rgpycrumbs.eon.con_splitter

Split multi-image .con files into per-image structures.

Added in version 0.0.2.

Attributes

_CON_SUFFIXES
ira_mod
CONSOLE

Classes

AlignMode	Defines structural alignment strategies.
SplitMode	Defines trajectory validation strictness.

Functions

_is_con_path(→ bool)
_read_trajectory_frames(→ tuple[list, list | None])	Load trajectory frames; CON/convel go through readcon to keep metadata.
_energy_from_atoms(→ float | None)
_apply_frame_energy(frame, energy)	Set per-frame total energy on a ConFrame copy-friendly handle.
_write_con_atoms(→ None)	Write one ASE structure as a CON file via readcon.
_write_con_frame(→ None)	Write a readcon ConFrame, optionally replacing positions from atoms.
align_path(frames, mode, iraconf)	Applies the selected alignment strategy to the image sequence.
con_splitter(neb_trajectory_file, mode, output_dir, ...)	Splits a multi-step trajectory file (.traj, .con, etc.) into

Module Contents

rgpycrumbs.eon.con_splitter._CON_SUFFIXES

rgpycrumbs.eon.con_splitter._is_con_path(path: pathlib.Path) → bool

rgpycrumbs.eon.con_splitter._read_trajectory_frames(path: pathlib.Path) → tuple[list, list | None]

Load trajectory frames; CON/convel go through readcon to keep metadata.

Returns (ase_atoms_list, con_frames_or_none). con_frames is populated only for .con/.convel inputs so writers can preserve per-frame energy.

rgpycrumbs.eon.con_splitter._energy_from_atoms(atoms) → float | None

rgpycrumbs.eon.con_splitter._apply_frame_energy(frame, energy: float | None)

Set per-frame total energy on a ConFrame copy-friendly handle.

Prefers set_energy / set_scalar_metadata (readcon>=0.13). Older wheels that expose only a read-only energy property are reconstructed with string metadata values accepted by the constructor.

rgpycrumbs.eon.con_splitter._write_con_atoms(dest: pathlib.Path, atoms, energy: float | None = None) → None

Write one ASE structure as a CON file via readcon.

rgpycrumbs.eon.con_splitter._write_con_frame(dest: pathlib.Path, frame, atoms=None, energy: float | None = None) → None

Write a readcon ConFrame, optionally replacing positions from atoms.

rgpycrumbs.eon.con_splitter.ira_mod

rgpycrumbs.eon.con_splitter.CONSOLE

class rgpycrumbs.eon.con_splitter.AlignMode

Bases: enum.Enum

Defines structural alignment strategies.

NONE = 'none'

ALL = 'all'

ENDPOINTS = 'endpoints'

class rgpycrumbs.eon.con_splitter.SplitMode

Bases: enum.Enum

Defines trajectory validation strictness.

NEB = 'neb'

FLEX = 'flex'

rgpycrumbs.eon.con_splitter.align_path(frames, mode: AlignMode, iraconf: rgpycrumbs.geom.api.alignment.IRAConfig)

Applies the selected alignment strategy to the image sequence.

rgpycrumbs.eon.con_splitter.con_splitter(neb_trajectory_file: pathlib.Path, mode: str, output_dir: pathlib.Path | None, images_per_path: int, path_index: int, center: bool, box_diagonal: tuple[float, float, float], align_type: str, use_ira: bool, ira_kmax: float, path_list_filename: str)

Splits a multi-step trajectory file (.traj, .con, etc.) into individual .con files for a single specified path.

This script reads a trajectory file, which may contain multiple NEB optimization steps (paths), and extracts only the frames corresponding to a single specified path.

It writes each frame of that path into a separate .con file (e.g., ipath_000.con, ipath_001.con, …).

It also generates a text file (default: ‘ipath.dat’) that lists the absolute paths of all created .con files.

This utility extracts specific optimization steps and applies physical chemistry refinements such as centering, cell overrides, and structural alignment (RMSD minimization).