distopia 0.3.0 compatibility changes

.github/actions/setup-deps/action.yaml

@@ -59,7 +59,7 @@ inputs:
   dask:
     default: 'dask'
   distopia:
-    default: 'distopia>=0.2.0'
+    default: 'distopia>=0.3.0'
   h5py:
     default: 'h5py>=2.10'
   hole2:

package/MDAnalysis/lib/_distopia.py

@@ -36,17 +36,15 @@
 else:
     HAS_DISTOPIA = True
 
-from .c_distances import (
-    calc_bond_distance_triclinic as _calc_bond_distance_triclinic_serial,
-)
+
 import warnings
 import numpy as np
 
 
 def calc_bond_distance_ortho(
     coords1, coords2: np.ndarray, box: np.ndarray, results: np.ndarray
 ) -> None:
-    distopia.calc_bonds_ortho_float(
+    distopia.calc_bonds_ortho(
         coords1, coords2, box[:3], results=results
     )
     # upcast is currently required, change for 3.0, see #3927
@@ -55,7 +53,7 @@
 def calc_bond_distance(
     coords1: np.ndarray, coords2: np.ndarray, results: np.ndarray
 ) -> None:
-    distopia.calc_bonds_no_box_float(
+    distopia.calc_bonds_no_box(
         coords1, coords2, results=results
     )
     # upcast is currently required, change for 3.0, see #3927
@@ -64,8 +62,69 @@
 def calc_bond_distance_triclinic(
     coords1: np.ndarray, coords2: np.ndarray, box: np.ndarray, results: np.ndarray
 ) -> None:
-    # redirect to serial backend
-    warnings.warn(
-        "distopia does not support triclinic boxes, using serial backend instead."
-    )
-    _calc_bond_distance_triclinic_serial(coords1, coords2, box, results)
+    distopia.calc_bonds_triclinic(coords1, coords2, box, results=results)
+
+
+def calc_angle(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_angles_no_box(coords1, coords2, coords3, results=results)
+
+def calc_angle_ortho(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_angles_ortho(coords1, coords2, coords3, box[:3], results=results)
+
+
+def calc_angle_triclinic(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+
+    distopia.calc_angles_triclinic(coords1, coords2, coords3, box, results=results)
+
+
+def calc_dihedral(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, coords4: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_dihedrals_no_box(coords1, coords2, coords3, coords4, results=results)
+
+def calc_dihedral_ortho(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, coords4: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_dihedrals_ortho(coords1, coords2, coords3, coords4, box[:3], results=results)
+
+def calc_dihedral_triclinic(
+    coords1: np.ndarray, coords2: np.ndarray, coords3: np.ndarray, coords4: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_dihedrals_triclinic(coords1, coords2, coords3, coords4, box, results=results)
+
+def calc_distance_array(
+    coords1: np.ndarray, coords2: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_distance_array_no_box(coords1, coords2, results=results)
+
+def calc_distance_array_ortho(
+    coords1: np.ndarray, coords2: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_distance_array_ortho(coords1, coords2, box[:3], results=results)
+
+def calc_distance_array_triclinic(
+    coords1: np.ndarray, coords2: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_distance_array_triclinic(coords1, coords2, box, results=results)
+
+def calc_self_distance_array(
+    coords: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_self_distance_array_no_box(coords, results=results)
+
+def calc_self_distance_array_ortho(
+    coords: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_self_distance_array_ortho(coords, box[:3], results=results)
+
+def calc_self_distance_array_triclinic(
+    coords: np.ndarray, box: np.ndarray, results: np.ndarray
+) -> None:
+    distopia.calc_self_distance_array_triclinic(coords, box, results=results)
+

package/MDAnalysis/lib/distances.py

@@ -61,14 +61,22 @@
 you wish to use is covered by distopia. For more information see the
 `distopia documentation`_.
 
