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

97.56

/pymatgen/entries/tests/test_correction_calculator.py

from __future__ import annotations

import os
import unittest

import pytest

from pymatgen.entries.correction_calculator import CorrectionCalculator
from pymatgen.util.testing import PymatgenTest


class CorrectionCalculatorTest(unittest.TestCase):
    def setUp(self):
        self.exclude_polyanions = [
            "SO4",
            "CO3",
            "NO3",
            "OCl3",
            "SiO4",
            "SeO3",
            "TiO3",
            "TiO4",
        ]

        self.normal_corrections = {
            "oxide": (-0.74, 0.0017),
            "peroxide": (-0.466, 0.0186),
            "superoxide": (-0.16, 0.0075),
            "S": (-0.639, 0.0121),
            "F": (-0.485, 0.0025),
            "Cl": (-0.593, 0.0016),
            "Br": (-0.538, 0.0022),
            "I": (-0.377, 0.0059),
            "N": (-0.344, 0.0084),
            "Se": (-0.473, 0.0341),
            "Si": (-0.406, 0.0621),
            "Sb": (-0.192, 0.0089),
            "Te": (-0.419, 0.024),
            "V": (-1.602, 0.006),
            "Cr": (-1.893, 0.0093),
            "Mn": (-1.588, 0.0051),
            "Fe": (-2.182, 0.009),
            "Co": (-1.535, 0.0059),
            "Ni": (-2.504, 0.0105),
            "W": (-4.57, 0.0181),
            "Mo": (-3.058, 0.0085),
            "H": (-0.178, 0.0013),
            "ozonide": (0, 0),
        }

        self.warnings_allowed_corrections = {
            "oxide": (-0.589, 0.0013),
            "peroxide": (-0.467, 0.019),
            "superoxide": (-0.16, 0.0075),
            "S": (-0.637, 0.0123),
            "F": (-0.481, 0.0025),
            "Cl": (-0.594, 0.0016),
            "Br": (-0.538, 0.0022),
            "I": (-0.376, 0.0059),
            "N": (-0.042, 0.0077),
            "Se": (-0.378, 0.0304),
            "Si": (-0.09, 0.0264),
            "Sb": (-0.197, 0.0089),
            "Te": (-0.42, 0.0238),
            "V": (-1.914, 0.0056),
            "Cr": (-2.227, 0.0089),
            "Mn": (-1.781, 0.0048),
            "Fe": (-2.214, 0.0081),
            "Co": (-1.549, 0.0055),
            "Ni": (-2.294, 0.0085),
            "W": (-5.263, 0.0173),
            "Mo": (-3.49, 0.008),
            "H": (-0.176, 0.0013),
            "ozonide": (0, 0),
        }

        self.no_uncertainties_corrections = {
            "oxide": (-0.749, 0.0198),
            "peroxide": (-0.466, 0.0492),
            "superoxide": (-0.155, 0.0545),
            "S": (-0.639, 0.0386),
            "F": (-0.444, 0.0206),
            "Cl": (-0.518, 0.0266),
            "Br": (-0.439, 0.0294),
            "I": (-0.29, 0.0327),
            "N": (-0.357, 0.0617),
            "Se": (-0.361, 0.0546),
            "Si": (-0.439, 0.1048),
            "Sb": (-0.286, 0.0775),
            "Te": (-0.457, 0.0524),
            "V": (-1.655, 0.0782),
            "Cr": (-1.836, 0.0699),
            "Mn": (-1.58, 0.071),
            "Fe": (-2.168, 0.0624),
            "Co": (-1.605, 0.0794),
            "Ni": (-2.516, 0.099),
            "W": (-4.553, 0.1235),
            "Mo": (-3.032, 0.1118),
            "H": (-0.137, 0.0313),
            "ozonide": (0, 0),
        }

        self.test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "correction_calculator")

    def tearDown(self):
        pass

    def test_normal_corrections(self):
        """
        Test that the values in MPCompatiblity.yaml are reproduced correctly.
        """
        exp_path = os.path.join(self.test_dir, "exp_compounds_norm.json.gz")
        calc_path = os.path.join(self.test_dir, "calc_compounds_norm.json.gz")

