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304 lines (275 loc) · 9.54 KB
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#!/usr/bin/env python
##############################################################################
#
# diffpy.structure Complex Modeling Initiative
# (c) 2016 Brookhaven Science Associates,
# Brookhaven National Laboratory.
# All rights reserved.
#
# File coded by: Pavol Juhas
#
# See AUTHORS.txt for a list of people who contributed.
# See LICENSE.txt for license information.
#
##############################################################################
"""Unit tests for the Atom class."""
import unittest
import numpy
import pytest
from diffpy.structure.atom import Atom
from diffpy.structure.lattice import Lattice
# ----------------------------------------------------------------------------
class TestAtom(unittest.TestCase):
def test___init__(self):
"""Check Atom.__init__()"""
a = Atom()
self.assertEqual("", a.element)
self.assertTrue((a.xyz == 0).all())
self.assertEqual("", a.label)
self.assertEqual(1.0, a.occupancy)
self.assertFalse(a.anisotropy)
self.assertTrue((a.U == 0).all())
self.assertTrue(a.lattice is None)
# check initialization with arguments
a1 = Atom("C", xyz=(1, 2, 3), Uisoequiv=0.005)
self.assertEqual("C", a1.element)
self.assertTrue(numpy.array_equal([1, 2, 3], a1.xyz))
self.assertFalse(a1.anisotropy)
self.assertEqual(0.005, a1.Uisoequiv)
# initialize with anisotropic displacement parameters
uani = numpy.identity(3, dtype=float) * numpy.array([1, 2, 3]) * 0.01
a2 = Atom("C", U=uani)
self.assertTrue(numpy.array_equal(uani, a2.U))
self.assertTrue(a2.anisotropy)
a3 = Atom("C", Uisoequiv=0.02, anisotropy=True)
self.assertTrue(a3.anisotropy)
self.assertEqual(a3.U[2, 2], 0.02)
self.assertRaises(ValueError, Atom, "C", Uisoequiv=0.02, U=uani)
return
# def test_msdLat(self):
# """check Atom.msdLat()
# """
# return
#
# def test_msdCart(self):
# """check Atom.msdCart()
# """
# return
#
# def test___repr__(self):
# """check Atom.__repr__()
# """
# return
#
# def test___copy__(self):
# """check Atom.__copy__()
# """
# return
def test_msdLat(self):
"""Check Atom.msdLat."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
atom_1 = Atom("C", [0, 0, 0], lattice=hexagonal, Uisoequiv=0.0123)
assert atom_1.msdLat([1, 2, 3]) == pytest.approx(0.0123, rel=0, abs=1e-15)
assert atom_1.msdLat([9, 0, -4]) == pytest.approx(0.0123, rel=0, abs=1e-15)
U = numpy.array(
[
[0.010, 0.002, 0.001],
[0.002, 0.020, 0.003],
[0.001, 0.003, 0.030],
],
dtype=float,
)
atom_2 = Atom("C", [0, 0, 0], lattice=hexagonal, U=U)
vc = numpy.array([1.2, -0.3, 0.7], dtype=float)
vl = hexagonal.fractional(vc)
assert atom_2.msdLat(vl) == pytest.approx(atom_2.msd_cart(vc), rel=1e-13, abs=1e-13)
def test_msdCart(self):
"""Check Atom.msdCart."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
atom_1 = Atom("C", [0, 0, 0], lattice=hexagonal, Uisoequiv=0.0456)
assert atom_1.msdCart([1, 0, 0]) == pytest.approx(0.0456, rel=0, abs=1e-15)
assert atom_1.msdCart([0, 5, -2]) == pytest.approx(0.0456, rel=0, abs=1e-15)
assert atom_1.msdCart([0, 5, -2]) == pytest.approx(0.0456, rel=0, abs=1e-15)
U = numpy.array(
[
[0.011, 0.001, 0.000],
[0.001, 0.019, 0.002],
[0.000, 0.002, 0.027],
],
dtype=float,
)
atom_2 = Atom("C", [0, 0, 0], lattice=hexagonal, U=U)
vc = numpy.array([0.4, 1.1, -0.6], dtype=float)
assert atom_2.msdCart(vc) == pytest.approx(atom_2.msdCart(3.7 * vc), rel=1e-13, abs=1e-13)
def test_xyz_cartn(self):
"""Check Atom.xyz_cartn property."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
a0 = Atom("C", [0, 0, 0], lattice=hexagonal)
a1 = Atom("C", [1, 1, 1], lattice=hexagonal)
self.assertTrue(all(a0.xyz_cartn == 0))
rc1 = numpy.array([0.75**0.5, 0.5, 1])
self.assertTrue(numpy.allclose(rc1, a1.xyz_cartn))
a1.xyz_cartn[2] = 0
self.assertTrue(numpy.allclose([1, 1, 0], a1.xyz))
a1.xyz_cartn[:2] = 0
self.assertTrue(all(a1.xyz == 0))
a3 = Atom("C", [1, 2, 3])
self.assertTrue(numpy.array_equal(a3.xyz, a3.xyz_cartn))
a3.xyz_cartn = 1.3
self.assertTrue(all(1.3 == a3.xyz_cartn))
self.assertTrue(all(1.3 == a3.xyz))
return
# def test__get_anisotropy(self):
# """check Atom._get_anisotropy()
# """
# return
#
# def test__set_anisotropy(self):
# """check Atom._set_anisotropy()
# """
# return
#
# def test__get_U(self):
# """check Atom._get_U()
# """
# return
#
# def test__set_U(self):
# """check Atom._set_U()
# """
# return
#
# def test__get_Uij(self):
# """check Atom._get_Uij()
# """
# return
#
# def test__set_Uij(self):
# """check Atom._set_Uij()
# """
# return
#
# def test__get_Uisoequiv(self):
# """check Atom._get_Uisoequiv()
# """
# return
#
# def test__set_Uisoequiv(self):
# """check Atom._set_Uisoequiv()
# """
# return
#
# def test__get_Bisoequiv(self):
# """check Atom._get_Bisoequiv()
# """
# return
#
# def test__set_Bisoequiv(self):
# """check Atom._set_Bisoequiv()
# """
# return
# End of class TestAtom
# ----------------------------------------------------------------------------
@pytest.mark.parametrize(
"uiso, lattice_vector",
[ # C1: isotropic displacement, msd is direction-independent in lattice coordinates.
