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

99.42

/pymatgen/io/feff/tests/test_sets.py

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


from __future__ import annotations

import os
import shutil
import unittest

import numpy as np
import pytest

from pymatgen.core.structure import Molecule, Structure
from pymatgen.io.cif import CifParser
from pymatgen.io.feff.inputs import Atoms, Header, Potential, Tags
from pymatgen.io.feff.sets import FEFFDictSet, MPELNESSet, MPEXAFSSet, MPXANESSet
from pymatgen.util.testing import PymatgenTest


class FeffInputSetTest(unittest.TestCase):
    @classmethod
    def setUpClass(cls):
        cls.header_string = """* This FEFF.inp file generated by pymatgen
TITLE comment: From cif file
TITLE Source:  CoO19128.cif
TITLE Structure Summary:  Co2 O2
TITLE Reduced formula:  CoO
TITLE space group: (P6_3mc), space number:  (186)
TITLE abc:  3.297078   3.297078   5.254213
TITLE angles: 90.000000  90.000000 120.000000
TITLE sites: 4
* 1 Co     0.333333     0.666667     0.503676
* 2 Co     0.666667     0.333333     0.003676
* 3 O     0.333333     0.666667     0.121324
* 4 O     0.666667     0.333333     0.621325"""
        cif_file = os.path.join(PymatgenTest.TEST_FILES_DIR, "CoO19128.cif")
        cls.structure = CifParser(cif_file).get_structures()[0]
        cls.absorbing_atom = "O"
        cls.mp_xanes = MPXANESSet(cls.absorbing_atom, cls.structure)

    def test_get_header(self):
        comment = "From cif file"
        header = str(self.mp_xanes.header(source="CoO19128.cif", comment=comment))
        print(header)

        ref = self.header_string.splitlines()
        last4 = [" ".join(l.split()[2:]) for l in ref[-4:]]
        for i, l in enumerate(header.splitlines()):
            if i < 9:
                assert l == ref[i]
            else:
                s = " ".join(l.split()[2:])
                assert s in last4

    def test_getfefftags(self):
        tags = self.mp_xanes.tags.as_dict()
        assert tags["COREHOLE"] == "FSR", "Failed to generate PARAMETERS string"

    def test_get_feffPot(self):
        POT = str(self.mp_xanes.potential)
        d, dr = Potential.pot_dict_from_string(POT)
        assert d["Co"] == 1, "Wrong symbols read in for Potential"

    def test_get_feff_atoms(self):
        atoms = str(self.mp_xanes.atoms)
        assert atoms.splitlines()[3].split()[4] == self.absorbing_atom, "failed to create ATOMS string"

    def test_to_and_from_dict(self):
        f1_dict = self.mp_xanes.as_dict()
        f2 = MPXANESSet.from_dict(f1_dict)
        assert f1_dict == f2.as_dict()

    def test_user_tag_settings(self):
        tags_dict_ans = self.mp_xanes.tags.as_dict()
        tags_dict_ans["COREHOLE"] = "RPA"
        tags_dict_ans["EDGE"] = "L1"
        user_tag_settings = {"COREHOLE": "RPA", "EDGE": "L1"}
        mp_xanes_2 = MPXANESSet(self.absorbing_atom, self.structure, user_tag_settings=user_tag_settings)
        assert mp_xanes_2.tags.as_dict() == tags_dict_ans

    def test_eels_to_from_dict(self):
        elnes = MPELNESSet(
            self.absorbing_atom,
            self.structure,
            radius=5.0,
            beam_energy=100,
            beam_direction=[1, 0, 0],
            collection_angle=7,
            convergence_angle=6,
        )
        elnes_dict = elnes.as_dict()
        elnes_2 = MPELNESSet.from_dict(elnes_dict)
        assert elnes_dict == elnes_2.as_dict()

