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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70.15

/pymatgen/command_line/tests/test_critic2_caller.py

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

from __future__ import annotations

import os
import unittest
from shutil import which

from pytest import approx

from pymatgen.command_line.critic2_caller import Critic2Analysis, Critic2Caller
from pymatgen.core.structure import Structure
from pymatgen.util.testing import PymatgenTest

__author__ = "Matthew Horton"
__version__ = "0.1"
__maintainer__ = "Matthew Horton"
__email__ = "mkhorton@lbl.gov"
__status__ = "Production"
__date__ = "July 2017"


@unittest.skipIf(not which("critic2"), "critic2 executable not present")
class Critic2CallerTest(unittest.TestCase):
    def test_from_path(self):
        # uses chgcars
        test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "bader")

        c2c = Critic2Caller.from_path(test_dir)

        # check we have some results!
        assert len(c2c._stdout) >= 500

        c2o = c2c.output

        # check we get our structure graph
        sg = c2o.structure_graph(include_critical_points=None)
        assert sg.get_coordination_of_site(0) == 4

        # check yt integration
        assert c2o.structure.site_properties["bader_volume"][0] == approx(66.0148355)
        assert c2o.structure.site_properties["bader_charge"][0] == approx(12.2229131)

        # test zpsp functionality
        # this is normally picked up from POTCARs, but since POTCARs not checked in with the
        # test suite, setting manually here
        c2o_dict = c2o.as_dict()
        c2o_dict["zpsp"] = {"Fe": 8.0, "O": 6.0}
        c2o = Critic2Analysis.from_dict(c2o_dict)
        # note: these values don't seem sensible physically, but seem to be correct with
        # respect to the input files (possibly bad/underconverged source data)
        assert c2o.structure.site_properties["bader_charge_transfer"][0] == approx(4.2229131)

        # alternatively, can also set when we do the analysis, but note that this will change
        # the analysis performed since augmentation charges are added in core regions
        c2c = Critic2Caller.from_path(test_dir, zpsp={"Fe": 8.0, "O": 6.0})

        # check yt integration
        assert c2o.structure.site_properties["bader_volume"][0] == approx(66.0148355)
        assert c2o.structure.site_properties["bader_charge"][0] == approx(12.2229131)
        assert c2o.structure.site_properties["bader_charge_transfer"][0] == approx(4.2229131)

    def test_from_structure(self):
        # uses promolecular density
        structure = Structure.from_file(
            os.path.join(
                PymatgenTest.TEST_FILES_DIR,
                "critic2/MoS2.cif",
            )
        )

        c2c = Critic2Caller.from_chgcar(structure)

        # check we have some results!
        assert len(c2c._stdout) >= 500


class Critic2AnalysisTest(unittest.TestCase):
    _multiprocess_shared_ = True

    def setUp(self):
        stdout_file = os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2_critic2_stdout.txt")
        stdout_file_new_format = os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2_critic2_stdout_new_format.txt")
        with open(stdout_file) as f:
            reference_stdout = f.read()
        with open(stdout_file_new_format) as f:
            reference_stdout_new_format = f.read()

        structure = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2.cif"))

        self.c2o = Critic2Analysis(structure, reference_stdout)
        self.c2o_new_format = Critic2Analysis(structure, reference_stdout_new_format)

    def test_properties_to_from_dict(self):
        assert len(self.c2o.critical_points) == 6
        assert len(self.c2o.nodes) == 14
        assert len(self.c2o.edges) == 10

        assert len(self.c2o_new_format.critical_points) == 6
        assert len(self.c2o_new_format.nodes) == 14
        assert len(self.c2o_new_format.edges) == 10

        # reference dictionary for c2o.critical_points[0].as_dict()
        # {'@class': 'CriticalPoint',
        #  '@module': 'pymatgen.command_line.critic2_caller',
        #  'coords': None,
        #  'field': 93848.0413,
        #  'field_gradient': 0.0,
        #  'field_hessian': [[-2593274446000.0, -3.873587547e-19, -1.704530713e-08],
        #                    [-3.873587547e-19, -2593274446000.0, 1.386877485e-18],
        #                    [-1.704530713e-08, 1.386877485e-18, -2593274446000.0]],
        #  'frac_coords': [0.333333, 0.666667, 0.213295],
        #  'index': 0,
        #  'multiplicity': 1.0,
        #  'point_group': 'D3h',
        #  'type': < CriticalPointType.nucleus: 'nucleus' >}

        assert str(self.c2o.critical_points[0].type) == "CriticalPointType.nucleus"

        # test connectivity
        assert self.c2o.edges[3] == {"from_idx": 1, "from_lvec": (0, 0, 0), "to_idx": 0, "to_lvec": (1, 0, 0)}
        # test as/from dict
        d = self.c2o.as_dict()
        assert set(d) == {
            "@module",
            "@class",
            "@version",
            "structure",
            "stdout",
            "stderr",
            "cpreport",
            "yt",
            "zpsp",
        }
        self.c2o.from_dict(d)

    def test_graph_output(self):
        sg = self.c2o.structure_graph()
        assert str(sg.structure[3].specie) == "Xbcp"
        assert set(list(sg.graph.edges(data=True))[0][2]) == {
            "to_jimage",
            "weight",
            "field",
            "laplacian",
            "ellipticity",
            "frac_coords",
        }


