conftest.py 9.56 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
from nomad.parsing.legacy import Backend
20
21
22
23
24
25
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
def run_normalize(backend: Backend) -> Backend:
30
31
32
33
34
35
36
37
38
39
40
    status, _ = backend.status

    assert status == 'ParseSuccess'

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


@pytest.fixture
41
42
def normalized_vasp_example(parsed_vasp_example: Backend) -> Backend:
    return run_normalize(parsed_vasp_example)
43
44
45


@pytest.fixture
46
47
def normalized_example(parsed_example: Backend) -> Backend:
    return run_normalize(parsed_example)
48
49
50


@pytest.fixture
51
52
def normalized_template_example(parsed_template_example) -> Backend:
    return run_normalize(parsed_template_example)
53
54


55
def run_normalize_for_structure(atoms: Atoms) -> Backend:
56
57
58
59
60
61
62
63
64
65
    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)

66
    return run_normalize(template)
67
68


Lauri Himanen's avatar
Lauri Himanen committed
69
@pytest.fixture(scope='session')
70
def single_point(two_d) -> Backend:
Lauri Himanen's avatar
Lauri Himanen committed
71
72
73
    return two_d


74
@pytest.fixture(scope='session')
75
def gw(two_d) -> Backend:
76
77
78
79
    parser_name = "parsers/template"
    filepath = "tests/data/normalizers/gw.json"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
80
    return backend
81
82


83
@pytest.fixture(scope='session')
84
def geometry_optimization() -> Backend:
85
86
87
88
    parser_name = "parsers/template"
    filepath = "tests/data/normalizers/fcc_crystal_structure.json"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
89
    return backend
90
91


92
@pytest.fixture(scope='session')
93
def molecular_dynamics(bulk) -> Backend:
94
    return bulk
95
96


97
@pytest.fixture(scope='session')
98
def phonon() -> Backend:
99
    parser_name = "parsers/phonopy"
100
    filepath = "tests/data/parsers/phonopy/phonopy-FHI-aims-displacement-01/control.in"
101
102
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
103
    return backend
Lauri Himanen's avatar
Lauri Himanen committed
104
105


106
@pytest.fixture(scope='session')
107
def bulk() -> Backend:
108
109
    parser_name = "parsers/cp2k"
    filepath = "tests/data/normalizers/cp2k_bulk_md/si_md.out"
110
111
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
112
    return backend
113
114
115


@pytest.fixture(scope='session')
116
def two_d() -> Backend:
Lauri Himanen's avatar
Lauri Himanen committed
117
    parser_name = "parsers/fhi-aims"
118
    filepath = "tests/data/normalizers/fhiaims_2d_singlepoint/aims.out"
Lauri Himanen's avatar
Lauri Himanen committed
119
120
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
121
    return backend
Lauri Himanen's avatar
Lauri Himanen committed
122
123
124


@pytest.fixture(scope='session')
125
def surface() -> Backend:
Lauri Himanen's avatar
Lauri Himanen committed
126
    parser_name = "parsers/fhi-aims"
127
128
129
    filepath = "tests/data/normalizers/fhiaims_surface_singlepoint/PBE-light+tight-rho2.out"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
130
    return backend
131
132
133


@pytest.fixture(scope='session')
134
def molecule() -> Backend:
135
136
137
138
    parser_name = "parsers/fhi-aims"
    filepath = "tests/data/normalizers/fhiaims_molecule_singlepoint/aims.out"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
139
    return backend
140
141
142


@pytest.fixture(scope='session')
143
def atom() -> Backend:
144
145
146
147
    parser_name = "parsers/gaussian"
    filepath = "tests/data/normalizers/gaussian_atom_singlepoint/m9b7.out"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
148
    return backend
149
150
151


@pytest.fixture(scope='session')
152
def one_d() -> Backend:
153
154
    parser_name = "parsers/exciting"
    filepath = "tests/data/normalizers/exciting_1d_singlepoint/INFO.OUT"
Lauri Himanen's avatar
Lauri Himanen committed
155
156
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
157
    return backend
158
159
160


@pytest.fixture(scope='session')
161
def bands_unpolarized_gap_indirect() -> Backend:
162
    parser_name = "parsers/vasp"
163
    filepath = "tests/data/normalizers/band_structure/unpolarized_gap/vasprun.xml.bands.xz"
164
165
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
166
    return backend
167
168
169