    def test_eels_tags_set(self):
        radius = 5.0
        user_eels_settings = {
            "ENERGY": "4 0.04 0.1",
            "BEAM_ENERGY": "200 1 0 1",
            "ANGLES": "2 3",
        }
        elnes = MPELNESSet(
            self.absorbing_atom,
            self.structure,
            radius=radius,
            user_eels_settings=user_eels_settings,
        )
        elnes_2 = MPELNESSet(
            self.absorbing_atom,
            self.structure,
            radius=radius,
            beam_energy=100,
            beam_direction=[1, 0, 0],
            collection_angle=7,
            convergence_angle=6,
        )
        assert elnes.tags["ELNES"]["ENERGY"] == user_eels_settings["ENERGY"]
        assert elnes.tags["ELNES"]["BEAM_ENERGY"] == user_eels_settings["BEAM_ENERGY"]
        assert elnes.tags["ELNES"]["ANGLES"] == user_eels_settings["ANGLES"]
        assert elnes_2.tags["ELNES"]["BEAM_ENERGY"] == [100, 0, 1, 1]
        assert elnes_2.tags["ELNES"]["BEAM_DIRECTION"] == [1, 0, 0]
        assert elnes_2.tags["ELNES"]["ANGLES"] == [7, 6]

    def test_charged_structure(self):
        # one Zn+2, 9 triflate, plus water
        # Molecule, net charge of -7
        xyz = os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_radial_shell.xyz")
        m = Molecule.from_file(xyz)
        m.set_charge_and_spin(-7)
        # Zn should not appear in the pot_dict
        with pytest.warns(UserWarning, match="ION tags"):
            MPXANESSet("Zn", m)
        s = self.structure.copy()
        s.set_charge(1)
        with pytest.raises(ValueError, match="not supported"):
            MPXANESSet("Co", s)

    def test_reciprocal_tags_and_input(self):
        user_tag_settings = {"RECIPROCAL": "", "KMESH": "1000"}
        elnes = MPELNESSet(self.absorbing_atom, self.structure, user_tag_settings=user_tag_settings)
        assert "RECIPROCAL" in elnes.tags
        assert elnes.tags["TARGET"] == 3
        assert elnes.tags["KMESH"] == "1000"
        assert elnes.tags["CIF"] == "Co2O2.cif"
        assert elnes.tags["COREHOLE"] == "RPA"
        all_input = elnes.all_input()
        assert "ATOMS" not in all_input
        assert "POTENTIALS" not in all_input
        elnes.write_input()
        structure = Structure.from_file("Co2O2.cif")
        assert self.structure.matches(structure)
        os.remove("HEADER")
        os.remove("PARAMETERS")
        os.remove("feff.inp")
        os.remove("Co2O2.cif")

    def test_small_system_EXAFS(self):
        exafs_settings = MPEXAFSSet(self.absorbing_atom, self.structure)
        assert not exafs_settings.small_system
        assert "RECIPROCAL" not in exafs_settings.tags

        user_tag_settings = {"RECIPROCAL": ""}
        exafs_settings_2 = MPEXAFSSet(
            self.absorbing_atom,
            self.structure,
            nkpts=1000,
            user_tag_settings=user_tag_settings,
        )
        assert not exafs_settings_2.small_system
        assert "RECIPROCAL" not in exafs_settings_2.tags

    def test_number_of_kpoints(self):
        user_tag_settings = {"RECIPROCAL": ""}
        elnes = MPELNESSet(
            self.absorbing_atom,
            self.structure,
            nkpts=1000,
            user_tag_settings=user_tag_settings,
        )
        assert elnes.tags["KMESH"] == [12, 12, 7]

    def test_large_systems(self):
        struct = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "La4Fe4O12.cif"))
        user_tag_settings = {"RECIPROCAL": "", "KMESH": "1000"}
        elnes = MPELNESSet("Fe", struct, user_tag_settings=user_tag_settings)
        assert "RECIPROCAL" not in elnes.tags
        assert "KMESH" not in elnes.tags
        assert "CIF" not in elnes.tags
        assert "TARGET" not in elnes.tags

    def test_postfeffset(self):
        self.mp_xanes.write_input(os.path.join(".", "xanes_3"))
        feff_dict_input = FEFFDictSet.from_directory(os.path.join(".", "xanes_3"))
        assert feff_dict_input.tags == Tags.from_file(os.path.join(".", "xanes_3/feff.inp"))
        assert str(feff_dict_input.header()) == str(Header.from_file(os.path.join(".", "xanes_3/HEADER")))
        feff_dict_input.write_input("xanes_3_regen")
        origin_tags = Tags.from_file(os.path.join(".", "xanes_3/PARAMETERS"))
        output_tags = Tags.from_file(os.path.join(".", "xanes_3_regen/PARAMETERS"))
        origin_mole = Atoms.cluster_from_file(os.path.join(".", "xanes_3/feff.inp"))
        output_mole = Atoms.cluster_from_file(os.path.join(".", "xanes_3_regen/feff.inp"))
        original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(np.float64)
        output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(np.float64)
        original_mole_shell = [x.species_string for x in origin_mole]
        output_mole_shell = [x.species_string for x in output_mole]

