4075885785

Build Type

push

github

Committed by Shyue Ping Ong

Commit Message

Merge branch 'master' of github.com:materialsproject/pymatgen

Run Details

96 of 96 new or added lines in 27 files covered. (100.0%)

81013 of 102710 relevant lines covered (78.88%)

0.79 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

68.0

/pymatgen/analysis/tests/test_wulff.py

from __future__ import annotations

import json
import os
import unittest

from pytest import approx

from pymatgen.analysis.wulff import WulffShape
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.coord import in_coord_list
from pymatgen.util.testing import PymatgenTest

__author__ = "Zihan Xu, Richard Tran, Balachandran Radhakrishnan"
__copyright__ = "Copyright 2013, The Materials Virtual Lab"
__version__ = "0.1"
__maintainer__ = "Zihan Xu"
__email__ = "zix009@eng.ucsd.edu"
__date__ = "May 05 2016"


class WulffShapeTest(PymatgenTest):
    def setUp(self):
        module_dir = os.path.dirname(os.path.abspath(__file__))
        with open(os.path.join(module_dir, "surface_samples.json")) as data_file:
            surface_properties = json.load(data_file)

        surface_energies, miller_indices = {}, {}
        for mpid in surface_properties:
            e_surf_list, miller_list = [], []
            for surface in surface_properties[mpid]["surfaces"]:
                e_surf_list.append(surface["surface_energy"])
                miller_list.append(surface["miller_index"])
            surface_energies[mpid] = e_surf_list
            miller_indices[mpid] = miller_list

        # In the case of a high anisotropy material
        # Nb: mp-8636
        latt_Nb = Lattice.cubic(2.992)
        # In the case of an fcc material
        # Ir: mp-101
        latt_Ir = Lattice.cubic(3.8312)
        # In the case of a hcp material
        # Ti: mp-72
        latt_Ti = Lattice.hexagonal(4.6000, 2.8200)
        self.ucell_Nb = Structure(
            latt_Nb,
            ["Nb", "Nb", "Nb", "Nb"],
            [[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
        )
        self.wulff_Nb = WulffShape(latt_Nb, miller_indices["mp-8636"], surface_energies["mp-8636"])

        self.ucell_Ir = Structure(
            latt_Nb,
            ["Ir", "Ir", "Ir", "Ir"],
            [[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
        )
        self.wulff_Ir = WulffShape(latt_Ir, miller_indices["mp-101"], surface_energies["mp-101"])

        self.ucell_Ti = Structure(
            latt_Ti,
            ["Ti", "Ti", "Ti"],
            [[0, 0, 0], [0.333333, 0.666667, 0.5], [0.666667, 0.333333, 0.5]],
        )
        self.wulff_Ti = WulffShape(latt_Ti, miller_indices["mp-72"], surface_energies["mp-72"])
        self.cube = WulffShape(Lattice.cubic(1), [(1, 0, 0)], [1])
        self.hex_prism = WulffShape(Lattice.hexagonal(2.63, 5.21), [(0, 0, 1), (1, 0, 0)], [0.35, 0.53])

        self.surface_properties = surface_properties

    @unittest.skipIf("DISPLAY" not in os.environ, "Need display")
    def test_get_plot(self):
        # Basic test, not really a unittest.
        self.wulff_Ti.get_plot()
        self.wulff_Nb.get_plot()
        self.wulff_Ir.get_plot()

    @unittest.skipIf("DISPLAY" not in os.environ, "Need display")
    def test_get_plotly(self):
        # Basic test, not really a unittest.
        self.wulff_Ti.get_plotly()
        self.wulff_Nb.get_plotly()
        self.wulff_Ir.get_plotly()

    def symm_check(self, ucell, wulff_vertices):
        """
        # Checks if the point group of the Wulff shape matches
        # the point group of its conventional unit cell

        Args:
            ucell (str): Unit cell that the Wulff shape is based on.
            wulff_vertices (list): List of all vertices on the Wulff
                shape. Use wulff.wulff_pt_list to obtain the list
                (see wulff_generator.py).

        return (bool)
        """
        space_group_analyzer = SpacegroupAnalyzer(ucell)
        symm_ops = space_group_analyzer.get_point_group_operations(cartesian=True)
        for point in wulff_vertices:
            for op in symm_ops:
                symm_point = op.operate(point)
                if in_coord_list(wulff_vertices, symm_point):
                    continue
                else:
                    return False
        return True

    def consistency_tests(self):
        # For a set of given values, these tests will
        # ensure that the general result given by the
        # algorithm does not change as the code is edited

        # For fcc Ir, make sure the (111) direction
        # is the most dominant facet on the Wulff shape

        fractional_areas = self.wulff_Ir.area_fraction_dict
        miller_list = [hkl for hkl in fractional_areas]
        area_list = [fractional_areas[hkl] for hkl in fractional_areas]
        assert miller_list[area_list.index(max(area_list))] == (1, 1, 1)

        # Overall weighted surface energy of fcc Nb should be
        # equal to the energy of the (310) surface, ie. fcc Nb
        # is anisotropic, the (310) surface is so low in energy,
        # its the only facet that exists in the Wulff shape

        Nb_area_fraction_dict = self.wulff_Nb.area_fraction_dict
        for hkl in Nb_area_fraction_dict:
            if hkl == (3, 1, 0):
                assert Nb_area_fraction_dict[hkl] == 1
            else:
                assert Nb_area_fraction_dict[hkl] == 0

        assert self.wulff_Nb.miller_energy_dict[(3, 1, 0)] == self.wulff_Nb.weighted_surface_energy

    def symmetry_test(self):
        # Maintains that all wulff shapes have the same point
        # groups as the conventional unit cell they were
        # derived from. This test should pass for all subsequent
        # updates of the surface_properties collection

        check_symmetry_Nb = self.symm_check(self.ucell_Nb, self.wulff_Nb.wulff_pt_list)
        check_symmetry_Ir = self.symm_check(self.ucell_Ir, self.wulff_Ir.wulff_pt_list)
        check_symmetry_Ti = self.symm_check(self.ucell_Ti, self.wulff_Ti.wulff_pt_list)
        assert check_symmetry_Nb
        assert check_symmetry_Ir
        assert check_symmetry_Ti

    def test_get_azimuth_elev(self):
        # Test out the viewing of the Wulff shape from Miller indices.
        azim, elev = self.wulff_Ir._get_azimuth_elev((0, 0, 1))
        assert azim == 0
        assert elev == 90
        azim, elev = self.wulff_Ir._get_azimuth_elev((1, 1, 1))
        assert azim == approx(45)

    def test_properties(self):
        # Simple test to check if the values of some
        # properties are consistent with what we already have

        wulff_shapes = {
            "mp-8636": self.wulff_Nb,
            "mp-72": self.wulff_Ti,
            "mp-101": self.wulff_Ir,
        }
        for mp_id, wulff in wulff_shapes.items():
            properties = self.surface_properties[mp_id]
            assert round(wulff.weighted_surface_energy, 3) == round(properties["weighted_surface_energy"], 3)
            assert round(wulff.shape_factor, 3) == round(properties["shape_factor"], 3)
            assert round(wulff.anisotropy, 3) == round(properties["surface_anisotropy"], 3)

    def test_corner_and_edges(self):
        # Test if it is returning the correct number of corner and edges
        self.assertArrayEqual(self.cube.tot_corner_sites, 8)
        self.assertArrayEqual(self.cube.tot_edges, 12)
        self.assertArrayEqual(self.hex_prism.tot_corner_sites, 12)
        self.assertArrayEqual(self.hex_prism.tot_edges, 18)


if __name__ == "__main__":
    unittest.main()

