encyclopedia.py 12.5 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.

from typing import Any

17
from nomad.normalizing.normalizer import Normalizer
18
19
from nomad.datamodel.encyclopedia import (
    EncyclopediaMetadata,
20
21
22
23
24
    Material,
    Method,
    Properties,
    Calculation,
)
25
from nomad.parsing.legacy import Backend
26
27
28
29
from nomad.normalizing.encyclopedia.context import Context
from nomad.normalizing.encyclopedia.material import MaterialBulkNormalizer, Material2DNormalizer, Material1DNormalizer
from nomad.normalizing.encyclopedia.method import MethodDFTNormalizer, MethodGWNormalizer
from nomad.normalizing.encyclopedia.properties import PropertiesNormalizer
30
from nomad import config
31
32
33
34
35
36


class EncyclopediaNormalizer(Normalizer):
    """
    This normalizer emulates the functionality of the old Encyclopedia backend.
    The data used by the encyclopedia have been assigned under new metainfo
37
    within a new section called "encyclopedia". In the future these separate
38
39
    metainfos could be absorbed into the existing metainfo hiearchy.
    """
40
    def __init__(self, backend: Backend):
41
        super().__init__(backend)
42
        self.backend: Backend = backend
43
44
45
46
47
48
49
50
51

    def calc_type(self, calc: Calculation) -> str:
        """Decides what type of calculation this is: single_point, md,
        geometry_optimization, etc.
        """
        calc_enums = Calculation.calculation_type.type
        calc_type = calc_enums.unavailable

        try:
52
            sccs = self.section_run.section_single_configuration_calculation
53
54
55
        except Exception:
            sccs = []
        try:
56
            frame_sequences = self.section_run.section_frame_sequence
57
58
59
60
61
62
63
64
        except Exception:
            frame_sequences = []

        n_scc = len(sccs)
        n_frame_seq = len(frame_sequences)

        # No sequences, only a few calculations
        if n_scc <= 3 and n_frame_seq == 0:
65
            program_name = self.section_run.program_name
66
67
68
69
70
71
72
73
74
75
76
77
            if program_name == "elastic":
                # TODO move to taylor expansion as soon as data is correct in archive
                calc_type = calc_enums.elastic_constants
            else:
                calc_type = calc_enums.single_point

        # One sequence. Currently calculations with multiple sequences are
        # unsupported.
        elif n_frame_seq == 1:
            frame_seq = frame_sequences[0]

            # See if sampling_method is present
78
79
            section_sampling_method = frame_seq.frame_sequence_to_sampling_ref
            if section_sampling_method is None:
80
81
82
83
84
85
86
                self.logger.info(
                    "Cannot determine encyclopedia run type because missing "
                    "value for frame_sequence_to_sampling_ref."
                )
                return calc_type

            # See if local frames are present
87
88
            frames = frame_seq.frame_sequence_local_frames_ref
            if not frames:
89
90
91
                self.logger.info("No frames referenced in section_frame_sequence_local_frames.")
                return calc_type

92
            sampling_method = section_sampling_method.sampling_method
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108

            if sampling_method == "molecular_dynamics":
                calc_type = calc_enums.molecular_dynamics
            if sampling_method == "geometry_optimization":
                calc_type = calc_enums.geometry_optimization
            if sampling_method == "taylor_expansion":
                calc_type = calc_enums.phonon_calculation

        calc.calculation_type = calc_type
        return calc_type

    def material_type(self, material: Material) -> tuple:
        # Try to fetch representative system
        system = None
        material_type = config.services.unavailable_value
        material_enums = Material.material_type.type
109
        try:
110
            system_idx = self.section_run.m_cache["representative_system_idx"]
111
112
113
        except (AttributeError, KeyError):
            pass
        else:
114
115
            # Try to find system type information from backend for the selected system.
            try:
116
117
                system = self.section_run.section_system[system_idx]
                stype = system.system_type
118
119
120
121
122
123
124
125
            except KeyError:
                pass
            else:
                if stype == material_enums.one_d or stype == material_enums.two_d:
                    material_type = stype
                # For bulk systems we also ensure that the symmetry information is available
                if stype == material_enums.bulk:
                    try:
126
                        system.section_symmetry[0]
127
128
129
130
131
132
133
134
                    except (KeyError, IndexError):
                        self.logger.info("Symmetry information is not available for a bulk system. No Encylopedia entry created.")
                    else:
                        material_type = stype

        material.material_type = material_type
        return system, material_type

135
    def method_type(self, method: Method) -> tuple:
136
137
        repr_method = None
        method_id = config.services.unavailable_value
138
        methods = self.section_run.section_method
139
140
141
142
        n_methods = len(methods)

        if n_methods == 1:
            repr_method = methods[0]
143
144
145
            method_id = repr_method.electronic_structure_method
            if method_id is None:
                method_id = config.services.unavailable_value
146
        elif n_methods > 1:
147
            for sec_method in methods:
148
                # GW
149
                electronic_structure_method = sec_method.electronic_structure_method
150
151
152
153
154
155
156
157
158
                if electronic_structure_method in {"G0W0", "scGW"}:
                    repr_method = sec_method
                    method_id = "GW"
                    break

