Source code for atomate2.common.flows.elastic

"""Flows for calculating elastic constants."""

from __future__ import annotations

from abc import ABC, abstractmethod
from dataclasses import dataclass, field
from typing import TYPE_CHECKING

from jobflow import Flow, Maker, OnMissing

from atomate2 import SETTINGS
from atomate2.common.jobs.elastic import (
    fit_elastic_tensor,
    generate_elastic_deformations,
    run_elastic_deformations,
)
from atomate2.common.jobs.utils import structure_to_conventional

if TYPE_CHECKING:
    from pathlib import Path

    from emmet.core.math import Matrix3D
    from pymatgen.core.structure import Structure

    from atomate2.forcefields.jobs import ForceFieldRelaxMaker
    from atomate2.vasp.jobs.base import BaseVaspMaker


[docs] @dataclass class BaseElasticMaker(Maker, ABC): """ Maker to calculate elastic constants. Calculate the elastic constant of a material. Initially, a tight structural relaxation is performed to obtain the structure in a state of approximately zero stress. Subsequently, perturbations are applied to the lattice vectors and the resulting stress tensor is calculated from DFT, while allowing for relaxation of the ionic degrees of freedom. Finally, constitutive relations from linear elasticity, relating stress and strain, are employed to fit the full 6x6 elastic tensor. From this, aggregate properties such as Voigt and Reuss bounds on the bulk and shear moduli are derived. .. Note:: It is heavily recommended to symmetrize the structure before passing it to this flow. Otherwise, the symmetry reduction routines will not be as effective at reducing the total number of deformations needed. Parameters ---------- name : str Name of the flows produced by this maker. order : int Order of the tensor expansion to be determined. Can be either 2 or 3. sym_reduce : bool Whether to reduce the number of deformations using symmetry. symprec : float Symmetry precision to use in the reduction of symmetry. bulk_relax_maker : .BaseVaspMaker or .ForceFieldRelaxMaker or None A maker to perform a tight relaxation on the bulk. Set to ``None`` to skip the bulk relaxation. elastic_relax_maker : .BaseVaspMaker or .ForceFieldRelaxMaker Maker used to generate elastic relaxations. max_failed_deformations: int or float Maximum number of deformations allowed to fail to proceed with the fitting of the elastic tensor. If an int the absolute number of deformations. If a float between 0 an 1 the maximum fraction of deformations. If None any number of deformations allowed. generate_elastic_deformations_kwargs : dict Keyword arguments passed to :obj:`generate_elastic_deformations`. fit_elastic_tensor_kwargs : dict Keyword arguments passed to :obj:`fit_elastic_tensor`. task_document_kwargs : dict Additional keyword args passed to :obj:`.ElasticDocument.from_stresses()`. """ name: str = "elastic" order: int = 2 sym_reduce: bool = True symprec: float = SETTINGS.SYMPREC bulk_relax_maker: BaseVaspMaker | ForceFieldRelaxMaker | None = None elastic_relax_maker: BaseVaspMaker | ForceFieldRelaxMaker = ( None # constant volume optimization ) max_failed_deformations: int | float | None = None generate_elastic_deformations_kwargs: dict = field(default_factory=dict) fit_elastic_tensor_kwargs: dict = field(default_factory=dict) task_document_kwargs: dict = field(default_factory=dict)
[docs] def make( self, structure: Structure, prev_dir: str | Path | None = None, equilibrium_stress: Matrix3D = None, conventional: bool = False, ) -> Flow: """Make flow to calculate the elastic constant. Parameters ---------- structure : .Structure A pymatgen structure. prev_dir : str or Path or None A previous vasp calculation directory to use for copying outputs. equilibrium_stress : tuple of tuple of float The equilibrium stress of the (relaxed) structure, if known. conventional : bool Whether to transform the structure into the conventional cell. """ jobs = [] if self.bulk_relax_maker is not None: # optionally relax the structure bulk_kwargs = {} if self.prev_calc_dir_argname is not None: bulk_kwargs[self.prev_calc_dir_argname] = prev_dir bulk = self.bulk_relax_maker.make(structure, **bulk_kwargs) jobs.append(bulk) structure = bulk.output.structure prev_dir = bulk.output.dir_name if equilibrium_stress is None: equilibrium_stress = bulk.output.output.stress if conventional: stc = structure_to_conventional(structure, self.symprec) jobs.append(stc) structure = stc.output deformations = generate_elastic_deformations( structure, order=self.order, sym_reduce=self.sym_reduce, symprec=self.symprec, **self.generate_elastic_deformations_kwargs, ) vasp_deformation_calcs = run_elastic_deformations( structure, deformations.output, elastic_relax_maker=self.elastic_relax_maker, prev_dir=prev_dir, ) fit_tensor = fit_elastic_tensor( structure, vasp_deformation_calcs.output, equilibrium_stress=equilibrium_stress, order=self.order, symprec=self.symprec if self.sym_reduce else None, max_failed_deformations=self.max_failed_deformations, **self.fit_elastic_tensor_kwargs, **self.task_document_kwargs, ) # allow some of the deformations to fail fit_tensor.config.on_missing_references = OnMissing.NONE jobs += [deformations, vasp_deformation_calcs, fit_tensor] return Flow( jobs=jobs, output=fit_tensor.output, name=self.name, )
@property @abstractmethod def prev_calc_dir_argname(self) -> str: """Name of argument informing static maker of previous calculation directory. As this differs between different DFT codes (e.g., VASP, CP2K), it has been left as a property to be implemented by the inheriting class. Note: this is only applicable if a relax_maker is specified; i.e., two calculations are performed for each ordering (relax -> static) """