4075885785

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push

github

Committed by Shyue Ping Ong

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

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98.59

/pymatgen/core/tests/test_interface.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.

from __future__ import annotations

import unittest

import numpy as np

from pymatgen.core.interface import Interface
from pymatgen.core.surface import SlabGenerator
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.util.testing import PymatgenTest


class InterfaceTest(PymatgenTest):
    def setUp(self):
        self.interface: Interface = self.get_structure("Si_SiO2_Interface")

    def test_basic_props(self):
        interface = self.interface
        assert isinstance(interface, Interface)

        assert len(interface.substrate_indices) == 14
        assert len(interface.film_indices) == 36
        assert len(interface.film_sites) == len(interface.film_indices)
        assert len(interface.substrate_sites) == len(interface.substrate_indices)
        assert interface.gap == 2.0
        assert np.allclose(interface.in_plane_offset, [0, 0])
        assert interface.vacuum_over_film == 20.0
        assert interface.film_termination == "O2_P6/mmm_4"
        assert interface.substrate_termination == "Si_P6/mmm_7"
        assert interface.film_layers == 6
        assert interface.substrate_layers == 2

        iface_dict = interface.as_dict()
        for k in [
            "lattice",
            "sites",
            "in_plane_offset",
            "gap",
            "vacuum_over_film",
            "interface_properties",
        ]:
            assert k in iface_dict
        assert isinstance(interface.from_dict(iface_dict), Interface)

    def test_gap_setter(self):
        interface = self.interface

        assert np.allclose(interface.gap, 2.0)

        max_sub_c = np.max(np.array([s.frac_coords for s in interface.substrate])[:, 2])
        min_film_c = np.min(np.array([f.frac_coords for f in interface.film])[:, 2])
        gap = (min_film_c - max_sub_c) * interface.lattice.c
        assert np.allclose(interface.gap, gap)

        interface.gap += 1

        assert np.allclose(interface.gap, 3.0)

        max_sub_c = np.max(np.array([s.frac_coords for s in interface.substrate])[:, 2])
        min_film_c = np.min(np.array([f.frac_coords for f in interface.film])[:, 2])
        gap = (min_film_c - max_sub_c) * interface.lattice.c
        assert np.allclose(interface.gap, gap)

    def test_in_plane_offset_setter(self):
        interface = self.interface
        init_coords = np.array(self.interface.frac_coords)
        interface.in_plane_offset = np.array([0.2, 0.2])

        assert np.allclose(interface.in_plane_offset, np.array([0.2, 0.2]))

        test_coords = np.array(init_coords)
        for i in interface.film_indices:
            test_coords[i] += [0.2, 0.2, 0]
        assert np.allclose(np.mod(test_coords, 1.0), np.mod(interface.frac_coords, 1.0))

    def test_vacuum_over_film_setter(self):
        interface = self.interface
        init_coords = self.interface.cart_coords

        assert interface.vacuum_over_film == 20

        interface.vacuum_over_film += 10

        assert interface.vacuum_over_film == 30
        assert np.allclose(init_coords, interface.cart_coords)

    def test_get_shifts_based_on_adsorbate_sites(self):
        # Only testing two tolerances as there appears to be significant numerical noise in this method
        assert len(self.interface.get_shifts_based_on_adsorbate_sites()) == 42
        assert len(self.interface.get_shifts_based_on_adsorbate_sites(tolerance=20.0)) == 1

    def test_from_slabs(self):
        si_struct = self.get_structure("Si")
        sio2_struct = self.get_structure("SiO2")
        si_conventional = SpacegroupAnalyzer(si_struct).get_conventional_standard_structure()
        sio2_conventional = SpacegroupAnalyzer(sio2_struct).get_conventional_standard_structure()

        si_slab = SlabGenerator(si_conventional, (1, 1, 1), 5, 10, reorient_lattice=True).get_slab()
        sio2_slab = SlabGenerator(sio2_conventional, (1, 0, 0), 5, 10, reorient_lattice=True).get_slab()

        interface = Interface.from_slabs(film_slab=si_slab, substrate_slab=sio2_slab)
        assert isinstance(interface, Interface)


