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# This file is part of xrayutilities.
#
# xrayutilities is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>.
#
# Copyright (C) 2017-2020 Dominik Kriegner <dominik.kriegner@gmail.com>
import math
import unittest
import numpy
import xrayutilities as xu
from numpy import arccos, cos, radians, sin, sqrt
class TestMaterialsTransform(unittest.TestCase):
@classmethod
def setUp(cls):
cls.a, cls.b, cls.c = numpy.random.rand(3) * 2 + 4
cls.alpha, cls.beta, cls.gamma = numpy.random.rand(3) * 60 + 60
cls.p1mat = xu.materials.Crystal(
'P1', xu.materials.SGLattice(1, cls.a, cls.b, cls.c,
cls.alpha, cls.beta, cls.gamma))
def test_q2hkl_hkl2q(self):
for i in range(3):
hkls = numpy.random.randint(-5, 6, 3)
qvec = self.p1mat.Q(hkls)
backhkl = self.p1mat.HKL(qvec)
for j in range(3):
self.assertAlmostEqual(hkls[j], backhkl[j], places=10)
def test_Bmatrix(self):
"""
check if our B matrix is compatible with the one from
Busing&Levy Acta Cryst. 22, 457 (1967)
"""
ca = cos(radians(self.alpha))
cb = cos(radians(self.beta))
cg = cos(radians(self.gamma))
sa = sin(radians(self.alpha))
sb = sin(radians(self.beta))
sg = sin(radians(self.gamma))
vh = sqrt(1 - ca**2-cb**2-cg**2 + 2*ca*cb*cg)
pi2 = numpy.pi * 2
ra, rb, rc = pi2*sa/(self.a*vh), pi2*sb/(self.b*vh), pi2*sg/(self.c*vh)
# cralpha = (cb*cg - ca)/(sb*sg)
crbeta = (ca*cg - cb)/(sa*sg)
crgamma = (ca*cb - cg)/(sa*sb)
b = numpy.zeros((3, 3))
b[0, 0] = ra
b[0, 1] = rb * crgamma
b[1, 1] = rb * sin(arccos(crgamma))
b[0, 2] = rc * crbeta
b[1, 2] = -rc * sin(arccos(crbeta)) * ca
b[2, 2] = pi2 / self.c
for j in range(9):
self.assertAlmostEqual(b.flat[j], self.p1mat.B.flat[j], places=10)
def test_Bmatrix_after_a_setter(self):
self.a = numpy.random.rand() * 2 + 4
self.p1mat.lattice.a = self.a
self.test_Bmatrix()
def test_Bmatrix_after_alpha_setter(self):
self.alpha = numpy.random.rand() * 60 + 60
self.p1mat.lattice.alpha = self.alpha
self.test_Bmatrix()
def test_Bmatrix_after_all_setters(self):
# change materials unit cell parameters to test setters
self.a, self.b, self.c = numpy.random.rand(3) * 2 + 4
self.alpha, self.beta, self.gamma = numpy.random.rand(3) * 60 + 60
self.p1mat.lattice.a = self.a
self.p1mat.lattice.b = self.b
self.p1mat.lattice.c = self.c
self.p1mat.lattice.alpha = self.alpha
self.p1mat.lattice.beta = self.beta
self.p1mat.lattice.gamma = self.gamma
self.test_Bmatrix()
def test_environment(self):
maxdist = max(self.a, self.b, self.c) + 0.01
e = self.p1mat.environment((0, 0, 0), maxdist=maxdist)
self.assertTrue(len(e) >= 4,
f"Length of environment must be >= 4, is {len(e)}")
for dis in (0.0, self.a, self.b, self.c):
found = False
for d, at, mult in e:
if numpy.isclose(d, dis):
found = True
self.assertTrue(found, "expected atomic distance not found")
def test_environment_Si(self):
a = xu.materials.Si.a
e = xu.materials.Si.environment(0.125, 0.125, 0.125)
self.assertAlmostEqual(e[0][0], a*math.sqrt(3)/8, places=10)
self.assertEqual(e[0][1], xu.materials.elements.Si)
self.assertAlmostEqual(e[0][2], 2.0)
def test_isequivalent(self):
hkl1 = (1, 2, 3)
materials = ['C', 'C_HOPG', 'TiO2', 'GeTe', 'Ag2Se']
hkl2lst = [((2, 1, -3), (2, 2, 3)),
((1, -3, 3), (1, -2, 3)),
((-2, 1, 3), (3, 2, 1)),
((1, 3, 2), (1, 3, -2)),
((1, -2, -3), (1, 3, 2))]
for mname, hkl2s in zip(materials, hkl2lst):
mat = getattr(xu.materials, mname)
self.assertTrue(mat.lattice.isequivalent(hkl1, hkl2s[0]))
self.assertFalse(mat.lattice.isequivalent(hkl1, hkl2s[1]))
if __name__ == '__main__':
unittest.main()
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