plt-neb

Visualizing NEB Landscapes

This tool generates 2D energy landscape plots from NEB calculations using gradient-enhanced surface interpolation.

Method

The default grad_imq surface method uses gradient-enhanced Inverse Multiquadric interpolation on 2D RMSD projections. This approach is described in:

  • R. Goswami, “Two-dimensional RMSD projections for reaction path visualization and validation,” MethodsX, p. 103851, Mar. 2026, doi: 10.1016/j.mex.2026.103851.

The method projects high-dimensional structures onto 2D RMSD coordinates (reactant distance r vs product distance p), then fits a smooth surface using energy values and their gradients for enhanced accuracy.

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

Troubleshooting

“No .dat files found” error

Problem: The script reports no input files matching the pattern.

Solution:

  1. Verify the input pattern matches your files:

    ls neb_*.dat

  2. Use the --input-pattern flag to specify a custom pattern:

    python -m rgpycrumbs.cli eon plt-neb --input-pattern "path/to/neb_*.dat"

“Index out of range” error

Problem: The --start or --end indices are outside the available data range.

Solution:

  1. Check available iterations:

    ls -1 neb_*.dat | wc -l

  2. Adjust indices to be within range (0 to N-1 where N is the number of files)

Plot appears empty

Problem: The plot window opens but shows no data.

Solution:

  1. Verify the .dat files contain valid energy data (column 2)

  2. Check that the energy values are not all identical

  3. Try with a smaller range first: --start 0 --end 5

Force-corrected interpolation fails

Problem: Hermite spline interpolation produces warnings or errors.

Solution:

  1. Ensure you have at least 3 data points

  2. Check that force data (column 4 in .dat) is present

  3. The script falls back to raw lines if spline fails - this is expected behavior

OCI-NEB/RONEB Options

MMF Peak Overlay

When eOn produces peak{NN}_pos.con files (from OCI-NEB mode-following), overlay them on the landscape:

rgpycrumbs eon plt-neb --plot-type landscape --mmf-peaks

Peaks are auto-detected in the current directory. Use --peak-dir to specify an explicit path:

rgpycrumbs eon plt-neb --plot-type landscape --mmf-peaks --peak-dir path/to/peaks/

Band Evolution

Show how the NEB band evolves across optimization iterations (requires write_movies=true data):

rgpycrumbs eon plt-neb --plot-type landscape --show-evolution

Older bands appear with lower opacity; the final band is most visible.

Structure Rendering

Rendering Backends

Four backends available via --strip-renderer:

Backend

Install

Style

xyzrender (default)

pip install xyzrender

Ball-and-stick, paton preset

ase

Built-in

Space-filling spheres

solvis

pip install solvis-tools

PyVista ball-and-stick, transparent bg

ovito

pip install ovito

OVITO off-screen

Viewing Angle

--rotation "0x,90y,0z" (default) sets the viewing angle for all backends. Uses ASE-style rotation syntax.

Perspective Tilt

--perspective-tilt 8 applies a small Rodrigues off-axis rotation (8 degrees) to reveal atoms hidden by orthographic projection overlap. Useful for ring structures where H atoms hide behind carbons.

See Also

API Reference

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