        assert np.allclose(original_mole_dist, output_mole_dist)
        assert origin_tags == output_tags
        assert original_mole_shell == output_mole_shell

        shutil.rmtree(os.path.join(".", "xanes_3"))
        shutil.rmtree(os.path.join(".", "xanes_3_regen"))

        reci_mp_xanes = MPXANESSet(self.absorbing_atom, self.structure, user_tag_settings={"RECIPROCAL": ""})
        reci_mp_xanes.write_input("xanes_reci")
        feff_reci_input = FEFFDictSet.from_directory(os.path.join(".", "xanes_reci"))
        assert "RECIPROCAL" in feff_reci_input.tags

        feff_reci_input.write_input("Dup_reci")
        assert os.path.exists(os.path.join(".", "Dup_reci", "HEADER"))
        assert os.path.exists(os.path.join(".", "Dup_reci", "feff.inp"))
        assert os.path.exists(os.path.join(".", "Dup_reci", "PARAMETERS"))
        assert not os.path.exists(os.path.join(".", "Dup_reci", "ATOMS"))
        assert not os.path.exists(os.path.join(".", "Dup_reci", "POTENTIALS"))

        tags_original = Tags.from_file(os.path.join(".", "xanes_reci/feff.inp"))
        tags_output = Tags.from_file(os.path.join(".", "Dup_reci/feff.inp"))
        assert tags_original == tags_output

        stru_orig = Structure.from_file(os.path.join(".", "xanes_reci/Co2O2.cif"))
        stru_reci = Structure.from_file(os.path.join(".", "Dup_reci/Co2O2.cif"))
        assert stru_orig == stru_reci

        shutil.rmtree(os.path.join(".", "Dup_reci"))
        shutil.rmtree(os.path.join(".", "xanes_reci"))

    def test_post_distdiff(self):
        feff_dict_input = FEFFDictSet.from_directory(os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test"))
        assert feff_dict_input.tags == Tags.from_file(
            os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test/feff.inp")
        )
        assert str(feff_dict_input.header()) == str(
            Header.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test/HEADER"))
        )
        feff_dict_input.write_input("feff_dist_regen")
        origin_tags = Tags.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test/PARAMETERS"))
        output_tags = Tags.from_file(os.path.join(".", "feff_dist_regen/PARAMETERS"))
        origin_mole = Atoms.cluster_from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test/feff.inp"))
        output_mole = Atoms.cluster_from_file(os.path.join(".", "feff_dist_regen/feff.inp"))
        original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(np.float64)
        output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(np.float64)
        original_mole_shell = [x.species_string for x in origin_mole]
        output_mole_shell = [x.species_string for x in output_mole]

        assert np.allclose(original_mole_dist, output_mole_dist)
        assert origin_tags == output_tags
        assert original_mole_shell == output_mole_shell

        shutil.rmtree(os.path.join(".", "feff_dist_regen"))


