File: electronic_structure.py

package info (click to toggle)
python-mp-api 0.45.3-4
  • links: PTS, VCS
  • area: main
  • in suites: forky, sid, trixie
  • size: 6,988 kB
  • sloc: python: 6,712; makefile: 14
file content (483 lines) | stat: -rw-r--r-- 18,330 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
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
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
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
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
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
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
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
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
from __future__ import annotations

import json
import warnings
from collections import defaultdict

from emmet.core.electronic_structure import (
    BSPathType,
    DOSProjectionType,
    ElectronicStructureDoc,
)
from monty.json import MontyDecoder
from pymatgen.analysis.magnetism.analyzer import Ordering
from pymatgen.core.periodic_table import Element
from pymatgen.electronic_structure.core import OrbitalType, Spin

from mp_api.client.core import BaseRester, MPRestError
from mp_api.client.core.utils import validate_ids


class ElectronicStructureRester(BaseRester[ElectronicStructureDoc]):
    suffix = "materials/electronic_structure"
    document_model = ElectronicStructureDoc  # type: ignore
    primary_key = "material_id"

    def search_electronic_structure_docs(self, *args, **kwargs):  # pragma: no cover
        """Deprecated."""
        warnings.warn(
            "MPRester.electronic_structure.search_electronic_structure_docs is deprecated. "
            "Please use MPRester.electronic_structure.search instead.",
            DeprecationWarning,
            stacklevel=2,
        )

        return self.search(*args, **kwargs)

    def search(
        self,
        material_ids: str | list[str] | None = None,
        band_gap: tuple[float, float] | None = None,
        chemsys: str | list[str] | None = None,
        efermi: tuple[float, float] | None = None,
        elements: list[str] | None = None,
        exclude_elements: list[str] | None = None,
        formula: str | list[str] | None = None,
        is_gap_direct: bool | None = None,
        is_metal: bool | None = None,
        magnetic_ordering: Ordering | None = None,
        num_elements: tuple[int, int] | None = None,
        num_chunks: int | None = None,
        chunk_size: int = 1000,
        all_fields: bool = True,
        fields: list[str] | None = None,
    ):
        """Query electronic structure docs using a variety of search criteria.

        Arguments:
            material_ids (str, List[str]): A single Material ID string or list of strings
                (e.g., mp-149, [mp-149, mp-13]).
            band_gap (Tuple[float,float]): Minimum and maximum band gap in eV to consider.
            chemsys (str, List[str]): A chemical system or list of chemical systems
                (e.g., Li-Fe-O, Si-*, [Si-O, Li-Fe-P]).
            efermi (Tuple[float,float]): Minimum and maximum fermi energy in eV to consider.
            elements (List[str]): A list of elements.
            exclude_elements (List[str]): A list of elements to exclude.
            formula (str, List[str]): A formula including anonymized formula
                or wild cards (e.g., Fe2O3, ABO3, Si*). A list of chemical formulas can also be passed
                (e.g., [Fe2O3, ABO3]).
            is_gap_direct (bool): Whether the material has a direct band gap.
            is_metal (bool): Whether the material is considered a metal.
            magnetic_ordering (Ordering): Magnetic ordering of the material.
            num_elements (Tuple[int,int]): Minimum and maximum number of elements to consider.
            num_chunks (int): Maximum number of chunks of data to yield. None will yield all possible.
            chunk_size (int): Number of data entries per chunk.
            all_fields (bool): Whether to return all fields in the document. Defaults to True.
            fields (List[str]): List of fields in EOSDoc to return data for.
                Default is material_id and last_updated if all_fields is False.

        Returns:
            ([ElectronicStructureDoc]) List of electronic structure documents
        """
        query_params = defaultdict(dict)  # type: dict

        if material_ids:
            if isinstance(material_ids, str):
                material_ids = [material_ids]

            query_params.update({"material_ids": ",".join(validate_ids(material_ids))})

        if formula:
            if isinstance(formula, str):
                formula = [formula]

            query_params.update({"formula": ",".join(formula)})

        if chemsys:
            if isinstance(chemsys, str):
                chemsys = [chemsys]

            query_params.update({"chemsys": ",".join(chemsys)})

        if elements:
            query_params.update({"elements": ",".join(elements)})

        if exclude_elements:
            query_params.update({"exclude_elements": ",".join(exclude_elements)})

        if band_gap:
            query_params.update(
                {"band_gap_min": band_gap[0], "band_gap_max": band_gap[1]}
            )

        if efermi:
            query_params.update({"efermi_min": efermi[0], "efermi_max": efermi[1]})

        if magnetic_ordering:
            query_params.update({"magnetic_ordering": magnetic_ordering.value})

        if num_elements:
            if isinstance(num_elements, int):
                num_elements = (num_elements, num_elements)
            query_params.update(
                {"nelements_min": num_elements[0], "nelements_max": num_elements[1]}
            )

        if is_gap_direct is not None:
            query_params.update({"is_gap_direct": is_gap_direct})

        if is_metal is not None:
            query_params.update({"is_metal": is_metal})

        query_params = {
            entry: query_params[entry]
            for entry in query_params
            if query_params[entry] is not None
        }

        return super()._search(
            num_chunks=num_chunks,
            chunk_size=chunk_size,
            all_fields=all_fields,
            fields=fields,
            **query_params,
        )


class BandStructureRester(BaseRester):
    suffix = "materials/electronic_structure/bandstructure"
    document_model = ElectronicStructureDoc  # type: ignore

    def search_bandstructure_summary(self, *args, **kwargs):  # pragma: no cover
        """Deprecated."""
        warnings.warn(
            "MPRester.electronic_structure_bandstructure.search_bandstructure_summary is deprecated. "
            "Please use MPRester.electronic_structure_bandstructure.search instead.",
            DeprecationWarning,
            stacklevel=2,
        )

        return self.search(*args, **kwargs)

    def search(
        self,
        band_gap: tuple[float, float] | None = None,
        efermi: tuple[float, float] | None = None,
        is_gap_direct: bool | None = None,
        is_metal: bool | None = None,
        magnetic_ordering: Ordering | None = None,
        path_type: BSPathType = BSPathType.setyawan_curtarolo,
        num_chunks: int | None = None,
        chunk_size: int = 1000,
        all_fields: bool = True,
        fields: list[str] | None = None,
    ):
        """Query band structure summary data in electronic structure docs using a variety of search criteria.

        Arguments:
            band_gap (Tuple[float,float]): Minimum and maximum band gap in eV to consider.
            efermi (Tuple[float,float]): Minimum and maximum fermi energy in eV to consider.
            is_gap_direct (bool): Whether the material has a direct band gap.
            is_metal (bool): Whether the material is considered a metal.
            magnetic_ordering (Ordering): Magnetic ordering of the material.
            path_type (BSPathType): k-path selection convention for the band structure.
            num_chunks (int): Maximum number of chunks of data to yield. None will yield all possible.
            chunk_size (int): Number of data entries per chunk.
            all_fields (bool): Whether to return all fields in the document. Defaults to True.
            fields (List[str]): List of fields in ElectronicStructureDoc to return data for.
                Default is material_id and last_updated if all_fields is False.

        Returns:
            ([ElectronicStructureDoc]) List of electronic structure documents
        """
        query_params = defaultdict(dict)  # type: dict

        query_params["path_type"] = path_type.value

        if band_gap:
            query_params.update(
                {"band_gap_min": band_gap[0], "band_gap_max": band_gap[1]}
            )

        if efermi:
            query_params.update({"efermi_min": efermi[0], "efermi_max": efermi[1]})

        if magnetic_ordering:
            query_params.update({"magnetic_ordering": magnetic_ordering.value})

        if is_gap_direct is not None:
            query_params.update({"is_gap_direct": is_gap_direct})

        if is_metal is not None:
            query_params.update({"is_metal": is_metal})

        query_params = {
            entry: query_params[entry]
            for entry in query_params
            if query_params[entry] is not None
        }

        return super()._search(
            num_chunks=num_chunks,
            chunk_size=chunk_size,
            all_fields=all_fields,
            fields=fields,
            **query_params,
        )

    def get_bandstructure_from_task_id(self, task_id: str):
        """Get the band structure pymatgen object associated with a given task ID.

        Arguments:
            task_id (str): Task ID for the band structure calculation

        Returns:
            bandstructure (BandStructure): BandStructure or BandStructureSymmLine object
        """
        decoder = MontyDecoder().decode if self.monty_decode else json.loads
        result = self._query_open_data(
            bucket="materialsproject-parsed",
            key=f"bandstructures/{task_id}.json.gz",
            decoder=decoder,
        )[0]

        if result:
            return result[0]["data"]
        else:
            raise MPRestError("No object found")

    def get_bandstructure_from_material_id(
        self,
        material_id: str,
        path_type: BSPathType = BSPathType.setyawan_curtarolo,
        line_mode=True,
    ):
        """Get the band structure pymatgen object associated with a Materials Project ID.

        Arguments:
            material_id (str): Materials Project ID for a material
            path_type (BSPathType): k-point path selection convention
            line_mode (bool): Whether to return data for a line-mode calculation

        Returns:
            bandstructure (Union[BandStructure, BandStructureSymmLine]): BandStructure or BandStructureSymmLine object
        """
        es_rester = ElectronicStructureRester(
            api_key=self.api_key,
            endpoint=self.base_endpoint,
            include_user_agent=self.include_user_agent,
            session=self.session,
            monty_decode=self.monty_decode,
            use_document_model=self.use_document_model,
            headers=self.headers,
            mute_progress_bars=self.mute_progress_bars,
        )

        if line_mode:
            bs_doc = es_rester.search(
                material_ids=material_id, fields=["bandstructure"]
            )
            if not bs_doc:
                raise MPRestError("No electronic structure data found.")

            bs_data = (
                bs_doc[0].bandstructure  # type: ignore
                if self.use_document_model
                else bs_doc[0]["bandstructure"]  # type: ignore
            )

            if bs_data is None:
                raise MPRestError(
                    f"No {path_type.value} band structure data found for {material_id}"
                )
            else:
                bs_data: dict = (
                    bs_data.model_dump() if self.use_document_model else bs_data  # type: ignore
                )

            if bs_data.get(path_type.value, None):
                bs_task_id = bs_data[path_type.value]["task_id"]
            else:
                raise MPRestError(
                    f"No {path_type.value} band structure data found for {material_id}"
                )
        else:
            bs_doc = es_rester.search(material_ids=material_id, fields=["dos"])

            if not bs_doc:
                raise MPRestError("No electronic structure data found.")

            bs_data = (
                bs_doc[0].dos  # type: ignore
                if self.use_document_model
                else bs_doc[0]["dos"]  # type: ignore
            )

            if bs_data is None:
                raise MPRestError(
                    f"No uniform band structure data found for {material_id}"
                )
            else:
                bs_data: dict = (
                    bs_data.model_dump() if self.use_document_model else bs_data  # type: ignore
                )

            if bs_data.get("total", None):
                bs_task_id = bs_data["total"]["1"]["task_id"]
            else:
                raise MPRestError(
                    f"No uniform band structure data found for {material_id}"
                )

        bs_obj = self.get_bandstructure_from_task_id(bs_task_id)

        if bs_obj:
            return bs_obj
        else:
            raise MPRestError("No band structure object found.")


class DosRester(BaseRester):
    suffix = "materials/electronic_structure/dos"
    document_model = ElectronicStructureDoc  # type: ignore

    def search_dos_summary(self, *args, **kwargs):  # pragma: no cover
        """Deprecated."""
        warnings.warn(
            "MPRester.electronic_structure_dos.search_dos_summary is deprecated. "
            "Please use MPRester.electronic_structure_dos.search instead.",
            DeprecationWarning,
            stacklevel=2,
        )

        return self.search(*args, **kwargs)

    def search(
        self,
        band_gap: tuple[float, float] | None = None,
        efermi: tuple[float, float] | None = None,
        element: Element | None = None,
        magnetic_ordering: Ordering | None = None,
        orbital: OrbitalType | None = None,
        projection_type: DOSProjectionType = DOSProjectionType.total,
        spin: Spin = Spin.up,
        num_chunks: int | None = None,
        chunk_size: int = 1000,
        all_fields: bool = True,
        fields: list[str] | None = None,
    ):
        """Query density of states summary data in electronic structure docs using a variety of search criteria.

