"""Set up geomopt commandline interface."""
from __future__ import annotations
from pathlib import Path
from typing import Annotated, Any
from typer import Context, Option, Typer
from typer_config import use_config
from janus_core.cli.types import (
Architecture,
CalcKwargs,
Device,
FilePrefix,
LogPath,
MinimizeKwargs,
ModelPath,
ReadKwargsLast,
StructPath,
Summary,
WriteKwargs,
)
from janus_core.cli.utils import yaml_converter_callback
app = Typer()
[docs]
def _set_minimize_kwargs(
minimize_kwargs: dict[str, Any],
opt_cell_lengths: bool,
pressure: float,
) -> None:
"""
Set minimize_kwargs dictionary values.
Parameters
----------
minimize_kwargs
Other keyword arguments to pass to geometry optimizer.
opt_cell_lengths
Whether to optimize cell vectors, as well as atomic positions, by setting
`hydrostatic_strain` in the filter function.
pressure
Scalar pressure when optimizing cell geometry, in GPa. Passed to the filter
function if either `opt_cell_lengths` or `opt_cell_fully` is True.
"""
minimize_kwargs.setdefault("opt_kwargs", {})
minimize_kwargs.setdefault("traj_kwargs", {})
# Check hydrostatic_strain and scalar pressure not duplicated
if "filter_kwargs" in minimize_kwargs:
if "hydrostatic_strain" in minimize_kwargs["filter_kwargs"]:
raise ValueError(
"'hydrostatic_strain' must be passed through the --opt-cell-lengths "
"option"
)
if "scalar_pressure" in minimize_kwargs["filter_kwargs"]:
raise ValueError(
"'scalar_pressure' must be passed through the --pressure option"
)
else:
minimize_kwargs["filter_kwargs"] = {}
# Set hydrostatic_strain and scalar pressure
minimize_kwargs["filter_kwargs"]["hydrostatic_strain"] = opt_cell_lengths
minimize_kwargs["filter_kwargs"]["scalar_pressure"] = pressure
[docs]
@app.command()
@use_config(yaml_converter_callback)
def geomopt(
# numpydoc ignore=PR02
ctx: Context,
struct: StructPath,
optimizer: Annotated[
str | None,
Option(help="Name of ASE optimizer function to use."),
] = "LBFGS",
fmax: Annotated[
float, Option(help="Maximum force for convergence, in eV/Å.")
] = 0.1,
steps: Annotated[int, Option(help="Maximum number of optimization steps.")] = 1000,
arch: Architecture = "mace_mp",
device: Device = "cpu",
model_path: ModelPath = None,
opt_cell_lengths: Annotated[
bool,
Option(help="Optimize cell vectors, as well as atomic positions."),
] = False,
opt_cell_fully: Annotated[
bool,
Option(
help="Fully optimize the cell vectors, angles, and atomic positions.",
),
] = False,
filter_func: Annotated[
str | None,
Option(
help=(
"Name of ASE filter/constraint function to use. If using "
"--opt-cell-lengths or --opt-cell-fully, defaults to "
"`FrechetCellFilter` if available, otherwise `ExpCellFilter`."
)
),
] = None,
pressure: Annotated[
float, Option(help="Scalar pressure when optimizing cell geometry, in GPa.")
] = 0.0,
symmetrize: Annotated[
bool, Option(help="Whether to refine symmetry after geometry optimization.")
] = False,
symmetry_tolerance: Annotated[
float,
Option(
help="Atom displacement tolerance for spglib symmetry determination, in Å."
),
] = 0.001,
file_prefix: FilePrefix = None,
out: Annotated[
Path | None,
Option(
help=(
"Path to save optimized structure. Default is inferred `file_prefix`."
),
),
] = None,
write_traj: Annotated[
bool,
Option(
help=(
"Whether to save a trajectory file of optimization frames. "
'If traj_kwargs["filename"] is not specified, it is inferred '
"from `file_prefix`."
),
),
] = False,
read_kwargs: ReadKwargsLast = None,
calc_kwargs: CalcKwargs = None,
minimize_kwargs: MinimizeKwargs = None,
write_kwargs: WriteKwargs = None,
log: LogPath = None,
tracker: Annotated[
bool, Option(help="Whether to save carbon emissions of calculation")
] = True,
summary: Summary = None,
) -> None:
"""
Perform geometry optimization and save optimized structure to file.
Parameters
----------
ctx
Typer (Click) Context. Automatically set.
struct
Path of structure to simulate.
optimizer
Name of optimization function from ase.optimize. Default is `LBFGS`.
fmax
Set force convergence criteria for optimizer, in eV/Å. Default is 0.1.
steps
Set maximum number of optimization steps to run. Default is 1000.
arch
MLIP architecture to use for geometry optimization.
Default is "mace_mp".
device
Device to run model on. Default is "cpu".
model_path
Path to MLIP model. Default is `None`.
opt_cell_lengths
Whether to optimize cell vectors, as well as atomic positions, by setting
`hydrostatic_strain` in the filter function. Default is False.
opt_cell_fully
Whether to fully optimize the cell vectors, angles, and atomic positions.
