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Add feature for multiple lattice parameters/phases in polycrystal_from_odf #16

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Sep 17, 2024
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Add feature for multiple lattice parameters/phases in polycrystal_from_odf #16

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Add feature for multiple lattice parameters/phases in polycrystal_fro…
vamatya Aug 29, 2024
c3e1dc9
1. Update definition for input parameters
vamatya Sep 2, 2024
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27 changes: 19 additions & 8 deletions xrd_simulator/templates.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,7 @@ def polycrystal_from_odf(
path_to_cif_file=None,
maximum_sampling_bin_seperation=np.radians(5.0),
strain_tensor=lambda x: np.zeros((3, 3)),
phase_fractions=None
):
"""Fill a cylinder with crystals from a given orientation density function.

Expand All @@ -117,11 +118,11 @@ def polycrystal_from_odf(
microns.
sample_bounding_cylinder_radius (:obj:`float`): Radius of sample cylinder in units of
microns.
unit_cell (:obj:`list` of :obj:`float`): Crystal unit cell representation of the form
[a,b,c,alpha,beta,gamma], where alpha,beta and gamma are in units of degrees while
unit_cell (:obj:`list of lists` of :obj:`float`): Crystal unit cell representation of the form
[[a,b,c,alpha,beta,gamma],], where alpha,beta and gamma are in units of degrees while
a,b and c are in units of anstrom.
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Can we add a sentence to each of these arguments which specify that "When unit_cell is an iterable with several instances of unit cell parameters, the polycrystal represents a multi-phase material."

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This is updated.

sgname (:obj:`string`): Name of space group , e.g 'P3221' for quartz, SiO2, for instance
path_to_cif_file (:obj:`string`): Path to CIF file. Defaults to None, in which case no structure
sgname (:obj:`list of strings`): Name of space group , e.g ['P3221',] for quartz, SiO2, for instance
path_to_cif_file (:obj:`list of strings`): [Path to CIF file,]. Defaults to None, in which case no structure
factors are computed.
maximum_sampling_bin_seperation (:obj:`float`): Discretization steplength of orientation
space using spherical coordinates over the unit quarternions in units of radians.
Expand All @@ -131,6 +132,8 @@ def polycrystal_from_odf(
strain_tensor(x) -> :obj:`numpy array` of shape ``(3,3)`` where input variable ``x`` is
a :obj:`numpy array` of shape ``(3,)`` representing a spatial coordinate in the
cylinder (x,y,z).
phase_fraction (:obj: `list` of :obj:`float`): Phase fraction represented as probability, summing up to 1.
Default None; will take even distribution of crystals.

Returns:
(:obj:`xrd_simulator.polycrystal.Polycrystal`)
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We also neeed to edit the example file. c.f docs/source/examples/example_polycrystal_from_odf.py

This example is included into the docs so it now needs to reflect the changes. I suggest to make it a simple 2-phase material example.

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I added a 2 phase example, albeit with trivial input values.

Expand Down Expand Up @@ -168,10 +171,18 @@ def polycrystal_from_odf(
)

mesh = TetraMesh._build_tetramesh(cylinder)

# Sample is uniformly single phase
phases = [Phase(unit_cell, sgname, path_to_cif_file)]
element_phase_map = np.zeros((mesh.number_of_elements,)).astype(int)

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This looks solid to me. :=)

Altough, we need to make the unit tests pass / add one for the case of multi phase.

phases = [Phase(uc, sg, cf) for uc, sg, cf in zip(unit_cell, sgname, path_to_cif_file)]
if len(phases) == 1:
# Sample is uniformly single phase
element_phase_map = np.zeros((mesh.number_of_elements,)).astype(int)
elif phase_fractions is None:
# Sample is uniformly distributed phases
element_phase_map = np.random.randint(len(phases), size=(mesh.number_of_elements,))
else :
# Sample is distributed by phase fraction
probabilities = np.array(phase_fractions)
element_phase_map = np.random.choice(len(phases), size=(mesh.number_of_elements,), p=probabilities)

# Sample spatial texture
orientation = _sample_ODF(
Expand Down
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