                # Methods linked to each other through references. Get all
                # linked methods, try to get electronic_structure_method from
                # each.
                try:
159
                    refs = sec_method.section_method_to_method_refs
160
161
162
163
164
                except KeyError:
                    pass
                else:
                    linked_methods = [sec_method]
                    for ref in refs:
165
166
                        method_to_method_kind = ref.method_to_method_kind
                        method_to_method_ref = ref.method_to_method_ref
167
                        if method_to_method_kind == "core_settings":
168
                            linked_methods.append(method_to_method_ref)
169
170

                    for i_method in linked_methods:
171
172
                        electronic_structure_method = i_method.electronic_structure_method
                        if electronic_structure_method is not None:
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
                            repr_method = sec_method
                            method_id = electronic_structure_method

        method.method_type = method_id
        return repr_method, method_id

    def fill(self, context: Context):
        # Fill structure related metainfo
        struct: Any = None
        if context.material_type == Material.material_type.type.bulk:
            struct = MaterialBulkNormalizer(self.backend, self.logger)
        elif context.material_type == Material.material_type.type.two_d:
            struct = Material2DNormalizer(self.backend, self.logger)
        elif context.material_type == Material.material_type.type.one_d:
            struct = Material1DNormalizer(self.backend, self.logger)
        if struct is not None:
            struct.normalize(context)

        # Fill method related metainfo
        method = None
        if context.method_type == Method.method_type.type.DFT or context.method_type == Method.method_type.type.DFTU:
            method = MethodDFTNormalizer(self._backend, self.logger)
        elif context.method_type == Method.method_type.type.GW:
            method = MethodGWNormalizer(self._backend, self.logger)
        if method is not None:
            method.normalize(context)

        # Fill properties related metainfo
        properties = PropertiesNormalizer(self.backend, self.logger)
        properties.normalize(context)

    def normalize(self, logger=None) -> None:
        """The caller will automatically log if the normalizer succeeds or ends
        up with an exception.
        """
208
209
        sec_enc = self.backend.entry_archive.section_metadata.m_create(EncyclopediaMetadata)
        status_enums = EncyclopediaMetadata.status.type
210

211
212
        # Do nothing if section_run is not present
        if self.section_run is None:
213
214
            status = status_enums.invalid_metainfo
            sec_enc.status = status
215
            self.logger.info(
216
217
                "required metainfo is missing or is invalid.",
                enc_status=status,
218
219
220
221
                invalid_metainfo="section_run",
            )
            return

222
223
224
225
226
227
228
229
230
231
232
233
        try:
            super().normalize(logger)

            # Initialise metainfo structure
            material = sec_enc.m_create(Material)
            method = sec_enc.m_create(Method)
            sec_enc.m_create(Properties)
            calc = sec_enc.m_create(Calculation)

            # Determine run type, stop if unknown
            calc_type = self.calc_type(calc)
            if calc_type == config.services.unavailable_value:
234
235
                status = status_enums.unsupported_calculation_type
                sec_enc.status = status
236
                self.logger.info(
237
238
                    "unsupported calculation type for encyclopedia",
                    enc_status=status,
239
240
241
                )
                return

242
            # Get the system type.
243
244
245
            material_enums = Material.material_type.type
            representative_system, material_type = self.material_type(material)
            if material_type != material_enums.bulk and material_type != material_enums.two_d and material_type != material_enums.one_d:
246
247
                status = status_enums.unsupported_material_type
                sec_enc.status = status
248
                self.logger.info(
249
250
                    "unsupported material type for encyclopedia",
                    enc_status=status,
251
                )
252
                return
253

254
255
256
            # Get the method type. For now, we allow unknown method type for
            # phonon calculations, as the method information is resolved at a
            # later stage.
257
            representative_method, method_type = self.method_type(method)
258
            if method_type == config.services.unavailable_value:
259
                sec_enc.status = status_enums.unsupported_method_type
260
261
                self.logger.info(
                    "unsupported method type for encyclopedia",
262
                    enc_status=status_enums.unsupported_method_type,
263
                )
264
265
266
                calc_enums = Calculation.calculation_type.type
                if calc_type != calc_enums.phonon_calculation:
                    return
267
268
269

            # Get representative scc
            try:
270
271
                representative_scc_idx = self.section_run.m_cache["representative_scc_idx"]
                representative_scc = self.section_run.section_single_configuration_calculation[representative_scc_idx]
272
            except Exception:
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
                representative_scc = None
                representative_scc_idx = None

            # Create one context that holds all details
            context = Context(
                material_type=material_type,
                method_type=method_type,
                calc_type=calc_type,
                representative_system=representative_system,
                representative_method=representative_method,
                representative_scc=representative_scc,
                representative_scc_idx=representative_scc_idx,
            )

            # Put the encyclopedia section into backend
            self.fill(context)
289

290
        except Exception:
291
292
            status = status_enums.failure
            sec_enc.status = status
293
            self.logger.error(
294
295
                "failed to process encyclopedia data due to an unhandlable exception",
                enc_status=status,
296
297
298
            )
            raise  # Reraise for the caller to log the exception as well
        else:
299
300
            status = status_enums.success
            sec_enc.status = status
301
            self.logger.info(
302
303
                "successfully created metainfo for encyclopedia.",
                enc_status=status,
304
            )