1	from __future__ import annotations	1✔
2
3	import json	1✔
4	import os	1✔
5	import unittest	1✔
6
7	from pytest import approx	1✔
8
9	from pymatgen.analysis.wulff import WulffShape	1✔
10	from pymatgen.core.lattice import Lattice	1✔
11	from pymatgen.core.structure import Structure	1✔
12	from pymatgen.symmetry.analyzer import SpacegroupAnalyzer	1✔
13	from pymatgen.util.coord import in_coord_list	1✔
14	from pymatgen.util.testing import PymatgenTest	1✔
15
16	__author__ = "Zihan Xu, Richard Tran, Balachandran Radhakrishnan"	1✔
17	__copyright__ = "Copyright 2013, The Materials Virtual Lab"	1✔
18	__version__ = "0.1"	1✔
19	__maintainer__ = "Zihan Xu"	1✔
20	__email__ = "zix009@eng.ucsd.edu"	1✔
21	__date__ = "May 05 2016"	1✔
22
23
24	class WulffShapeTest(PymatgenTest):	1✔
25	def setUp(self):	1✔
26	module_dir = os.path.dirname(os.path.abspath(__file__))	1✔
27	with open(os.path.join(module_dir, "surface_samples.json")) as data_file:	1✔
28	surface_properties = json.load(data_file)	1✔
29
30	surface_energies, miller_indices = {}, {}	1✔
31	for mpid in surface_properties:	1✔
32	e_surf_list, miller_list = [], []	1✔
33	for surface in surface_properties[mpid]["surfaces"]:	1✔
34	e_surf_list.append(surface["surface_energy"])	1✔
35	miller_list.append(surface["miller_index"])	1✔
36	surface_energies[mpid] = e_surf_list	1✔
37	miller_indices[mpid] = miller_list	1✔
38
39	# In the case of a high anisotropy material
40	# Nb: mp-8636
41	latt_Nb = Lattice.cubic(2.992)	1✔
42	# In the case of an fcc material
43	# Ir: mp-101
44	latt_Ir = Lattice.cubic(3.8312)	1✔
45	# In the case of a hcp material
46	# Ti: mp-72
47	latt_Ti = Lattice.hexagonal(4.6000, 2.8200)	1✔
48	self.ucell_Nb = Structure(	1✔
49	latt_Nb,
50	["Nb", "Nb", "Nb", "Nb"],
51	[[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
52	)
53	self.wulff_Nb = WulffShape(latt_Nb, miller_indices["mp-8636"], surface_energies["mp-8636"])	1✔
54
55	self.ucell_Ir = Structure(	1✔
56	latt_Nb,
57	["Ir", "Ir", "Ir", "Ir"],
58	[[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
59	)
60	self.wulff_Ir = WulffShape(latt_Ir, miller_indices["mp-101"], surface_energies["mp-101"])	1✔
61
62	self.ucell_Ti = Structure(	1✔
63	latt_Ti,
64	["Ti", "Ti", "Ti"],
65	[[0, 0, 0], [0.333333, 0.666667, 0.5], [0.666667, 0.333333, 0.5]],
66	)
67	self.wulff_Ti = WulffShape(latt_Ti, miller_indices["mp-72"], surface_energies["mp-72"])	1✔
68	self.cube = WulffShape(Lattice.cubic(1), [(1, 0, 0)], [1])	1✔
69	self.hex_prism = WulffShape(Lattice.hexagonal(2.63, 5.21), [(0, 0, 1), (1, 0, 0)], [0.35, 0.53])	1✔
70
71	self.surface_properties = surface_properties	1✔
72
73	@unittest.skipIf("DISPLAY" not in os.environ, "Need display")	1✔
74	def test_get_plot(self):	1✔
75	# Basic test, not really a unittest.
76	self.wulff_Ti.get_plot()	×
77	self.wulff_Nb.get_plot()	×
78	self.wulff_Ir.get_plot()	×
79
80	@unittest.skipIf("DISPLAY" not in os.environ, "Need display")	1✔
81	def test_get_plotly(self):	1✔
82	# Basic test, not really a unittest.
83	self.wulff_Ti.get_plotly()	×
84	self.wulff_Nb.get_plotly()	×
85	self.wulff_Ir.get_plotly()	×
86
87	def symm_check(self, ucell, wulff_vertices):	1✔
88	"""
89	# Checks if the point group of the Wulff shape matches
90	# the point group of its conventional unit cell
91
92	Args:
93	ucell (str): Unit cell that the Wulff shape is based on.
94	wulff_vertices (list): List of all vertices on the Wulff
95	shape. Use wulff.wulff_pt_list to obtain the list
96	(see wulff_generator.py).
97
98	return (bool)
99	"""
100	space_group_analyzer = SpacegroupAnalyzer(ucell)	×
