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root/OpenMD/trunk/src/math/SquareMatrix3.hpp

Comparing trunk/src/math/SquareMatrix3.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 47 | Line 47
47		*/
48		#ifndef MATH_SQUAREMATRIX3_HPP
49		#define  MATH_SQUAREMATRIX3_HPP
50	<
50	>	#include <vector>
51		#include "Quaternion.hpp"
52		#include "SquareMatrix.hpp"
53		#include "Vector3.hpp"
54		#include "utils/NumericConstant.hpp"
55	<	namespace oopse {
55	>	namespace OpenMD {
56
57		template<typename Real>
58		class SquareMatrix3 : public SquareMatrix<Real, 3> {
#	Line 166 | Line 166 | namespace oopse {
166		void setupRotMat(Real w, Real x, Real y, Real z) {
167		Quaternion<Real> q(w, x, y, z);
168		*this = q.toRotationMatrix3();
169	+	}
170	+
171	+	void setupSkewMat(Vector3<Real> v) {
172	+	setupSkewMat(v[0], v[1], v[2]);
173	+	}
174	+
175	+	void setupSkewMat(Real v1, Real v2, Real v3) {
176	+	this->data_[0][0] = 0;
177	+	this->data_[0][1] = -v3;
178	+	this->data_[0][2] = v2;
179	+	this->data_[1][0] = v3;
180	+	this->data_[1][1] = 0;
181	+	this->data_[1][2] = -v1;
182	+	this->data_[2][0] = -v2;
183	+	this->data_[2][1] = v1;
184	+	this->data_[2][2] = 0;
185	+
186	+
187		}
188
189	+
190	+
191		/**
192		* Returns the quaternion from this rotation matrix
193		* @return the quaternion from this rotation matrix
#	Line 188 | Line 208 | namespace oopse {
208		q[3] = (this->data_[0][1] - this->data_[1][0]) * s;
209		} else {
210
211	<	ad1 = fabs( this->data_[0][0] );
212	<	ad2 = fabs( this->data_[1][1] );
213	<	ad3 = fabs( this->data_[2][2] );
211	>	ad1 = this->data_[0][0];
212	>	ad2 = this->data_[1][1];
213	>	ad3 = this->data_[2][2];
214
215		if( ad1 >= ad2 && ad1 >= ad3 ){
216
#	Line 224 | Line 244 | namespace oopse {
244		* @return the euler angles in a vector
245		* @exception invalid rotation matrix
246		* We use so-called "x-convention", which is the most common definition.
247	<	* In this convention, the rotation given by Euler angles (phi, theta, psi), where the first
248	<	* rotation is by an angle phi about the z-axis, the second is by an angle
249	<	* theta (0 <= theta <= 180)about the x-axis, and thethird is by an angle psi about the
250	<	* z-axis (again).
247	>	* In this convention, the rotation given by Euler angles (phi, theta,
248	>	* psi), where the first rotation is by an angle phi about the z-axis,
249	>	* the second is by an angle theta (0 <= theta <= 180) about the x-axis,
250	>	* and the third is by an angle psi about the z-axis (again).
251		*/
252		Vector3<Real> toEulerAngles() {
253		Vector3<Real> myEuler;
#	Line 239 | Line 259 | namespace oopse {
259
260		// set the tolerance for Euler angles and rotation elements
261
262	<	theta = acos(std::min(1.0, std::max(-1.0,this->data_[2][2])));
262	>	theta = acos(std::min((RealType)1.0, std::max((RealType)-1.0,this->data_[2][2])));
263		ctheta = this->data_[2][2];
264		stheta = sqrt(1.0 - ctheta * ctheta);
265
266	<	// when sin(theta) is close to 0, we need to consider singularity
267	<	// In this case, we can assign an arbitary value to phi (or psi), and then determine
268	<	// the psi (or phi) or vice-versa. We'll assume that phi always gets the rotation, and psi is 0
269	<	// in cases of singularity.
266	>	// when sin(theta) is close to 0, we need to consider
267	>	// singularity In this case, we can assign an arbitary value to
268	>	// phi (or psi), and then determine the psi (or phi) or
269	>	// vice-versa. We'll assume that phi always gets the rotation,
270	>	// and psi is 0 in cases of singularity.
271		// we use atan2 instead of atan, since atan2 will give us -Pi to Pi.
272	<	// Since 0 <= theta <= 180, sin(theta) will be always non-negative. Therefore, it never
273	<	// change the sign of both of the parameters passed to atan2.
272	>	// Since 0 <= theta <= 180, sin(theta) will be always
273	>	// non-negative. Therefore, it will never change the sign of both of
274	>	// the parameters passed to atan2.
275
276	<	if (fabs(stheta) <= oopse::epsilon){
276	>	if (fabs(stheta) < 1e-6){
277		psi = 0.0;
278		phi = atan2(-this->data_[1][0], this->data_[0][0]);
279		}
#	Line 263 | Line 285 | namespace oopse {
285
286		//wrap phi and psi, make sure they are in the range from 0 to 2*Pi
287		if (phi < 0)
288	<	phi += M_PI;
288	>	phi += 2.0 * M_PI;
289
290		if (psi < 0)
291	<	psi += M_PI;
