src/hydrodynamics/Ellipsoid.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#ifndef HYDRODYNAMICS_ELLIPSOID_HPP
#define HYDRODYNAMICS_ELLIPSOID_HPP
#include "hydrodynamics/Shape.hpp"
#include "math/SquareMatrix3.hpp"
namespace OpenMD {
  
  /** @class Ellipsoid 
   *
   * An ellipsoid in OpenMD is restricted to having two equal
   * equatorial semi-axes.  OpenMD treats the "special" axis as the
   * z-coordinate in the body fixed reference frame.  That is:
   *
   *   z^2 / a^2  +  (x^2 + y^2) / b^2   = 1
   *
   * If a >= b, the ellipsoid is a prolate spheroid, and if a < b, 
   * the ellipsoid is oblate.  Ellipsoids are specified in the constructor 
   * using an axial length (a), and a equatorial length (b).  A Vector3d 
   * can be used to position the center of the ellipsoid, and a rotation 
   * matrix can also be used to orient the ellipsoid to a preferred lab-fixed
   * coordinate frame.
   */
  class Ellipsoid : public Shape{
  public:
    Ellipsoid(Vector3d origin, RealType rAxial, RealType rEquatorial, Mat3x3d rotMat);
    virtual bool isInterior(Vector3d pos);
    virtual std::pair<Vector3d, Vector3d> getBoundingBox();
    virtual bool hasAnalyticalSolution() {return true;}
    
    virtual HydroProp* getHydroProp(RealType viscosity, RealType temperature);
    
    RealType getRAxial() {return rAxial_;}
    RealType getREquatorial() {return rEquatorial_;}
    RealType getRMajor() {return rMajor_;}
    RealType getRMinor() {return rMinor_;}
    
  private:
    
    Vector3d origin_;
    RealType rAxial_;
    RealType rEquatorial_;
    RealType rMajor_;
    RealType rMinor_;
    Mat3x3d rotMat_;
  };  
}

#endif
Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	3690 byte(s)
Log Message:	Creating busticated version of OpenMD
#	Content
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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#ifndef HYDRODYNAMICS_ELLIPSOID_HPP
43	#define HYDRODYNAMICS_ELLIPSOID_HPP
44	#include "hydrodynamics/Shape.hpp"
45	#include "math/SquareMatrix3.hpp"
46	namespace OpenMD {
47
48	/** @class Ellipsoid
49	*
50	* An ellipsoid in OpenMD is restricted to having two equal
51	* equatorial semi-axes. OpenMD treats the "special" axis as the
52	* z-coordinate in the body fixed reference frame. That is:
53	*
54	* z^2 / a^2 + (x^2 + y^2) / b^2 = 1
55	*
56	* If a >= b, the ellipsoid is a prolate spheroid, and if a < b,
57	* the ellipsoid is oblate. Ellipsoids are specified in the constructor
58	* using an axial length (a), and a equatorial length (b). A Vector3d
59	* can be used to position the center of the ellipsoid, and a rotation
60	* matrix can also be used to orient the ellipsoid to a preferred lab-fixed
61	* coordinate frame.
62	*/
63	class Ellipsoid : public Shape{
64	public:
65	Ellipsoid(Vector3d origin, RealType rAxial, RealType rEquatorial, Mat3x3d rotMat);
66	virtual bool isInterior(Vector3d pos);
67	virtual std::pair<Vector3d, Vector3d> getBoundingBox();
68	virtual bool hasAnalyticalSolution() {return true;}
69
70	virtual HydroProp* getHydroProp(RealType viscosity, RealType temperature);
71
72	RealType getRAxial() {return rAxial_;}
73	RealType getREquatorial() {return rEquatorial_;}
74	RealType getRMajor() {return rMajor_;}
75	RealType getRMinor() {return rMinor_;}
76
77	private:
78
79	Vector3d origin_;
80	RealType rAxial_;
81	RealType rEquatorial_;
82	RealType rMajor_;
83	RealType rMinor_;
84	Mat3x3d rotMat_;
85	};
86	}
87
88	#endif