        calculator = CorrectionCalculator(exclude_polyanions=self.exclude_polyanions)
        corrs = calculator.compute_from_files(exp_path, calc_path)

        assert corrs == self.normal_corrections

    def test_warnings_options(self):
        """
        Test that compounds can be included/excluded using the allow_{warning} optional parameters.
        """
        exp_path = os.path.join(self.test_dir, "exp_compounds_norm.json.gz")
        calc_path = os.path.join(self.test_dir, "calc_compounds_norm.json.gz")

        calculator = CorrectionCalculator(max_error=1, exclude_polyanions=[], allow_unstable=True)
        corrs = calculator.compute_from_files(exp_path, calc_path)

        assert corrs == self.warnings_allowed_corrections

    def test_no_uncertainties(self):
        """
        Test that corrections can be calculated with no uncertainties.
        """
        exp_path = os.path.join(self.test_dir, "exp_no_error_compounds.json.gz")
        calc_path = os.path.join(self.test_dir, "calc_compounds_norm.json.gz")

        calculator = CorrectionCalculator(exclude_polyanions=self.exclude_polyanions)
        corrs = calculator.compute_from_files(exp_path, calc_path)

        assert corrs == self.no_uncertainties_corrections

    def test_missing_entry_response(self):
        """
        Test that correct error is raised (ValueError) if the input is missing a computed entry.
        """
        exp_path = os.path.join(self.test_dir, "exp_compounds_norm.json.gz")
        calc_path = os.path.join(self.test_dir, "calc_missing_compounds.json.gz")

        calculator = CorrectionCalculator(exclude_polyanions=self.exclude_polyanions)
        with pytest.raises(ValueError):
            calculator.compute_from_files(exp_path, calc_path)


