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Fix k-value/k-vector units for non-cubic systems #793

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Fix k-value/k-vector units for non-cubic systems #793

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5f8d785
Additional explanation and example in diffraction docs.
andkerr Jun 15, 2021
805aadf
Docs edit.
andkerr Jun 15, 2021
04a6583
Docs edit.
andkerr Jun 15, 2021
8e3adbc
Docs edit.
andkerr Jun 15, 2021
03761e8
Create empty tests w/ TODOs.
andkerr Jun 16, 2021
12e016f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 16, 2021
7ca562f
Add intersphinx reference to vector_vector_rotation.
bdice Jun 24, 2021
f7947be
Update code snippet.
bdice Jun 24, 2021
d4e3840
Merge branch 'master' into fix/non-cubic-diffraction
bdice Jun 24, 2021
a5fddf9
updated tests to cover more systems and better align with Tim's imple…
andkerr Aug 30, 2021
d591406
Merge branch 'fix/non-cubic-diffraction' of https://github.com/glotze…
andkerr Aug 30, 2021
732f63f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 30, 2021
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1 change: 1 addition & 0 deletions doc/source/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -320,6 +320,7 @@
"MDAnalysis": ("https://docs.mdanalysis.org/stable", None),
"ovito": ("https://www.ovito.org/docs/current/python/", None),
"pytest": ("https://docs.pytest.org/en/stable", None),
"rowan": ("https://rowan.readthedocs.io/en/stable/", None),
}

autodoc_default_options = {
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23 changes: 21 additions & 2 deletions freud/diffraction.pyx
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Expand Up @@ -169,7 +169,7 @@ cdef class DiffractionPattern(_Compute):
roll_shift -= 0.5 / zoom

box_matrix = box.to_matrix()
ss = np.max(box_matrix) * inv_shear
ss = np.max(box_matrix[:, 0:2]) * inv_shear

shift_matrix = np.array(
[[1, 0, -roll],
Expand Down Expand Up @@ -217,6 +217,23 @@ cdef class DiffractionPattern(_Compute):
Whether to erase the previously computed values before adding
the new computations; if False, will accumulate data (Default
value: True).

For a target view axis in Cartesian coordinates, `rowan
<https://rowan.readthedocs.io/en/latest/index.html>`__ provides
:py:func:`rowan.vector_vector_rotation`, a function that will return
the necessary quaternion for rotating the default view orientation to
the desired axis.

Example::

>>> import rowan
>>> import numpy as np
>>> default_view_axis = np.array([0, 0, 1])
>>> desired_view_axis = np.array([1, 1, 1])
>>> view_orientation = rowan.vector_vector_rotation(
... default_view_axis, desired_view_axis
... )

"""
if reset:
self._diffraction = np.zeros((self.output_size, self.output_size))
Expand Down Expand Up @@ -277,7 +294,9 @@ cdef class DiffractionPattern(_Compute):

# Cache the view orientation and box matrix scale factor for
# lazy evaluation of k-values and k-vectors
self._box_matrix_scale_factor = np.max(system.box.to_matrix())
self._box_matrix_scale_factor = np.max(
rowan.rotate(view_orientation, system.box.to_matrix())[:, 0:2]
)
self._view_orientation = view_orientation
self._k_scale_factor = 2 * np.pi * self.output_size / (self._box_matrix_scale_factor * zoom)
self._k_values_cached = False
Expand Down
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