diff --git a/.gitignore b/.gitignore index 79393ff4..0ec9944d 100644 --- a/.gitignore +++ b/.gitignore @@ -135,3 +135,5 @@ dmypy.json docs_build examples/wip* + +.vscode diff --git a/.vscode/settings.json b/.vscode/settings.json index e3cb091b..effbcfc9 100644 --- a/.vscode/settings.json +++ b/.vscode/settings.json @@ -1,7 +1,9 @@ { "restructuredtext.confPath": "", "esbonio.sphinx.confDir": "", - "python.testing.pytestArgs": [], + "python.testing.pytestArgs": [ + "tests" + ], "python.testing.unittestEnabled": false, "python.testing.pytestEnabled": true, "python.formatting.provider": "black" diff --git a/dash_app/chempot_selection.py b/dash_app/chempot_selection.py deleted file mode 100644 index 7e684a03..00000000 --- a/dash_app/chempot_selection.py +++ /dev/null @@ -1,98 +0,0 @@ -import click -import dash -import numpy as np -import plotly.express as px -from dash import dcc, html -from dash.dependencies import Input, Output -from monty.serialization import loadfn -from pymatgen.core import Element - - -@click.command() -@click.argument("filename", type=click.Path(exists=True)) -def main(filename: str) -> None: - fed = loadfn(filename) - - def chempot_plot(bulk_formula): - """ - Draw the chemical potentia plot - """ - cpd = fed.chempot_diagram - def_set = set(fed.chempot_diagram.elements) - {Element("Ga"), Element("O")} - def_el = next(iter(def_set)) - cpd.limits = {def_el: [-4, 0]} - cpd = cpd.from_dict(cpd.as_dict()) - - fig = cpd.get_plot(formulas_to_draw=[bulk_formula]) - fig.update_traces(hoverinfo="skip") - x, y, z = cpd.domains[bulk_formula].T - fig.add_scatter3d(x=x, y=y, z=z, mode="markers") - return fig - - external_stylesheets = ["https://codepen.io/chriddyp/pen/bWLwgP.css"] - app = dash.Dash(__name__, external_stylesheets=external_stylesheets) - - app.layout = html.Div( - className="row", - children=[ - html.H1( - "Select chemical potential limit to obtain the formation energy diagram." - ), - html.Div( - children=[ - dcc.Graph( - id="chempot", - figure=chempot_plot("Ga2O3"), - style={"display": "inline-block"}, - ), - dcc.Graph(id="formation-en", style={"display": "inline-block"}), - ] - ), - ], - ) - - @app.callback(Output("formation-en", "figure"), Input("chempot", "clickData")) - def select_chempot(clickData): - if clickData is None: - form_en_plot = px.line( - x=[ - 0, - ], - y=[0], - ) - else: - cp_point = clickData["points"][0] - chempot = [cp_point["x"], cp_point["y"], cp_point["z"]] - cp_dict = fed._parse_chempots(chempot) - form_en = np.array(fed.get_transitions(cp_dict, 0, 5)) - - form_en_plot = px.line(x=form_en[:, 0], y=form_en[:, 1]) - form_en_plot.update_yaxes(range=[-3, 8]) - custom_layout = { - "width": 500, - "height": 700, - "hovermode": "closest", - "paper_bgcolor": "rgba(256,256,256,100)", - "plot_bgcolor": "rgba(0,0,0,0)", - "xaxis_title": "Fermi level (eV)", - "yaxis_title": "Formation energy (eV)", - "showlegend": True, - "legend": { - "orientation": "v", - "x": 0.1, - "y": 0.99, - "traceorder": "reversed", - "xanchor": "left", - "yanchor": "top", - }, - "xaxis": {"gridcolor": "#dbdbdb", "gridwidth": 2, "showline": True}, - "yaxis": {"gridcolor": "#dbdbdb", "gridwidth": 2, "showline": True}, - } - form_en_plot.update_layout(custom_layout) - return form_en_plot - - app.run_server(debug=True, use_reloader=True) - - -if __name__ == "__main__": - main() diff --git a/dash_app/formation_en_Mn_Ga.json b/dash_app/formation_en_Mn_Ga.json deleted file mode 100644 index 48928012..00000000 --- a/dash_app/formation_en_Mn_Ga.json +++ /dev/null @@ -1,23631 +0,0 @@ -{ - "@module": "pymatgen.analysis.defects2.thermo", - "@class": "FormationEnergyDiagram", - "@version": null, - "bulk_entry": { - "@module": "pymatgen.entries.computed_entries", - "@class": "ComputedStructureEntry", - "energy": -954.75229092, - "composition": { - "Ga": 64.0, - "O": 96.0 - }, - "entry_id": "vasprun-2022-06-19 15:40:09.100544", - "correction": 0.0, - "energy_adjustments": [], - "parameters": { - "potcar_symbols": [ - "PAW_PBE Ga_d 06Jul2010", - "PAW_PBE O 08Apr2002" - ], - 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0.848482099608345 - ], - "label": "O", - "properties": { - "magmom": -0.04 - } - } - ] - } - } - ], - "band_gap": null -} diff --git a/pymatgen/analysis/defects/ccd.py b/pymatgen/analysis/defects/ccd.py index beaebbe2..76ba138c 100644 --- a/pymatgen/analysis/defects/ccd.py +++ b/pymatgen/analysis/defects/ccd.py @@ -4,14 +4,18 @@ import logging from ctypes import Structure from dataclasses import dataclass -from typing import Tuple +from typing import Optional, Tuple import numpy as np +import numpy.typing as npt from monty.json import MSONable -from numpy.typing import ArrayLike +from pymatgen.electronic_structure.core import Spin +from pymatgen.io.vasp.outputs import WSWQ, BandStructure, Procar, Vasprun, Waveder from scipy import constants as const from scipy.optimize import curve_fit +from .utils import get_localized_state, sort_positive_definite + # Copyright (c) Pymatgen Development Team. # Distributed under the terms of the MIT License. @@ -20,112 +24,364 @@ __maintainer__ = "Jimmy Shen" __email__ = "jmmshn@gmail.com" __date__ = "Mar 15, 2022" -__logger = logging.getLogger(__name__) +_logger = logging.getLogger(__name__) HBAR = const.hbar / const.e # in units of eV.s EV2J = const.e # 1 eV in Joules AMU2KG = const.physical_constants["atomic mass constant"][0] ANGS2M = 1e-10 # angstrom in meters +KB = const.k / const.e # Boltzmann constant in eV/K -__all__ = ["ConfigurationCoordinateDiagram", "get_dQ"] +# __all__ = ["ConfigurationCoordinateDiagram", "HarmonicDefect", "get_dQ"] @dataclass -class ConfigurationCoordinateDiagram(MSONable): - """A class representing a configuration coordinate diagram. +class HarmonicDefect(MSONable): + """A class representing the a harmonic defect vibronic state. + + The vibronic part of a defect is often catured by a simple harmonic oscillator. + This class store a representation of the SHO as well as some additional information for book-keeping purposes. + + Attributes: + omega: The vibronic frequency of the phonon state in in the same units as the energy vs. Q plot. + charge: The charge state. This should be the charge of the defect + simulation that gave rise to the minimum of the parabola. + distortions: The distortion of the structure in units of amu^{-1/2} Angstrom^{-1}. + This object's internal reference for the distoration should always be relaxed structure. + structures: The list of structures that were used to compute the distortions. + energies: The potential energy surface obtained by distorting the structure.A + defect_band_index: The index of the defect band. + relaxed_indices: The indices of the relaxed defect structure. + relaxed_bandstructure: The band structure of the relaxed defect calculation. + """ + + omega: float + charge_state: int + distortions: Optional[list[float]] = None + structures: Optional[list[Structure]] = None + energies: Optional[list[float]] = None + defect_band_index: Optional[int] = None + relaxed_index: Optional[int] = None + relaxed_bandstructure: Optional[BandStructure] = None + + @classmethod + def from_vaspruns( + cls, + vasp_runs: list[Vasprun], + charge_state: int, + relaxed_index: int | None = None, + defect_band_index: int | None = None, + procar: Procar | None = None, + store_bandstructure: bool = False, + get_band_structure_kwargs: dict | None = None, + **kwargs, + ) -> HarmonicDefect: + """Create a HarmonicDefectPhonon from a list of vasprun. + + .. note:: + The constructor check that you have the vaspruns sorted by the distortions + but does not perform the sorting for you. This serves as a safety check to + ensure that the vaspruns are properly ordered. + + Args: + vasp_runs: A list of Vasprun objects. + charge_state: The charge state for the defect. + relaxed_index: The index of the relaxed structure in the list of structures. + defect_band_index: The index of the defect band (0-indexed). + procar: A Procar object. Used to identify the defect band if the defect_band_index is not provided. + store_bandstructure: Whether to store the bandstructure of the relaxed defect calculation. + Defaults to False to save space. + get_band_structure_kwargs: Keyword arguments to pass to the ``get_band_structure`` method. + **kwargs: Additional keyword arguments to pass to the constructor. + + Returns: + A HarmonicDefect object. + """ + + def _parse_vasprun(vasprun: Vasprun): + energy = vasprun.final_energy + struct = vasprun.final_structure + return (energy, struct) + + energy_struct = list(map(_parse_vasprun, vasp_runs)) + unsorted_e = [e for e, _ in energy_struct] + + if relaxed_index is None: + # Use the vasprun with the lowest energy + relaxed_index = np.argmin([e for e, _ in energy_struct]) + + sorted_list, distortions = sort_positive_definite( + energy_struct, + energy_struct[relaxed_index], + energy_struct[-1], + lambda x, y: get_dQ(x[1], y[1]), + ) + energies, structures = list(zip(*sorted_list)) + + if not np.allclose(unsorted_e, energies, atol=1e-99): + raise ValueError("The vaspruns should already be in order.") + + omega = _get_omega( + Q=distortions, + E=energies, + Q0=distortions[relaxed_index], + E0=energies[relaxed_index], + ) + + if defect_band_index is None and procar is not None: + bandstructure = vasp_runs[relaxed_index].get_band_structure() + loc_res = get_localized_state(bandstructure=bandstructure, procar=procar) + _, (_, defect_band_index) = min(loc_res.items(), key=lambda x: x[1]) + + if store_bandstructure: + get_band_structure_kwargs = get_band_structure_kwargs or {} + bs = vasp_runs[relaxed_index].get_band_structure( + **get_band_structure_kwargs + ) + else: + bs = None + + return cls( + omega=omega, + charge_state=charge_state, + structures=structures, + distortions=distortions, + energies=energies, + defect_band_index=defect_band_index, + relaxed_index=relaxed_index, + relaxed_bandstructure=bs, + **kwargs, + ) + + @property + def omega_eV(self) -> float: + """Get the vibronic frequency of the phonon state in (eV).""" + return self.omega * HBAR * np.sqrt(EV2J / (ANGS2M**2 * AMU2KG)) + + def occupation(self, t: npt.ArrayLike | float) -> npt.ArrayLike: + """Calculate the phonon occupation. + + Args: + t: The temperature in Kelvin. + """ + return 1.0 / (1 - np.exp(-self.omega_eV / KB * t)) + + def get_elph_me( + self, + wswqs: list[WSWQ], + ) -> npt.NDArray: + """Calculate the electron phonon matrix elements. + + Combine the data from the WSWQs to calculate the electron phonon matrix elements. + The matrix elements are calculated by combining the finite difference from the matrix overlaps. + + d() / dQ + + And the eignvalue difference. + + Args: + wswqs: A list of WSWQ objects, assuming that they match the order of the distortions. + bandstructure: The bandstructure of the relaxed defect calculation. + + Returns: + npt.NDArray: The electron phonon matrix elements. + """ + if self.defect_band_index is None: + raise ValueError("The ``defect_band_index`` must be already be set.") + + # It's either [..., defect_band_index, :] or [..., defect_band_index] + # Which band index is the "correct" one might not be super important since + # the matrix is symmetric in the first-order theory we are working in. + # TODO: I should really read my thesis. + slopes = _get_wswq_slope(self.distortions, wswqs)[ + ..., self.defect_band_index, : + ] + ediffs = self._get_ediff(output_order="skb") + return np.multiply(slopes, ediffs) + + def _get_ediff(self, output_order="skb") -> npt.NDArray: + """Compute the eigenvalue difference to the defect band. + + Args: + band_structure: The band structure of the relaxed defect calculation. + output_order: The order of the output. Defaults to "skb" (spin, kpoint, band]). + You can also use "bks" (band, kpoint, spin). + + Returns: + The eigenvalue difference to the defect band in the order specified by output_order. + """ + if self.defect_band_index is None: + raise ValueError( # pragma: no cover + "The ``defect_band_index`` must be set before ``ediff`` can be computed." + ) + if self.relaxed_bandstructure is None: + raise ValueError( # pragma: no cover + "The ``relaxed_bandstructure`` must be set before ``ediff`` can be computed." + ) + + ediffs_ = _get_ks_ediff( + bandstructure=self.relaxed_bandstructure, + defect_band_index=self.defect_band_index, + ) + ediffs_stack = [ + ediffs_[Spin.up].T, + ] + if Spin.down in ediffs_.keys(): + ediffs_stack.append(ediffs_[Spin.down].T) + ediffs = np.stack(ediffs_stack) + + if output_order == "skb": + return ediffs + elif output_order == "bks": + return ediffs.transpose((2, 1, 0)) + else: + raise ValueError( + "Invalid output_order, choose from 'skb' or 'bks'." + ) # pragma: no cover + - Based on the NONRAD code: - M. E. Turiansky et al.: Comput. Phys. Commun. 267, 108056 (2021). +@dataclass +class OpticalHarmonicDefect(HarmonicDefect): + """Representation of Harmonic defect with optical (dipole) matrix elements. - Since configuration coordinate diagrams always represent some kind of a process - in a defect. We will call one state `gs` for ground state and another state `es` - for excited state. The ground state is always lower in energy than the excited - state. + The dipole matrix elements are computed by VASP and reported in the WAVEDER file. Attributes: - charge_gs (int): The charge of the ground state. - charge_es (int): The charge of the excited state. - dQ (float): The configurational difference between the relaxed structures of the - ground state and the excited state. - dE (float): The energy difference between the ground state and the - excited state. - Q_gs (ArrayLike): The list of the configurational coordinates of the - ground state. - Q_es (ArrayLike): The list of the configurational coordinates of the - excited state. - energies_gs (ArrayLike): The list of the energies of the ground state. - energies_es (ArrayLike): The list of the energies of the excited state. - omega_gs (float): The frequency of the harmonic oscillator of the ground state. - omega_es (float): The frequency of the harmonic oscillator of the excited state. + omega: The vibronic frequency of the phonon state in in the same units as the energy vs. Q plot. + charge: The charge state. This should be the charge of the defect + simulation that gave rise to the minimum of the parabola. + distortions: The distortion of the structure in units of amu^{-1/2} Angstrom^{-1}. + This object's internal reference for the distoration should always be relaxed structure. + structures: The list of structures that were used to compute the distortions. + energies: The potential energy surface obtained by distorting the structure.A + defect_band_index: The index of the defect band. + relaxed_indices: The indices of the relaxed defect structure. + relaxed_bandstructure: The band structure of the relaxed defect calculation. + waveder: The WAVEDER object containing the dipole matrix elements. """ - charge_gs: int - charge_es: int - # distortions in units of [amu^{1/2} Angstrom] - dQ: float - Q_gs: ArrayLike - Q_es: ArrayLike - # energies in units of [eV] - energies_gs: ArrayLike - energies_es: ArrayLike - # zero-phonon line energy in units of [eV] - dE: float - # electron-phonon matrix element Wif in units of - # eV amu^{-1/2} Angstrom^{-1} for each bulk_index - - def __post_init__(self): - """After all the attributes. - - Perform the following: - - convert fields to numpy arrays - - reference the gs to zero and es to dE - - compute the frequencies of the harmonic oscillators defined by curves + # TODO: use kw_only once we drop Python < 3.10 + waveder: Waveder | None = None + + @classmethod + def from_vaspruns_and_waveder( + cls, + vasp_runs: list[Vasprun], + waveder: Waveder, + charge_state: int, + relaxed_index: int | None = None, + defect_band_index: int | None = None, + procar: Procar | None = None, + get_band_structure_kwargs: dict | None = None, + **kwargs, + ) -> OpticalHarmonicDefect: + """Create a HarmonicDefectPhonon from a list of vasprun. + + .. note:: + The constructor check that you have the vaspruns sorted by the distortions + but does not order it for you. + + Args: + vasp_runs: A list of Vasprun objects. + charge_state: The charge state for the defect. + relaxed_index: The index of the relaxed structure in the list of structures. + defect_band_index: The index of the defect band (0-indexed). + procar: The Procar object for the defect calculation. + + Returns: + An OpticalHarmonicDefect object. """ - self.Q_gs = np.array(self.Q_gs) - self.Q_es = np.array(self.Q_es) - self.energies_gs = np.array(self.energies_gs) - self.energies_es = np.array(self.energies_es) - - # reference energies to zero: - idx_zero = np.argmin(np.abs(self.Q_gs)) - idx_Q = np.argmin(np.abs(self.Q_es - self.dQ)) - self.energies_gs -= self.energies_gs[idx_zero] - self.energies_es -= self.energies_es[idx_Q] - self.dE - # get frequencies - self.omega_gs = _get_omega(self.Q_gs, self.energies_gs, 0, 0) - self.omega_es = _get_omega(self.Q_es, self.energies_es, self.dQ, self.dE) - - def fit_gs(self, Q): - """Fit the ground state energy to