4075885785

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push

github

Committed by Shyue Ping Ong

Commit Message

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

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37.1

/pymatgen/command_line/tests/test_mcsqs_caller.py

from __future__ import annotations

import os
import unittest
from shutil import which

import pytest
from monty.serialization import loadfn

from pymatgen.command_line.mcsqs_caller import run_mcsqs
from pymatgen.core.structure import Structure
from pymatgen.util.testing import PymatgenTest

__author__ = "Handong Ling, Rachel Woods-Robinson"
__maintainer__ = "Handong Ling, Rachel Woods-Robinson"
__email__ = "handongling@berkeley.edu, rwoodsrobinson@lbl.gov"


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


@unittest.skipIf(not (which("mcsqs") and which("str2cif")), "mcsqs executable not present")
class McsqsCallerTest(PymatgenTest):
    def setUp(self):
        self.pztstructs = loadfn(os.path.join(test_dir, "pztstructs.json"))
        self.pztstructs2 = loadfn(os.path.join(test_dir, "pztstructs2.json"))
        self.struct = self.get_structure("Pb2TiZrO6")
        self.perfect_match_zzn_rs = loadfn(os.path.join(test_dir, "perfect_match_zzn_rs.json"))

    def test_mcsqs_caller_supercell(self):
        struct = self.struct.copy()
        struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})
        sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=[2, 1, 1], search_time=0.01, instances=1)

        matches = [sqs.bestsqs.matches(s) for s in self.pztstructs]
        assert True in matches

        assert isinstance(sqs.bestsqs, Structure)

        # ensures specific keys are present in cluster parsing for use in atomate
        assert set(sqs.clusters[0]) == {
            "multiplicity",
            "coordinates",
            "longest_pair_length",
            "num_points_in_cluster",
        }
        assert set(sqs.clusters[0]["coordinates"][0]) == {"cluster_function", "coordinates", "num_possible_species"}

    def test_mcsqs_caller_total_atoms(self):
        struct = self.struct.copy()
        struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})
        sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=1)

        matches = [sqs.bestsqs.matches(s) for s in self.pztstructs2]
        assert True in matches

    def test_mcsqs_caller_total_atoms_auto_instances(self):
        struct = self.struct.copy()
        struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})
        sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=None)

        matches = [sqs.bestsqs.matches(s) for s in self.pztstructs2]
        assert True in matches

    def test_mcsqs_caller_parallel(self):
        # explicitly test with four instances

        struct = self.struct.copy()
        struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})
        sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=4)

        matches = [sqs.bestsqs.matches(s) for s in self.pztstructs2]
        assert True in matches

    def test_mcsqs_perfect_match_error(self):
        scale = 32 / self.perfect_match_zzn_rs.num_sites
        sqs = run_mcsqs(
            self.perfect_match_zzn_rs,
            {2: 6, 3: 4},
            scaling=scale,
            search_time=1,
            instances=1,
        )

        assert sqs.objective_function == "Perfect_match"

    def test_mcsqs_perfect_match_error_parallel(self):
        scale = 32 / self.perfect_match_zzn_rs.num_sites
        sqs = run_mcsqs(
            self.perfect_match_zzn_rs,
            {2: 6, 3: 4},
            scaling=scale,
            search_time=1,
            instances=4,
        )

        assert sqs.objective_function == "Perfect_match"

    def test_mcsqs_caller_runtime_error(self):
        struct = self.struct.copy()
        struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})
        struct.replace_species({"Pb": {"Ti": 0.2, "Pb": 0.8}})
        struct.replace_species({"O": {"F": 0.8, "O": 0.2}})
        with pytest.raises(RuntimeError):
            run_mcsqs(struct, {2: 6, 3: 4}, 10, 0.000001)