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 os	1✔
7	import unittest	1✔
8	from shutil import which	1✔
9
10	from pytest import approx	1✔
11
12	from pymatgen.command_line.critic2_caller import Critic2Analysis, Critic2Caller	1✔
13	from pymatgen.core.structure import Structure	1✔
14	from pymatgen.util.testing import PymatgenTest	1✔
15
16	__author__ = "Matthew Horton"	1✔
17	__version__ = "0.1"	1✔
18	__maintainer__ = "Matthew Horton"	1✔
19	__email__ = "mkhorton@lbl.gov"	1✔
20	__status__ = "Production"	1✔
21	__date__ = "July 2017"	1✔
22
23
24	@unittest.skipIf(not which("critic2"), "critic2 executable not present")	1✔
25	class Critic2CallerTest(unittest.TestCase):	1✔
26	def test_from_path(self):	1✔
27	# uses chgcars
28	test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "bader")	×
29
30	c2c = Critic2Caller.from_path(test_dir)	×
31
32	# check we have some results!
33	assert len(c2c._stdout) >= 500	×
34
35	c2o = c2c.output	×
36
37	# check we get our structure graph
38	sg = c2o.structure_graph(include_critical_points=None)	×
39	assert sg.get_coordination_of_site(0) == 4	×
40
41	# check yt integration
42	assert c2o.structure.site_properties["bader_volume"][0] == approx(66.0148355)	×
43	assert c2o.structure.site_properties["bader_charge"][0] == approx(12.2229131)	×
44
45	# test zpsp functionality
46	# this is normally picked up from POTCARs, but since POTCARs not checked in with the
47	# test suite, setting manually here
48	c2o_dict = c2o.as_dict()	×
49	c2o_dict["zpsp"] = {"Fe": 8.0, "O": 6.0}	×
50	c2o = Critic2Analysis.from_dict(c2o_dict)	×
51	# note: these values don't seem sensible physically, but seem to be correct with
52	# respect to the input files (possibly bad/underconverged source data)
53	assert c2o.structure.site_properties["bader_charge_transfer"][0] == approx(4.2229131)	×
54
55	# alternatively, can also set when we do the analysis, but note that this will change
56	# the analysis performed since augmentation charges are added in core regions
57	c2c = Critic2Caller.from_path(test_dir, zpsp={"Fe": 8.0, "O": 6.0})	×
58
59	# check yt integration
60	assert c2o.structure.site_properties["bader_volume"][0] == approx(66.0148355)	×
61	assert c2o.structure.site_properties["bader_charge"][0] == approx(12.2229131)	×
62	assert c2o.structure.site_properties["bader_charge_transfer"][0] == approx(4.2229131)	×
63
64	def test_from_structure(self):	1✔
65	# uses promolecular density
66	structure = Structure.from_file(	×
67	os.path.join(
68	PymatgenTest.TEST_FILES_DIR,
69	"critic2/MoS2.cif",
70	)
71	)
72
73	c2c = Critic2Caller.from_chgcar(structure)	×
74
75	# check we have some results!
76	assert len(c2c._stdout) >= 500	×
77
78
79	class Critic2AnalysisTest(unittest.TestCase):	1✔
80	_multiprocess_shared_ = True	1✔
81
82	def setUp(self):	1✔
83	stdout_file = os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2_critic2_stdout.txt")	1✔
84	stdout_file_new_format = os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2_critic2_stdout_new_format.txt")	1✔
85	with open(stdout_file) as f:	1✔
86	reference_stdout = f.read()	1✔
87	with open(stdout_file_new_format) as f:	1✔
88	reference_stdout_new_format = f.read()	1✔
89
90	structure = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2.cif"))	1✔
91
92	self.c2o = Critic2Analysis(structure, reference_stdout)	1✔
93	self.c2o_new_format = Critic2Analysis(structure, reference_stdout_new_format)	1✔
94
95	def test_properties_to_from_dict(self):	1✔
96	assert len(self.c2o.critical_points) == 6	1✔
97	assert len(self.c2o.nodes) == 14	1✔
98	assert len(self.c2o.edges) == 10	1✔
99
100	assert len(self.c2o_new_format.critical_points) == 6	1✔
101	assert len(self.c2o_new_format.nodes) == 14	1✔
102	assert len(self.c2o_new_format.edges) == 10	1✔
103
104	# reference dictionary for c2o.critical_points[0].as_dict()
105	# {'@class': 'CriticalPoint',
106	# '@module': 'pymatgen.command_line.critic2_caller',
107	# 'coords': None,
108	# 'field': 93848.0413,
109	# 'field_gradient': 0.0,
110	# 'field_hessian': [[-2593274446000.0, -3.873587547e-19, -1.704530713e-08],
111	# [-3.873587547e-19, -2593274446000.0, 1.386877485e-18],
112	# [-1.704530713e-08, 1.386877485e-18, -2593274446000.0]],
113	# 'frac_coords': [0.333333, 0.666667, 0.213295],
114	# 'index': 0,
115	# 'multiplicity': 1.0,
116	# 'point_group': 'D3h',
117	# 'type': < CriticalPointType.nucleus: 'nucleus' >}
118
119	assert str(self.c2o.critical_points[0].type) == "CriticalPointType.nucleus"	1✔
120
121	# test connectivity
122	assert self.c2o.edges[3] == {"from_idx": 1, "from_lvec": (0, 0, 0), "to_idx": 0, "to_lvec": (1, 0, 0)}	1✔
123	# test as/from dict
124	d = self.c2o.as_dict()	1✔
125	assert set(d) == {	1✔
126	"@module",
127	"@class",
128	"@version",
129	"structure",
130	"stdout",
131	"stderr",
132	"cpreport",
133	"yt",
134	"zpsp",
135	}
136	self.c2o.from_dict(d)	1✔
137
138	def test_graph_output(self):	1✔
139	sg = self.c2o.structure_graph()	1✔
140	assert str(sg.structure[3].specie) == "Xbcp"	1✔
141	assert set(list(sg.graph.edges(data=True))[0][2]) == {	1✔
142	"to_jimage",
143	"weight",
144	"field",
145	"laplacian",
146	"ellipticity",
147	"frac_coords",
148	}
149
150
151	if __name__ == "__main__":	1✔
152	unittest.main()	×

materialsproject / pymatgen / 4075885785

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