chemparseplot.parse.eon.dimer_trajectory

Dimer/saddle search trajectory parser for eOn output.

Reads structured per-iteration data from climb.dat (TSV) and concatenated trajectory from climb.con (movie file), as produced by eOn with write_movies=true.

.. versionadded:: 1.5.0

Module Contents

Classes

DimerTrajectoryData

Container for a dimer/saddle search trajectory.

Functions

parse_climb_dat	Read the structured climb.dat TSV file.
parse_climb_con	Read concatenated structures from the climb.con movie file.
_find_initial_structure	Locate the initial/reactant structure in the job directory.
_load_mode_dat	Load eigenvector from mode.dat (Nx3 whitespace-separated).
load_dimer_trajectory	Load a complete dimer/saddle search trajectory from an eOn job directory.

Data

log

API

chemparseplot.parse.eon.dimer_trajectory.log

‘getLogger(…)’

class chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData

Container for a dimer/saddle search trajectory.

Attributes

atoms_list Per-iteration structures from the movie file. dat_df Polars DataFrame with per-iteration metrics from climb.dat. initial_atoms Starting structure (from reactant.con or pos.con). saddle_atoms Final saddle point structure (from saddle.con), or None. mode_vector Eigenvector at the saddle (from mode.dat), or None.

atoms_list: list[ase.Atoms]

None

dat_df: polars.DataFrame

None

initial_atoms: ase.Atoms

None

saddle_atoms: ase.Atoms | None

None

mode_vector: numpy.ndarray | None

None

chemparseplot.parse.eon.dimer_trajectory.parse_climb_dat(path: pathlib.Path) → polars.DataFrame

Read the structured climb.dat TSV file.

Parameters

path Path to the climb.dat file.

Returns

pl.DataFrame DataFrame with columns matching the TSV header.

chemparseplot.parse.eon.dimer_trajectory.parse_climb_con(path: pathlib.Path) → list[ase.Atoms]

Read concatenated structures from the climb.con movie file.

Parameters

path Path to the climb or climb.con file.

Returns

list[Atoms] List of ASE Atoms objects, one per iteration.

chemparseplot.parse.eon.dimer_trajectory._find_initial_structure(job_dir: pathlib.Path) → ase.Atoms | None

Locate the initial/reactant structure in the job directory.

chemparseplot.parse.eon.dimer_trajectory._load_mode_dat(path: pathlib.Path) → numpy.ndarray | None

Load eigenvector from mode.dat (Nx3 whitespace-separated).

chemparseplot.parse.eon.dimer_trajectory.load_dimer_trajectory(job_dir: pathlib.Path) → chemparseplot.parse.eon.dimer_trajectory.DimerTrajectoryData

Load a complete dimer/saddle search trajectory from an eOn job directory.

Expects the job to have been run with write_movies=true.

Parameters

job_dir Path to the eOn job output directory containing climb, climb.dat, saddle.con, etc.

Returns

DimerTrajectoryData Combined trajectory data.

Raises

FileNotFoundError If required files (climb, climb.dat) are missing.