Merge pull request #943 from glotzerlab/fix/noncubic-diffraction

Fix/noncubic diffraction

ChangeLog.md

@@ -8,6 +8,7 @@ and this project adheres to
 
 ### Added
 * (breaking) Some `freud.diffraction.StaticStructureFactorDebye` property names changed to be more descriptive.
+* `freud.diffraction.DiffractionPattern` now raises an exception when used with non-cubic boxes.
 
 ### Fixed
 * `freud.diffraction.StaticStructureFactorDebye` implementation now gives `S_k[0] = N`.

doc/source/reference/credits.rst

@@ -329,6 +329,7 @@ Tommy Waltmann
 * Remove CI build configurations from CircleCI which were already covered by CIBuildWheel.
 * Change property names in ``StaticStructureFactorDebye`` class.
 * Reformat static structure factor tests.
+* ``DiffractionPattern`` now raises an error when used with non-cubic boxes.
 
 Maya Martirossyan
 

freud/box.pyx

@@ -592,6 +592,20 @@ cdef class Box:
 
         return np.array(l_contains_mask).astype(bool)
 
+    @property
+    def cubic(self):
+        """bool: Whether the box is a cube."""
+        return (
+            not self.is2D
+            and np.allclose(
+                [self.Lx, self.Lx, self.Ly, self.Ly, self.Lz, self.Lz],
+                [self.Ly, self.Lz, self.Lx, self.Lz, self.Lx, self.Ly],
+                rtol=1e-5,
+                atol=1e-5,
+            )
+            and np.allclose(0, [self.xy, self.yz, self.xz], rtol=1e-5, atol=1e-5)
+        )
+
     @property
     def periodic(self):
         r""":math:`\left(3, \right)` :class:`numpy.ndarray`: Get or set the

freud/diffraction.pyx

@@ -565,6 +565,9 @@ cdef class DiffractionPattern(_Compute):
     `GIXStapose application <https://github.com/cmelab/GIXStapose>`_ and its
     predecessor, diffractometer :cite:`Jankowski2017`.
 
+    Note:
+        freud only supports diffraction patterns for cubic boxes.
+
     Args:
         grid_size (unsigned int):
             Resolution of the diffraction grid (Default value = 512).
@@ -731,6 +734,10 @@ cdef class DiffractionPattern(_Compute):
 
         system = freud.locality.NeighborQuery.from_system(system)
 
+        if not system.box.cubic:
+            raise ValueError("freud.diffraction.DiffractionPattern only "
+                             "supports cubic boxes")
+
         if view_orientation is None:
             view_orientation = np.array([1., 0., 0., 0.])
         view_orientation = freud.util._convert_array(

tests/test_box_Box.py

@@ -374,6 +374,21 @@ def test_vectors(self):
         npt.assert_allclose(box.get_box_vector(2), [xz * Lz, yz * Lz, Lz])
         npt.assert_allclose(box.v3, [xz * Lz, yz * Lz, Lz])
 
+    @pytest.mark.parametrize(
+        "box_params, answer",
+        [
+            (dict(Lx=1, Ly=1, Lz=1), True),
+            (dict(Lx=2, Ly=1, Lz=4), False),
+            (dict(Lx=1, Ly=1, Lz=1, xz=0.25), False),
+            (dict(Lx=3, Ly=3, Lz=3), True),
+            (dict(Lx=3, Ly=3, Lz=3, yz=0.01), False),
+            (dict(Lx=0.01, Ly=1, Lz=10000, xy=0.75), False),
+        ],
+    )
+    def test_cubic(self, box_params, answer):
+        box = freud.box.Box(**box_params)
+        assert box.cubic is answer
+
     def test_periodic(self):
         box = freud.box.Box(1, 2, 3, 0, 0, 0)
         npt.assert_array_equal(box.periodic, True)

tests/test_diffraction_DiffractionPattern.py

@@ -285,3 +285,13 @@ def test_cubic_system_parameterized(self):
                                 ideal_peaks[peak] = True
 
                     assert all(ideal_peaks.values())
+
+    @pytest.mark.parametrize(
+        "noncubic_box_params", [dict(Lx=3, Ly=4, Lz=1), dict(Lx=3, Ly=3, Lz=3, xy=0.21)]
+    )
+    def test_noncubic_system(self, noncubic_box_params):
+        box = freud.box.Box(**noncubic_box_params)
+        points = [[0, 0, 0]]
+        dp = freud.diffraction.DiffractionPattern()
+        with pytest.raises(ValueError):
+            dp.compute((box, points))