`chemparseplot.plot.neb`¶

Module Contents¶

Classes¶

SmoothingParams

Functions¶

`render_structure_to_image`	Renders an ASE atoms object to a numpy image array.
`plot_structure_strip`	Renders a horizontal gallery of atomic structures.
`plot_structure_inset`	Plots a single structure as an annotation inset.
`plot_energy_path`	Plots 1D energy profile with optional Hermite spline interpolation.
`plot_eigenvalue_path`	Plots 1D eigenvalue profile.
`_augment_minima_points`	Creates a ‘collar’ of synthetic points around the endpoints. This forces the RBF interpolator to curve upwards around these points, preventing artificial wells (overshooting) where the physics dictates a minimum.
`_augment_with_gradients`	Uses projected gradients to create helper points slightly offset from the path. This effectively tells the RBF interpolator the local slope.
`plot_landscape_surface`	Plots the 2D landscape surface using RBF or Grid interpolation.
`plot_landscape_path_overlay`	Overlays the colored path line on the landscape.

Data¶

`log`
`InsetImagePos`
`MIN_PATH_LENGTH`

API¶

chemparseplot.plot.neb.log¶: ‘getLogger(…)’

chemparseplot.plot.neb.InsetImagePos¶: ‘namedtuple(…)’

class chemparseplot.plot.neb.SmoothingParams¶

window_length: int¶: 5

polyorder: int¶: 2

chemparseplot.plot.neb.MIN_PATH_LENGTH¶: 1e-06

chemparseplot.plot.neb.render_structure_to_image(atoms, zoom, rotation)¶: Renders an ASE atoms object to a numpy image array.

chemparseplot.plot.neb.plot_structure_strip(ax, atoms_list, labels, zoom=0.3, rotation='0x,90y,0z', theme_color='black', max_cols=6)¶: Renders a horizontal gallery of atomic structures.

chemparseplot.plot.neb.plot_structure_inset(ax, atoms, x, y, xybox, rad, zoom=0.4, rotation='0x,90y,0z', arrow_props=None)¶: Plots a single structure as an annotation inset.

chemparseplot.plot.neb.plot_energy_path(ax, rc, energy, f_para, color, alpha, zorder, method='hermite', smoothing=None)¶: Plots 1D energy profile with optional Hermite spline interpolation.

chemparseplot.plot.neb.plot_eigenvalue_path(ax, rc, eigenvalue, color, alpha, zorder, grid_color='white')¶: Plots 1D eigenvalue profile.

chemparseplot.plot.neb._augment_minima_points(rmsd_r, rmsd_p, z_data, radius=0.01, dE=0.02, num_pts=12)¶: Creates a ‘collar’ of synthetic points around the endpoints. This forces the RBF interpolator to curve upwards around these points, preventing artificial wells (overshooting) where the physics dictates a minimum.

chemparseplot.plot.neb._augment_with_gradients(r, p, z, gr, gp, epsilon=0.05)¶

Uses projected gradients to create helper points slightly offset from the path. This effectively tells the RBF interpolator the local slope.

Creates 4 helper points for every real point: (r +/- eps, p) and (r, p +/- eps)

chemparseplot.plot.neb.plot_landscape_surface(ax, rmsd_r, rmsd_p, grad_r, grad_p, z_data, step_data=None, method='grad_matern', rbf_smooth=None, cmap='viridis', show_pts=True)¶

Plots the 2D landscape surface using RBF or Grid interpolation.

Unified pipeline:

Hyperparameter Optimization: Learn LS/Noise on the ‘clean’ final path.
Augmentation: Add synthetic points (minima rings) and helper points (gradients).
Final Fit: Generate surface using learned params + augmented data.

chemparseplot.plot.neb.plot_landscape_path_overlay(ax, r, p, z, cmap, z_label)¶: Overlays the colored path line on the landscape.

chemparseplot.plot.neb¶