From b3c674d934c29b66bfa885dd538ecf43709052d4 Mon Sep 17 00:00:00 2001 From: Sean Kavanagh Date: Thu, 15 Aug 2024 19:21:29 -0400 Subject: [PATCH] Add `get_doped_chempots_from_entries` convenience function to `doped.chemical_potentials` --- doped/chemical_potentials.py | 114 +++++++++++++++++++++++++---------- 1 file changed, 81 insertions(+), 33 deletions(-) diff --git a/doped/chemical_potentials.py b/doped/chemical_potentials.py index 2bb1131a..30ebaaed 100644 --- a/doped/chemical_potentials.py +++ b/doped/chemical_potentials.py @@ -9,7 +9,7 @@ import itertools import os import warnings -from collections.abc import Iterable +from collections.abc import Iterable, Sequence from copy import deepcopy from pathlib import Path from typing import Any, Optional, Union @@ -1681,6 +1681,77 @@ def __init__( _name_entries_and_handle_duplicates(self.entries) # set entry names +def get_doped_chempots_from_entries( + entries: Sequence[Union[ComputedEntry, ComputedStructureEntry, PDEntry]], + composition: Union[str, Composition, ComputedEntry], + sort_by: Optional[str] = None, + single_chempot_limit: bool = False, +) -> dict: + r""" + Given a list of ``ComputedEntry``\s / ``ComputedStructureEntry``\s / + ``PDEntry``\s and the bulk ``composition``, returns the chemical potential + limits dictionary in the ``doped`` format (i.e. ``{"limits": [{'limit': + [chempot_dict]}], ...}``) for the host material. + + Args: + entries (list[ComputedEntry]): + List of ``ComputedEntry``\s / ``ComputedStructureEntry``\s / + ``PDEntry``\s for the chemical system, from which to determine + the chemical potential limits for the host material (``composition``). + composition (str, Composition, ComputedEntry): + Composition of the host material either as a string + (e.g. 'LiFePO4') a ``pymatgen`` ``Composition`` object (e.g. + ``Composition('LiFePO4')``), or a ``ComputedEntry`` object. + sort_by (str): + If set, will sort the chemical potential limits in the output + ``DataFrame`` according to the chemical potential of the specified + element (from element-rich to element-poor conditions). + single_chempot_limit (bool): + If set to ``True``, only returns the first chemical potential limit + in the calculated chemical potentials dictionary. Mainly intended for + internal ``doped`` usage when the host material is calculated to be + unstable with respect to the competing phases. + + Returns: + dict: + Dictionary of chemical potential limits in the ``doped`` format. + """ + if isinstance(composition, (str, Composition)): + composition = Composition(composition) + else: + composition = composition.composition + + phase_diagram = PhaseDiagram( + entries, + list(map(Element, composition.elements)), # preserve bulk comp element ordering + ) + chem_lims = phase_diagram.get_all_chempots(composition.reduced_composition) + chem_lims_iterator = list(chem_lims.items())[:1] if single_chempot_limit else chem_lims.items() + + # remove Element to make it JSONable: + no_element_chem_lims = {k: {str(kk): vv for kk, vv in v.items()} for k, v in chem_lims_iterator} + + if sort_by is not None: + no_element_chem_lims = dict( + sorted(no_element_chem_lims.items(), key=lambda x: x[1][sort_by], reverse=True) + ) + + chempots = { + "limits": no_element_chem_lims, + "elemental_refs": {str(el): ent.energy_per_atom for el, ent in phase_diagram.el_refs.items()}, + "limits_wrt_el_refs": {}, + } + + # relate the limits to the elemental energies + for limit, chempot_dict in chempots["limits"].items(): + relative_chempot_dict = copy.deepcopy(chempot_dict) + for e in relative_chempot_dict: + relative_chempot_dict[e] -= chempots["elemental_refs"][e] + chempots["limits_wrt_el_refs"].update({limit: relative_chempot_dict}) + + return chempots + + class CompetingPhasesAnalyzer: # TODO: Allow parsing using pymatgen ComputedEntries as well, to aid interoperability with # high-througput architectures like AiiDA or atomate2. See: @@ -2151,7 +2222,7 @@ def calculate_chempots( self._intrinsic_phase_diagram = PhaseDiagram( intrinsic_phase_diagram_entries, - map(Element, self.bulk_composition.elements), + list(map(Element, self.bulk_composition.elements)), # preserve bulk comp element ordering ) # check if it's stable and if not, warn user and downshift to get _least_ unstable point on convex @@ -2179,38 +2250,15 @@ def calculate_chempots( ) self._intrinsic_phase_diagram = PhaseDiagram( [*intrinsic_phase_diagram_entries, renormalised_bulk_pde], - map(Element, self.bulk_composition.elements), + list(map(Element, self.bulk_composition.elements)), # preserve bulk comp element ordering ) - chem_lims = self._intrinsic_phase_diagram.get_all_chempots(self.bulk_composition) - - # remove Element to make it JSONable: - no_element_chem_lims = {k: {str(kk): vv for kk, vv in v.items()} for k, v in chem_lims.items()} - - if unstable_host: - no_element_chem_lims = { - k: {str(kk): vv for kk, vv in v.items()} for k, v in list(chem_lims.items())[:1] - } - - if sort_by is not None: - no_element_chem_lims = dict( - sorted(no_element_chem_lims.items(), key=lambda x: x[1][sort_by], reverse=True) - ) - - self._intrinsic_chempots = { - "limits": no_element_chem_lims, - "elemental_refs": { - str(el): ent.energy_per_atom for el, ent in self._intrinsic_phase_diagram.el_refs.items() - }, - "limits_wrt_el_refs": {}, - } - - # relate the limits to the elemental energies - for limit, chempot_dict in self._intrinsic_chempots["limits"].items(): - relative_chempot_dict = copy.deepcopy(chempot_dict) - for e in relative_chempot_dict: - relative_chempot_dict[e] -= self._intrinsic_chempots["elemental_refs"][e] - self._intrinsic_chempots["limits_wrt_el_refs"].update({limit: relative_chempot_dict}) + self._intrinsic_chempots = get_doped_chempots_from_entries( + self._intrinsic_phase_diagram.entries, + self.bulk_composition, + sort_by=sort_by, + single_chempot_limit=unstable_host, + ) # get chemical potentials as pandas dataframe chemical_potentials = [] @@ -2340,7 +2388,7 @@ def intrinsic_chempots(self) -> dict: return self._intrinsic_chempots @property - def intrinsic_phase_diagram(self) -> dict: + def intrinsic_phase_diagram(self) -> PhaseDiagram: """ Returns the calculated intrinsic phase diagram. """