Default is False.
filter_func
Name of filter function from ase.filters or ase.constraints, to apply
constraints to atoms. If using --opt-cell-lengths or --opt-cell-fully, defaults
to `FrechetCellFilter` if available, otherwise `ExpCellFilter`.
pressure
Scalar pressure when optimizing cell geometry, in GPa. Passed to the filter
function if either `opt_cell_lengths` or `opt_cell_fully` is True. Default is
0.0.
symmetrize
Whether to refine symmetry after geometry optimization. Default is False.
symmetry_tolerance
Atom displacement tolerance for spglib symmetry determination, in Å.
Default is 0.001.
file_prefix
Prefix for output files, including directories. Default directory is
./janus_results, and default filename prefix is inferred from the input
stucture filename.
out
Path to save optimized structure, or last structure if optimization did not
converge. Default is inferred from `file_prefix`.
write_traj
Whether to save a trajectory file of optimization frames.
If traj_kwargs["filename"] is not specified, it is inferred from `file_prefix`.
read_kwargs
Keyword arguments to pass to ase.io.read. By default,
read_kwargs["index"] is -1.
calc_kwargs
Keyword arguments to pass to the selected calculator. Default is {}.
minimize_kwargs
Other keyword arguments to pass to geometry optimizer. Default is {}.
write_kwargs
Keyword arguments to pass to ase.io.write when saving optimized structure.
Default is {}.
log
Path to write logs to. Default is inferred from `file_prefix`.
tracker
Whether to save carbon emissions of calculation in log file and summary.
Default is True.
summary
Path to save summary of inputs, start/end time, and carbon emissions. Default
is inferred from `file_prefix`.
config
Path to yaml configuration file to define the above options. Default is None.
"""
from janus_core.calculations.geom_opt import GeomOpt
from janus_core.cli.utils import (
carbon_summary,
check_config,
end_summary,
get_config,
get_struct_info,
parse_typer_dicts,
set_read_kwargs_index,
start_summary,
)
# Check options from configuration file are all valid
check_config(ctx)
[read_kwargs, calc_kwargs, minimize_kwargs, write_kwargs] = parse_typer_dicts(
[read_kwargs, calc_kwargs, minimize_kwargs, write_kwargs]
)
# Set initial config
all_kwargs = {
"read_kwargs": read_kwargs.copy(),
"calc_kwargs": calc_kwargs.copy(),
"minimize_kwargs": minimize_kwargs.copy(),
"write_kwargs": write_kwargs.copy(),
}
config = get_config(params=ctx.params, all_kwargs=all_kwargs)
# Read only first structure by default and ensure only one image is read
set_read_kwargs_index(read_kwargs)
# Check optimized structure path not duplicated
if "filename" in write_kwargs:
raise ValueError("'filename' must be passed through the --out option")
if out:
write_kwargs["filename"] = out
_set_minimize_kwargs(minimize_kwargs, opt_cell_lengths, pressure)
if opt_cell_fully or opt_cell_lengths:
# Use default filter unless filter function explicitly passed
opt_cell_fully_dict = {"filter_func": filter_func} if filter_func else {}
else:
if filter_func:
raise ValueError(
"--opt-cell-lengths or --opt-cell-fully must be set to use a filter "
"function"
)
# Override default filter function with None
opt_cell_fully_dict = {"filter_func": None}
log_kwargs = {"filemode": "w"}
if log:
log_kwargs["filename"] = log
# Dictionary of inputs for optimize function
optimize_kwargs = {
"struct": struct,
"arch": arch,
"device": device,
"model_path": model_path,
"read_kwargs": read_kwargs,
"calc_kwargs": calc_kwargs,
"attach_logger": True,
"log_kwargs": log_kwargs,
"track_carbon": tracker,
"optimizer": optimizer,
"fmax": fmax,
"steps": steps,
"symmetrize": symmetrize,
"symmetry_tolerance": symmetry_tolerance,
"file_prefix": file_prefix,
**opt_cell_fully_dict,
**minimize_kwargs,
"write_results": True,
"write_kwargs": write_kwargs,
"write_traj": write_traj,
}
# Set up geometry optimization
optimizer = GeomOpt(**optimize_kwargs)
# Set summary and log files
summary = optimizer._build_filename("geomopt-summary.yml", filename=summary)
log = optimizer.log_kwargs["filename"]
# Add structure, MLIP information, and log to info
info = get_struct_info(
struct=optimizer.struct,
struct_path=struct,
)
output_files = optimizer.output_files
# Save summary information before optimization begins
start_summary(
command="geomopt",
summary=summary,
info=info,
config=config,
output_files=output_files,
)
# Run geometry optimization and save output structure
optimizer.run()
# Save carbon summary
if tracker:
carbon_summary(summary=summary, log=log)
# Time after optimization has finished
end_summary(summary)