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

1	# Copyright (c) Pymatgen Development Team.
2	# Distributed under the terms of the MIT License.
3
4
5	from __future__ import annotations	1✔
6
7	import os	1✔
8	import shutil	1✔
9	import unittest	1✔
10
11	import numpy as np	1✔
12	import pytest	1✔
13
14	from pymatgen.core.structure import Molecule, Structure	1✔
15	from pymatgen.io.cif import CifParser	1✔
16	from pymatgen.io.feff.inputs import Atoms, Header, Potential, Tags	1✔
17	from pymatgen.io.feff.sets import FEFFDictSet, MPELNESSet, MPEXAFSSet, MPXANESSet	1✔
18	from pymatgen.util.testing import PymatgenTest	1✔
19
20
21	class FeffInputSetTest(unittest.TestCase):	1✔
22	@classmethod	1✔
23	def setUpClass(cls):	1✔
24	cls.header_string = """* This FEFF.inp file generated by pymatgen	1✔
25	TITLE comment: From cif file
26	TITLE Source: CoO19128.cif
27	TITLE Structure Summary: Co2 O2
28	TITLE Reduced formula: CoO
29	TITLE space group: (P6_3mc), space number: (186)
30	TITLE abc: 3.297078 3.297078 5.254213
31	TITLE angles: 90.000000 90.000000 120.000000
32	TITLE sites: 4
33	* 1 Co 0.333333 0.666667 0.503676
34	* 2 Co 0.666667 0.333333 0.003676
35	* 3 O 0.333333 0.666667 0.121324
36	* 4 O 0.666667 0.333333 0.621325"""
37	cif_file = os.path.join(PymatgenTest.TEST_FILES_DIR, "CoO19128.cif")	1✔
38	cls.structure = CifParser(cif_file).get_structures()[0]	1✔
39	cls.absorbing_atom = "O"	1✔
40	cls.mp_xanes = MPXANESSet(cls.absorbing_atom, cls.structure)	1✔
41
42	def test_get_header(self):	1✔
43	comment = "From cif file"	1✔
44	header = str(self.mp_xanes.header(source="CoO19128.cif", comment=comment))	1✔
45	print(header)	1✔
46
47	ref = self.header_string.splitlines()	1✔
48	last4 = [" ".join(l.split()[2:]) for l in ref[-4:]]	1✔
49	for i, l in enumerate(header.splitlines()):	1✔
50	if i < 9:	1✔
51	assert l == ref[i]	1✔
52	else:
53	s = " ".join(l.split()[2:])	1✔
54	assert s in last4	1✔
55
56	def test_getfefftags(self):	1✔
57	tags = self.mp_xanes.tags.as_dict()	1✔
58	assert tags["COREHOLE"] == "FSR", "Failed to generate PARAMETERS string"	1✔
59
60	def test_get_feffPot(self):	1✔
61	POT = str(self.mp_xanes.potential)	1✔
62	d, dr = Potential.pot_dict_from_string(POT)	1✔
63	assert d["Co"] == 1, "Wrong symbols read in for Potential"	1✔
64
65	def test_get_feff_atoms(self):	1✔
66	atoms = str(self.mp_xanes.atoms)	1✔
67	assert atoms.splitlines()[3].split()[4] == self.absorbing_atom, "failed to create ATOMS string"	1✔
68
69	def test_to_and_from_dict(self):	1✔
70	f1_dict = self.mp_xanes.as_dict()	1✔
71	f2 = MPXANESSet.from_dict(f1_dict)	1✔
72	assert f1_dict == f2.as_dict()	1✔
73
74	def test_user_tag_settings(self):	1✔
75	tags_dict_ans = self.mp_xanes.tags.as_dict()	1✔
76	tags_dict_ans["COREHOLE"] = "RPA"	1✔
77	tags_dict_ans["EDGE"] = "L1"	1✔
78	user_tag_settings = {"COREHOLE": "RPA", "EDGE": "L1"}	1✔
79	mp_xanes_2 = MPXANESSet(self.absorbing_atom, self.structure, user_tag_settings=user_tag_settings)	1✔
80	assert mp_xanes_2.tags.as_dict() == tags_dict_ans	1✔
81
82	def test_eels_to_from_dict(self):	1✔
83	elnes = MPELNESSet(	1✔
84	self.absorbing_atom,
85	self.structure,
86	radius=5.0,
87	beam_energy=100,
88	beam_direction=[1, 0, 0],
89	collection_angle=7,
90	convergence_angle=6,
91	)
92	elnes_dict = elnes.as_dict()	1✔
93	elnes_2 = MPELNESSet.from_dict(elnes_dict)	1✔
94	assert elnes_dict == elnes_2.as_dict()	1✔
95
96	def test_eels_tags_set(self):	1✔
97	radius = 5.0	1✔
98	user_eels_settings = {	1✔
99	"ENERGY": "4 0.04 0.1",
100	"BEAM_ENERGY": "200 1 0 1",
101	"ANGLES": "2 3",
102	}
103	elnes = MPELNESSet(	1✔
104	self.absorbing_atom,
105	self.structure,
106	radius=radius,
107	user_eels_settings=user_eels_settings,
108	)
109	elnes_2 = MPELNESSet(	1✔
110	self.absorbing_atom,
111	self.structure,
112	radius=radius,
113	beam_energy=100,
114	beam_direction=[1, 0, 0],
115	collection_angle=7,
116	convergence_angle=6,
117	)
118	assert elnes.tags["ELNES"]["ENERGY"] == user_eels_settings["ENERGY"]	1✔
119	assert elnes.tags["ELNES"]["BEAM_ENERGY"] == user_eels_settings["BEAM_ENERGY"]	1✔
120	assert elnes.tags["ELNES"]["ANGLES"] == user_eels_settings["ANGLES"]	1✔
121	assert elnes_2.tags["ELNES"]["BEAM_ENERGY"] == [100, 0, 1, 1]	1✔
122	assert elnes_2.tags["ELNES"]["BEAM_DIRECTION"] == [1, 0, 0]	1✔
123	assert elnes_2.tags["ELNES"]["ANGLES"] == [7, 6]	1✔
124
125	def test_charged_structure(self):	1✔
126	# one Zn+2, 9 triflate, plus water
127	# Molecule, net charge of -7
128	xyz = os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_radial_shell.xyz")	1✔
129	m = Molecule.from_file(xyz)	1✔
130	m.set_charge_and_spin(-7)	1✔
131	# Zn should not appear in the pot_dict
132	with pytest.warns(UserWarning, match="ION tags"):	1✔
133	MPXANESSet("Zn", m)	1✔
134	s = self.structure.copy()	1✔
135	s.set_charge(1)	1✔
136	with pytest.raises(ValueError, match="not supported"):	1✔
137	MPXANESSet("Co", s)	1✔
138
139	def test_reciprocal_tags_and_input(self):	1✔
140	user_tag_settings = {"RECIPROCAL": "", "KMESH": "1000"}	1✔
141	elnes = MPELNESSet(self.absorbing_atom, self.structure, user_tag_settings=user_tag_settings)	1✔
142	assert "RECIPROCAL" in elnes.tags	1✔
143	assert elnes.tags["TARGET"] == 3	1✔
144	assert elnes.tags["KMESH"] == "1000"	1✔
145	assert elnes.tags["CIF"] == "Co2O2.cif"	1✔
146	assert elnes.tags["COREHOLE"] == "RPA"	1✔
147	all_input = elnes.all_input()	1✔
148	assert "ATOMS" not in all_input	1✔
149	assert "POTENTIALS" not in all_input	1✔
150	elnes.write_input()	1✔
151	structure = Structure.from_file("Co2O2.cif")	1✔
152	assert self.structure.matches(structure)	1✔
153	os.remove("HEADER")	1✔
154	os.remove("PARAMETERS")	1✔
155	os.remove("feff.inp")	1✔
156	os.remove("Co2O2.cif")	1✔
157
158	def test_small_system_EXAFS(self):	1✔
159	exafs_settings = MPEXAFSSet(self.absorbing_atom, self.structure)	1✔
160	assert not exafs_settings.small_system	1✔
161	assert "RECIPROCAL" not in exafs_settings.tags	1✔
162
163	user_tag_settings = {"RECIPROCAL": ""}	1✔
164	exafs_settings_2 = MPEXAFSSet(	1✔
165	self.absorbing_atom,
166	self.structure,
167	nkpts=1000,
168	user_tag_settings=user_tag_settings,
169	)
170	assert not exafs_settings_2.small_system	1✔
171	assert "RECIPROCAL" not in exafs_settings_2.tags	1✔
172
173	def test_number_of_kpoints(self):	1✔
174	user_tag_settings = {"RECIPROCAL": ""}	1✔
175	elnes = MPELNESSet(	1✔
176	self.absorbing_atom,
177	self.structure,
178	nkpts=1000,
179	user_tag_settings=user_tag_settings,
180	)
181	assert elnes.tags["KMESH"] == [12, 12, 7]	1✔
182
183	def test_large_systems(self):	1✔
184	struct = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "La4Fe4O12.cif"))	1✔
185	user_tag_settings = {"RECIPROCAL": "", "KMESH": "1000"}	1✔
186	elnes = MPELNESSet("Fe", struct, user_tag_settings=user_tag_settings)	1✔
187	assert "RECIPROCAL" not in elnes.tags	1✔
188	assert "KMESH" not in elnes.tags	1✔
189	assert "CIF" not in elnes.tags	1✔
190	assert "TARGET" not in elnes.tags	1✔
191
192	def test_postfeffset(self):	1✔
193	self.mp_xanes.write_input(os.path.join(".", "xanes_3"))	1✔
194	feff_dict_input = FEFFDictSet.from_directory(os.path.join(".", "xanes_3"))	1✔
195	assert feff_dict_input.tags == Tags.from_file(os.path.join(".", "xanes_3/feff.inp"))	1✔
196	assert str(feff_dict_input.header()) == str(Header.from_file(os.path.join(".", "xanes_3/HEADER")))	1✔
197	feff_dict_input.write_input("xanes_3_regen")	1✔