@pytest.fixture(scope='session')
170
def bands_polarized_no_gap() -> Backend:
171
    parser_name = "parsers/vasp"
172
    filepath = "tests/data/normalizers/band_structure/polarized_no_gap/vasprun.xml.bands.xz"
173
174
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
175
    return backend
176
177
178


@pytest.fixture(scope='session')
179
def bands_unpolarized_no_gap() -> Backend:
180
    parser_name = "parsers/vasp"
181
    filepath = "tests/data/normalizers/band_structure/unpolarized_no_gap/vasprun.xml.bands.xz"
182
183
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
184
    return backend
185
186
187


@pytest.fixture(scope='session')
188
def bands_polarized_gap_indirect() -> Backend:
189
    parser_name = "parsers/vasp"
190
    filepath = "tests/data/normalizers/band_structure/polarized_gap/vasprun.xml.bands.xz"
191
192
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
193
    return backend
194
195


Lauri Himanen's avatar
Lauri Himanen committed
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
@pytest.fixture(scope='session')
def dos_si_vasp() -> Backend:
    parser_name = "parsers/vasp"
    filepath = "tests/data/normalizers/dos/dos_si_vasp/vasprun.xml.relax2.xz"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def dos_si_exciting() -> Backend:
    parser_name = "parsers/exciting"
    filepath = "tests/data/normalizers/dos/dos_si_exciting/INFO.OUT"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def dos_si_fhiaims() -> Backend:
    parser_name = "parsers/fhi-aims"
    filepath = "tests/data/normalizers/dos/dos_si_fhiaims/aims.log"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


223
@pytest.fixture(scope='session')
224
def dos_polarized_vasp() -> Backend:
225
226
227
228
    parser_name = "parsers/vasp"
    filepath = "tests/data/normalizers/dos/polarized_vasp/vasprun.xml.relax2.xz"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
229
    return backend
230
231
232


@pytest.fixture(scope='session')
233
def dos_unpolarized_vasp() -> Backend:
234
235
236
237
    parser_name = "parsers/vasp"
    filepath = "tests/data/normalizers/dos/unpolarized_vasp/vasprun.xml.xz"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
238
    return backend
239
240
241


@pytest.fixture(scope='session')
242
def hash_exciting() -> Backend:
243
244
245
246
    parser_name = "parsers/exciting"
    filepath = "tests/data/normalizers/hashes/exciting/INFO.OUT"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
247
    return backend
248
249
250


@pytest.fixture(scope='session')
251
def hash_vasp(bands_unpolarized_gap_indirect) -> Backend:
252
    return bands_unpolarized_gap_indirect
253
254
255


@pytest.fixture(scope='session')
256
257
def band_path_cF(bands_unpolarized_gap_indirect) -> Backend:
    """Band structure calculation for a cP Bravais lattice.
258
259
    """
    return bands_unpolarized_gap_indirect
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305


@pytest.fixture(scope='session')
def band_path_tP() -> Backend:
    """Band structure calculation for a tP Bravais lattice.
    """
    parser_name = "parsers/vasp"
    filepath = "tests/data/normalizers/band_structure/tP/vasprun.xml.bands.xz"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def band_path_hP() -> Backend:
    """Band structure calculation for a hP Bravais lattice.
    """
    parser_name = "parsers/vasp"
    filepath = "tests/data/normalizers/band_structure/hP/vasprun.xml.bands.xz"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def band_path_mP_nonstandard() -> Backend:
    """Band structure calculation for a mP Bravais lattice with a non-standard
    lattice ordering.
    """
    parser_name = "parsers/vasp"
    filepath = "tests/data/normalizers/band_structure/mP_nonstandard/vasprun.xml.bands.xz"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend


@pytest.fixture(scope='session')
def band_path_cF_nonstandard() -> Backend:
    """Band structure calculation for a mP Bravais lattice with a non-standard
    lattice ordering.
    """
    parser_name = "parsers/exciting"
    filepath = "tests/data/normalizers/band_structure/cF_nonstandard/INFO.OUT"
    backend = parse_file((parser_name, filepath))
    backend = run_normalize(backend)
    return backend