Source code for pymatgen.apps.battery.insertion_battery

# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.


"""
This module is used for analysis of materials with potential application as
intercalation batteries.
"""

__author__ = "Anubhav Jain, Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"


import itertools
from dataclasses import dataclass
from typing import Iterable, Dict

from monty.dev import deprecated
from scipy.constants import N_A

from pymatgen.analysis.phase_diagram import PDEntry, PhaseDiagram
from pymatgen.apps.battery.battery_abc import AbstractElectrode, AbstractVoltagePair
from pymatgen.core.composition import Composition
from pymatgen.core.periodic_table import Element
from pymatgen.core.units import Charge, Time
from pymatgen.entries.computed_entries import ComputedEntry


[docs]@dataclass class InsertionElectrode(AbstractElectrode): """ A set of topotactically related compounds, with different amounts of a single element, e.g. TiO2 and LiTiO2, that can be used to define an insertion battery electrode. """ _stable_entries: Iterable[ComputedEntry] _unstable_entries: Iterable[ComputedEntry]
[docs] @classmethod def from_entries(cls, entries, working_ion_entry, strip_structures=False): """ Create a new InsertionElectrode. Args: entries: A list of ComputedStructureEntries (or subclasses) representing the different topotactic states of the battery, e.g. TiO2 and LiTiO2. working_ion_entry: A single ComputedEntry or PDEntry representing the element that carries charge across the battery, e.g. Li. strip_structures: Since the electrode document only uses volume we can make the electrode object significantly leaner by dropping the structure data. If this parameter is set to True, the ComputedStructureEntry will be replaced with ComputedEntry and the volume will be stored in ComputedEntry.data['volume'] """ if strip_structures: ents = [] for ient in entries: dd = ient.as_dict() ent = ComputedEntry.from_dict(dd) ent.data["volume"] = ient.structure.volume ents.append(ent) entries = ents _working_ion = working_ion_entry.composition.elements[0] _working_ion_entry = working_ion_entry # Prepare to make phase diagram: determine elements and set their energy # to be very high elements = set() for entry in entries: elements.update(entry.composition.elements) # Set an artificial energy for each element for convex hull generation element_energy = max([entry.energy_per_atom for entry in entries]) + 10 pdentries = [] pdentries.extend(entries) pdentries.extend([PDEntry(Composition({el: 1}), element_energy) for el in elements]) # Make phase diagram to determine which entries are stable vs. unstable pd = PhaseDiagram(pdentries) def lifrac(e): return e.composition.get_atomic_fraction(_working_ion) # stable entries ordered by amount of Li asc _stable_entries = tuple(sorted([e for e in pd.stable_entries if e in entries], key=lifrac)) # unstable entries ordered by amount of Li asc _unstable_entries = tuple(sorted([e for e in pd.unstable_entries if e in entries], key=lifrac)) # create voltage pairs _vpairs = tuple( InsertionVoltagePair.from_entries( _stable_entries[i], _stable_entries[i + 1], working_ion_entry, ) for i in range(len(_stable_entries) - 1) ) framework = _vpairs[0].framework return cls( voltage_pairs=_vpairs, working_ion_entry=_working_ion_entry, _stable_entries=_stable_entries, _unstable_entries=_unstable_entries, _framework_formula=framework.reduced_formula, )
[docs] def get_stable_entries(self, charge_to_discharge=True): """ Get the stable entries. Args: charge_to_discharge: order from most charge to most discharged state? Default to True. Returns: A list of stable entries in the electrode, ordered by amount of the working ion. """ list_copy = list(self._stable_entries) return list_copy if charge_to_discharge else list_copy.reverse()
