OpenMD 3.0
Molecular Dynamics in the Open
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AlphaHull.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).
39 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
40 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
41 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
42 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
43 */
44
45#ifndef MATH_ALPHAHULL_HPP_
46#define MATH_ALPHAHULL_HPP_
47
48#include <config.h>
49
50#include <cassert>
51#include <string>
52#include <vector>
53
54#include "math/Hull.hpp"
55#include "math/Triangle.hpp"
56#include "math/Vector3.hpp"
57
58namespace OpenMD {
59
60 /**
61 * @class AlphaHull
62 * @brief Compute alpha complex or alpha shape
63 *
64 * Builds the alpha shape (H. Edelsbrunner and P.Mucke,
65 * "Three-dimensional Alpha Shapes," ACM Trans. Graph. 13, 1994) from a
66 * set of atomic locations using the Qhull library,
67 * http://www.qhull.org/
68 *
69 * For a given value of \f$\alpha\f$, the \f$\alpha\f$-shape
70 * includes all of the tetrahedra in the Delaunay triangulation
71 * which have an empty circumsphere with radius equal or smaller
72 * than \f$\alpha\f$. To carry out this calculation, all points are
73 * lifted to 4D so that each point is \f$(x, y, z, x^2+y^2+z^2)\f$.
74 * The convex hull is computed in 4D, and tetrahedral facets with
75 * circumsphere radii larger than \f$\alpha\f$ are removed.
76 *
77 * \param alpha the circumsphere radius to test tetrahedra for elimination
78 */
79 class AlphaHull : public Hull {
80 public:
81 AlphaHull(RealType alpha);
82 virtual ~AlphaHull() {};
83
84 void computeHull(std::vector<StuntDouble*> bodydoubles);
85
86 /* Total area of Hull*/
87 RealType getArea() { return area_; }
88
89 /* Total Volume enclosed by Hull */
90 RealType getVolume() { return volume_; }
91
92 vector<Triangle> getMesh() { return Triangles_; }
93
94 protected:
95 int dim_;
96 RealType alpha_;
97 const std::string options_;
98
99 private:
100 // These variables are private so that each new hull returns
101 // information about itself.
102 RealType volume_;
103 RealType area_;
104 std::vector<Triangle> Triangles_;
105 };
106} // namespace OpenMD
107
108#endif
Compute alpha complex or alpha shape.
Definition AlphaHull.hpp:79
This basic Periodic Table class was originally taken from the data.cpp file in OpenBabel.