Plotting NEB paths

Visualizing path trajectories

rgpycrumbs eon plt-neb

Main entry point for NEB plot script.

Usage

rgpycrumbs eon plt-neb [OPTIONS]

Options

--input-dat-pattern <input_dat_pattern>

Glob pattern for input data files.

--input-path-pattern <input_path_pattern>

Glob pattern for input path files.

--con-file <con_file>

Path to .con trajectory file.

--additional-con <additional_con>

Path(s) to additional .con file(s) and the label to highlight, use an empty string to default to the file name.

--plot-type <plot_type>

Type of plot to generate: ‘profile’ (1D path) or ‘landscape’ (2D RMSD plot).

Options:

profile | landscape

--rbf-smoothing <rbf_smoothing>

Smoothing term for 2D RBF, defaults to 10% of the minimum RMSD range.

--rounding <rounding>

Data rounding term for 2D plots.

Default:

3

--landscape-mode <landscape_mode>

For landscape plot: ‘path’ (only 1D path) or ‘surface’ (interpolated 2D surface).

Options:

path | surface

--landscape-path <landscape_path>

Last uses an interpolation only on the last path, otherwise use all points.

Options:

last | all

--rc-mode <rc_mode>

Reaction coordinate for profile plot: ‘path’ (file’s RC) or ‘rmsd’ (RMSD from reactant).

Options:

path | rmsd | index

--plot-structures <plot_structures>

Structures to render on the path. Requires –con-file.

Options:

none | all | crit_points

--surface-type <surface_type>

Interpolation method for the 2D surface.

Options:

grid | rbf

--show-pts, --no-show-pts

Show all paths from the optimization on the RMSD 2D plot.

--plot-mode <plot_mode>

Quantity to plot on y-axis (profile) or color (landscape): ‘energy’ or ‘eigenvalue’.

Options:

energy | eigenvalue

-o, --output-file <output_file>

Output image filename. If not provided, plot is shown interactively.

--start <start>

Start file index for profile plot.

--end <end>

End file index for profile plot.

--normalize-rc

Normalize reaction coordinate.

--title <title>

Plot title.

--xlabel <xlabel>

X-axis label (overrides default).

--ylabel <ylabel>

Y-axis label (overrides default).

--theme <theme>

The plotting theme to use.

Options:

cmc.batlow | ruhi

--cmap-profile <cmap_profile>

Colormap for profile plot (overrides theme default).

--cmap-landscape <cmap_landscape>

Colormap for landscape plot (overrides theme default).

--facecolor <facecolor>

Background color (overrides theme default).

--fontsize-base <fontsize_base>

Base font size (overrides theme default).

--figsize <figsize>

Figure width, height in inches.

Default:

10, 7

--fig-height <fig_height>

Figure height in inches. Must be used with –aspect-ratio.

--aspect-ratio <aspect_ratio>

Figure aspect ratio (width/height). Must be used with –fig-height.

--dpi <dpi>

Resolution in Dots Per Inch.

Default:

200

--zoom-ratio <zoom_ratio>

Scale the inset image.

Default:

0.4

--ase-rotation <ase_rotation>

ASE rotation string for structure insets (e.g., ‘45x,30y,0z’).

Default:

'0x, 90y, 0z'

--arrow-head-length <arrow_head_length>

Arrow head length for insets (points).

Default:

0.2

--arrow-head-width <arrow_head_width>

Arrow head width for insets (points).

Default:

0.3

--arrow-tail-width <arrow_tail_width>

Arrow tail width for insets (points).

Default:

0.1

--highlight-last, --no-highlight-last

Highlight last path (uses theme’s ‘highlight_color’).

--spline-method <spline_method>

Spline interpolation method for energy profiles.

Options:

hermite | spline

--savgol-window <savgol_window>

Savitzky-Golay filter window length (for Hermite spline).

--savgol-order <savgol_order>

Savitzky-Golay filter polynomial order (for Hermite spline).

--draw-reactant <draw_reactant>

Positioning for the reactant inset (x, y, rad).

Default:

15, 60, 0.1

--draw-saddle <draw_saddle>

Positioning for the saddle inset (x, y, rad).

Default:

15, 60, 0.1

--draw-product <draw_product>

Positioning for the product inset (x, y, rad).

Default:

15, 60, 0.1

--cache-file <cache_file>

Parquet file to cache RMSD calculations (speeds up re-runs).

--force-recompute

Ignore cache and force re-calculation of RMSD.

--show-legend

Show the legends for additional con.

--ira-kmax <ira_kmax>

kmax factor for IRA.

Usage

To plot a specific range of neb_*.dat files and save the output:

To show the plot interactively without saving:

python -m rgpycrumbs.cli eon plt-neb --start 280

API Reference

For developer details and source code see rgpycrumbs.eon.plt_neb.