198	origin_tags = Tags.from_file(os.path.join(".", "xanes_3/PARAMETERS"))	1✔
199	output_tags = Tags.from_file(os.path.join(".", "xanes_3_regen/PARAMETERS"))	1✔
200	origin_mole = Atoms.cluster_from_file(os.path.join(".", "xanes_3/feff.inp"))	1✔
201	output_mole = Atoms.cluster_from_file(os.path.join(".", "xanes_3_regen/feff.inp"))	1✔
202	original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(np.float64)	1✔
203	output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(np.float64)	1✔
204	original_mole_shell = [x.species_string for x in origin_mole]	1✔
205	output_mole_shell = [x.species_string for x in output_mole]	1✔
206
207	assert np.allclose(original_mole_dist, output_mole_dist)	1✔
208	assert origin_tags == output_tags	1✔
209	assert original_mole_shell == output_mole_shell	1✔
210
211	shutil.rmtree(os.path.join(".", "xanes_3"))	1✔
212	shutil.rmtree(os.path.join(".", "xanes_3_regen"))	1✔
213
214	reci_mp_xanes = MPXANESSet(self.absorbing_atom, self.structure, user_tag_settings={"RECIPROCAL": ""})	1✔
215	reci_mp_xanes.write_input("xanes_reci")	1✔
216	feff_reci_input = FEFFDictSet.from_directory(os.path.join(".", "xanes_reci"))	1✔
217	assert "RECIPROCAL" in feff_reci_input.tags	1✔
218
219	feff_reci_input.write_input("Dup_reci")	1✔
220	assert os.path.exists(os.path.join(".", "Dup_reci", "HEADER"))	1✔
221	assert os.path.exists(os.path.join(".", "Dup_reci", "feff.inp"))	1✔
222	assert os.path.exists(os.path.join(".", "Dup_reci", "PARAMETERS"))	1✔
223	assert not os.path.exists(os.path.join(".", "Dup_reci", "ATOMS"))	1✔
224	assert not os.path.exists(os.path.join(".", "Dup_reci", "POTENTIALS"))	1✔
225
226	tags_original = Tags.from_file(os.path.join(".", "xanes_reci/feff.inp"))	1✔
227	tags_output = Tags.from_file(os.path.join(".", "Dup_reci/feff.inp"))	1✔
228	assert tags_original == tags_output	1✔
229
230	stru_orig = Structure.from_file(os.path.join(".", "xanes_reci/Co2O2.cif"))	1✔
231	stru_reci = Structure.from_file(os.path.join(".", "Dup_reci/Co2O2.cif"))	1✔
232	assert stru_orig == stru_reci	1✔
233
234	shutil.rmtree(os.path.join(".", "Dup_reci"))	1✔
235	shutil.rmtree(os.path.join(".", "xanes_reci"))	1✔
236
237	def test_post_distdiff(self):	1✔
238	feff_dict_input = FEFFDictSet.from_directory(os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test"))	1✔
239	assert feff_dict_input.tags == Tags.from_file(	1✔
240	os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test/feff.inp")
241	)
242	assert str(feff_dict_input.header()) == str(	1✔
243	Header.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test/HEADER"))
244	)
245	feff_dict_input.write_input("feff_dist_regen")	1✔
246	origin_tags = Tags.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test/PARAMETERS"))	1✔
247	output_tags = Tags.from_file(os.path.join(".", "feff_dist_regen/PARAMETERS"))	1✔
248	origin_mole = Atoms.cluster_from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "feff_dist_test/feff.inp"))	1✔
249	output_mole = Atoms.cluster_from_file(os.path.join(".", "feff_dist_regen/feff.inp"))	1✔
250	original_mole_dist = np.array(origin_mole.distance_matrix[0, :]).astype(np.float64)	1✔
251	output_mole_dist = np.array(output_mole.distance_matrix[0, :]).astype(np.float64)	1✔
252	original_mole_shell = [x.species_string for x in origin_mole]	1✔
253	output_mole_shell = [x.species_string for x in output_mole]	1✔
254
255	assert np.allclose(original_mole_dist, output_mole_dist)	1✔
256	assert origin_tags == output_tags	1✔
257	assert original_mole_shell == output_mole_shell	1✔
258
259	shutil.rmtree(os.path.join(".", "feff_dist_regen"))	1✔
260
261
262	if __name__ == "__main__":	1✔
263	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