Decahedron.hpp

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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
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 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
/*! \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() = default;
 
    //! 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
  };
}  // namespace OpenMD
 
#endif