1	from __future__ import annotations	1✔
2
3	import os	1✔
4	import unittest	1✔
5	from shutil import which	1✔
6
7	import pytest	1✔
8	from monty.serialization import loadfn	1✔
9
10	from pymatgen.command_line.mcsqs_caller import run_mcsqs	1✔
11	from pymatgen.core.structure import Structure	1✔
12	from pymatgen.util.testing import PymatgenTest	1✔
13
14	__author__ = "Handong Ling, Rachel Woods-Robinson"	1✔
15	__maintainer__ = "Handong Ling, Rachel Woods-Robinson"	1✔
16	__email__ = "handongling@berkeley.edu, rwoodsrobinson@lbl.gov"	1✔
17
18
19	test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "mcsqs")	1✔
20
21
22	@unittest.skipIf(not (which("mcsqs") and which("str2cif")), "mcsqs executable not present")	1✔
23	class McsqsCallerTest(PymatgenTest):	1✔
24	def setUp(self):	1✔
25	self.pztstructs = loadfn(os.path.join(test_dir, "pztstructs.json"))	×
26	self.pztstructs2 = loadfn(os.path.join(test_dir, "pztstructs2.json"))	×
27	self.struct = self.get_structure("Pb2TiZrO6")	×
28	self.perfect_match_zzn_rs = loadfn(os.path.join(test_dir, "perfect_match_zzn_rs.json"))	×
29
30	def test_mcsqs_caller_supercell(self):	1✔
31	struct = self.struct.copy()	×
32	struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})	×
33	sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=[2, 1, 1], search_time=0.01, instances=1)	×
34
35	matches = [sqs.bestsqs.matches(s) for s in self.pztstructs]	×
36	assert True in matches	×
37
38	assert isinstance(sqs.bestsqs, Structure)	×
39
40	# ensures specific keys are present in cluster parsing for use in atomate
41	assert set(sqs.clusters[0]) == {	×
42	"multiplicity",
43	"coordinates",
44	"longest_pair_length",
45	"num_points_in_cluster",
46	}
47	assert set(sqs.clusters[0]["coordinates"][0]) == {"cluster_function", "coordinates", "num_possible_species"}	×
48
49	def test_mcsqs_caller_total_atoms(self):	1✔
50	struct = self.struct.copy()	×
51	struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})	×
52	sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=1)	×
53
54	matches = [sqs.bestsqs.matches(s) for s in self.pztstructs2]	×
55	assert True in matches	×
56
57	def test_mcsqs_caller_total_atoms_auto_instances(self):	1✔
58	struct = self.struct.copy()	×
59	struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})	×
60	sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=None)	×
61
62	matches = [sqs.bestsqs.matches(s) for s in self.pztstructs2]	×
63	assert True in matches	×
64
65	def test_mcsqs_caller_parallel(self):	1✔
66	# explicitly test with four instances
67
68	struct = self.struct.copy()	×
69	struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})	×
70	sqs = run_mcsqs(struct, {2: 6, 3: 4}, scaling=2, search_time=0.01, instances=4)	×
71
72	matches = [sqs.bestsqs.matches(s) for s in self.pztstructs2]	×
73	assert True in matches	×
74
75	def test_mcsqs_perfect_match_error(self):	1✔
76	scale = 32 / self.perfect_match_zzn_rs.num_sites	×
77	sqs = run_mcsqs(	×
78	self.perfect_match_zzn_rs,
79	{2: 6, 3: 4},
80	scaling=scale,
81	search_time=1,
82	instances=1,
83	)
84
85	assert sqs.objective_function == "Perfect_match"	×
86
87	def test_mcsqs_perfect_match_error_parallel(self):	1✔
88	scale = 32 / self.perfect_match_zzn_rs.num_sites	×
89	sqs = run_mcsqs(	×
90	self.perfect_match_zzn_rs,
91	{2: 6, 3: 4},
92	scaling=scale,
93	search_time=1,
94	instances=4,
95	)
96
97	assert sqs.objective_function == "Perfect_match"	×
98
99	def test_mcsqs_caller_runtime_error(self):	1✔
100	struct = self.struct.copy()	×
101	struct.replace_species({"Ti": {"Ti": 0.5, "Zr": 0.5}, "Zr": {"Ti": 0.5, "Zr": 0.5}})	×
102	struct.replace_species({"Pb": {"Ti": 0.2, "Pb": 0.8}})	×
103	struct.replace_species({"O": {"F": 0.8, "O": 0.2}})	×
104	with pytest.raises(RuntimeError):	×
105	run_mcsqs(struct, {2: 6, 3: 4}, 10, 0.000001)	×

materialsproject / pymatgen / 4075885785

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