a parabola.""" - E0 = 0 - omega = _fit_parabola(self.Q_gs, self.energies_gs, 0, E0) - return 0.5 * omega**2 * (Q) ** 2 + E0 - - def fit_es(self, Q): - """Fit the excited state energy to a parabola.""" - E0 = self.dE - omega = _fit_parabola(self.Q_es, self.energies_es, self.dQ, E0) - return 0.5 * omega**2 * (Q - self.dQ) ** 2 + E0 - - def plot(self, ax=None, show=True, **kwargs): - """Plot the configuration coordinate diagram.""" - import matplotlib.pyplot as plt - - if ax is None: - fig, ax = plt.subplots() - (l_gs,) = ax.plot(self.Q_gs, self.energies_gs, "o", label="gs", **kwargs) - (l_es,) = ax.plot(self.Q_es, self.energies_es, "o", label="es", **kwargs) - - qq = np.linspace(self.Q_gs.min() - 0.2, self.Q_es.max() + 0.2, 100) - ax.plot(qq, self.fit_gs(qq), "-", color=l_gs.get_color()) - ax.plot(qq, self.fit_es(qq), "-", color=l_es.get_color()) - - ax.set_xlabel("Q [amu^{1/2} Angstrom]") - ax.set_ylabel("Energy [eV]") - ax.legend() - if show: - plt.show() - return ax + obj = super().from_vaspruns( + vasp_runs, + charge_state, + relaxed_index, + waveder=waveder, + defect_band_index=defect_band_index, + procar=procar, + store_bandstructure=True, + get_band_structure_kwargs=get_band_structure_kwargs, + **kwargs, + ) + if obj.defect_band_index is None: + raise ValueError( # pragma: no cover + "You must provide `defect_band_index` or PROCAR to help indetify the `defect_band_index`." + ) + if obj.relaxed_bandstructure is None: + raise ValueError( # pragma: no cover + "The bandstructure was not populated properly check the constructor of the parent." + ) + return obj + + @classmethod + def from_vaspruns( + cls, + vasp_runs: list[Vasprun], + charge_state: int, + relaxed_index: int | None = None, + defect_band_index: int | None = None, + procar: Procar | None = None, + store_bandstructure: bool = False, + get_band_structure_kwargs: dict | None = None, + **kwargs, + ) -> HarmonicDefect: + """Not implemented.""" + raise NotImplementedError("Use from_vaspruns_and_waveder instead.") + + def _get_defect_dipoles(self) -> npt.NDArray: + """Get the dipole matrix elements for the defect. + + Returns: + The dipole matrix elements for the defect. The indices are: + ``[band index, k-point index, spin index, cart. direction]``. + """ + return self.waveder.cder_data[self.defect_band_index, ...] + + def _get_spectra(self) -> npt.NDArray: + """Get the spectra for the defect. + + Args: + bandstructure: The band structure of the relaxed defect calculation. + shift: The shift to apply to the spectra. + """ + return self._get_ediff(output_order="bks") + + +# @dataclass +# class ConfigurationCoordinateDiagram(MSONable): +# """A class representing a configuration coordinate diagram. + +# The configuration coordinate diagram represents two parabolas with some finite configuration shift ``dQ``. +# The two defects are ``sorted`` in the sense that the defect with the lower ``charge_state`` +# is designated as ``defect_state_0``. + +# Attributes: +# phonon_mode_0 : The defect with the lower charge state. +# phonon_mode_1 : The defect with the higher charge state. +# dQ : The finite configuration shift. +# """ +# phonon_mode_0: HarmonicDefect +# phonon_mode_1: HarmonicDefect +# dQ: float + +# def __post_init__(self): +# """Post-initialization.""" +# if abs(self.phonon_mode_0.charge_state - self.phonon_mode_1.charge_state) != 1: +# raise ValueError( +# "The charge states of the two defects must be 1 apart. " +# "Got {} and {}".format(self.phonon_mode_0.charge_state, self.phonon_mode_1.charge_state) +# ) +# if self.phonon_mode_0.charge_state > self.phonon_mode_1.charge_state: +# self.phonon_mode_0, self.phonon_mode_1 = self.phonon_mode_1, self.phonon_mode_0 + +# @property +# def omega0_eV(self) -> float: +# """The vibronic frequency of the defect with the lower charge state.""" +# return self.phonon_mode_0.omega_eV + +# @property +# def omega1_eV(self) -> float: +# """The vibronic frequency of the defect with the higher charge state.""" +# return self.phonon_mode_1.omega_eV def get_dQ(ground: Structure, excited: Structure) -> float: @@ -151,8 +407,8 @@ def get_dQ(ground: Structure, excited: Structure) -> float: def _get_omega( - Q: ArrayLike, - energy: ArrayLike, + Q: npt.ArrayLike, + E: npt.ArrayLike, Q0: float, E0: float, ) -> float: @@ -162,24 +418,67 @@ def _get_omega( Args: Q: array of Q values (amu^{1/2} Angstrom) corresponding to each vasprun - energy: array of energy values (eV) corresponding to each vasprun - Q0: fix the value of the minimum of the parabola + E: array of energy values (eV) corresponding to each vasprun + Q0: fix the x-value of the minimum of the parabola + E0: fix the y-value of the minimum of the parabola Returns: omega: the harmonic phonon frequency in (eV) """ - popt = _fit_parabola(Q, energy, Q0, E0) - return HBAR * popt[0] * np.sqrt(EV2J / (ANGS2M**2 * AMU2KG)) + popt = _fit_parabola(Q, E, Q0, E0) + return popt[0] def _fit_parabola( - Q: ArrayLike, energy: ArrayLike, Q0: float, E0: float + Q: npt.ArrayLike, energy: npt.ArrayLike, Q0: float, E0: float ) -> Tuple[float, float, float]: """Fit the parabola to the data.""" def f(Q, omega): - """The parabola function.""" + """Get the parabola function.""" return 0.5 * omega**2 * (Q - Q0) ** 2 + E0 popt, _ = curve_fit(f, Q, energy) return popt + + +def _get_wswq_slope(distortions: list[float], wswqs: list[WSWQ]) -> npt.NDArray: + """Get the slopes of the overlap matrixs vs. Q. + + Args: + distortions: List of Q values (amu^{1/2} Angstrom). + wswqs: List of WSWQ objects. + + Returns: + npt.NDArray: slope matrix with the same shape as the ``WSWQ.data``. + """ + yy = np.stack([np.abs(ww.data) * np.sign(qq) for qq, ww in zip(distortions, wswqs)]) + _, *oldshape = yy.shape + return np.polyfit(distortions, yy.reshape(yy.shape[0], -1), deg=1)[0].reshape( + *oldshape + ) + + +def _get_ks_ediff( + bandstructure: BandStructure, + defect_band_index: int, +) -> dict[Spin, npt.NDArray]: + """Calculate the Kohn-Sham energy between the defect state. + + Get the eigenvalue differences to the defect band. Report this difference + on each k-point and each spin, the result should be shape [nspins, nkpoints, nbands]. + + Args: + bandstructure: A BandStructure object. + defect_band_index: The index of the defect band. + + Returns: + npt.NDArray: The Kohn-Sham energy difference between the defect state and other states. + Indexed the same way as ``bandstructure.bands``. + """ + res = dict() + for k, kpt_bands in bandstructure.bands.items(): + e_at_def_band = kpt_bands[defect_band_index, :] + e_diff = kpt_bands - e_at_def_band + res[k] = e_diff + return res diff --git a/pymatgen/analysis/defects/utils.py b/pymatgen/analysis/defects/utils.py index d105f4c6..1e42f905 100644 --- a/pymatgen/analysis/defects/utils.py +++ b/pymatgen/analysis/defects/utils.py @@ -1,6 +1,7 @@ """Utilities for defects module.""" from __future__ import annotations +import bisect import collections import logging import math @@ -8,7 +9,7 @@ from copy import deepcopy from functools import cached_property from pathlib import Path -from typing import Generator +from typing import Any, Callable, Generator import numpy as np from monty.json import MSONable @@ -17,7 +18,8 @@ from pymatgen.analysis.local_env import cn_opt_params from pymatgen.analysis.structure_matcher import StructureMatcher from pymatgen.core import Lattice, Structure -from pymatgen.io.vasp import VolumetricData +from pymatgen.electronic_structure.core import Spin +from pymatgen.io.vasp.outputs import BandStructure, Procar, VolumetricData from pymatgen.io.vasp.sets import get_valid_magmom_struct from scipy.cluster.hierarchy import fcluster, linkage from scipy.spatial.distance import squareform @@ -516,3 +518,92 @@ def filter_and_group( res.append((avg_chg, [self.local_minima[idx] for idx in lab_groups[lab]])) return res + + +def get_localized_state( + bandstructure: BandStructure, + procar: Procar, + k_index: int | None = None, + band_window: int = 5, +) -> dict[Spin, tuple[float, int]]: + """Find the index of the localized state. + + Find the band index with the lowest inverse participation ratio (IPR) in a small window + around the fermi level. Since some of the core states can be very localized, + we should only search near the valence. + + Args: + bandstructure: The bandstructure object. + The band just below the fermi level is used as the center of band window. + procar: The procar object. + k_index: The index of the k-point to use. If None, the IPR is averaged over all k-points. + band_range: The number of bands above