# Expected the msd_latt equals Uisoequiv for any direction.
(0.0123, [1, 2, 3]),
],
)
def test_msd_latt_isotropic(uiso, lattice_vector):
"""Check Atom.msd_latt()."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
atom = Atom("C", [0, 0, 0], lattice=hexagonal, Uisoequiv=uiso)
actual = atom.msd_latt(lattice_vector)
expected = pytest.approx(uiso, rel=0, abs=1e-15)
assert actual == expected
@pytest.mark.parametrize(
"U, cartesian_vector",
[ # C2: anisotropic displacement with same physical direction expressed in lattice vs cartesian coords
# Expected msd_latt(fractional(cartesian_vector)) == msd_cart(cartesian_vector)
(
numpy.array(
[
[0.010, 0.002, 0.001],
[0.002, 0.020, 0.003],
[0.001, 0.003, 0.030],
],
dtype=float,
),
numpy.array([1.2, -0.3, 0.7], dtype=float),
),
(
numpy.array(
[
[0.018, -0.001, 0.002],
[-0.001, 0.012, 0.004],
[0.002, 0.004, 0.025],
],
dtype=float,
),
numpy.array([-0.8, 0.9, 0.1], dtype=float),
),
],
)
def test_msd_latt_anisotropic(U, cartesian_vector):
"""Check Atom.msd_latt() anisotropic coordinate-invariance."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
atom = Atom("C", [0, 0, 0], lattice=hexagonal, U=U)
lattice_vector = hexagonal.fractional(cartesian_vector)
actual = atom.msd_latt(lattice_vector)
expected = pytest.approx(atom.msd_cart(cartesian_vector), rel=1e-13, abs=1e-13)
assert actual == expected
@pytest.mark.parametrize(
"uiso, cartesian_vector",
[ # C1: isotropic displacement with msd is direction-independent in cartesian coordinates
# Expected msd_cart equals Uisoequiv for any direction
(0.0456, [0, 5, -2]),
],
)
def test_msd_cart_isotropic(uiso, cartesian_vector):
"""Check Atom.msd_cart()."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
atom = Atom("C", [0, 0, 0], lattice=hexagonal, Uisoequiv=uiso)
actual = atom.msd_cart(cartesian_vector)
expected = pytest.approx(uiso, rel=0, abs=1e-15)
assert actual == expected
@pytest.mark.parametrize(
"U, cartesian_vector, scale",
[ # C2: anisotropic displacement with msd_cart normalizes direction vector internally
# Expected msd_cart(cartesian_vector) == msd_cart(scale * cartesian_vector)
(
numpy.array(
[
[0.011, 0.001, 0.000],
[0.001, 0.019, 0.002],
[0.000, 0.002, 0.027],
],
dtype=float,
),
numpy.array([0.4, 1.1, -0.6], dtype=float),
3.7,
),
(
numpy.array(
[
[0.020, 0.003, -0.001],
[0.003, 0.014, 0.002],
[-0.001, 0.002, 0.009],
],
dtype=float,
),
numpy.array([2.0, -1.0, 0.5], dtype=float),
0.25,
),
],
)
def test_msd_cart_anisotropic(U, cartesian_vector, scale):
"""Check Atom.msd_cart() anisotropic normalization invariance."""
hexagonal = Lattice(1, 1, 1, 90, 90, 120)
atom = Atom("C", [0, 0, 0], lattice=hexagonal, U=U)
actual = atom.msd_cart(cartesian_vector)
expected = pytest.approx(atom.msd_cart(scale * cartesian_vector), rel=1e-13, abs=1e-13)
assert actual == expected
if __name__ == "__main__":
unittest.main()
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