101	symm_ops = space_group_analyzer.get_point_group_operations(cartesian=True)	×
102	for point in wulff_vertices:	×
103	for op in symm_ops:	×
104	symm_point = op.operate(point)	×
105	if in_coord_list(wulff_vertices, symm_point):	×
106	continue	×
107	else:
108	return False	×
109	return True	×
110
111	def consistency_tests(self):	1✔
112	# For a set of given values, these tests will
113	# ensure that the general result given by the
114	# algorithm does not change as the code is edited
115
116	# For fcc Ir, make sure the (111) direction
117	# is the most dominant facet on the Wulff shape
118
119	fractional_areas = self.wulff_Ir.area_fraction_dict	×
120	miller_list = [hkl for hkl in fractional_areas]	×
121	area_list = [fractional_areas[hkl] for hkl in fractional_areas]	×
122	assert miller_list[area_list.index(max(area_list))] == (1, 1, 1)	×
123
124	# Overall weighted surface energy of fcc Nb should be
125	# equal to the energy of the (310) surface, ie. fcc Nb
126	# is anisotropic, the (310) surface is so low in energy,
127	# its the only facet that exists in the Wulff shape
128
129	Nb_area_fraction_dict = self.wulff_Nb.area_fraction_dict	×
130	for hkl in Nb_area_fraction_dict:	×
131	if hkl == (3, 1, 0):	×
132	assert Nb_area_fraction_dict[hkl] == 1	×
133	else:
134	assert Nb_area_fraction_dict[hkl] == 0	×
135
136	assert self.wulff_Nb.miller_energy_dict[(3, 1, 0)] == self.wulff_Nb.weighted_surface_energy	×
137
138	def symmetry_test(self):	1✔
139	# Maintains that all wulff shapes have the same point
140	# groups as the conventional unit cell they were
141	# derived from. This test should pass for all subsequent
142	# updates of the surface_properties collection
143
144	check_symmetry_Nb = self.symm_check(self.ucell_Nb, self.wulff_Nb.wulff_pt_list)	×
145	check_symmetry_Ir = self.symm_check(self.ucell_Ir, self.wulff_Ir.wulff_pt_list)	×
146	check_symmetry_Ti = self.symm_check(self.ucell_Ti, self.wulff_Ti.wulff_pt_list)	×
147	assert check_symmetry_Nb	×
148	assert check_symmetry_Ir	×
149	assert check_symmetry_Ti	×
150
151	def test_get_azimuth_elev(self):	1✔
152	# Test out the viewing of the Wulff shape from Miller indices.
153	azim, elev = self.wulff_Ir._get_azimuth_elev((0, 0, 1))	1✔
154	assert azim == 0	1✔
155	assert elev == 90	1✔
156	azim, elev = self.wulff_Ir._get_azimuth_elev((1, 1, 1))	1✔
157	assert azim == approx(45)	1✔
158
159	def test_properties(self):	1✔
160	# Simple test to check if the values of some
161	# properties are consistent with what we already have
162
163	wulff_shapes = {	1✔
164	"mp-8636": self.wulff_Nb,
165	"mp-72": self.wulff_Ti,
166	"mp-101": self.wulff_Ir,
167	}
168	for mp_id, wulff in wulff_shapes.items():	1✔
169	properties = self.surface_properties[mp_id]	1✔
170	assert round(wulff.weighted_surface_energy, 3) == round(properties["weighted_surface_energy"], 3)	1✔
171	assert round(wulff.shape_factor, 3) == round(properties["shape_factor"], 3)	1✔
172	assert round(wulff.anisotropy, 3) == round(properties["surface_anisotropy"], 3)	1✔
173
174	def test_corner_and_edges(self):	1✔
175	# Test if it is returning the correct number of corner and edges
176	self.assertArrayEqual(self.cube.tot_corner_sites, 8)	1✔
177	self.assertArrayEqual(self.cube.tot_edges, 12)	1✔
178	self.assertArrayEqual(self.hex_prism.tot_corner_sites, 12)	1✔
179	self.assertArrayEqual(self.hex_prism.tot_edges, 18)	1✔
180
181
182	if __name__ == "__main__":	1✔
183	unittest.main()	×

materialsproject / pymatgen / 4075885785

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous