-
Notifications
You must be signed in to change notification settings - Fork 65
/
electrode.py
406 lines (322 loc) · 13 KB
/
electrode.py
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
import re
from datetime import datetime
from typing import List, Union, Dict
from collections import defaultdict
from monty.json import MontyDecoder
from pydantic import BaseModel, Field, validator
from pymatgen.apps.battery.battery_abc import AbstractElectrode
from pymatgen.apps.battery.conversion_battery import ConversionElectrode
from pymatgen.apps.battery.insertion_battery import InsertionElectrode
from pymatgen.core import Composition, Structure
from pymatgen.core.periodic_table import Element
from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
from emmet.core.mpid import MPID
class VoltagePairDoc(BaseModel):
"""
Data for individual voltage steps.
Note: Each voltage step is represented as a sub_electrode (ConversionElectrode/InsertionElectrode)
object to gain access to some basic statistics about the voltage step
"""
max_delta_volume: float = Field(
None,
description="Volume changes in % for a particular voltage step using: "
"max(charge, discharge) / min(charge, discharge) - 1",
)
average_voltage: float = Field(
None, description="The average voltage in V for a particular voltage step."
)
capacity_grav: float = Field(None, description="Gravimetric capacity in mAh/g.")
capacity_vol: float = Field(None, description="Volumetric capacity in mAh/cc.")
energy_grav: float = Field(
None, description="Gravimetric energy (Specific energy) in Wh/kg."
)
energy_vol: float = Field(
None, description="Volumetric energy (Energy Density) in Wh/l."
)
fracA_charge: float = Field(
None, description="Atomic fraction of the working ion in the charged state."
)
fracA_discharge: float = Field(
None, description="Atomic fraction of the working ion in the discharged state."
)
@classmethod
def from_sub_electrode(cls, sub_electrode: AbstractElectrode, **kwargs):
"""
Convert A pymatgen electrode object to a document
"""
return cls(**sub_electrode.get_summary_dict(), **kwargs)
class InsertionVoltagePairDoc(VoltagePairDoc):
"""
Features specific to insertion electrode
"""
formula_charge: str = Field(
None, description="The chemical formula of the charged material."
)
formula_discharge: str = Field(
None, description="The chemical formula of the discharged material."
)
stability_charge: float = Field(
None, description="The energy above hull of the charged material."
)
stability_discharge: float = Field(
None, description="The energy above hull of the discharged material."
)
id_charge: Union[MPID, int, None] = Field(
None, description="The material-id of the charged structure."
)
id_discharge: Union[MPID, int, None] = Field(
None, description="The material-id of the discharged structure."
)
class EntriesCompositionSummary(BaseModel):
"""
Composition summary data for all material entries associated with this electrode.
Included to enable better searching via the API.
"""
all_formulas: List[str] = Field(
None,
description="Reduced formulas for material entries across all voltage pairs.",
)
all_chemsys: List[str] = Field(
None,
description="Chemical systems for material entries across all voltage pairs.",
)
all_formula_anonymous: List[str] = Field(
None,
description="Anonymous formulas for material entries across all voltage pairs.",
)
all_elements: List[Element] = Field(
None, description="Elements in material entries across all voltage pairs.",
)
all_composition_reduced: Dict = Field(
None,
description="Composition reduced data for entries across all voltage pairs.",
)
@classmethod
def from_compositions(cls, compositions: List[Composition]):
all_formulas = list({comp.reduced_formula for comp in compositions})
all_chemsys = list({comp.chemical_system for comp in compositions})
all_formula_anonymous = list({comp.anonymized_formula for comp in compositions})
all_elements = sorted(compositions)[-1].elements
all_composition_reduced = defaultdict(set)
for comp in compositions:
comp_red = comp.get_reduced_composition_and_factor()[0].as_dict()
for ele, num in comp_red.items():
all_composition_reduced[ele].add(num)
return cls(
all_formulas=all_formulas,
all_chemsys=all_chemsys,
all_formula_anonymous=all_formula_anonymous,
all_elements=all_elements,
all_composition_reduced=all_composition_reduced,
)
class InsertionElectrodeDoc(InsertionVoltagePairDoc):
"""
Insertion electrode
"""
battery_id: str = Field(None, description="The id for this battery document.")
battery_formula: str = Field(
None,
description="Reduced formula with working ion range produced by combining the charge and discharge formulas.",
)
framework_formula: str = Field(
None, description="The id for this battery document."