and blow the fermi level to include in the search window. + + Returns: + dict[Spin, tuple(float, int)]: + The inverse participation ratio (IPR) and the index for each spin channel. + """ + res = dict() + for spin in bandstructure.bands.keys(): + # last band that is fully below the fermi level + last_occ_idx = bisect.bisect_left( + bandstructure.bands[spin].max(1), bandstructure.efermi + ) + lbound = max(last_occ_idx - band_window, 0) + if k_index is None: + # average over all k + ipr = np.average( + [ + _get_ipr(spin, ik, procar) + for ik in range(len(bandstructure.kpoints)) + ], + axis=0, + ) + else: + ipr = _get_ipr(spin, k_index, procar) + + idx = ipr[lbound:].argmin() + lbound + res[spin] = (ipr[idx], idx) + return res + + +def _get_ipr(spin, k_index, procar): + states = procar.data[spin][k_index, ...] + flat_states = states.reshape(states.shape[0], -1) + return 1 / np.sum(flat_states**2, axis=1) + + +def sort_positive_definite( + list_in: list, ref1: Any, ref2: Any, dist: Callable +) -> tuple[list, list[float]]: + """Sort a list where we can only compute a positive-definite distance. + + Sometimes, we can only compute a positive-definite distance between two objects. + (E.g., the displacement between two structures). In these cases, standard + sorting algorithms will not work. Here, we accept two reference points to give + some sense of direction. We then sort the list based on the distance between the + reference points. Note: this only works if the list falls on a line of some sort. + + Args: + list_in: The list to sort. + ref1: The first reference point, this will be the `zero` point. + ref2: The second reference point, this will determine the direction. + dist: Some positive definite distance function. + + Returns: + - the sorted list of objects. + - the signed distance in the chosen direction. + """ + d1 = [dist(el, ref1) for el in list_in] + d2 = [dist(el, ref2) for el in list_in] + D0 = dist(ref1, ref2) + + d_vs_s = [] + for q1, q2, el in zip(d1, d2, list_in): + sign = +1 + if q1 < q2 and q2 > D0: + sign = -1 + d_vs_s.append((sign * q1, el)) + d_vs_s.sort() + distances, sorted_list = list(zip(*d_vs_s)) + return sorted_list, distances diff --git a/pyproject.toml b/pyproject.toml index a5369337..44a3068d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -16,7 +16,7 @@ classifiers = [ "Topic :: Scientific/Engineering", ] dependencies = [ - "pymatgen>=2022.7.19", + 'pymatgen@git+https://github.com/jmmshn/pymatgen@get_elphon', "dscribe>=1.2.1", "scikit-image>=0.19.3", ] @@ -42,7 +42,7 @@ docs = [ ] strict = [ - "pymatgen==2022.7.19", + 'pymatgen@git+https://github.com/jmmshn/pymatgen@get_elphon', "dscribe==1.2.1", "scikit-image==0.19.3", ] @@ -99,7 +99,6 @@ show_missing = true skip_covered = true [tool.pydocstyle] -convention = 'google' -match = '^pymatgen/(?!_).*\.py' -inherit = false -add-ignore= "D107, " +convention="google" +match="^((?!(test|docs)).)*$" +add-ignore="D107," diff --git a/tests/conftest.py b/tests/conftest.py index fcba466f..5a6c9f81 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -5,7 +5,7 @@ from monty.serialization import loadfn from pymatgen.core import Structure from pymatgen.core.periodic_table import Specie -from pymatgen.io.vasp import Chgcar, Locpot, Vasprun +from pymatgen.io.vasp.outputs import WSWQ, Chgcar, Locpot, Procar, Vasprun, Waveder from pymatgen.analysis.defects.core import PeriodicSite, Substitution from pymatgen.analysis.defects.thermo import DefectEntry @@ -93,3 +93,19 @@ def get_data(q): @pytest.fixture(scope="session") def chgcar_fe3o4(test_dir): return Chgcar.from_file(test_dir / "CHGCAR.Fe3O4.vasp") + + +@pytest.fixture(scope="session") +def v_ga(test_dir): + res = dict() + for q1, q2 in [(0, -1), (-1, 0)]: + ccd_dir = test_dir / f"V_Ga/ccd_{q1}_{q2}" + vaspruns = [Vasprun(ccd_dir / f"vasprun.xml.{i}.gz") for i in [0, 1, 2]] + wswqs = [WSWQ.from_file(ccd_dir / f"WSWQ.