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, 234107 (2008).          
 * [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
 *
 *  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 $Id$
 *
 */

#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(RealType 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_; } 
    
    vector<Triangle> getMesh(){ return Triangles_; }
    void printHull(const std::string& geomFileName);
    
  protected:
    int dim_;
    RealType alpha_;
    const std::string options_;
    
  private:
    // These variables are private so that each new hull returns
    // information about itself.
    RealType volume_;
    RealType area_;
    std::vector<Triangle> Triangles_;

  };
}
#endif
Revision:	2056
Committed:	Fri Feb 20 15:12:07 2015 UTC (10 years, 2 months ago) by gezelter
File size:	3397 byte(s)
Log Message:	Fixes to HullFinder (and by extension to RNEMD) for getSurfaceArea() call. Adding Multipass Correlation Function (unused right now).
#	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, 234107 (2008).
38	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
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 $Id$
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	namespace OpenMD {
64	class AlphaHull : public Hull {
65	public:
66
67	AlphaHull(RealType alpha);
68	virtual ~AlphaHull(){};
69
70	void computeHull( std::vector<StuntDouble*> bodydoubles );
71
72	/* Total area of Hull*/
73	RealType getArea(){ return area_; }
74
75	/* Total Volume enclosed by Hull */
76	RealType getVolume(){ return volume_; }
77
78	vector<Triangle> getMesh(){ return Triangles_; }
79	void printHull(const std::string& geomFileName);
80
81	protected:
82	int dim_;
83	RealType alpha_;
84	const std::string options_;
85
86	private:
87	// These variables are private so that each new hull returns
88	// information about itself.
89	RealType volume_;
90	RealType area_;
91	std::vector<Triangle> Triangles_;
92
93	};
94	}
95	#endif