"""Set up eos commandline interface."""
from __future__ import annotations
from typing import Annotated, get_args
from click import Choice
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,
Tracker,
WriteKwargs,
)
from janus_core.cli.utils import yaml_converter_callback
from janus_core.helpers.janus_types import EoSNames
app = Typer()
[docs]
@app.command()
@use_config(yaml_converter_callback, param_help="Path to configuration file.")
def eos(
# numpydoc ignore=PR02
ctx: Context,
# Calculation
struct: StructPath,
min_volume: Annotated[
float,
Option(help="Minimum volume scale factor.", rich_help_panel="Calculation"),
] = 0.95,
max_volume: Annotated[
float,
Option(help="Maximum volume scale factor.", rich_help_panel="Calculation"),
] = 1.05,
n_volumes: Annotated[
int, Option(help="Number of volumes.", rich_help_panel="Calculation")
] = 7,
eos_type: Annotated[
str,
Option(
click_type=Choice(get_args(EoSNames)),
help="Type of fit for equation of state.",
rich_help_panel="Calculation",
),
] = "birchmurnaghan",
minimize: Annotated[
bool,
Option(
help="Whether to minimize initial structure before calculations.",
rich_help_panel="Calculation",
),
] = True,
minimize_all: Annotated[
bool,
Option(
help="Whether to minimize all generated structures for calculations.",
rich_help_panel="Calculation",
),
] = False,
fmax: Annotated[
float,
Option(
help="Maximum force for optimization convergence.",
rich_help_panel="Calculation",
),
] = 0.1,
minimize_kwargs: MinimizeKwargs = None,
write_structures: Annotated[
bool,
Option(
help="Whether to write out all genereated structures.",
rich_help_panel="Calculation",
),
] = False,
plot_to_file: Annotated[
bool,
Option(
help="Whether to plot equation of state.",
rich_help_panel="Calculation",
),
] = False,
# MLIP Calculator
arch: Architecture = "mace_mp",
device: Device = "cpu",
model_path: ModelPath = None,
calc_kwargs: CalcKwargs = None,
# Structure I/O
file_prefix: FilePrefix = None,
read_kwargs: ReadKwargsLast = None,
write_kwargs: WriteKwargs = None,
# Logging/summary
log: LogPath = None,
tracker: Tracker = True,
summary: Summary = None,
) -> None:
"""
Calculate equation of state and write out results.
Parameters
----------
ctx
Typer (Click) Context. Automatically set.
struct
Path of structure to simulate.
min_volume
Minimum volume scale factor. Default is 0.95.
max_volume
Maximum volume scale factor. Default is 1.05.
n_volumes
Number of volumes to use. Default is 7.
eos_type
Type of fit for equation of state. Default is "birchmurnaghan".
minimize
Whether to minimize initial structure before calculations. Default is True.
minimize_all
Whether to optimize geometry for all generated structures. Default is False.
fmax
Set force convergence criteria for optimizer in units eV/Å.
Default is 0.1.
minimize_kwargs
Other keyword arguments to pass to geometry optimizer. Default is {}.
write_structures
True to write out all genereated structures. Default is False.
plot_to_file
Whether to save plot equation of state to svg. Default is False.
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`.
calc_kwargs
Keyword arguments to pass to the selected calculator. Default is {}.
file_prefix
Prefix for output files, including directories. Default directory is
./janus_results, and default filename prefix is inferred from the input
stucture filename.
read_kwargs
Keyword arguments to pass to ase.io.read. By default,
read_kwargs["index"] is -1.
write_kwargs
Keyword arguments to pass to ase.io.write to save generated structures.
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.eos import EoS
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 fmax option not duplicated
if "fmax" in minimize_kwargs:
raise ValueError("'fmax' must be passed through the --fmax option")
minimize_kwargs["fmax"] = fmax
log_kwargs = {"filemode": "w"}
if log:
log_kwargs["filename"] = log
# Dictionary of inputs for EoS class
eos_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,
"min_volume": min_volume,
"max_volume": max_volume,
"n_volumes": n_volumes,
"eos_type": eos_type,
"minimize": minimize,
"minimize_all": minimize_all,
"minimize_kwargs": minimize_kwargs,
"write_structures": write_structures,
"write_kwargs": write_kwargs,
"plot_to_file": plot_to_file,
"file_prefix": file_prefix,
}
# Initialise EoS
equation_of_state = EoS(**eos_kwargs)
# Set summary and log files
summary = equation_of_state._build_filename("eos-summary.yml", filename=summary)
log = equation_of_state.log_kwargs["filename"]
# Add structure, MLIP information, and log to info
info = get_struct_info(
struct=equation_of_state.struct,
struct_path=struct,
)
output_files = equation_of_state.output_files
# Save summary information before calculations begin
start_summary(
command="eos",
summary=summary,
info=info,
config=config,
output_files=output_files,
)
# Run equation of state calculations
equation_of_state.run()
# Save carbon summary
if tracker:
carbon_summary(summary=summary, log=log)
# Time after calculations have finished
end_summary(summary)