-.. Table:: Functions available using the `distopia`_ backend.
-    :align: center
-
-    +-------------------------------------+-----------------------------------+
-    | Functions                           | Notes                             |
-    +=====================================+===================================+
-    | MDAnalysis.lib.distances.calc_bonds | Doesn't support triclinic boxes   |
-    +-------------------------------------+-----------------------------------+
+.. table:: Functions available using the `distopia`_ backend.
+   :align: center
+
+   +-----------------------------------------------+
+   | Functions                                     |
+   +===============================================+
+   | MDAnalysis.lib.distances.calc_bonds           |
+   +-----------------------------------------------+
+   | MDAnalysis.lib.distances.calc_angles          |
+   +-----------------------------------------------+
+   | MDAnalysis.lib.distances.calc_dihedrals       |
+   +-----------------------------------------------+
+   | MDAnalysis.lib.distances.distance_array       | 
+   +-----------------------------------------------+
+   | MDAnalysis.lib.distances.self_distance_array  |
+   +-----------------------------------------------+
 
 If `distopia`_ is installed, the functions in this table will accept the key
 'distopia' for the `backend` keyword argument. If the distopia backend is
@@ -83,7 +91,7 @@
 
 .. Note::
     Due to the use of Instruction Set Architecture (`ISA`_) specific SIMD
-    intrinsics in distopia via `VCL2`_, the precision of your results may
+    intrinsics in distopia via `HWY`_, the precision of your results may
     depend on the ISA available on your machine. However, in all tested cases
     distopia satisfied the accuracy thresholds used to the functions in this
     module. Please document any issues you encounter with distopia's accuracy
@@ -92,7 +100,7 @@
 .. _distopia: https://github.com/MDAnalysis/distopia
 .. _distopia documentation: https://www.mdanalysis.org/distopia
 .. _ISA: https://en.wikipedia.org/wiki/Instruction_set_architecture
-.. _VCL2: https://github.com/vectorclass/version2
+.. _HWY: https://github.com/google/highway
 .. _relevant distopia issue: https://github.com/MDAnalysis/mdanalysis/issues/3915
 
 .. versionadded:: 0.13.0
@@ -101,6 +109,8 @@
    :class:`~MDAnalysis.core.groups.AtomGroup` or an :class:`np.ndarray`
 .. versionchanged:: 2.5.0
    Interface to the `distopia`_ package added.
+.. versionchanged:: 2.7.0
+    Distopia support greatly expanded.
 
 Functions
 ---------
@@ -303,6 +313,11 @@
     distances = _check_result_array(result, (refnum, confnum))
     if len(distances) == 0:
         return distances
+
+    if backend == 'distopia':
+        distances = distances.astype(np.float32)
+        box = np.asarray(box).astype(np.float32) if box is not None else None
+
     if box is not None:
         boxtype, box = check_box(box)
         if boxtype == 'ortho':
@@ -318,6 +333,9 @@
              args=(reference, configuration, distances),
              backend=backend)
 
+    if backend == 'distopia':
+        distances = distances.astype(np.float64)
+
     return distances
 
 
@@ -1484,13 +1502,14 @@
     """
     numatom = coords1.shape[0]
     bondlengths = _check_result_array(result, (numatom,))
+    if backend == 'distopia':
+        bondlengths = bondlengths.astype(np.float32)
+        box = np.asarray(box).astype(np.float32) if box is not None else None
 
     if numatom > 0:
         if box is not None:
             boxtype, box = check_box(box)
             if boxtype == "ortho":
-                if backend == 'distopia':
-                    bondlengths = bondlengths.astype(np.float32)
                 _run(
                     "calc_bond_distance_ortho",
                     args=(coords1, coords2, box, bondlengths),
@@ -1598,6 +1617,10 @@
     numatom = coords1.shape[0]
     angles = _check_result_array(result, (numatom,))
 
+    if backend == 'distopia':
+        angles = angles.astype(np.float32)
+        box = np.asarray(box).astype(np.float32) if box is not None else None
+
     if numatom > 0:
         if box is not None:
             boxtype, box = check_box(box)
@@ -1614,6 +1637,8 @@
                    args=(coords1, coords2, coords3, angles),
                    backend=backend)
 
+    if backend == 'distopia':
+        angles = angles.astype(np.float64)
     return angles
 
 
@@ -1716,6 +1741,10 @@
     numatom = coords1.shape[0]
     dihedrals = _check_result_array(result, (numatom,))
 
+    if backend == 'distopia':
+        dihedrals = dihedrals.astype(np.float32)
+        box = np.asarray(box).astype(np.float32) if box is not None else None
+
     if numatom > 0:
         if box is not None:
             boxtype, box = check_box(box)
@@ -1731,7 +1760,8 @@
             _run("calc_dihedral",
                  args=(coords1, coords2, coords3, coords4, dihedrals),
                  backend=backend)
-
+    if backend == 'distopia':
+        dihedrals = dihedrals.astype(np.float64)
     return dihedrals