Plotting ChemGP figures¶

CLI Reference¶

rgpycrumbs chemgp plt-gp¶

ChemGP figure generation from HDF5 data.

Usage

rgpycrumbs chemgp plt-gp [OPTIONS] COMMAND [ARGS]...

batch¶

Generate multiple plots from a TOML config.

Usage

rgpycrumbs chemgp plt-gp batch [OPTIONS]

Options

-c, --config <config_path>¶: Required TOML config listing plots to generate.

-b, --base-dir <base_dir>¶: Base directory for relative paths in config.

--dpi <dpi>¶: Output resolution.

convergence¶

Force/energy convergence vs oracle calls.

Usage

rgpycrumbs chemgp plt-gp convergence [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

fps¶

FPS subset visualization (PCA scatter).

Usage

rgpycrumbs chemgp plt-gp fps [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

landscape¶

2D NEB reaction landscape via plt-neb (RMSD coordinates).

Usage

rgpycrumbs chemgp plt-gp landscape [OPTIONS]

Options

--dat-pattern <dat_pattern>¶: Glob pattern for .dat files (eON format).

--con-pattern <con_pattern>¶: Glob pattern for .con path files (eON format).

-d, --source-dir <source_dir>¶: Directory containing .dat/.con files.

-o, --output <output_path>¶: Required Output PDF path.

-W, --width <width>¶

-H, --height <height>¶

--dpi <dpi>¶

--surface-type <surface_type>¶: Surface interpolation method for plt-neb.

--landscape-mode <landscape_mode>¶

Options:: path | surface

--plot-structures <plot_structures>¶

--project-path, --no-project-path¶

--additional-con <additional_con>¶: (path, label) pairs for extra path overlays.

--augment-dat <augment_dat>¶: Glob for extra .dat surface data.

--augment-con <augment_con>¶: Glob for extra .con surface data.

--zoom-ratio <zoom_ratio>¶: Structure image zoom ratio.

--ase-rotation <ase_rotation>¶: ASE rotation string for structures.

nll¶

MAP-NLL landscape in hyperparameter space.

Usage

rgpycrumbs chemgp plt-gp nll [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

profile¶

NEB energy profile (image index vs delta E).

Usage

rgpycrumbs chemgp plt-gp profile [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

quality¶

GP surrogate quality progression (multi-panel).

Usage

rgpycrumbs chemgp plt-gp quality [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

--n-points <n_points>¶

rff¶

RFF approximation quality vs exact GP.

Usage

rgpycrumbs chemgp plt-gp rff [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

sensitivity¶

Hyperparameter sensitivity grid (3x3).

Usage

rgpycrumbs chemgp plt-gp sensitivity [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

surface¶

2D PES contour plot.

Usage

rgpycrumbs chemgp plt-gp surface [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

--clamp-lo <clamp_lo>¶

--clamp-hi <clamp_hi>¶

--contour-step <contour_step>¶

trust¶

Trust region illustration (1D slice).

Usage

rgpycrumbs chemgp plt-gp trust [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

variance¶

GP variance overlaid on PES.

Usage

rgpycrumbs chemgp plt-gp variance [OPTIONS]

Options

--dpi <dpi>¶: Output resolution.

-H, --height <height>¶: Figure height in inches.

-W, --width <width>¶: Figure width in inches.

-o, --output <output_path>¶: Required Output PDF path.

-i, --input <input_path>¶: Required HDF5 data file.

Overview¶

plt-gp reads HDF5 files produced by ChemGP (the Rust crate chemgp-core) and generates publication-quality PDF figures via chemparseplot.

Subcommand	Plot type	Backend
convergence	Oracle calls vs force/energy	plotnine
surface	2D PES contour + NEB path overlay	matplotlib
quality	GP surrogate progression (multi-panel)	matplotlib
rff	RFF vs exact GP error (two-panel)	plotnine
nll	MAP-NLL landscape in hyperparameter space	matplotlib
sensitivity	3x3 hyperparameter sensitivity grid	matplotlib
trust	Trust region illustration (1D slice)	matplotlib
variance	GP variance hatching on PES	matplotlib
fps	FPS subset PCA scatter	plotnine
profile	NEB energy profile across images	plotnine
landscape	2D NEB landscape (delegates to plt-neb)	matplotlib
batch	TOML-driven batch figure generation	(all)

Common Options¶

All single-plot subcommands accept:

--input / -i: Path to the HDF5 file (required)
--output / -o: Output PDF/PNG path (required)
--width: Figure width in inches (default varies by type)
--height: Figure height in inches (default varies by type)
--dpi: Resolution (default 300)

Single-Plot Usage¶

# Convergence curve from a minimize run
rgpycrumbs chemgp plt-gp convergence -i output/leps_minimize.h5 -o convergence.pdf

# 2D surface with NEB path overlay
rgpycrumbs chemgp plt-gp surface -i output/leps_neb.h5 -o surface.pdf

# NLL landscape
rgpycrumbs chemgp plt-gp nll -i output/leps_nll.h5 -o nll.pdf

Batch Mode¶

Define a TOML config listing all plots, then generate them in one command:

rgpycrumbs chemgp plt-gp batch --config figures.toml

See the batch tutorial for a worked example with a full TOML config.

Energy Clamping¶

Surface and quality plots auto-detect clamping ranges from the filename:

Files containing mb use [-200, 50]
Files containing leps use [-5, 5]

Override with --clamp-lo and --clamp-hi flags on the subcommand, or clamp_lo / clamp_hi keys in the TOML config.

API Reference¶

For developer details and source code see rgpycrumbs.chemgp.plt_gp.

The plotting functions themselves live in chemparseplot at chemparseplot.plot.chemgp.