{i}.gz") for i in [0, 1, 2]] + res[(q1, q2)] = { + "vaspruns": vaspruns, + "procar": Procar(ccd_dir / "PROCAR.1.gz"), + "waveder": Waveder(ccd_dir / "WAVEDER.1"), + "wswqs": wswqs, + } + return res diff --git a/tests/test_ccd.py b/tests/test_ccd.py index b50e5cb5..6b11c3ee 100644 --- a/tests/test_ccd.py +++ b/tests/test_ccd.py @@ -1,19 +1,78 @@ +from collections import namedtuple + +import numpy as np import pytest +from pymatgen.analysis.defects.ccd import _get_wswq_slope + + +def test_HarmonicDefect(v_ga): + from pymatgen.analysis.defects.ccd import HarmonicDefect + + vaspruns = v_ga[(0, -1)]["vaspruns"] + procar = v_ga[(0, -1)]["procar"] + hd0 = HarmonicDefect.from_vaspruns(vaspruns, charge_state=0, procar=procar) + pytest.approx(hd0.distortions[1], 0.0) + pytest.approx(hd0.omega_eV, 0.032680) + wswqs = v_ga[(0, -1)]["wswqs"] + # check for ValueError + with pytest.raises(ValueError): + elph_me = hd0.get_elph_me(wswqs=wswqs) + + hd0 = HarmonicDefect.from_vaspruns( + vaspruns, charge_state=0, procar=procar, store_bandstructure=True + ) + elph_me = hd0.get_elph_me(wswqs=wswqs) + assert np.allclose(elph_me[..., 138], 0.0) # ediff should be zero for defect band + assert np.linalg.norm(elph_me[..., 139]) > 0 -def test_ccd(test_dir): - from pymatgen.analysis.defects.ccd import ConfigurationCoordinateDiagram - ccd = ConfigurationCoordinateDiagram( - charge_gs=0, - charge_es=1, - dQ=1.0, - dE=2, - Q_gs=(-0.2, 0.0, 0.2), - Q_es=(0.8, 1.0, 1.2), - energies_es=(1.2, 1.0, 1.2), - energies_gs=(1.2, 1.0, 1.2), +def test_OpticalHarmonicDefect(v_ga): + from pymatgen.analysis.defects.ccd import OpticalHarmonicDefect + + vaspruns = v_ga[(0, -1)]["vaspruns"] + procar = v_ga[(0, -1)]["procar"] + wavder = v_ga[(0, -1)]["waveder"] + hd0 = OpticalHarmonicDefect.from_vaspruns_and_waveder( + vaspruns, + waveder=wavder, + charge_state=0, + procar=procar, ) - # check that plot runs without error don't show - ccd.plot(show=False) - assert ccd.omega_es == pytest.approx(ccd.omega_gs) + + # the non-optical part should behave the same + wswqs = v_ga[(0, -1)]["wswqs"] + elph_me = hd0.get_elph_me(wswqs=wswqs) + assert np.allclose(elph_me[..., 138], 0.0) # ediff should be zero for defect band + assert np.linalg.norm(elph_me[..., 139]) > 0 + + # # check that waveder is symmetric + def is_symm(waveder, i, j): + assert ( + np.max( + np.abs( + np.abs(waveder.cder_data[i, j, :, :]) + - np.abs(waveder.cder_data[j, i, :, :]) + ) + ) + <= 1e-10 + ) + + is_symm(hd0.waveder, 123, 42) + is_symm(hd0.waveder, 138, 69) + + nbands_spectra, *_ = hd0._get_spectra().shape + nbands_dipole, *_ = hd0._get_defect_dipoles().shape + assert nbands_spectra == nbands_dipole + + +def test_wswq_slope(): + mats = [np.ones((3, 5)), np.zeros((3, 5)), np.ones((3, 5))] + FakeWSWQ = namedtuple("FakeWSWQ", ["data"]) + fake_wswqs = [FakeWSWQ(data=m) for m in mats] + + res = _get_wswq_slope([-0.5, 0, 0.5], fake_wswqs) + np.allclose(res, np.ones((3, 5)) * 2) + + res = _get_wswq_slope([1.0, 0, -1.0], fake_wswqs) + np.allclose(res, np.ones((3, 5)) * -1) diff --git a/tests/test_files/V_Ga/ccd_-1_0/PROCAR.1.gz b/tests/test_files/V_Ga/ccd_-1_0/PROCAR.1.gz new file mode 100644 index 00000000..b4898f59 Binary files /dev/null and b/tests/test_files/V_Ga/ccd_-1_0/PROCAR.1.gz differ diff --git a/tests/test_files/V_Ga/ccd_-1_0/WAVEDER.1 b/tests/test_files/V_Ga/ccd_-1_0/WAVEDER.1 new file mode 100644 index 00000000..ec5ab91b Binary files /dev/null and b/tests/test_files/V_Ga/ccd_-1_0/WAVEDER.1 differ diff --git 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a/tests/test_files/V_Ga/ccd_0_-1/vasprun.xml.2.gz b/tests/test_files/V_Ga/ccd_0_-1/vasprun.xml.2.gz new file mode 100644 index 00000000..8156778f Binary files /dev/null and b/tests/test_files/V_Ga/ccd_0_-1/vasprun.xml.2.gz differ diff --git a/tests/test_utils.py b/tests/test_utils.py index 655c6961..e97c0042 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -7,6 +7,7 @@ cluster_nodes, get_avg_chg, get_local_extrema, + get_localized_state, ) @@ -68,3 +69,20 @@ def test_chgcar_insertion(chgcar_fe3o4): fpos = sorted(group) pytest.approx(avg_chg, ref_chg) assert np.allclose(fpos, ref_fpos) + + +def test_get_localized_states(v_ga): + vaspruns = v_ga[(0, -1)]["vaspruns"] + procar = v_ga[(0, -1)]["procar"] + vr = vaspruns[1] + bs = vr.get_band_structure() + res = get_localized_state(bs, procar=procar) + _, (_, min_indx) = min(res.items(), key=lambda x: x[1]) + assert min_indx == 138 + + vaspruns = v_ga[(-1, 0)]["vaspruns"] + procar = v_ga[(-1, 0)]["procar"] + vr = vaspruns[1] + bs = vr.get_band_structure() + res = get_localized_state(bs, procar=procar) + assert min_indx == 138