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>

using namespace std;
namespace OpenMD {
  class AlphaHull : public Hull {
  public:
    
    AlphaHull(RealType alpha);    
    virtual ~AlphaHull(){};
    
    void computeHull( 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:
    RealType volume_;
    RealType area_;
    Mat3x3d boundingBox_;
    int dim_;
    RealType alpha_;
    const std::string options_;
    
  private:
    vector<Triangle> Triangles_;
  };
}
#endif
Revision:	1866
Committed:	Thu Apr 25 14:32:56 2013 UTC (12 years ago) by gezelter
File size:	3335 byte(s)
Log Message:	Fixes for Qhull static build strangeness
#	User	Rev	Content
1	chuckv	1402	/* 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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
38	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
39			* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
40	chuckv	1402	*
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	gezelter	1442	* @version $Id$
48	chuckv	1402	*
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	gezelter	1858	using namespace std;
64	chuckv	1402	namespace OpenMD {
65			class AlphaHull : public Hull {
66			public:
67	gezelter	1858
68			AlphaHull(RealType alpha);
69	chuckv	1402	virtual ~AlphaHull(){};
70	gezelter	1858
71			void computeHull( vector<StuntDouble*> bodydoubles );
72
73	chuckv	1402	/* Total area of Hull*/
74	gezelter	1858	RealType getArea(){ return area_; }
75
76	chuckv	1402	/* Total Volume enclosed by Hull */
77			RealType getVolume(){ return volume_; }
78	gezelter	1858
79			vector<Triangle> getMesh(){ return Triangles_; }
80	chuckv	1402	void printHull(const std::string& geomFileName);
81	gezelter	1858
82	chuckv	1402	protected:
83			RealType volume_;
84			RealType area_;
85	gezelter	1858	Mat3x3d boundingBox_;
86	chuckv	1402	int dim_;
87	gezelter	1858	RealType alpha_;
88	chuckv	1402	const std::string options_;
89
90			private:
91	gezelter	1858	vector<Triangle> Triangles_;
92	chuckv	1402	};
93			}
94	gezelter	1858	#endif