Source code for pymatgen.apps.battery.conversion_battery

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

This module contains the classes to build a ConversionElectrode.

from scipy.constants import N_A

from pymatgen.core.periodic_table import Element
from pymatgen.core.units import Charge, Time

from pymatgen.analysis.reaction_calculator import BalancedReaction
from pymatgen.core.composition import Composition
from pymatgen.apps.battery.battery_abc import AbstractElectrode, \
from pymatgen.analysis.phase_diagram import PhaseDiagram
from monty.json import MontyDecoder

[docs]class ConversionElectrode(AbstractElectrode): """ Class representing a ConversionElectrode. """ def __init__(self, voltage_pairs, working_ion_entry, initial_comp): """ General constructor for ConversionElectrode. However, it is usually easier to construct a ConversionElectrode using one of the static constructors provided. Args: voltage_pairs: The voltage pairs making up the Conversion Electrode. working_ion_entry: A single ComputedEntry or PDEntry representing the element that carries charge across the battery, e.g. Li. initial_comp: Starting composition for ConversionElectrode. """ self._composition = initial_comp self._working_ion_entry = working_ion_entry ion_el = self._working_ion_entry.composition.elements[0] self._working_ion = ion_el.symbol self._vpairs = voltage_pairs
[docs] @staticmethod def from_composition_and_pd(comp, pd, working_ion_symbol="Li", allow_unstable=False): """ Convenience constructor to make a ConversionElectrode from a composition and a phase diagram. Args: comp: Starting composition for ConversionElectrode, e.g., Composition("FeF3") pd: A PhaseDiagram of the relevant system (e.g., Li-Fe-F) working_ion_symbol: Element symbol of working ion. Defaults to Li. allow_unstable: Allow compositions that are unstable """ working_ion = Element(working_ion_symbol) entry = None working_ion_entry = None for e in pd.stable_entries: if e.composition.reduced_formula == comp.reduced_formula: entry = e elif e.is_element and \ e.composition.reduced_formula == working_ion_symbol: working_ion_entry = e if not allow_unstable and not entry: raise ValueError("Not stable compound found at composition {}." .format(comp)) profile = pd.get_element_profile(working_ion, comp) # Need to reverse because voltage goes form most charged to most # discharged. profile.reverse() if len(profile) < 2: return None working_ion_entry = working_ion_entry working_ion = working_ion_entry.composition.elements[0].symbol normalization_els = {} for el, amt in comp.items(): if el != Element(working_ion): normalization_els[el] = amt vpairs = [ConversionVoltagePair.from_steps(profile[i], profile[i + 1], normalization_els) for i in range(len(profile) - 1)] return ConversionElectrode(vpairs, working_ion_entry, comp)
[docs] @staticmethod def from_composition_and_entries(comp, entries_in_chemsys, working_ion_symbol="Li", allow_unstable=False): """ Convenience constructor to make a ConversionElectrode from a composition and all entries in a chemical system. Args: comp: Starting composition for ConversionElectrode, e.g., Composition("FeF3") entries_in_chemsys: Sequence containing all entries in a chemical system. E.g., all Li-Fe-F containing entries. working_ion_symbol: Element symbol of working ion. Defaults to Li. """ pd = PhaseDiagram(entries_in_chemsys) return ConversionElectrode.from_composition_and_pd(comp, pd, working_ion_symbol, allow_unstable)
[docs] def get_sub_electrodes(self, adjacent_only=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 Returns: A list of ConversionElectrode objects """ if adjacent_only: return [self.__class__(self._vpairs[i:i + 1], self._working_ion_entry, self._composition) for i in range(len(self._vpairs))] sub_electrodes = [] for i in range(len(self._vpairs)): for j in range(i, len(self._vpairs)): sub_electrodes.append(self.__class__(self._vpairs[i:j + 1], self._working_ion_entry, self._composition)) return sub_electrodes
@property def composition(self) -> Composition: """ Returns: Composition """ return self._composition @property def working_ion(self) -> Element: """ The working ion as an Element object """ return self._working_ion_entry.composition.elements[0] @property def working_ion_entry(self): """ Returns: Working ion as an entry. """ return self._working_ion_entry @property def voltage_pairs(self): """ Returns: All voltage pairs. """ return self._vpairs
[docs] def is_super_electrode(self, conversion_electrode): """ Checks if a particular conversion electrode is a sub electrode of the current electrode. Starting from a more lithiated state may result in a subelectrode that is essentially on the same path. For example, a ConversionElectrode formed by starting from an FePO4 composition would be a super_electrode of a ConversionElectrode formed from an LiFePO4 composition. """ for pair1 in conversion_electrode: rxn1 = pair1.rxn all_formulas1 = set([rxn1.all_comp[i].reduced_formula for i in range(len(rxn1.all_comp)) if abs(rxn1.coeffs[i]) > 1e-5]) for pair2 in self: rxn2 = pair2.rxn all_formulas2 = set([rxn2.all_comp[i].reduced_formula for i in range(len(rxn2.all_comp)) if abs(rxn2.coeffs[i]) > 1e-5]) if all_formulas1 == all_formulas2: break else: return False return True
def __eq__(self, conversion_electrode): """ Check if two electrodes are exactly the same: """ if len(self) != len(conversion_electrode): return False for pair1 in conversion_electrode: rxn1 = pair1.rxn all_formulas1 = set([rxn1.all_comp[i].reduced_formula for i in range(len(rxn1.all_comp)) if abs(rxn1.coeffs[i]) > 1e-5]) for pair2 in self: rxn2 = pair2.rxn all_formulas2 = set([rxn2.all_comp[i].reduced_formula for i in range(len(rxn2.all_comp)) if abs(rxn2.coeffs[i]) > 1e-5]) if all_formulas1 == all_formulas2: break else: return False return True def __hash__(self): return 7 def __str__(self): return self.__repr__() def __repr__(self): output = ["Conversion electrode with formula {} and nsteps {}".format( self._composition.reduced_formula, self.num_steps), "Avg voltage {} V, min voltage {} V, max voltage {} V".format( self.get_average_voltage(), self.min_voltage, self.max_voltage), "Capacity (grav.) {} mAh/g, capacity (vol.) {} Ah/l".format( self.get_capacity_grav(), self.get_capacity_vol()), "Specific energy {} Wh/kg, energy density {} Wh/l".format( self.get_specific_energy(), self.get_energy_density())] return "\n".join(output)
[docs] @classmethod def from_dict(cls, d): """ Args: d (dict): Dict representation Returns: ConversionElectrode """ dec = MontyDecoder() return cls(dec.process_decoded(d["voltage_pairs"]), dec.process_decoded(d["working_ion_entry"]), Composition(d["initial_comp"]))
[docs] def as_dict(self): """ Returns: MSONable dict. """ return {"@module": self.__class__.__module__, "@class": self.__class__.__name__, "voltage_pairs": [v.as_dict() for v in self._vpairs], "working_ion_entry": self.working_ion_entry.as_dict(), "initial_comp": self._composition.as_dict()}
[docs] def get_summary_dict(self, print_subelectrodes=True): """ Args: print_subelectrodes: Also print data on all the possible subelectrodes Returns: a summary of this electrode"s properties in dictionary format """ d = {} framework_comp = Composition({k: v for k, v in self._composition.items() if k.symbol != self.working_ion.symbol}) d["framework"] = framework_comp.to_data_dict d["framework_pretty"] = framework_comp.reduced_formula d["average_voltage"] = self.get_average_voltage() d["max_voltage"] = self.max_voltage d["min_voltage"] = self.min_voltage d["max_delta_volume"] = self.max_delta_volume d["max_instability"] = 0 d["max_voltage_step"] = self.max_voltage_step d["nsteps"] = self.num_steps d["capacity_grav"] = self.get_capacity_grav() d["capacity_vol"] = self.get_capacity_vol() d["energy_grav"] = self.get_specific_energy() d["energy_vol"] = self.get_energy_density() d["working_ion"] = self.working_ion.symbol d["reactions"] = [] d["reactant_compositions"] = [] comps = [] frac = [] for pair in self._vpairs: rxn = pair.rxn frac.append(pair.frac_charge) frac.append(pair.frac_discharge) d["reactions"].append(str(rxn)) for i in range(len(rxn.coeffs)): if abs(rxn.coeffs[i]) > 1e-5 and rxn.all_comp[i] not in comps: comps.append(rxn.all_comp[i]) if abs(rxn.coeffs[i]) > 1e-5 and \ rxn.all_comp[i].reduced_formula != d["working_ion"]: reduced_comp = rxn.all_comp[i].reduced_composition comp_dict = reduced_comp.as_dict() d["reactant_compositions"].append(comp_dict) d["fracA_charge"] = min(frac) d["fracA_discharge"] = max(frac) d["nsteps"] = self.num_steps 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
[docs]class ConversionVoltagePair(AbstractVoltagePair): """ A VoltagePair representing a Conversion Reaction with a defined voltage. Typically not initialized directly but rather used by ConversionElectrode. """ def __init__(self, balanced_rxn, voltage, mAh, vol_charge, vol_discharge, mass_charge, mass_discharge, frac_charge, frac_discharge, entries_charge, entries_discharge, working_ion_entry): """ Args: balanced_rxn (BalancedReaction): BalancedReaction for the step voltage (float): Voltage for the step mAh (float): Capacity of the step vol_charge (float): Volume of charged state vol_discharge (float): Volume of discharged state mass_charge (float): Mass of charged state mass_discharge (float): Mass of discharged state frac_charge (float): Fraction of working ion in the charged state frac_discharge (float): Fraction of working ion in the discharged state entries_charge ([ComputedEntry]): Entries in the charged state entries_discharge ([ComputedEntry]): Entries in discharged state working_ion_entry (ComputedEntry): Entry of the working ion. """ self._working_ion_entry = working_ion_entry working_ion = self._working_ion_entry.composition.elements[0].symbol self._voltage = voltage self._mAh = mAh self._vol_charge = vol_charge self._mass_charge = mass_charge self._mass_discharge = mass_discharge self._vol_discharge = vol_discharge self._frac_charge = frac_charge self._frac_discharge = frac_discharge self._rxn = balanced_rxn self._working_ion = working_ion self._entries_charge = entries_charge self._entries_discharge = entries_discharge
[docs] @staticmethod def from_steps(step1, step2, normalization_els): """ Creates a ConversionVoltagePair from two steps in the element profile from a PD analysis. Args: step1: Starting step step2: Ending step normalization_els: Elements to normalize the reaction by. To ensure correct capacities. """ working_ion_entry = step1["element_reference"] working_ion = working_ion_entry.composition.elements[0].symbol working_ion_valence = max(Element(working_ion).oxidation_states) voltage = (-step1["chempot"] + working_ion_entry.energy_per_atom) / working_ion_valence mAh = (step2["evolution"] - step1["evolution"]) * Charge(1, "e").to("C") * Time(1, "s").to("h") * \ N_A * 1000 * working_ion_valence licomp = Composition(working_ion) prev_rxn = step1["reaction"] reactants = {comp: abs(prev_rxn.get_coeff(comp)) for comp in prev_rxn.products if comp != licomp} curr_rxn = step2["reaction"] products = {comp: abs(curr_rxn.get_coeff(comp)) for comp in curr_rxn.products if comp != licomp} reactants[licomp] = (step2["evolution"] - step1["evolution"]) rxn = BalancedReaction(reactants, products) for el, amt in normalization_els.items(): if rxn.get_el_amount(el) > 1e-6: rxn.normalize_to_element(el, amt) break prev_mass_dischg = sum([prev_rxn.all_comp[i].weight * abs(prev_rxn.coeffs[i]) for i in range(len(prev_rxn.all_comp))]) / 2 vol_charge = sum([abs(prev_rxn.get_coeff(e.composition)) * e.structure.volume for e in step1["entries"] if e.composition.reduced_formula != working_ion]) mass_discharge = sum([curr_rxn.all_comp[i].weight * abs(curr_rxn.coeffs[i]) for i in range(len(curr_rxn.all_comp))]) / 2 mass_charge = prev_mass_dischg mass_discharge = mass_discharge vol_discharge = sum([abs(curr_rxn.get_coeff(e.composition)) * e.structure.volume for e in step2["entries"] if e.composition.reduced_formula != working_ion]) totalcomp = Composition({}) for comp in prev_rxn.products: if comp.reduced_formula != working_ion: totalcomp += comp * abs(prev_rxn.get_coeff(comp)) frac_charge = totalcomp.get_atomic_fraction(Element(working_ion)) totalcomp = Composition({}) for comp in curr_rxn.products: if comp.reduced_formula != working_ion: totalcomp += comp * abs(curr_rxn.get_coeff(comp)) frac_discharge = totalcomp.get_atomic_fraction(Element(working_ion)) rxn = rxn entries_charge = step2["entries"] entries_discharge = step1["entries"] return ConversionVoltagePair(rxn, voltage, mAh, vol_charge, vol_discharge, mass_charge, mass_discharge, frac_charge, frac_discharge, entries_charge, entries_discharge, working_ion_entry)
@property def working_ion(self): """ Returns: working ion """ return self._working_ion @property def entries_charge(self): """ Returns: Entries pertaining to charged electrode. """ return self._entries_charge @property def entries_discharge(self): """ Returns: Entries pertaining to discharged electrode. """ return self._entries_discharge @property def frac_charge(self): """ Returns: Amount of working ion at charge """ return self._frac_charge @property def frac_discharge(self): """ Returns: Amount of working ion at discharge """ return self._frac_discharge @property def rxn(self): """ Returns: Reaction representing the conversion. """ return self._rxn @property def voltage(self): """ Returns: Voltage of electrode """ return self._voltage @property def mAh(self): """ Returns: Energy in mAh. """ return self._mAh @property def mass_charge(self): """ Returns: Mass of charged electrode. """ return self._mass_charge @property def mass_discharge(self): """ Returns: Mass of discharged electrode. """ return self._mass_discharge @property def vol_charge(self): """ Returns: Volume of charged electrode. """ return self._vol_charge @property def vol_discharge(self): """ Returns: Volume of discharged electrode. """ return self._vol_discharge @property def working_ion_entry(self): """ Returns: Working ion entry """ return self._working_ion_entry def __repr__(self): output = ["Conversion voltage pair with working ion {}".format( self._working_ion_entry.composition.reduced_formula), "Reaction : {}".format(self._rxn), "V = {}, mAh = {}".format(self.voltage, self.mAh), "frac_charge = {}, frac_discharge = {}".format( self.frac_charge, self.frac_discharge), "mass_charge = {}, mass_discharge = {}".format( self.mass_charge, self.mass_discharge), "vol_charge = {}, vol_discharge = {}".format( self.vol_charge, self.vol_discharge)] return "\n".join(output) def __str__(self): return self.__repr__()
[docs] @classmethod def from_dict(cls, d): """ Args: d (dict): Dict representation Returns: ConversionVoltagePair """ dec = MontyDecoder() working_ion_entry = dec.process_decoded(d["working_ion_entry"]) balanced_rxn = dec.process_decoded(d["balanced_rxn"]) entries_charge = dec.process_decoded(d["entries_charge"]) entries_discharge = dec.process_decoded(d["entries_discharge"]) return ConversionVoltagePair(balanced_rxn, d["voltage"], d["mAh"], d["vol_charge"], d["vol_discharge"], d["mass_charge"], d["mass_discharge"], d["frac_charge"], d["frac_discharge"], entries_charge, entries_discharge, working_ion_entry)
[docs] def as_dict(self): """ Returns: MSONable dict """ return {"@module": self.__class__.__module__, "@class": self.__class__.__name__, "working_ion_entry": self._working_ion_entry.as_dict(), "voltage": self._voltage, "mAh": self._mAh, "vol_charge": self._vol_charge, "mass_charge": self._mass_charge, "mass_discharge": self._mass_discharge, "vol_discharge": self._vol_discharge, "frac_charge": self._frac_charge, "frac_discharge": self._frac_discharge, "balanced_rxn": self._rxn.as_dict(), "entries_charge": [e.as_dict() for e in self._entries_charge], "entries_discharge": [e.as_dict() for e in self._entries_discharge]}