OpenMD 3.0
Molecular Dynamics in the Open
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Decahedron.hpp
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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] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
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42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45/*! \file Decahedron.hpp
46 \brief Decahedron cluster structure generator
47*/
48
49/* Original copyright & license text:
50
51Copyright (c) 2011, Dmitry
52Copyright (c) 2009, Richard Brown
53Copyright (c) 2011, Evgeny Pr
54All rights reserved.
55
56Redistribution and use in source and binary forms, with or without
57modification, are permitted provided that the following conditions are
58met:
59
60 * Redistributions of source code must retain the above copyright
61 notice, this list of conditions and the following disclaimer.
62 * Redistributions in binary form must reproduce the above copyright
63 notice, this list of conditions and the following disclaimer in
64 the documentation and/or other materials provided with the distribution
65
66THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
67AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
68IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
69ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
70LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
71CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
72SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
73INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
74CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
75ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
76POSSIBILITY OF SUCH DAMAGE.
77
78*/
79
80#ifndef CLUSTERS_DECAHEDRON_HPP
81#define CLUSTERS_DECAHEDRON_HPP
82
83#include <vector>
84
85#include "math/Vector3.hpp"
86
87using namespace std;
88namespace OpenMD {
89
90 //! Creates the regular decahedron, Ino decahedron, or truncated
91 //! (Marks) decahedron structures (depending on the parameters).
92 /*!
93 (Heavily modified from Matlab code from:
94 Dmitry, Richard Brown, and Evgeny Pr)
95
96 */
97 class Decahedron {
98 public:
99 //! Default constructor
100 Decahedron(int columnAtoms, int shells, int twinAtoms);
101 virtual ~Decahedron() = default;
102
103 //! Get the generated points in the cluster.
104 virtual vector<Vector3d> getPoints();
105
106 protected:
107 //! Generate the rings of the Decahedron.
108 vector<Vector3d> truncatedRing(int n, int k);
109
110 int N_; // number of atoms in the central atomic column
111 int M_; // number of {002} shells
112 int K_; // number of atomic columns along twin boundary
113
114 vector<Vector3d> Points;
115 vector<Vector3d> Basis; // Basis vectors of the Decahedron
116 };
117
119 public:
120 RegularDecahedron(int shells) : Decahedron(shells - 1, shells, shells) {}
121 };
122
123 class InoDecahedron : public Decahedron {
124 public:
125 InoDecahedron(int columnAtoms, int shells) :
126 Decahedron(columnAtoms, shells, columnAtoms) {}
127 };
128
130 public:
131 CurlingStoneDecahedron(int columnAtoms, int shells, int twinAtoms,
132 int truncatedPlanes);
133 vector<Vector3d> getPoints();
134
135 private:
136 int T_; // number of truncated planes snipped from top and bottom
137 };
138} // namespace OpenMD
139
140#endif
vector< Vector3d > getPoints()
Get the generated points in the cluster.
Creates the regular decahedron, Ino decahedron, or truncated (Marks) decahedron structures (depending...
virtual vector< Vector3d > getPoints()
Get the generated points in the cluster.
vector< Vector3d > truncatedRing(int n, int k)
Generate the rings of the Decahedron.
Decahedron(int columnAtoms, int shells, int twinAtoms)
Default constructor.
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.