[docs] def get_unstable_entries(self, charge_to_discharge=True): """ Returns the unstable entries for the electrode. Args: charge_to_discharge: Order from most charge to most discharged state? Defaults to True. Returns: A list of unstable entries in the electrode, ordered by amount of the working ion. """ list_copy = list(self._unstable_entries) return list_copy if charge_to_discharge else list_copy.reverse()
[docs] def get_all_entries(self, charge_to_discharge=True): """ Return all entries input for the electrode. Args: charge_to_discharge: order from most charge to most discharged state? Defaults to True. Returns: A list of all entries in the electrode (both stable and unstable), ordered by amount of the working ion. """ all_entries = list(self.get_stable_entries()) all_entries.extend(self.get_unstable_entries()) # sort all entries by amount of working ion ASC all_entries = sorted( all_entries, key=lambda e: e.composition.get_atomic_fraction(self.working_ion), ) return all_entries if charge_to_discharge else all_entries.reverse()
@property def fully_charged_entry(self): """ The most charged entry along the topotactic path. """ return self._stable_entries[0] @property def fully_discharged_entry(self): """ The most discharged entry along the topotactic path. """ return self._stable_entries[-1]
[docs] def get_max_instability(self, min_voltage=None, max_voltage=None): """ The maximum instability along a path for a specific voltage range. Args: min_voltage: The minimum allowable voltage. max_voltage: The maximum allowable voltage. Returns: Maximum decomposition energy of all compounds along the insertion path (a subset of the path can be chosen by the optional arguments) """ data = [] for pair in self._select_in_voltage_range(min_voltage, max_voltage): if pair.decomp_e_charge is not None: data.append(pair.decomp_e_charge) if pair.decomp_e_discharge is not None: data.append(pair.decomp_e_discharge) return max(data) if len(data) > 0 else None
[docs] def get_min_instability(self, min_voltage=None, max_voltage=None): """ The minimum instability along a path for a specific voltage range. Args: min_voltage: The minimum allowable voltage. max_voltage: The maximum allowable voltage. Returns: Minimum decomposition energy of all compounds along the insertion path (a subset of the path can be chosen by the optional arguments) """ data = [] for pair in self._select_in_voltage_range(min_voltage, max_voltage): if pair.decomp_e_charge is not None: data.append(pair.decomp_e_charge) if pair.decomp_e_discharge is not None: data.append(pair.decomp_e_discharge) return min(data) if len(data) > 0 else None
[docs] def get_max_muO2(self, min_voltage=None, max_voltage=None): """ Maximum critical oxygen chemical potential along path. Args: min_voltage: The minimum allowable voltage. max_voltage: The maximum allowable voltage. Returns: Maximum critical oxygen chemical of all compounds along the insertion path (a subset of the path can be chosen by the optional arguments). """ data = [] for pair in self._select_in_voltage_range(min_voltage, max_voltage): if pair.muO2_discharge is not None: data.extend([d["chempot"] for d in pair.muO2_discharge]) if pair.muO2_charge is not None: data.extend([d["chempot"] for d in pair.muO2_discharge]) return max(data) if len(data) > 0 else None
[docs] def get_min_muO2(self, min_voltage=None, max_voltage=None): """ Minimum critical oxygen chemical potential along path. Args: min_voltage: The minimum allowable voltage for a given step max_voltage: The maximum allowable voltage allowable for a given step Returns: Minimum critical oxygen chemical of all compounds along the insertion path (a subset of the path can be chosen by the optional arguments). """ data = [] for pair in self._select_in_voltage_range(min_voltage, max_voltage): if pair.muO2_discharge is not None: data.extend([d["chempot"] for d in pair.muO2_discharge]) if pair.muO2_charge is not None: data.extend([d["chempot"] for d in pair.muO2_discharge]) return min(data) if len(data) > 0 else None
[docs] def get_sub_electrodes(self, adjacent_only=True, include_myself=True): """ If this electrode contains multiple voltage steps, then it is possible to use only a subset of the voltage steps to define other electrodes. For example, an LiTiO2 electrode might contain three subelectrodes: [LiTiO2 --> TiO2, LiTiO2 --> Li0.5TiO2, Li0.5TiO2 --> TiO2] This method can be used to return all the subelectrodes with some options Args: adjacent_only: Only return electrodes from compounds that are adjacent on the convex hull, i.e. no electrodes returned will have multiple voltage steps if this is set True. include_myself: Include this identical electrode in the list of results. Returns: A list of InsertionElectrode objects """ battery_list = [] pair_it = ( self.voltage_pairs if adjacent_only else itertools.combinations_with_replacement(self.voltage_pairs, 2) ) ion = self.working_ion for pair in pair_it: entry_charge = pair.entry_charge if adjacent_only else pair[0].entry_charge entry_discharge = pair.entry_discharge if adjacent_only else pair[1].entry_discharge chg_frac = entry_charge.composition.get_atomic_fraction(ion) dischg_frac = entry_discharge.composition.get_atomic_fraction(ion) def in_range(entry): frac = entry.composition.get_atomic_fraction(ion) return chg_frac <= frac <= dischg_frac if ( include_myself or entry_charge != self.fully_charged_entry or entry_discharge != self.fully_discharged_entry ): unstable_entries = filter(in_range, self.get_unstable_entries()) stable_entries = filter(in_range, self.get_stable_entries()) all_entries = list(stable_entries) all_entries.extend(unstable_entries) battery_list.append(self.__class__.from_entries(all_entries, self.working_ion_entry)) return battery_list
[docs] def get_summary_dict(self, print_subelectrodes=True) -> Dict: """ Generate a summary dict. Populates the summary dict with the basic information from the parent method then populates more information. Since the parent method calls self.get_summary_dict(print_subelectrodes=True) for the subelectrodes. The current methode will be called from within super().get_summary_dict. Args: print_subelectrodes: Also print data on all the possible subelectrodes. Returns: A summary of this electrode"s properties in dict format. """ d = super().get_summary_dict(print_subelectrodes=print_subelectrodes) chg_comp = self.fully_charged_entry.composition dischg_comp = self.fully_discharged_entry.composition d.update( { "id_charge": self.fully_charged_entry.entry_id, "formula_charge": chg_comp.reduced_formula, "id_discharge": self.fully_discharged_entry.entry_id, "formula_discharge": dischg_comp.reduced_formula, "max_instability": self.get_max_instability(), "min_instability": self.get_min_instability(), "material_ids": [itr_ent.entry_id for itr_ent in self.get_all_entries()], "stable_material_ids": [itr_ent.entry_id for itr_ent in self.get_stable_entries()], "unstable_material_ids": [itr_ent.entry_id for itr_ent in self.get_unstable_entries()], } ) if all("decomposition_energy" in itr_ent.data for itr_ent in self.get_all_entries()): d.update( { "stability_charge": self.fully_charged_entry.data["decomposition_energy"], "stability_discharge": self.fully_discharged_entry.data["decomposition_energy"], "stability_data": { itr_ent.entry_id: itr_ent.data["decomposition_energy"] for itr_ent in self.get_all_entries() }, } ) if all("muO2" in itr_ent.data for itr_ent in self.get_all_entries()): d.update({"muO2_data": {itr_ent.entry_id: itr_ent.data["muO2"] for itr_ent in self.get_all_entries()}}) return d
