rgpycrumbs.eon.plt_neb¶

Plots Nudged Elastic Band (NEB) reaction paths and landscapes.

Added in version 0.0.2.

This script provides a command-line interface (CLI) to visualize data generated from NEB calculations. It can plot:

Energy/Eigenvalue Profiles: Shows the evolution of the energy or lowest eigenvalue along the reaction coordinate. It can overlay multiple paths (e.g., from different optimization steps) and use a physically-motivated Hermite spline interpolation using force data.
2D Reaction Landscapes: Plots the path on a 2D coordinate system defined by the Root Mean Square Deviation (RMSD) from the reactant and product structures. This requires the ‘ira_mod’ library. It can also interpolate and display the 2D energy/eigenvalue surface.

The script can also render atomic structures from a .con file as insets on the plots for key points (reactant, saddle, product).

This script follows the guidelines laid out here: https://realpython.com/python-script-structure/

Attributes¶

`ensure_import`
`compute_projection_basis`
`log`
`DEFAULT_INPUT_PATTERN`
`DEFAULT_PATH_PATTERN`
`IRA_KMAX_DEFAULT`
`NEB_LANDSCAPE_STRIP_ZOOM_MULT`
`NEB_PROFILE_STRIP_ZOOM_MULT`
`NEB_LANDSCAPE_STRIP_MAX_COLS`
`NEB_PROFILE_STRIP_HEIGHT_IN`
`NEB_PROFILE_MAIN_HEIGHT_IN`
`plot_neb`

`adjust_text`(args, *kwargs)	Lazy adjustText (ensure_import when AUTO_DEPS is on).
`plot_neb_from_settings`(→ pathlib.Path \| None)	Run the eOn NEB plot pipeline from a resolved settings mapping.
`main`(ctx, config, **params)	CLI entry: merge flags/config then run plot_neb_from_settings.

rgpycrumbs.eon.plt_neb.adjust_text(*args, **kwargs)[source]¶: Lazy adjustText (ensure_import when AUTO_DEPS is on).

rgpycrumbs.eon.plt_neb.plot_neb_from_settings(settings: dict[str, Any]) → pathlib.Path | None[source]¶

Run the eOn NEB plot pipeline from a resolved settings mapping.

Prefer plot_neb() for library callers. This entry is the shared implementation used by the Click CLI after resolve_from_click.

settings:: Mapping from rgpycrumbs.eon.plot_config.merge_plot_settings() (or resolve_from_click).

Added in version 1.10.2.

rgpycrumbs.eon.plt_neb.main(ctx, config, **params)[source]¶: CLI entry: merge flags/config then run plot_neb_from_settings.