Skip to content

Bugfix for get_points_in_sphere (Superceded by #60) #57

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
wants to merge 2 commits into from
Closed

Bugfix for get_points_in_sphere (Superceded by #60) #57

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
d1449db
Change as discussed in #56
pc494 Jan 28, 2020
133e2d2
Makes a local import global
pc494 Jan 28, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 5 additions & 4 deletions diffsims/utils/sim_utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
from scipy.constants import h, m_e, e, c, pi
import collections
import diffpy.structure
from itertools import product

from transforms3d.axangles import axangle2mat
from transforms3d.euler import mat2euler
Expand Down Expand Up @@ -372,7 +373,7 @@ def simulate_rotated_structure(diffraction_generator, structure, rotation_matrix
stdbase = structure.lattice.stdbase
stdbase_inverse = np.linalg.inv(stdbase)
rotation_matrix_diffpy = stdbase_inverse @ rotation_matrix @ stdbase

lattice_rotated = diffpy.structure.lattice.Lattice(
*structure.lattice.abcABG(),
baserot=rotation_matrix_diffpy)
Expand Down Expand Up @@ -407,16 +408,16 @@ def get_points_in_sphere(reciprocal_lattice, reciprocal_radius):
spot_distances : numpy.array
Distance of reciprocal lattice points in sphere from the origin.
"""
a, b, c = reciprocal_lattice.a, reciprocal_lattice.b, reciprocal_lattice.c
standard_base = diffpy.structure.lattice.Lattice(base=reciprocal_lattice.stdbase)
a, b, c = standard_base.a, standard_base.b, standard_base.c
h_max = np.floor(reciprocal_radius / a)
k_max = np.floor(reciprocal_radius / b)
l_max = np.floor(reciprocal_radius / c)
from itertools import product
h_list = np.arange(-h_max, h_max + 1) #arange has a non-inclusive endpoint
k_list = np.arange(-k_max, k_max + 1)
l_list = np.arange(-l_max, l_max + 1)
potential_points = np.asarray(list(product(h_list, k_list, l_list)))
in_sphere = np.abs(reciprocal_lattice.dist(potential_points, [0, 0, 0])) < reciprocal_radius
in_sphere = np.abs(standard_base.dist(potential_points, [0, 0, 0])) < reciprocal_radius
spot_indicies = potential_points[in_sphere]
spot_coords = reciprocal_lattice.cartesian(spot_indicies)
spot_distances = reciprocal_lattice.dist(spot_indicies, [0, 0, 0])
Expand Down