@deprecated( replacement=get_summary_dict, message="Name and logic changed, as_dict_summary will be removed in a future release.", ) def as_dict_summary(self, print_subelectrodes=True): """ Generate a summary dict. Args: print_subelectrodes: Also print data on all the possible subelectrodes. Returns: A summary of this electrode"s properties in dict format. """ chg_comp = self.fully_charged_entry.composition dischg_comp = self.fully_discharged_entry.composition ion = self.working_ion d = { "average_voltage": self.get_average_voltage(), "max_voltage": self.max_voltage, "min_voltage": self.min_voltage, "max_delta_volume": self.max_delta_volume, "max_voltage_step": self.max_voltage_step, "capacity_grav": self.get_capacity_grav(), "capacity_vol": self.get_capacity_vol(), "energy_grav": self.get_specific_energy(), "energy_vol": self.get_energy_density(), "working_ion": self.working_ion.symbol, "nsteps": self.num_steps, "framework": self.voltage_pairs[0].framework.to_data_dict, "formula_charge": chg_comp.reduced_formula, "id_charge": self.fully_charged_entry.entry_id, "formula_discharge": dischg_comp.reduced_formula, "id_discharge": self.fully_discharged_entry.entry_id, "fracA_charge": chg_comp.get_atomic_fraction(ion), "fracA_discharge": dischg_comp.get_atomic_fraction(ion), "max_instability": self.get_max_instability(), "min_instability": self.get_min_instability(), "material_ids": [itr_ent.entry_id for itr_ent in self.get_all_entries()], "stable_material_ids": [itr_ent.entry_id for itr_ent in self.get_stable_entries()], "unstable_material_ids": [itr_ent.entry_id for itr_ent in self.get_unstable_entries()], } if all("decomposition_energy" in itr_ent.data for itr_ent in self.get_all_entries()): d.update( { "stability_charge": self.fully_charged_entry.data["decomposition_energy"], "stability_discharge": self.fully_discharged_entry.data["decomposition_energy"], "stability_data": { itr_ent.entry_id: itr_ent.data["decomposition_energy"] for itr_ent in self.get_all_entries() }, } ) if all("muO2" in itr_ent.data for itr_ent in self.get_all_entries()): d.update({"muO2_data": {itr_ent.entry_id: itr_ent.data["muO2"] for itr_ent in self.get_all_entries()}}) if print_subelectrodes: def f_dict(c): return c.get_summary_dict(print_subelectrodes=False) d["adj_pairs"] = list(map(f_dict, self.get_sub_electrodes(adjacent_only=True))) d["all_pairs"] = list(map(f_dict, self.get_sub_electrodes(adjacent_only=False))) return d def __str__(self): return self.__repr__() def __repr__(self): output = [] chg_form = self.fully_charged_entry.composition.reduced_formula dischg_form = self.fully_discharged_entry.composition.reduced_formula output.append("InsertionElectrode with endpoints at {} and {}".format(chg_form, dischg_form)) output.append("Avg. volt. = {} V".format(self.get_average_voltage())) output.append("Grav. cap. = {} mAh/g".format(self.get_capacity_grav())) output.append("Vol. cap. = {}".format(self.get_capacity_vol())) return "\n".join(output)
[docs] @classmethod def from_dict_legacy(cls, d): """ Args: d (dict): Dict representation Returns: InsertionElectrode """ from monty.json import MontyDecoder dec = MontyDecoder() return cls( dec.process_decoded(d["entries"]), dec.process_decoded(d["working_ion_entry"]), )
[docs] def as_dict_legacy(self): """ Returns: MSONAble dict """ return { "@module": self.__class__.__module__, "@class": self.__class__.__name__, "entries": [entry.as_dict() for entry in self.get_all_entries()], "working_ion_entry": self.working_ion_entry.as_dict(), }
[docs]@dataclass class InsertionVoltagePair(AbstractVoltagePair): """ Defines an Insertion Voltage Pair. """ entry_charge: ComputedEntry entry_discharge: ComputedEntry
[docs] @classmethod def from_entries(cls, entry1, entry2, working_ion_entry): """ Args: entry1: Entry corresponding to one of the entries in the voltage step. entry2: Entry corresponding to the other entry in the voltage step. working_ion_entry: A single ComputedEntry or PDEntry representing the element that carries charge across the battery, e.g. Li. """ # initialize some internal variables working_element = working_ion_entry.composition.elements[0] entry_charge = entry1 entry_discharge = entry2 if entry_charge.composition.get_atomic_fraction(working_element) > entry2.composition.get_atomic_fraction( working_element ): (entry_charge, entry_discharge) = (entry_discharge, entry_charge) comp_charge = entry_charge.composition comp_discharge = entry_discharge.composition ion_sym = working_element.symbol frame_charge_comp = Composition({el: comp_charge[el] for el in comp_charge if el.symbol != ion_sym}) frame_discharge_comp = Composition({el: comp_discharge[el] for el in comp_discharge if el.symbol != ion_sym}) # Data validation # check that the ion is just a single element if not working_ion_entry.composition.is_element: raise ValueError("VoltagePair: The working ion specified must be " "an element") # check that at least one of the entries contains the working element if ( not comp_charge.get_atomic_fraction(working_element) > 0 and not comp_discharge.get_atomic_fraction(working_element) > 0 ): raise ValueError("VoltagePair: The working ion must be present in " "one of the entries") # check that the entries do not contain the same amount of the workin # element if comp_charge.get_atomic_fraction(working_element) == comp_discharge.get_atomic_fraction(working_element): raise ValueError("VoltagePair: The working ion atomic percentage " "cannot be the same in both the entries") # check that the frameworks of the entries are equivalent if not frame_charge_comp.reduced_formula == frame_discharge_comp.reduced_formula: raise ValueError("VoltagePair: the specified entries must have the" " same compositional framework") # Initialize normalization factors, charged and discharged entries valence_list = Element(ion_sym).oxidation_states working_ion_valence = abs(max(valence_list)) ( framework, norm_charge, ) = frame_charge_comp.get_reduced_composition_and_factor() norm_discharge = frame_discharge_comp.get_reduced_composition_and_factor()[1] # Initialize normalized properties if hasattr(entry_charge, "structure"): _vol_charge = entry_charge.structure.volume / norm_charge else: _vol_charge = entry_charge.data.get("volume") if hasattr(entry_discharge, "structure"): _vol_discharge = entry_discharge.structure.volume / norm_discharge else: _vol_discharge = entry_discharge.data.get("volume") comp_charge = entry_charge.composition comp_discharge = entry_discharge.composition _mass_charge = comp_charge.weight / norm_charge _mass_discharge = comp_discharge.weight / norm_discharge _num_ions_transferred = (comp_discharge[working_element] / norm_discharge) - ( comp_charge[working_element] / norm_charge ) _voltage = ( ((entry_charge.energy / norm_charge) - (entry_discharge.energy / norm_discharge)) / _num_ions_transferred + working_ion_entry.energy_per_atom ) / working_ion_valence _mAh = _num_ions_transferred * Charge(1, "e").to("C") * Time(1, "s").to("h") * N_A * 1000 * working_ion_valence _frac_charge = comp_charge.get_atomic_fraction(working_element) _frac_discharge = comp_discharge.get_atomic_fraction(working_element) vpair = cls( voltage=_voltage, mAh=_mAh, mass_charge=_mass_charge, mass_discharge=_mass_discharge, vol_charge=_vol_charge, vol_discharge=_vol_discharge, frac_charge=_frac_charge, frac_discharge=_frac_discharge, working_ion_entry=working_ion_entry, entry_charge=entry_charge, entry_discharge=entry_discharge, _framework_formula=framework.reduced_formula, ) # Step 4: add (optional) hull and muO2 data vpair.decomp_e_charge = entry_charge.data.get("decomposition_energy", None) vpair.decomp_e_discharge = entry_discharge.data.get("decomposition_energy", None) vpair.muO2_charge = entry_charge.data.get("muO2", None) vpair.muO2_discharge = entry_discharge.data.get("muO2", None) return vpair
def __repr__(self): output = [ "Insertion voltage pair with working ion {}".format(self.working_ion_entry.composition.reduced_formula), "V = {}, mAh = {}".format(self.voltage, self.mAh), "mass_charge = {}, mass_discharge = {}".format(self.mass_charge, self.mass_discharge), "vol_charge = {}, vol_discharge = {}".format(self.vol_charge, self.vol_discharge), "frac_charge = {}, frac_discharge = {}".format(self.frac_charge, self.frac_discharge), ] return "\n".join(output) def __str__(self): return self.__repr__()