)
host_structure: Structure = Field(
None, description="Host structure (structure without the working ion)"
)
adj_pairs: List[InsertionVoltagePairDoc] = Field(
None, description="Returns all the Voltage Steps"
)
working_ion: Element = Field(
None, description="The working ion as an Element object"
)
num_steps: int = Field(
None,
description="The number of distinct voltage steps in from fully charge to "
"discharge based on the stable intermediate states",
)
max_voltage_step: float = Field(
None, description="Maximum absolute difference in adjacent voltage steps"
)
last_updated: datetime = Field(
None,
description="Timestamp for the most recent calculation for this Material document",
)
framework: Composition = Field(
None, description="The chemical compositions of the host framework"
)
elements: List[Element] = Field(
None,
description="The atomic species contained in this electrode (not including the working ion).",
)
nelements: int = Field(
None,
description="The number of elements in the material (not including the working ion).",
)
chemsys: str = Field(
None,
description="The chemical system this electrode belongs to (not including the working ion)",
)
material_ids: List[MPID] = Field(
None,
description="The ids of all structures that matched to the present host lattice, regardless of stability. "
"The stable entries can be found in the adjacent pairs.",
)
formula_anonymous: str = Field(
None,
title="Anonymous Formula",
description="Anonymized representation of the formula (not including the working ion)",
)
entries_composition_summary: EntriesCompositionSummary = Field(
None,
description="Composition summary data for all material in entries across all voltage pairs.",
)
electrode_object: InsertionElectrode = Field(
None, description="The pymatgen electrode object"
)
warnings: List[str] = Field([], description="Any warnings related to this material")
# Make sure that the datetime field is properly formatted
@validator("last_updated", pre=True)
def last_updated_dict_ok(cls, v):
return MontyDecoder().process_decoded(v)
@classmethod
def from_entries(
cls,
grouped_entries: List[ComputedStructureEntry],
working_ion_entry: ComputedEntry,
battery_id: str,
) -> Union["InsertionElectrodeDoc", None]:
try:
ie = InsertionElectrode.from_entries(
entries=grouped_entries,
working_ion_entry=working_ion_entry,
strip_structures=True,
)
except IndexError:
return None
# First get host structure
d = ie.get_summary_dict()
least_wion_ent = next(
item for item in grouped_entries if item.entry_id == d["id_charge"]
)
host_structure = least_wion_ent.structure.copy()
host_structure.remove_species([d["working_ion"]])
d["material_ids"] = d["stable_material_ids"] + d["unstable_material_ids"]
d["num_steps"] = d.pop("nsteps", None)
d["last_updated"] = datetime.utcnow()
elements = sorted(host_structure.composition.elements)
chemsys = "-".join(sorted(map(str, elements)))
framework = Composition(d["framework_formula"])
discharge_comp = Composition(d["formula_discharge"])
working_ion_ele = Element(d["working_ion"])
battery_formula = cls.get_battery_formula(
Composition(d["formula_charge"]), discharge_comp, working_ion_ele,
)
compositions = []
for doc in d["adj_pairs"]:
compositions.append(Composition(doc["formula_charge"]))
compositions.append(Composition(doc["formula_discharge"]))
entries_composition_summary = EntriesCompositionSummary.from_compositions(
compositions
)
# Check if more than one working ion per transition metal and warn
warnings = []
transition_metal_fraction = sum(
[
discharge_comp.get_atomic_fraction(element)
for element in discharge_comp
if element.is_transition_metal
]
)
if (
discharge_comp.get_atomic_fraction(working_ion_ele)
/ transition_metal_fraction
> 1.0
):
warnings.append("More than one working ion per transition metal")
return cls(
battery_id=battery_id,
host_structure=host_structure.as_dict(),
framework=framework,
battery_formula=battery_formula,
electrode_object=ie.as_dict(),
elements=elements,
nelements=len(elements),
chemsys=chemsys,
formula_anonymous=framework.anonymized_formula,
entries_composition_summary=entries_composition_summary,
warnings=warnings,
**d,
)
@staticmethod
def get_battery_formula(
charge_comp: Composition, discharge_comp: Composition, working_ion: Element
):
working_ion_subscripts = []
for comp in [charge_comp, discharge_comp]:
comp_dict = comp.get_el_amt_dict()
working_ion_num = (
comp_dict.pop(working_ion.value)
if working_ion.value in comp_dict
else 0
)
temp_comp = Composition.from_dict(comp_dict)
(temp_reduced, n) = temp_comp.get_reduced_composition_and_factor()
new_subscript = re.sub(".00$", "", "{:.2f}".format(working_ion_num / n))
if new_subscript != "0":
new_subscript = new_subscript.rstrip("0")
working_ion_subscripts.append(new_subscript)
return (
working_ion.value
+ "-".join(working_ion_subscripts)
+ temp_reduced.reduced_formula
)
class ConversionVoltagePairDoc(VoltagePairDoc):
"""
Features specific to conversion electrode
"""
reactions: List[str] = Field(
None,
description="The reaction(s) the characterizes that particular voltage step.",
)
class ConversionElectrodeDoc(ConversionVoltagePairDoc):
battery_id: str = Field(None, description="The id for this battery document.")
adj_pairs: List[ConversionVoltagePairDoc] = Field(
None, description="Returns all the adjacent Voltage Steps"
)
working_ion: Element = Field(
None, description="The working ion as an Element object"
)
num_steps: int = Field(
None,
description="The number of distinct voltage steps in from fully charge to "
"discharge based on the stable intermediate states",
)
max_voltage_step: float = Field(
None, description="Maximum absolute difference in adjacent voltage steps"
)
last_updated: datetime = Field(
None,
description="Timestamp for the most recent calculation for this Material document",
)
# Make sure that the datetime field is properly formatted
@validator("last_updated", pre=True)
def last_updated_dict_ok(cls, v):
return MontyDecoder().process_decoded(v)
@classmethod
def from_composition_and_entries(
cls,
composition: Composition,
entries: List[ComputedEntry],
working_ion_symbol: str,
task_id: MPID,
):
ce = ConversionElectrode.from_composition_and_entries(
comp=composition,
entries_in_chemsys=entries,
working_ion_symbol=working_ion_symbol,
)
d = ce.get_summary_dict()
d["num_steps"] = d.pop("nsteps", None)
d["last_updated"] = datetime.utcnow()
return cls(task_id=task_id, framework=Composition(d["framework_formula"]), **d)