rgpycrumbs.eon.plt_neb_stitch

Stitch multi-segment NEB paths into ONE band and plot it (1D + 2D).

Added in version 0.0.3.

This CLI assembles several NEB segments that share an absolute-energy axis into a single continuous reaction band (deduplicating shared junction frames and removing per-segment minimization offsets), then renders both the 1D energy profile (with the xyzrender structure strip) and the 2D reaction-valley landscape on the stitched band by reusing the existing plt-neb plotter.

The stitching itself lives in chemparseplot.parse.eon.stitch.stitch_neb_segments().

Example:

python -m rgpycrumbs.cli --dev eon plt-neb-stitch \
    --segment "geo2 -> well:results/02_neb/si3n4_g2g1/neb.con:0:7" \
    --segment "well -> geo1_R:results/02_neb/si3n4_g2g1_mid/neb.con:0:" \
    --segment "geo1_R -> N2 loss:results/02_neb/si3n4_cluster/neb.con:0:" \
    --saddle-override "well -> geo1_R:results/03_saddle/si3n4_g2g1_mid/saddle.con:-29432.165003" \
    --out-dir results/02_neb/si3n4_resolved \
    --profile-output results/03_figures/si3n4_resolved-1d-path.png \
    --landscape-output results/03_figures/si3n4_resolved-2d-landscape.png

Attributes

warn_on_direct_script_import
log
PLT_NEB

Functions

_parse_segment(→ tuple[str, str, int | None, int | None])	Parse LABEL:CON_PATH:START:END (END may be empty for 'to the end').
_parse_override(→ tuple[str, str, float])	Parse LABEL:CON_PATH:ENERGY (absolute saddle energy in eV).
_run_plt_neb(→ int)	Dispatch to the existing plt-neb plotter, inheriting the environment.
main(segments, saddle_overrides, out_dir, ...)	Stitch NEB segments and plot the combined 1D profile and 2D landscape.

Module Contents

rgpycrumbs.eon.plt_neb_stitch.warn_on_direct_script_import = None

rgpycrumbs.eon.plt_neb_stitch.log

rgpycrumbs.eon.plt_neb_stitch.PLT_NEB

rgpycrumbs.eon.plt_neb_stitch._parse_segment(spec: str) → tuple[str, str, int | None, int | None]

Parse LABEL:CON_PATH:START:END (END may be empty for ‘to the end’).

rgpycrumbs.eon.plt_neb_stitch._parse_override(spec: str) → tuple[str, str, float]

Parse LABEL:CON_PATH:ENERGY (absolute saddle energy in eV).

rgpycrumbs.eon.plt_neb_stitch._run_plt_neb(args: list[str]) → int

Dispatch to the existing plt-neb plotter, inheriting the environment.

rgpycrumbs.eon.plt_neb_stitch.main(segments, saddle_overrides, out_dir, profile_output, landscape_output, sp_label, profile_title, landscape_title, plot_structures, strip_renderer, facecolor, figsize, dpi, fontsize_base, zoom_ratio, rotation, ira_kmax)

Stitch NEB segments and plot the combined 1D profile and 2D landscape.