        Arguments:
            band_gap (Tuple[float,float]): Minimum and maximum band gap in eV to consider.
            efermi (Tuple[float,float]): Minimum and maximum fermi energy in eV to consider.
            element (Element): Element for element-projected dos data.
            magnetic_ordering (Ordering): Magnetic ordering of the material.
            orbital (OrbitalType): Orbital for orbital-projected dos data.
            projection_type (DOSProjectionType): Projection type of dos data. Default is the total dos.
            spin (Spin): Spin channel of dos data. If non spin-polarized data is stored in Spin.up
            num_chunks (int): Maximum number of chunks of data to yield. None will yield all possible.
            chunk_size (int): Number of data entries per chunk.
            all_fields (bool): Whether to return all fields in the document. Defaults to True.
            fields (List[str]): List of fields in EOSDoc to return data for.
                Default is material_id and last_updated if all_fields is False.

        Returns:
            ([ElectronicStructureDoc]) List of electronic structure documents
        """
        query_params = defaultdict(dict)  # type: dict

        query_params["projection_type"] = projection_type.value
        query_params["spin"] = spin.value

        if element:
            query_params["element"] = element.value

        if orbital:
            query_params["orbital"] = orbital.value

        if band_gap:
            query_params.update(
                {"band_gap_min": band_gap[0], "band_gap_max": band_gap[1]}
            )

        if efermi:
            query_params.update({"efermi_min": efermi[0], "efermi_max": efermi[1]})

        if magnetic_ordering:
            query_params.update({"magnetic_ordering": magnetic_ordering.value})

        query_params = {
            entry: query_params[entry]
            for entry in query_params
            if query_params[entry] is not None
        }

        return super()._search(
            num_chunks=num_chunks,
            chunk_size=chunk_size,
            all_fields=all_fields,
            fields=fields,
            **query_params,
        )

    def get_dos_from_task_id(self, task_id: str):
        """Get the density of states pymatgen object associated with a given calculation ID.

        Arguments:
            task_id (str): Task ID for the density of states calculation

        Returns:
            bandstructure (CompleteDos): CompleteDos object
        """
        decoder = MontyDecoder().decode if self.monty_decode else json.loads
        result = self._query_open_data(
            bucket="materialsproject-parsed",
            key=f"dos/{task_id}.json.gz",
            decoder=decoder,
        )[0]

        if result:
            return result[0]["data"]  # type: ignore
        else:
            raise MPRestError("No object found")

    def get_dos_from_material_id(self, material_id: str):
        """Get the complete density of states pymatgen object associated with a Materials Project ID.

        Arguments:
            material_id (str): Materials Project ID for a material

        Returns:
            dos (CompleteDos): CompleteDos object
        """
        es_rester = ElectronicStructureRester(
            api_key=self.api_key,
            endpoint=self.base_endpoint,
            include_user_agent=self.include_user_agent,
            session=self.session,
            monty_decode=self.monty_decode,
            use_document_model=self.use_document_model,
            headers=self.headers,
            mute_progress_bars=self.mute_progress_bars,
        )

        dos_doc = es_rester.search(material_ids=material_id, fields=["dos"])
        if not dos_doc:
            return None

        dos_data: dict = (
            dos_doc[0].model_dump() if self.use_document_model else dos_doc[0]  # type: ignore
        )

        if dos_data["dos"]:
            dos_task_id = dos_data["dos"]["total"]["1"]["task_id"]
        else:
            raise MPRestError(f"No density of states data found for {material_id}")

        dos_obj = self.get_dos_from_task_id(dos_task_id)

        if dos_obj:
            return dos_obj
        else:
            raise MPRestError("No density of states object found.")