src/math/AlphaHull.hpp

/* Copyright (c) 2008, 2009 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).                        
 *
 *
 *  AlphaHull.hpp
 *
 *  Purpose: To calculate alphahull, hull volume using the QuickHull algorithm provided by QHull.
 *
 *  Created by Charles F. Vardeman II on 16 Dec 2009.
 *  @author  Charles F. Vardeman II
 *  @version $Id: ConvexHull.hpp,v 1.19 2009-11-25 20:02:01 gezelter Exp $
 *
 */

#ifndef MATH_ALPHAHULL_HPP_
#define MATH_ALPHAHULL_HPP_

#include "math/Vector3.hpp"
#include "config.h"
#include "math/Hull.hpp"
#include "math/Triangle.hpp"

#include <cassert>
#include <vector>
#include <string>


namespace OpenMD {
  class AlphaHull : public Hull {
  public:

    AlphaHull(double alpha);    
    virtual ~AlphaHull(){};

    void computeHull( std::vector<StuntDouble*> bodydoubles );

    /* Total area of Hull*/
    RealType getArea(){return area_;}

    /* Total Volume enclosed by Hull */
    RealType getVolume(){ return volume_; } 

    std::vector<Triangle> getMesh(){return Triangles_;}
    void printHull(const std::string& geomFileName);

  protected:
    RealType volume_;
    RealType area_;
    int dim_;
    double alpha_;
    const std::string options_;
    
  private:
    std::vector<Triangle> Triangles_;
  };
}
#endif /*MATH_CONVEXHULL_HPP_*/
Revision:	1402
Committed:	Fri Jan 8 17:15:27 2010 UTC (15 years, 3 months ago) by chuckv
File size:	3298 byte(s)
Log Message:	Added preliminary code for Alpha Hull calculation using qhull. Added preliminary support to SMIPD to support Alpha Hull. Alpha Hull does not yet add the correct things to triangle to be returned to SMPID. Preliminary changes for shadow hamiltonian integrator. Chages to md files so they will work in openMD.
#	Content
1	/* Copyright (c) 2008, 2009 The University of Notre Dame. All Rights Reserved.
2	*
3	* The University of Notre Dame grants you ("Licensee") a
4	* non-exclusive, royalty free, license to use, modify and
5	* redistribute this software in source and binary code form, provided
6	* that the following conditions are met:
7	*
8	* 1. Redistributions of source code must retain the above copyright
9	* notice, this list of conditions and the following disclaimer.
10	*
11	* 2. Redistributions in binary form must reproduce the above copyright
12	* notice, this list of conditions and the following disclaimer in the
13	* documentation and/or other materials provided with the
14	* distribution.
15	*
16	* This software is provided "AS IS," without a warranty of any
17	* kind. All express or implied conditions, representations and
18	* warranties, including any implied warranty of merchantability,
19	* fitness for a particular purpose or non-infringement, are hereby
20	* excluded. The University of Notre Dame and its licensors shall not
21	* be liable for any damages suffered by licensee as a result of
22	* using, modifying or distributing the software or its
23	* derivatives. In no event will the University of Notre Dame or its
24	* licensors be liable for any lost revenue, profit or data, or for
25	* direct, indirect, special, consequential, incidental or punitive
26	* damages, however caused and regardless of the theory of liability,
27	* arising out of the use of or inability to use software, even if the
28	* University of Notre Dame has been advised of the possibility of
29	* such damages.
30	*
31	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
32	* research, please cite the appropriate papers when you publish your
33	* work. Good starting points are:
34	*
35	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
36	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
37	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
38	* [4] Vardeman & Gezelter, in progress (2009).
39	*
40	*
41	* AlphaHull.hpp
42	*
43	* Purpose: To calculate alphahull, hull volume using the QuickHull algorithm provided by QHull.
44	*
45	* Created by Charles F. Vardeman II on 16 Dec 2009.
46	* @author Charles F. Vardeman II
47	* @version $Id: ConvexHull.hpp,v 1.19 2009-11-25 20:02:01 gezelter Exp $
48	*
49	*/
50
51	#ifndef MATH_ALPHAHULL_HPP_
52	#define MATH_ALPHAHULL_HPP_
53
54	#include "math/Vector3.hpp"
55	#include "config.h"
56	#include "math/Hull.hpp"
57	#include "math/Triangle.hpp"
58
59	#include <cassert>
60	#include <vector>
61	#include <string>
62
63
64	namespace OpenMD {
65	class AlphaHull : public Hull {
66	public:
67
68	AlphaHull(double alpha);
69	virtual ~AlphaHull(){};
70
71	void computeHull( std::vector<StuntDouble*> bodydoubles );
72
73	/* Total area of Hull*/
74	RealType getArea(){return area_;}
75
76	/* Total Volume enclosed by Hull */
77	RealType getVolume(){ return volume_; }
78
79	std::vector<Triangle> getMesh(){return Triangles_;}
80	void printHull(const std::string& geomFileName);
81
82	protected:
83	RealType volume_;
84	RealType area_;
85	int dim_;
86	double alpha_;
87	const std::string options_;
88
89	private:
90	std::vector<Triangle> Triangles_;
91	};
92	}
93	#endif /MATH_CONVEXHULL_HPP_/