#!/usr/bin/env python3
"""Seed eOn dimer saddle searches from every peak of a converged NEB band.
.. versionadded:: 1.8.0
Reads a converged NEB band (``neb.con``), finds all interior local maxima of
the energy profile, and writes one ``job=saddle_search`` seed directory per
peak under ``out-dir/peak_<NN>/`` (pos.con, direction.dat, displacement.con,
config.ini). See :mod:`rgpycrumbs.eon.seed_dimers` for the library API.
"""
# /// script
# requires-python = ">=3.11"
# dependencies = [
# "click",
# "numpy",
# "scipy",
# "rich",
# "ase",
# "readcon>=0.7.0",
# "rgpycrumbs>=1.10.2",
# ]
# ///
import logging
from pathlib import Path
import click
try:
from rgpycrumbs._aux import warn_on_direct_script_import
except ImportError: # pragma: no cover - direct script execution without package root
[docs]
warn_on_direct_script_import = None
if warn_on_direct_script_import is not None:
warn_on_direct_script_import(__name__, "rgpycrumbs eon gen-dimer")
try:
from .seed_dimers import seed_dimers_from_peaks
except ImportError: # pragma: no cover - direct script execution
from rgpycrumbs.eon.seed_dimers import seed_dimers_from_peaks
logging.basicConfig(level=logging.INFO, format="%(message)s")
@click.command()
@click.option(
"--neb-con",
required=True,
type=click.Path(exists=True, dir_okay=False, path_type=Path),
help="Converged NEB band (neb.con) with per-image energies.",
)
@click.option(
"--out-dir",
required=True,
type=click.Path(file_okay=False, path_type=Path),
help="Parent dir; each peak gets out-dir/peak_<NN>/.",
)
@click.option(
"--settings",
"settings_name",
required=True,
help="Name of the NWChem .nwi settings fragment referenced by config.ini.",
)
@click.option("--socket", required=True, help="Unix socket path for [SocketNWChemPot].")
@click.option(
"--peak-files-dir",
type=click.Path(exists=True, file_okay=False, path_type=Path),
default=None,
help="Dir with eOn peak{MM}_pos.con + peak{MM}_mode.dat to seed direction.dat.",
)
@click.option(
"--prominence",
type=float,
default=0.02,
show_default=True,
help="scipy.signal.find_peaks prominence on the energy profile.",
)
@click.option(
"--rmsd-tol",
type=float,
default=0.1,
show_default=True,
help="Max RMSD (A) for an eOn peak geometry to match a NEB peak frame.",
)
[docs]
def main(
neb_con: Path,
out_dir: Path,
settings_name: str,
socket: str,
peak_files_dir: Path | None,
prominence: float,
rmsd_tol: float,
):
"""Seed one eOn dimer saddle search per interior NEB peak."""
seed_dirs, summary = seed_dimers_from_peaks(
neb_con=neb_con,
out_dir=out_dir,
settings_name=settings_name,
socket=socket,
peak_files_dir=peak_files_dir,
prominence=prominence,
rmsd_tol=rmsd_tol,
)
if not seed_dirs:
click.echo("No interior peaks found; no seed directories written.", err=True)
return
click.echo(f"Created {len(seed_dirs)} dimer seed dir(s) under {out_dir}:")
for seed in summary:
click.echo(
f" peak_{seed.peak_index:02d} image={seed.image_index} "
f"E={seed.energy:.4f} dE={seed.energy_vs_reactant:.4f} "
f"mode={seed.mode_source} -> {seed.seed_dir}"
)
if __name__ == "__main__":
main()
