conftest.py 4.61 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
# Copyright 2018 Markus Scheidgen
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#   http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an"AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import pytest

17
18
from ase import Atoms

19
20
21
22
23
24
25
from nomad.parsing import LocalBackend
from nomad.normalizing import normalizers

from tests.test_parsing import parsed_vasp_example  # pylint: disable=unused-import
from tests.test_parsing import parsed_template_example  # pylint: disable=unused-import
from tests.test_parsing import parsed_example  # pylint: disable=unused-import
from tests.test_parsing import parse_file
26
from tests.test_parsing import parsed_template_no_system  # pylint: disable=unused-import
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54


def run_normalize(backend: LocalBackend) -> LocalBackend:
    status, _ = backend.status

    assert status == 'ParseSuccess'

    for normalizer_class in normalizers:
        normalizer = normalizer_class(backend)
        normalizer.normalize()
    return backend


@pytest.fixture
def normalized_vasp_example(parsed_vasp_example: LocalBackend) -> LocalBackend:
    return run_normalize(parsed_vasp_example)


@pytest.fixture
def normalized_example(parsed_example: LocalBackend) -> LocalBackend:
    return run_normalize(parsed_example)


@pytest.fixture
def normalized_template_example(parsed_template_example) -> LocalBackend:
    return run_normalize(parsed_template_example)


55
56
57
58
59
60
61
62
63
64
65
66
67
68
def run_normalize_for_structure(atoms: Atoms) -> LocalBackend:
    template = parsed_template_no_system()

    # Fill structural information
    gid = template.openSection("section_system")
    template.addArrayValues("atom_positions", atoms.get_positions() * 1E-10)
    template.addArrayValues("atom_labels", atoms.get_chemical_symbols())
    template.addArrayValues("simulation_cell", atoms.get_cell() * 1E-10)
    template.addArrayValues("configuration_periodic_dimensions", atoms.get_pbc())
    template.closeSection("section_system", gid)

    return run_normalize(template)


69
70
@pytest.fixture(scope='session')
def geometry_optimization() -> LocalBackend:
71
72
73
74
    parser_name = "parsers/template"
    filepath = "tests/data/normalizers/fcc_crystal_structure.json"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
75
    return backend
76
77


78
@pytest.fixture(scope='session')
79
80
def molecular_dynamics(bulk) -> LocalBackend:
    return bulk
81
82


83
84
@pytest.fixture(scope='session')
def phonon() -> LocalBackend:
85
    parser_name = "parsers/phonopy"
86
    filepath = "tests/data/parsers/phonopy/phonopy-FHI-aims-displacement-01/control.in"
87
88
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
89
    return backend
Lauri Himanen's avatar
Lauri Himanen committed
90
91


92
93
@pytest.fixture(scope='session')
def bulk() -> LocalBackend:
94
95
    parser_name = "parsers/cp2k"
    filepath = "tests/data/normalizers/cp2k_bulk_md/si_md.out"
96
97
98
99
100
101
102
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def two_d() -> LocalBackend:
Lauri Himanen's avatar
Lauri Himanen committed
103
    parser_name = "parsers/fhi-aims"
104
    filepath = "tests/data/normalizers/fhiaims_2d_singlepoint/aims.out"
Lauri Himanen's avatar
Lauri Himanen committed
105
106
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
107
    return backend
Lauri Himanen's avatar
Lauri Himanen committed
108
109
110
111
112


@pytest.fixture(scope='session')
def surface() -> LocalBackend:
    parser_name = "parsers/fhi-aims"
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
    filepath = "tests/data/normalizers/fhiaims_surface_singlepoint/PBE-light+tight-rho2.out"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def molecule() -> LocalBackend:
    parser_name = "parsers/fhi-aims"
    filepath = "tests/data/normalizers/fhiaims_molecule_singlepoint/aims.out"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def atom() -> LocalBackend:
    parser_name = "parsers/gaussian"
    filepath = "tests/data/normalizers/gaussian_atom_singlepoint/m9b7.out"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def one_d() -> LocalBackend:
    parser_name = "parsers/exciting"
    filepath = "tests/data/normalizers/exciting_1d_singlepoint/INFO.OUT"
Lauri Himanen's avatar
Lauri Himanen committed
141
142
143
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend