src/clusters/Icosahedron.hpp

/*
 * Copyright (c) 2013 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).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

/*! \file Icosahedron.hpp
    \brief Icosahedron cluster structure generator
*/

#ifndef CLUSTERS_ICOSAHEDRON_HPP
#define CLUSTERS_ICOSAHEDRON_HPP

#include <string>
#include <vector>
#include "utils/Tuple.hpp"
#include "math/Vector3.hpp"

using namespace std;
namespace OpenMD{

    //! Create the Mackay icosahedron structure.
    /*!
        (Heavily modified from code from Yanting Wang date 07/21/2003)
    */
  
  class Icosahedron {
  public:
    //! Default constructor
    Icosahedron();
    virtual ~Icosahedron();
    
    //! Calculate number of particles in an icosahedron with nShells shells.
    int getNpoints(int nShells);
    
    //! Get the generated points in an icosahedron with nShells shells.
    vector<Vector3d> getPoints(int nShells);
    
  protected:
    //! Create nth layer particles.
    vector<Vector3d> ih( int n );
    //! Calculate number of particles on the nth layer.
    int np( int n );
    
    vector<Vector3d> Points;
    vector<pair<int, int> > Edges;
    vector<tuple3<int, int, int> > Facets;
    vector<Vector3d> Basis; // Basis vectors of the edges
  };
}

#endif
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	3295 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	Content
1	/*
2	* Copyright (c) 2013 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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	/*! \file Icosahedron.hpp
44	\brief Icosahedron cluster structure generator
45	*/
46
47	#ifndef CLUSTERS_ICOSAHEDRON_HPP
48	#define CLUSTERS_ICOSAHEDRON_HPP
49
50	#include <string>
51	#include <vector>
52	#include "utils/Tuple.hpp"
53	#include "math/Vector3.hpp"
54
55	using namespace std;
56	namespace OpenMD{
57
58	//! Create the Mackay icosahedron structure.
59	/*!
60	(Heavily modified from code from Yanting Wang date 07/21/2003)
61	*/
62
63	class Icosahedron {
64	public:
65	//! Default constructor
66	Icosahedron();
67	virtual ~Icosahedron();
68
69	//! Calculate number of particles in an icosahedron with nShells shells.
70	int getNpoints(int nShells);
71
72	//! Get the generated points in an icosahedron with nShells shells.
73	vector<Vector3d> getPoints(int nShells);
74
75	protected:
76	//! Create nth layer particles.
77	vector<Vector3d> ih( int n );
78	//! Calculate number of particles on the nth layer.
79	int np( int n );
80
81	vector<Vector3d> Points;
82	vector<pair<int, int> > Edges;
83	vector<tuple3<int, int, int> > Facets;
84	vector<Vector3d> Basis; // Basis vectors of the edges
85	};
86	}
87
88	#endif