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

1	# Copyright (c) Pymatgen Development Team.
2	# Distributed under the terms of the MIT License.
3
4	from __future__ import annotations	1✔
5
6	import unittest	1✔
7
8	import numpy as np	1✔
9
10	from pymatgen.core.interface import Interface	1✔
11	from pymatgen.core.surface import SlabGenerator	1✔
12	from pymatgen.symmetry.analyzer import SpacegroupAnalyzer	1✔
13	from pymatgen.util.testing import PymatgenTest	1✔
14
15
16	class InterfaceTest(PymatgenTest):	1✔
17	def setUp(self):	1✔
18	self.interface: Interface = self.get_structure("Si_SiO2_Interface")	1✔
19
20	def test_basic_props(self):	1✔
21	interface = self.interface	1✔
22	assert isinstance(interface, Interface)	1✔
23
24	assert len(interface.substrate_indices) == 14	1✔
25	assert len(interface.film_indices) == 36	1✔
26	assert len(interface.film_sites) == len(interface.film_indices)	1✔
27	assert len(interface.substrate_sites) == len(interface.substrate_indices)	1✔
28	assert interface.gap == 2.0	1✔
29	assert np.allclose(interface.in_plane_offset, [0, 0])	1✔
30	assert interface.vacuum_over_film == 20.0	1✔
31	assert interface.film_termination == "O2_P6/mmm_4"	1✔
32	assert interface.substrate_termination == "Si_P6/mmm_7"	1✔
33	assert interface.film_layers == 6	1✔
34	assert interface.substrate_layers == 2	1✔
35
36	iface_dict = interface.as_dict()	1✔
37	for k in [	1✔
38	"lattice",
39	"sites",
40	"in_plane_offset",
41	"gap",
42	"vacuum_over_film",
43	"interface_properties",
44	]:
45	assert k in iface_dict	1✔
46	assert isinstance(interface.from_dict(iface_dict), Interface)	1✔
47
48	def test_gap_setter(self):	1✔
49	interface = self.interface	1✔
50
51	assert np.allclose(interface.gap, 2.0)	1✔
52
53	max_sub_c = np.max(np.array([s.frac_coords for s in interface.substrate])[:, 2])	1✔
54	min_film_c = np.min(np.array([f.frac_coords for f in interface.film])[:, 2])	1✔
55	gap = (min_film_c - max_sub_c) * interface.lattice.c	1✔
56	assert np.allclose(interface.gap, gap)	1✔
57
58	interface.gap += 1	1✔
59
60	assert np.allclose(interface.gap, 3.0)	1✔
61
62	max_sub_c = np.max(np.array([s.frac_coords for s in interface.substrate])[:, 2])	1✔
63	min_film_c = np.min(np.array([f.frac_coords for f in interface.film])[:, 2])	1✔
64	gap = (min_film_c - max_sub_c) * interface.lattice.c	1✔
65	assert np.allclose(interface.gap, gap)	1✔
66
67	def test_in_plane_offset_setter(self):	1✔
68	interface = self.interface	1✔
69	init_coords = np.array(self.interface.frac_coords)	1✔
70	interface.in_plane_offset = np.array([0.2, 0.2])	1✔
71
72	assert np.allclose(interface.in_plane_offset, np.array([0.2, 0.2]))	1✔
73
74	test_coords = np.array(init_coords)	1✔
75	for i in interface.film_indices:	1✔
76	test_coords[i] += [0.2, 0.2, 0]	1✔
77	assert np.allclose(np.mod(test_coords, 1.0), np.mod(interface.frac_coords, 1.0))	1✔
78
79	def test_vacuum_over_film_setter(self):	1✔
80	interface = self.interface	1✔
81	init_coords = self.interface.cart_coords	1✔
82
83	assert interface.vacuum_over_film == 20	1✔
84
85	interface.vacuum_over_film += 10	1✔
86
87	assert interface.vacuum_over_film == 30	1✔
88	assert np.allclose(init_coords, interface.cart_coords)	1✔
89
90	def test_get_shifts_based_on_adsorbate_sites(self):	1✔
91	# Only testing two tolerances as there appears to be significant numerical noise in this method
92	assert len(self.interface.get_shifts_based_on_adsorbate_sites()) == 42	1✔
93	assert len(self.interface.get_shifts_based_on_adsorbate_sites(tolerance=20.0)) == 1	1✔
94
95	def test_from_slabs(self):	1✔
96	si_struct = self.get_structure("Si")	1✔
97	sio2_struct = self.get_structure("SiO2")	1✔
98	si_conventional = SpacegroupAnalyzer(si_struct).get_conventional_standard_structure()	1✔
99	sio2_conventional = SpacegroupAnalyzer(sio2_struct).get_conventional_standard_structure()	1✔
100
101	si_slab = SlabGenerator(si_conventional, (1, 1, 1), 5, 10, reorient_lattice=True).get_slab()	1✔
102	sio2_slab = SlabGenerator(sio2_conventional, (1, 0, 0), 5, 10, reorient_lattice=True).get_slab()	1✔
103
104	interface = Interface.from_slabs(film_slab=si_slab, substrate_slab=sio2_slab)	1✔
105	assert isinstance(interface, Interface)	1✔
106
107
108	if __name__ == "__main__":	1✔
109	unittest.main()	×

materialsproject / pymatgen / 4075885785

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