot;
380	>	for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
381	>	atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
382	>	}
383	>
384		}
305	–
306	–	for(j = 0; j < 3; j++)
307	–	refCOM[j] /= mass;
385
386	<	// Next, move the origin of the reference coordinate system to the COM:
386	>	void RigidBody::updateAtomVel(int frame) {
387	>	Mat3x3d skewMat;;
388
389	<	for (i = 0; i < myAtoms.size(); i++) {
390	<	apos = refCoords[i];
313	<	for (j=0; j < 3; j++) {
314	<	apos[j] = apos[j] - refCOM[j];
315	<	}
316	<	refCoords[i] = apos;
317	<	}
389	>	Vector3d ji = getJ(frame);
390	>	Mat3x3d I =  getI();
391
392	<	// Moment of Inertia calculation
392	>	skewMat(0, 0) =0;
393	>	skewMat(0, 1) = ji[2] /I(2, 2);
394	>	skewMat(0, 2) = -ji[1] /I(1, 1);
395
396	<	for (i = 0; i < 3; i++)
397	<	for (j = 0; j < 3; j++)
398	<	Itmp[i][j] = 0.0;
324	<
325	<	for (it = 0; it < myAtoms.size(); it++) {
396	>	skewMat(1, 0) = -ji[2] /I(2, 2);
397	>	skewMat(1, 1) = 0;
398	>	skewMat(1, 2) = ji[0]/I(0, 0);
399
400	<	mtmp = myAtoms[it]->getMass();
401	<	ptmp = refCoords[it];
402	<	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;
400	>	skewMat(2, 0) =ji[1] /I(1, 1);
401	>	skewMat(2, 1) = -ji[0]/I(0, 0);
402	>	skewMat(2, 2) = 0;
403
404	<	Itmp[i][j] -= mtmp * ptmp.vec[i]*ptmp.vec[j];
405	<	}
339	<	}
340	<	}
341	<
342	<	diagonalize3x3(Itmp, evals, sU);
343	<
344	<	// zero out I and then fill the diagonals with the moments of inertia:
404	>	Mat3x3d mat = (getA(frame) * skewMat).transpose();
405	>	Vector3d rbVel = getVel(frame);
406
346	–	n_linear_coords = 0;
407
408	<	for (i = 0; i < 3; i++) {
409	<	for (j = 0; j < 3; j++) {
410	<	I[i][j] = 0.0;
408	>	Vector3d velRot;
409	>	for (unsigned int i = 0 ; i < refCoords_.size(); ++i) {
410	>	atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
411		}
352	–	I[i][i] = evals[i];
412
354	–	if (fabs(evals[i]) < momIntTol) {
355	–	is_linear = true;
356	–	n_linear_coords++;
357	–	linear_axis = i;
358	–	}
413		}
414
415	<	if (n_linear_coords > 1) {
416	<	sprintf( painCave.errMsg,
417	<	"RigidBody error.\n"
418	<	"\tOOPSE found more than one axis in this rigid body with a vanishing \n"
419	<	"\tmoment of inertia.  This can happen in one of three ways:\n"
420	<	"\t 1) Only one atom was specified, or \n"
421	<	"\t 2) All atoms were specified at the same location, or\n"
422	<	"\t 3) The programmers did something stupid.\n"
423	<	"\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
424	<	);
425	<	painCave.isFatal = 1;
426	<	simError();
415	>
416	>
417	>	bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
418	>	if (index < atoms_.size()) {
419	>
420	>	Vector3d ref = body2Lab(refCoords_[index]);
421	>	pos = getPos() + ref;
422	>	return true;
423	>	} else {
424	>	std::cerr << index << " is an invalid index, current rigid body contains "
425	>	<< atoms_.size() << "atoms" << std::endl;
426	>	return false;
427	>	}
428		}
429	<
430	<	// renormalize column vectors:
431	<
432	<	for (i=0; i < 3; i++) {
433	<	len = 0.0;
434	<	for (j = 0; j < 3; j++) {
435	<	len += sU[i][j]*sU[i][j];
429	>
430	>	bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
431	>	std::vector<Atom*>::iterator i;
432	>	i = std::find(atoms_.begin(), atoms_.end(), atom);
433	>	if (i != atoms_.end()) {
434	>	//RigidBody class makes sure refCoords_ and atoms_ match each other
435	>	Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
436	>	pos = getPos() + ref;
437	>	return true;
438	>	} else {
439	>	std::cerr << "Atom " << atom->getGlobalIndex()
440	>	<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
441	>	return false;
442		}
382	–	len = sqrt(len);
383	–	for (j = 0; j < 3; j++) {
384	–	sU[i][j] /= len;
385	–	}
443		}
444	<	}
444	>	bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
445
446	<	void RigidBody::doEulerToRotMat(vec3 &euler, mat3x3 &myA ){
446	>	//velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
447
448	<	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);
448	>	if (index < atoms_.size()) {
449
450	<	}
450	>	Vector3d velRot;
451	>	Mat3x3d skewMat;;
452	>	Vector3d ref = refCoords_[index];
453	>	Vector3d ji = getJ();
454	>	Mat3x3d I =  getI();
455
456	<	void RigidBody::calcForcesAndTorques() {
456	>	skewMat(0, 0) =0;
457	>	skewMat(0, 1) = ji[2] /I(2, 2);
458	>	skewMat(0, 2) = -ji[1] /I(1, 1);
459
460	<	// Convert Atomic forces and torques to total forces and torques:
461	<	int i, j;
462	<	double apos[3];
416	<	double afrc[3];
417	<	double atrq[3];
418	<	double rpos[3];
460	>	skewMat(1, 0) = -ji[2] /I(2, 2);
461	>	skewMat(1, 1) = 0;
462	>	skewMat(1, 2) = ji[0]/I(0, 0);
463
464	<	zeroForces();
465	<
466	<	for (i = 0; i < myAtoms.size(); i++) {
464	>	skewMat(2, 0) =ji[1] /I(1, 1);
465	>	skewMat(2, 1) = -ji[0]/I(0, 0);
466	>	skewMat(2, 2) = 0;
467
468	<	myAtoms[i]->getPos(apos);
425	<	myAtoms[i]->getFrc(afrc);
468	>	velRot = (getA() * skewMat).transpose() * ref;
469
470	<	for (j=0; j<3; j++) {
471	<	rpos[j] = apos[j] - pos[j];
472	<	frc[j] += afrc[j];
470	>	vel =getVel() + velRot;
471	>	return true;
472	>
473	>	} else {
474	>	std::cerr << index << " is an invalid index, current rigid body contains "
475	>	<< atoms_.size() << "atoms" << std::endl;
476	>	return false;
477		}
478	<
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];
478	>	}
479
480	<	// If the atom has a torque associated with it, then we also need to
437	<	// migrate the torques onto the center of mass:
480	>	bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
481
482	<	if (myAtoms[i]->isDirectional()) {
482	>	std::vector<Atom*>::iterator i;
483	>	i = std::find(atoms_.begin(), atoms_.end(), atom);
484	>	if (i != atoms_.end()) {
485	>	return getAtomVel(vel, i - atoms_.begin());
486	>	} else {
487	>	std::cerr << "Atom " << atom->getGlobalIndex()
488	>	<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
489	>	return false;
490	>	}
491	>	}
492
493	<	myAtoms[i]->getTrq(atrq);
494	<
495	<	for (j=0; j<3; j++)
496	<	trq[j] += atrq[j];
493	>	bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
494	>	if (index < atoms_.size()) {
495	>
496	>	coor = refCoords_[index];
497	>	return true;
498	>	} else {
499	>	std::cerr << index << " is an invalid index, current rigid body contains "
500	>	<< atoms_.size() << "atoms" << std::endl;
501	>	return false;
502		}
503	+
504		}
505
506	<	// Convert Torque to Body-fixed coordinates:
507	<	// (Actually, on second thought, don't.  Integrator does this now.)
508	<	// lab2Body(trq);
506	>	bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
507	>	std::vector<Atom*>::iterator i;
508	>	i = std::find(atoms_.begin(), atoms_.end(), atom);
509	>	if (i != atoms_.end()) {
510	>	//RigidBody class makes sure refCoords_ and atoms_ match each other
511	>	coor = refCoords_[i - atoms_.begin()];
512	>	return true;
513	>	} else {
514	>	std::cerr << "Atom " << atom->getGlobalIndex()
515	>	<<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
516	>	return false;
517	>	}
518
519	<	}
519	>	}
520
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];
521
522	<	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	<	}
522	>	void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
523
524	<	void RigidBody::getGrad( double grad[6] ) {
524	>	Vector3d coords;
525	>	Vector3d euler;
526	>
527
528	<	double myEuler[3];
529	<	double phi, theta, psi;
530	<	double cphi, sphi, ctheta, stheta;
531	<	double ephi[3];
532	<	double etheta[3];
533	<	double epsi[3];
528	>	atoms_.push_back(at);
529	>
530	>	if( !ats->havePosition() ){
531	>	sprintf( painCave.errMsg,
532	>	"RigidBody error.\n"
533	>	"\tAtom %s does not have a position specified.\n"
534	>	"\tThis means RigidBody cannot set up reference coordinates.\n",
535	>	ats->getType().c_str() );
536	>	painCave.isFatal = 1;
537	>	simError();
538	>	}
539
540	<	this->getEulerAngles(myEuler);
540	>	coords[0] = ats->getPosX();
541	>	coords[1] = ats->getPosY();
542	>	coords[2] = ats->getPosZ();
543
544	<	phi = myEuler[0];
492	<	theta = myEuler[1];
493	<	psi = myEuler[2];
544	>	refCoords_.push_back(coords);
545
546	<	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;
546	>	RotMat3x3d identMat = RotMat3x3d::identity();
547
548	<	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];
548	>	if (at->isDirectional()) {
549
550	<	grad[3] = 0.0;
551	<	grad[4] = 0.0;
552	<	grad[5] = 0.0;
553	<
554	<	for (int j = 0; j < 3; j++ ) {
550	>	if( !ats->haveOrientation() ){
551	>	sprintf( painCave.errMsg,
552	>	"RigidBody error.\n"
553	>	"\tAtom %s does not have an orientation specified.\n"
554	>	"\tThis means RigidBody cannot set up reference orientations.\n",
555	>	ats->getType().c_str() );
556	>	painCave.isFatal = 1;
557	>	simError();
558	>	}
559
560	<	grad[3] += trq[j]*ephi[j];
561	<	grad[4] += trq[j]*etheta[j];
562	<	grad[5] += trq[j]*epsi[j];
526	<
527	<	}
528	<
529	<	}
560	>	euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
561	>	euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
562	>	euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;
563
564	<	/**
565	<	* 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++) {
564	>	RotMat3x3d Atmp(euler);
565	>	refOrients_.push_back(Atmp);
566
567	<	mtmp = myAtoms[i]->getMass();
568	<	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;
567	>	}else {
568	>	refOrients_.push_back(identMat);
569		}
632	–
633	–	}
570
571	<	for(j = 0; j < 3; j++) {
636	<	pos[j] /= mass;
637	<	vel[j] /= mass;
571	>
572		}
573
574		}
575
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 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1797 by gezelter, Mon Sep 10 20:58:00 2012 UTC

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