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¶

main(input_dat_pattern, input_path_pattern, con_file, ...)

Main entry point for NEB plot script.

rgpycrumbs.eon.plt_neb.main(input_dat_pattern, input_path_pattern, con_file, additional_con, source, input_traj, input_h5, plot_type, landscape_mode, landscape_path, project_path, rc_mode, plot_structures, rbf_smoothing, show_pts, plot_mode, surface_type, n_inducing, output_file, start, end, normalize_rc, title, xlabel, ylabel, highlight_last, theme, cmap_profile, cmap_landscape, facecolor, fontsize_base, figsize, fig_height, aspect_ratio, dpi, zoom_ratio, ase_rotation, strip_renderer, arrow_head_length, arrow_head_width, arrow_tail_width, spline_method, draw_reactant, draw_saddle, draw_product, show_legend, cache_file, force_recompute, ira_kmax, sp_file, augment_dat, augment_con)[source]¶: Main entry point for NEB plot script.