""" Define equation of state flows. https://github.com/materialsvirtuallab/matcalc/blob/main/matcalc/eos.py """ from __future__ import annotations from typing import TYPE_CHECKING import numpy as np from ase import Atoms from ase.filters import * # type: ignore from ase.optimize import * # type: ignore from ase.optimize.optimize import Optimizer from prefect import flow from prefect.futures import wait from prefect.runtime import flow_run, task_run from pymatgen.analysis.eos import BirchMurnaghan from mlip_arena.models import MLIPEnum from mlip_arena.tasks.optimize import run as OPT if TYPE_CHECKING: from ase.filters import Filter def generate_flow_run_name(): flow_name = flow_run.flow_name parameters = flow_run.parameters atoms = parameters["atoms"] calculator_name = parameters["calculator_name"] return f"{flow_name}: {atoms.get_chemical_formula()} - {calculator_name}" def generate_task_run_name(): task_name = task_run.task_name parameters = task_run.parameters atoms = parameters["atoms"] calculator_name = parameters["calculator_name"] return f"{task_name}: {atoms.get_chemical_formula()} - {calculator_name}" # https://docs.prefect.io/3.0/develop/write-tasks#custom-retry-behavior # @task(task_run_name=generate_task_run_name) @flow(flow_run_name=generate_flow_run_name, validate_parameters=False) def fit( atoms: Atoms, calculator_name: str | MLIPEnum, calculator_kwargs: dict | None, device: str | None = None, optimizer: Optimizer | str = "BFGSLineSearch", # type: ignore optimizer_kwargs: dict | None = None, filter: Filter | str | None = None, filter_kwargs: dict | None = None, criterion: dict | None = None, max_abs_strain: float = 0.1, npoints: int = 11, ): """ Compute the equation of state (EOS) for the given atoms and calculator. Args: atoms: The input atoms. calculator_name: The name of the calculator to use. calculator_kwargs: Additional kwargs to pass to the calculator. device: The device to use. optimizer: The optimizer to use. optimizer_kwargs: Additional kwargs to pass to the optimizer. filter: The filter to use. filter_kwargs: Additional kwargs to pass to the filter. criterion: The criterion to use. max_abs_strain: The maximum absolute strain to use. npoints: The number of points to sample. Returns: A dictionary containing the EOS data and the bulk modulus. """ first_relax = OPT( atoms=atoms, calculator_name=calculator_name, calculator_kwargs=calculator_kwargs, device=device, optimizer=optimizer, optimizer_kwargs=optimizer_kwargs, filter=filter, filter_kwargs=filter_kwargs, criterion=criterion, ) relaxed = first_relax["atoms"] # p0 = relaxed.get_positions() c0 = relaxed.get_cell() factors = np.linspace(1 - max_abs_strain, 1 + max_abs_strain, npoints) ** (1 / 3) futures = [] for f in factors: atoms = relaxed.copy() atoms.set_cell(c0 * f, scale_atoms=True) future = OPT.submit( atoms=atoms, calculator_name=calculator_name, calculator_kwargs=calculator_kwargs, device=device, optimizer=optimizer, optimizer_kwargs=optimizer_kwargs, filter=None, filter_kwargs=None, criterion=criterion, ) futures.append(future) wait(futures) volumes = [ f.result()["atoms"].get_volume() for f in futures if isinstance(f.result(), dict) ] energies = [ f.result()["atoms"].get_potential_energy() for f in futures if isinstance(f.result(), dict) ] volumes, energies = map( list, zip( *sorted(zip(volumes, energies, strict=True), key=lambda i: i[0]), strict=True, ), ) bm = BirchMurnaghan(volumes=volumes, energies=energies) bm.fit() return { "eos": {"volumes": volumes, "energies": energies}, "K": bm.b0_GPa, }