291	>	psi += 2.0 * M_PI;
292
293		myEuler[0] = phi;
294		myEuler[1] = theta;
#	Line 298 | Line 320 | namespace oopse {
320		*/
321		SquareMatrix3<Real>  inverse() const {
322		SquareMatrix3<Real> m;
323	<	double det = determinant();
324	<	if (fabs(det) <= oopse::epsilon) {
323	>	RealType det = determinant();
324	>	if (fabs(det) <= OpenMD::epsilon) {
325		//"The method was called on a matrix with |determinant| <= 1e-6.",
326		//"This is a runtime or a programming error in your application.");
327	<	}
327	>	std::vector<int> zeroDiagElementIndex;
328	>	for (int i =0; i < 3; ++i) {
329	>	if (fabs(this->data_[i][i]) <= OpenMD::epsilon) {
330	>	zeroDiagElementIndex.push_back(i);
331	>	}
332	>	}
333
334	<	m(0, 0) = this->data_[1][1]*this->data_[2][2] - this->data_[1][2]*this->data_[2][1];
335	<	m(1, 0) = this->data_[1][2]*this->data_[2][0] - this->data_[1][0]*this->data_[2][2];
336	<	m(2, 0) = this->data_[1][0]*this->data_[2][1] - this->data_[1][1]*this->data_[2][0];
337	<	m(0, 1) = this->data_[2][1]*this->data_[0][2] - this->data_[2][2]*this->data_[0][1];
311	<	m(1, 1) = this->data_[2][2]*this->data_[0][0] - this->data_[2][0]*this->data_[0][2];
312	<	m(2, 1) = this->data_[2][0]*this->data_[0][1] - this->data_[2][1]*this->data_[0][0];
313	<	m(0, 2) = this->data_[0][1]*this->data_[1][2] - this->data_[0][2]*this->data_[1][1];
314	<	m(1, 2) = this->data_[0][2]*this->data_[1][0] - this->data_[0][0]*this->data_[1][2];
315	<	m(2, 2) = this->data_[0][0]*this->data_[1][1] - this->data_[0][1]*this->data_[1][0];
334	>	if (zeroDiagElementIndex.size() == 2) {
335	>	int index = zeroDiagElementIndex[0];
336	>	m(index, index) = 1.0 / this->data_[index][index];
337	>	}else if (zeroDiagElementIndex.size() == 1) {
338
339	<	m /= det;
339	>	int a = (zeroDiagElementIndex[0] + 1) % 3;
340	>	int b = (zeroDiagElementIndex[0] + 2) %3;
341	>	RealType denom = this->data_[a][a] * this->data_[b][b] - this->data_[b][a]*this->data_[a][b];
342	>	m(a, a) = this->data_[b][b] /denom;
343	>	m(b, a) = -this->data_[b][a]/denom;
344	>
345	>	m(a,b) = -this->data_[a][b]/denom;
346	>	m(b, b) = this->data_[a][a]/denom;
347	>
348	>	}
349	>
350	>	/*
351	>	for(std::vector<int>::iterator iter = zeroDiagElementIndex.begin(); iter != zeroDiagElementIndex.end() ++iter) {
352	>	if (this->data_[*iter][0] > OpenMD::epsilon || this->data_[*iter][1] ||this->data_[*iter][2] ||
353	>	this->data_[0][*iter] > OpenMD::epsilon || this->data_[1][*iter] ||this->data_[2][*iter] ) {
354	>	std::cout << "can not inverse matrix" << std::endl;
355	>	}
356	>	}
357	>	*/
358	>	} else {
359	>
360	>	m(0, 0) = this->data_[1][1]*this->data_[2][2] - this->data_[1][2]*this->data_[2][1];
361	>	m(1, 0) = this->data_[1][2]*this->data_[2][0] - this->data_[1][0]*this->data_[2][2];
362	>	m(2, 0) = this->data_[1][0]*this->data_[2][1] - this->data_[1][1]*this->data_[2][0];
363	>	m(0, 1) = this->data_[2][1]*this->data_[0][2] - this->data_[2][2]*this->data_[0][1];
364	>	m(1, 1) = this->data_[2][2]*this->data_[0][0] - this->data_[2][0]*this->data_[0][2];
365	>	m(2, 1) = this->data_[2][0]*this->data_[0][1] - this->data_[2][1]*this->data_[0][0];
366	>	m(0, 2) = this->data_[0][1]*this->data_[1][2] - this->data_[0][2]*this->data_[1][1];
367	>	m(1, 2) = this->data_[0][2]*this->data_[1][0] - this->data_[0][0]*this->data_[1][2];
368	>	m(2, 2) = this->data_[0][0]*this->data_[1][1] - this->data_[0][1]*this->data_[1][0];
369	>
370	>	m /= det;
371	>	}
372		return m;
373		}
374	+
375	+	SquareMatrix3<Real> transpose() const{
376	+	SquareMatrix3<Real> result;
377	+
378	+	for (unsigned int i = 0; i < 3; i++)
379	+	for (unsigned int j = 0; j < 3; j++)
380	+	result(j, i) = this->data_[i][j];
381	+
382	+	return result;
383	+	}
384		/**
385		* Extract the eigenvalues and eigenvectors from a 3x3 matrix.
386		* The eigenvectors (the columns of V) will be normalized.
#	Line 499 | Line 563 | namespace oopse {
563		}
564
565
566	<	typedef SquareMatrix3<double> Mat3x3d;
567	<	typedef SquareMatrix3<double> RotMat3x3d;
566	>	typedef SquareMatrix3<RealType> Mat3x3d;
567	>	typedef SquareMatrix3<RealType> RotMat3x3d;
568
569	<	} //namespace oopse
569	>	} //namespace OpenMD
570		#endif // MATH_SQUAREMATRIX_HPP
571

Comparing trunk/src/math/SquareMatrix3.hpp (property svn:keywords):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC

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