src/clusters/Decahedron.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 Decahedron.hpp
    \brief Decahedron cluster structure generator
*/

/* Original copyright & license text:

Copyright (c) 2011, Dmitry
Copyright (c) 2009, Richard Brown
Copyright (c) 2011, Evgeny Pr
All rights reserved.

Redistribution and use in source and binary forms, with or without 
modification, are permitted provided that the following conditions are 
met:

    * Redistributions of source code must retain the above copyright 
      notice, this list of conditions and the following disclaimer.
    * 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 BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE 
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
POSSIBILITY OF SUCH DAMAGE.

*/


#ifndef CLUSTERS_DECAHEDRON_HPP
#define CLUSTERS_DECAHEDRON_HPP

#include <vector>
#include "math/Vector3.hpp"

using namespace std;
namespace OpenMD{

    //! Creates the regular decahedron, Ino decahedron, or truncated
    //! (Marks) decahedron structures (depending on the parameters).
    /*!
        (Heavily modified from Matlab code from: 
        Dmitry, Richard Brown, and Evgeny Pr)

    */
  class Decahedron {
  public:
    //! Default constructor
    Decahedron(int columnAtoms, int shells, int twinAtoms);
    virtual ~Decahedron();
    
    //! Get the generated points in the cluster.
    virtual vector<Vector3d> getPoints();
    
  protected:
    //! Generate the rings of the Decahedron.
    vector<Vector3d> truncatedRing( int n, int k );
    
    int N_; // number of atoms in the central atomic column
    int M_; // number of {002} shells
    int K_; // number of atomic columns along twin boundary

    vector<Vector3d> Points;
    vector<Vector3d> Basis; // Basis vectors of the Decahedron
  };

  class RegularDecahedron : public Decahedron {
  public:
    RegularDecahedron(int shells) : Decahedron(shells-1, shells, shells) {}
  };

  class InoDecahedron : public Decahedron {
  public:
    InoDecahedron(int columnAtoms, int shells) : 
      Decahedron(columnAtoms, shells, columnAtoms) {}
  };

  class CurlingStoneDecahedron : public Decahedron {
  public:
    CurlingStoneDecahedron(int columnAtoms, int shells, int twinAtoms, int truncatedPlanes);
    vector<Vector3d> getPoints();
  private:
    int T_; // number of truncated planes snipped from top and bottom
  };
    
}

#endif
Revision:	1862
Committed:	Fri Apr 12 20:45:04 2013 UTC (12 years ago) by gezelter
File size:	5315 byte(s)
Log Message:	Adding nanoparticle generators, fixing a Qhull static link bug
#	User	Rev	Content
1	gezelter	1862	/*
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 Decahedron.hpp
44			\brief Decahedron cluster structure generator
45			*/
46
47			/* Original copyright & license text:
48
49			Copyright (c) 2011, Dmitry
50			Copyright (c) 2009, Richard Brown
51			Copyright (c) 2011, Evgeny Pr
52			All rights reserved.
53
54			Redistribution and use in source and binary forms, with or without
55			modification, are permitted provided that the following conditions are
56			met:
57
58			* Redistributions of source code must retain the above copyright
59			notice, this list of conditions and the following disclaimer.
60			* Redistributions in binary form must reproduce the above copyright
61			notice, this list of conditions and the following disclaimer in
62			the documentation and/or other materials provided with the distribution
63
64			THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
65			AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
66			IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
67			ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
68			LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
69			CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
70			SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
71			INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
72			CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
73			ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
74			POSSIBILITY OF SUCH DAMAGE.
75
76			*/
77
78
79			#ifndef CLUSTERS_DECAHEDRON_HPP
80			#define CLUSTERS_DECAHEDRON_HPP
81
82			#include <vector>
83			#include "math/Vector3.hpp"
84
85			using namespace std;
86			namespace OpenMD{
87
88			//! Creates the regular decahedron, Ino decahedron, or truncated
89			//! (Marks) decahedron structures (depending on the parameters).
90			/*!
91			(Heavily modified from Matlab code from:
92			Dmitry, Richard Brown, and Evgeny Pr)
93
94			*/
95			class Decahedron {
96			public:
97			//! Default constructor
98			Decahedron(int columnAtoms, int shells, int twinAtoms);
99			virtual ~Decahedron();
100
101			//! Get the generated points in the cluster.
102			virtual vector<Vector3d> getPoints();
103
104			protected:
105			//! Generate the rings of the Decahedron.
106			vector<Vector3d> truncatedRing( int n, int k );
107
108			int N_; // number of atoms in the central atomic column
109			int M_; // number of {002} shells
110			int K_; // number of atomic columns along twin boundary
111
112			vector<Vector3d> Points;
113			vector<Vector3d> Basis; // Basis vectors of the Decahedron
114			};
115
116			class RegularDecahedron : public Decahedron {
117			public:
118			RegularDecahedron(int shells) : Decahedron(shells-1, shells, shells) {}
119			};
120
121			class InoDecahedron : public Decahedron {
122			public:
123			InoDecahedron(int columnAtoms, int shells) :
124			Decahedron(columnAtoms, shells, columnAtoms) {}
125			};
126
127			class CurlingStoneDecahedron : public Decahedron {
128			public:
129			CurlingStoneDecahedron(int columnAtoms, int shells, int twinAtoms, int truncatedPlanes);
130			vector<Vector3d> getPoints();
131			private:
132			int T_; // number of truncated planes snipped from top and bottom
133			};
134
135			}
136
137			#endif