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

1	from __future__ import annotations	1✔
2
3	import os	1✔
4	import unittest	1✔
5
6	import pytest	1✔
7
8	from pymatgen.entries.correction_calculator import CorrectionCalculator	1✔
9	from pymatgen.util.testing import PymatgenTest	1✔
10
11
12	class CorrectionCalculatorTest(unittest.TestCase):	1✔
13	def setUp(self):	1✔
14	self.exclude_polyanions = [	1✔
15	"SO4",
16	"CO3",
17	"NO3",
18	"OCl3",
19	"SiO4",
20	"SeO3",
21	"TiO3",
22	"TiO4",
23	]
24
25	self.normal_corrections = {	1✔
26	"oxide": (-0.74, 0.0017),
27	"peroxide": (-0.466, 0.0186),
28	"superoxide": (-0.16, 0.0075),
29	"S": (-0.639, 0.0121),
30	"F": (-0.485, 0.0025),
31	"Cl": (-0.593, 0.0016),
32	"Br": (-0.538, 0.0022),
33	"I": (-0.377, 0.0059),
34	"N": (-0.344, 0.0084),
35	"Se": (-0.473, 0.0341),
36	"Si": (-0.406, 0.0621),
37	"Sb": (-0.192, 0.0089),
38	"Te": (-0.419, 0.024),
39	"V": (-1.602, 0.006),
40	"Cr": (-1.893, 0.0093),
41	"Mn": (-1.588, 0.0051),
42	"Fe": (-2.182, 0.009),
43	"Co": (-1.535, 0.0059),
44	"Ni": (-2.504, 0.0105),
45	"W": (-4.57, 0.0181),
46	"Mo": (-3.058, 0.0085),
47	"H": (-0.178, 0.0013),
48	"ozonide": (0, 0),
49	}
50
51	self.warnings_allowed_corrections = {	1✔
52	"oxide": (-0.589, 0.0013),
53	"peroxide": (-0.467, 0.019),
54	"superoxide": (-0.16, 0.0075),
55	"S": (-0.637, 0.0123),
56	"F": (-0.481, 0.0025),
57	"Cl": (-0.594, 0.0016),
58	"Br": (-0.538, 0.0022),
59	"I": (-0.376, 0.0059),
60	"N": (-0.042, 0.0077),
61	"Se": (-0.378, 0.0304),
62	"Si": (-0.09, 0.0264),
63	"Sb": (-0.197, 0.0089),
64	"Te": (-0.42, 0.0238),
65	"V": (-1.914, 0.0056),
66	"Cr": (-2.227, 0.0089),
67	"Mn": (-1.781, 0.0048),
68	"Fe": (-2.214, 0.0081),
69	"Co": (-1.549, 0.0055),
70	"Ni": (-2.294, 0.0085),
71	"W": (-5.263, 0.0173),
72	"Mo": (-3.49, 0.008),
73	"H": (-0.176, 0.0013),
74	"ozonide": (0, 0),
75	}
76
77	self.no_uncertainties_corrections = {	1✔
78	"oxide": (-0.749, 0.0198),
79	"peroxide": (-0.466, 0.0492),
80	"superoxide": (-0.155, 0.0545),
81	"S": (-0.639, 0.0386),
82	"F": (-0.444, 0.0206),
83	"Cl": (-0.518, 0.0266),
84	"Br": (-0.439, 0.0294),
85	"I": (-0.29, 0.0327),
86	"N": (-0.357, 0.0617),
87	"Se": (-0.361, 0.0546),
88	"Si": (-0.439, 0.1048),
89	"Sb": (-0.286, 0.0775),
90	"Te": (-0.457, 0.0524),
91	"V": (-1.655, 0.0782),
92	"Cr": (-1.836, 0.0699),
93	"Mn": (-1.58, 0.071),
94	"Fe": (-2.168, 0.0624),
95	"Co": (-1.605, 0.0794),
96	"Ni": (-2.516, 0.099),
97	"W": (-4.553, 0.1235),
98	"Mo": (-3.032, 0.1118),
99	"H": (-0.137, 0.0313),
100	"ozonide": (0, 0),
101	}
102
103	self.test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "correction_calculator")	1✔
104
105	def tearDown(self):	1✔
106	pass	1✔
107
108	def test_normal_corrections(self):	1✔
109	"""
110	Test that the values in MPCompatiblity.yaml are reproduced correctly.
111	"""
112	exp_path = os.path.join(self.test_dir, "exp_compounds_norm.json.gz")	1✔
113	calc_path = os.path.join(self.test_dir, "calc_compounds_norm.json.gz")	1✔
114
115	calculator = CorrectionCalculator(exclude_polyanions=self.exclude_polyanions)	1✔
116	corrs = calculator.compute_from_files(exp_path, calc_path)	1✔
117
118	assert corrs == self.normal_corrections	1✔
119
120	def test_warnings_options(self):	1✔
121	"""
122	Test that compounds can be included/excluded using the allow_{warning} optional parameters.
123	"""
124	exp_path = os.path.join(self.test_dir, "exp_compounds_norm.json.gz")	1✔
125	calc_path = os.path.join(self.test_dir, "calc_compounds_norm.json.gz")	1✔
126
127	calculator = CorrectionCalculator(max_error=1, exclude_polyanions=[], allow_unstable=True)	1✔
128	corrs = calculator.compute_from_files(exp_path, calc_path)	1✔
129
130	assert corrs == self.warnings_allowed_corrections	1✔
131
132	def test_no_uncertainties(self):	1✔
133	"""
134	Test that corrections can be calculated with no uncertainties.
135	"""
136	exp_path = os.path.join(self.test_dir, "exp_no_error_compounds.json.gz")	1✔
137	calc_path = os.path.join(self.test_dir, "calc_compounds_norm.json.gz")	1✔
138
139	calculator = CorrectionCalculator(exclude_polyanions=self.exclude_polyanions)	1✔
140	corrs = calculator.compute_from_files(exp_path, calc_path)	1✔
141
142	assert corrs == self.no_uncertainties_corrections	1✔
143
144	def test_missing_entry_response(self):	1✔
145	"""
146	Test that correct error is raised (ValueError) if the input is missing a computed entry.
147	"""
148	exp_path = os.path.join(self.test_dir, "exp_compounds_norm.json.gz")	1✔
149	calc_path = os.path.join(self.test_dir, "calc_missing_compounds.json.gz")	1✔
150
151	calculator = CorrectionCalculator(exclude_polyanions=self.exclude_polyanions)	1✔
152	with pytest.raises(ValueError):	1✔
153	calculator.compute_from_files(exp_path, calc_path)	1✔
154
155
156	if __name__ == "__main__":	1✔
157	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