|
48 | 48 |
|
49 | 49 | "OpenMP" :mod:`c_distances_openmp` parallel implementation in C/Cython
|
50 | 50 | with OpenMP
|
51 |
| - "distopia" `_distopia` SIMD-accelerated implementation |
| 51 | +
|
| 52 | + "distopia" `_distopia` SIMD-accelerated implementation |
| 53 | + with the `distopia`_ library |
52 | 54 | ========== ========================= ======================================
|
53 | 55 |
|
| 56 | +
|
54 | 57 | Use of the distopia library
|
55 | 58 | ---------------------------
|
56 | 59 |
|
|
65 | 68 | .. table:: Functions available using the `distopia`_ backend.
|
66 | 69 | :align: center
|
67 | 70 |
|
68 |
| - +-----------------------------------------------+ |
69 |
| - | Functions | |
70 |
| - +===============================================+ |
71 |
| - | MDAnalysis.lib.distances.calc_bonds | |
72 |
| - +-----------------------------------------------+ |
73 |
| - | MDAnalysis.lib.distances.calc_angles | |
74 |
| - +-----------------------------------------------+ |
75 |
| - | MDAnalysis.lib.distances.calc_dihedrals | |
76 |
| - +-----------------------------------------------+ |
77 |
| - | MDAnalysis.lib.distances.distance_array | |
78 |
| - +-----------------------------------------------+ |
79 |
| - | MDAnalysis.lib.distances.self_distance_array | |
80 |
| - +-----------------------------------------------+ |
| 71 | + +-------------------------------------------------------+ |
| 72 | + | Functions | |
| 73 | + +=======================================================+ |
| 74 | + | :func:`MDAnalysis.lib.distances.calc_bonds` | |
| 75 | + +-------------------------------------------------------+ |
| 76 | + | :func:`MDAnalysis.lib.distances.calc_angles` | |
| 77 | + +-------------------------------------------------------+ |
| 78 | + | :func:`MDAnalysis.lib.distances.calc_dihedrals` | |
| 79 | + +-------------------------------------------------------+ |
| 80 | + | :func:`MDAnalysis.lib.distances.distance_array` | |
| 81 | + +-------------------------------------------------------+ |
| 82 | + | :func:`MDAnalysis.lib.distances.self_distance_array` | |
| 83 | + +-------------------------------------------------------+ |
81 | 84 |
|
82 | 85 | If `distopia`_ is installed, the functions in this table will accept the key
|
83 |
| -'distopia' for the `backend` keyword argument. If the distopia backend is |
84 |
| -selected the `distopia` library will be used to calculate the distances. Note |
85 |
| -that for functions listed in this table **distopia is not the default backend |
86 |
| -and must be selected.** |
| 86 | +'distopia' for the `backend` keyword argument. The variable |
| 87 | +:data:`HAS_DISTOPIA` is set to ``True`` if distopia is available. |
| 88 | +
|
| 89 | +If the distopia backend is selected the `distopia` library will be used to |
| 90 | +calculate the distances. Note that for functions listed in this table |
| 91 | +**distopia is not the default backend and must be explicitly selected.** |
87 | 92 |
|
88 | 93 |
|
89 | 94 | .. Note::
|
|
109 | 114 | .. versionchanged:: 2.9.0
|
110 | 115 | Distopia support greatly expanded (with distopia ≥ 0.4.0).
|
111 | 116 |
|
| 117 | +Constants |
| 118 | +--------- |
| 119 | +.. data:: HAS_DISTOPIA |
| 120 | +
|
| 121 | + This variable is ``True`` if the :mod:`distopia` package has been |
| 122 | + installed and is available as a `backend`. Otherwise it is |
| 123 | + ``False``. |
| 124 | +
|
112 | 125 | Functions
|
113 | 126 | ---------
|
114 | 127 | .. autofunction:: distance_array
|
|
124 | 137 | .. autofunction:: augment_coordinates(coordinates, box, r)
|
125 | 138 | .. autofunction:: undo_augment(results, translation, nreal)
|
126 | 139 | .. autofunction:: minimize_vectors(vectors, box)
|
| 140 | +
|
127 | 141 | """
|
128 | 142 | import numpy as np
|
129 | 143 | import numpy.typing as npt
|
|
0 commit comments