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_base.py
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_base.py
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"""Base jobs for espresso."""
from __future__ import annotations
from pathlib import Path
from typing import TYPE_CHECKING
from ase.atoms import Atoms
from ase.io.espresso import Namelist
from ase.io.espresso_namelist.keys import ALL_KEYS
from quacc.calculators.espresso.espresso import (
Espresso,
EspressoProfile,
EspressoTemplate,
)
from quacc.calculators.espresso.utils import (
prepare_copy_files,
remove_conflicting_kpts_kspacing,
)
from quacc.runners.ase import Runner
from quacc.schemas.ase import summarize_opt_run, summarize_run
from quacc.utils.dicts import recursive_dict_merge
if TYPE_CHECKING:
from typing import Any
from ase.calculators.genericfileio import GenericFileIOCalculator
from quacc.runners.ase import OptParams
from quacc.schemas._aliases.ase import RunSchema
from quacc.utils.files import Filenames, SourceDirectory
def run_and_summarize(
atoms: Atoms | None = None,
preset: str | None = None,
template: EspressoTemplate | None = None,
profile: EspressoProfile | None = None,
calc_defaults: dict[str, Any] | None = None,
calc_swaps: dict[str, Any] | None = None,
additional_fields: dict[str, Any] | None = None,
copy_files: (
SourceDirectory
| list[SourceDirectory]
| dict[SourceDirectory, Filenames]
| None
) = None,
) -> RunSchema:
"""
Base function to carry out espresso recipes.
Parameters
----------
atoms
Atoms object
preset
Name of the preset to use
template
EspressoTemplate to use
profile
EspressoProfile to use
calc_defaults
The default calculator parameters.
calc_swaps
Custom kwargs for the espresso calculator. Set a value to
`quacc.Remove` to remove a pre-existing key entirely. For a list of available
keys, refer to the [ase.calculators.espresso.Espresso][] calculator.
additional_fields
Any additional fields to supply to the summarizer.
copy_files
Files to copy (and decompress) from source to the runtime directory.
Returns
-------
RunSchema
Dictionary of results from [quacc.schemas.ase.summarize_run][]
"""
atoms = Atoms() if atoms is None else atoms
calc = prepare_calc(
atoms,
preset=preset,
template=template,
profile=profile,
calc_defaults=calc_defaults,
calc_swaps=calc_swaps,
)
updated_copy_files = prepare_copy(
copy_files=copy_files,
calc_params=calc.user_calc_params,
binary=calc.template.binary,
)
geom_file = template.outputname if template.binary == "pw" else None
final_atoms = Runner(atoms, calc, copy_files=updated_copy_files).run_calc(
geom_file=geom_file
)
return summarize_run(
final_atoms, atoms, move_magmoms=True, additional_fields=additional_fields
)
def run_and_summarize_opt(
atoms: Atoms | None = None,
preset: str | None = None,
template: EspressoTemplate | None = None,
profile: EspressoProfile | None = None,
calc_defaults: dict[str, Any] | None = None,
calc_swaps: dict[str, Any] | None = None,
opt_defaults: dict[str, Any] | None = None,
opt_params: OptParams | None = None,
additional_fields: dict[str, Any] | None = None,
copy_files: (
SourceDirectory
| list[SourceDirectory]
| dict[SourceDirectory, Filenames]
| None
) = None,
) -> RunSchema:
"""
Base function to carry out espresso recipes with ASE optimizers.
Parameters
----------
atoms
Atoms object
preset
Name of the preset to use
template
EspressoTemplate to use
profile
EspressoProfile to use
calc_defaults
The default calculator parameters.
calc_swaps
Custom kwargs for the espresso calculator. Set a value to
`quacc.Remove` to remove a pre-existing key entirely. For a list of available
keys, refer to the [ase.calculators.espresso.Espresso][] calculator.
opt_defaults
The default optimization parameters.
opt_params
Dictionary of parameters to pass to the optimizer. pass "optimizer"
to change the optimizer being used. "fmax" and "max_steps" are commonly
used keywords. See the ASE documentation for more information.
additional_fields
Any additional fields to supply to the summarizer.
copy_files
Files to copy (and decompress) from source to the runtime directory.
Returns
-------
RunSchema
Dictionary of results from [quacc.schemas.ase.summarize_run][]
"""
atoms = Atoms() if atoms is None else atoms
calc = prepare_calc(
atoms,
preset=preset,
template=template,
profile=profile,
calc_defaults=calc_defaults,
calc_swaps=calc_swaps,
)
updated_copy_files = prepare_copy(
copy_files=copy_files,
calc_params=calc.user_calc_params,
binary=calc.template.binary,
)
opt_flags = recursive_dict_merge(opt_defaults, opt_params)
dyn = Runner(atoms, calc, copy_files=updated_copy_files).run_opt(**opt_flags)
return summarize_opt_run(
dyn, move_magmoms=True, additional_fields=additional_fields
)
def prepare_calc(
atoms: Atoms,
preset: str | None = None,
template: EspressoTemplate | None = None,
profile: EspressoProfile | None = None,
calc_defaults: dict[str, Any] | None = None,
calc_swaps: dict[str, Any] | None = None,
) -> GenericFileIOCalculator:
"""
Commonly used preparation function to merge parameters
and create an Espresso calculator accordingly.
Parameters
----------
atoms
Atoms object
preset
Name of the preset to use
template
EspressoTemplate to use
profile
EspressoProfile to use
calc_defaults
The default calculator parameters.
calc_swaps
Custom kwargs for the espresso calculator. Set a value to
`quacc.Remove` to remove a pre-existing key entirely. For a list of available
keys, refer to the [ase.calculators.espresso.Espresso][] calculator.
Returns
-------
GenericFileIOCalculator
The Espresso calculator.
"""
calc_defaults = calc_defaults or {}
calc_swaps = calc_swaps or {}
calc_defaults["input_data"] = Namelist(calc_defaults.get("input_data"))
calc_swaps["input_data"] = Namelist(calc_swaps.get("input_data"))
binary = template.binary if template else "pw"
if binary in ALL_KEYS:
calc_defaults["input_data"].to_nested(binary=binary, **calc_defaults)
calc_swaps["input_data"].to_nested(binary=binary, **calc_swaps)
calc_defaults = remove_conflicting_kpts_kspacing(calc_defaults, calc_swaps)
calc_flags = recursive_dict_merge(calc_defaults, calc_swaps)
return Espresso(
input_atoms=atoms,
preset=preset,
template=template,
profile=profile,
**calc_flags,
)
def prepare_copy(
copy_files: (
SourceDirectory
| list[SourceDirectory]
| dict[SourceDirectory, Filenames]
| None
) = None,
calc_params: dict[str, Any] | None = None,
binary: str = "pw",
) -> dict[SourceDirectory, Filenames] | None:
"""
Function that will prepare the files to copy.
Parameters
----------
copy_files
Files to copy (and decompress) from source to the runtime directory.
calc_params
The calculator parameters.
binary
The binary to use.
Returns
-------
dict
Dictionary of files to copy.
"""
if isinstance(copy_files, (str, Path)):
copy_files = [copy_files]
if isinstance(copy_files, list):
exact_files_to_copy = prepare_copy_files(calc_params, binary=binary)
return {source: exact_files_to_copy for source in copy_files}
return copy_files