`plt-saddle`¶

Visualizing Dimer/Saddle Search Optimization¶

This tool generates 2D optimization landscape plots and convergence profiles from dimer or saddle point search calculations. Like plt-min and plt-neb, it uses the shared renderer-option bundle for structure strips and viewing controls.

Library API¶

from rgpycrumbs.eon import plot_saddle, plot

# Job directory (write_movies=true)
plot_saddle(job_dir="results/", plot_type="profile", output="out.pdf")

# Live object frames (Matter.movie_frames / MinModeSaddleSearch.climb_frames)
# or a ConFrame sequence with kind="saddle"
plot(frames, kind="saddle", plot_type="profile", output="out.pdf")

Same pipeline as the CLI. Heavy deps stage via ensure_import when RGPYCRUMBS_AUTO_DEPS is on (library entries enable it by default).

Method¶

Uses the same gradient-enhanced surface interpolation as NEB landscapes, but with different reference structures and axis labels. The (s, d) projection maps into optimization progress (s) and lateral deviation (d), where s represents how far along the path from initial to saddle, and d represents wasted sideways motion.

Requires eOn output with write_movies=true and a climb concatenated movie. Metadata-rich full CON movies are treated as the canonical structured source; climb.dat is retained as a compatibility and export layer when present.

Plot Types¶

Energy/Eigenvalue Profile¶

rgpycrumbs eon plt-saddle --job-dir results/ --plot-type profile

Shows energy delta and eigenvalue vs iteration. Useful for checking convergence behavior.

2D Optimization Landscape¶

rgpycrumbs eon plt-saddle --job-dir results/ --plot-type landscape

Projects the dimer trajectory into (s, d) coordinates using RMSD from the initial structure and saddle point.

Convergence Panel¶

rgpycrumbs eon plt-saddle --job-dir results/ --plot-type convergence

Side-by-side plots of force norm and step size vs iteration.

Options¶

Option	Default	Description
`--job-dir`	(required)	eOn output directory
`--plot-type`	`profile`	`profile`, `landscape`, `convergence`, `mode-evolution`
`--ref-product`	None	Optional product .con for (initial, product) reference pair
`--project-path`	True	Project into (s, d) coordinates
`--surface-type`	`grad_matern`	Surface fitting method
`--ira-kmax`	14.0	IRA kmax for RMSD calculation
`--energy-unit`	`eV`	Presentation unit: `eV`, `kcal/mol`, `kJ/mol`
`--theme`	`ruhi`	Plot theme
`--plot-structures`	`none`	Structure strip below landscape: `none`, `endpoints`
`--strip-renderer`	`xyzrender`	Renderer backend for structure strips
`--xyzrender-config`	`paton`	xyzrender preset for strip rendering
`--rotation`	`auto`	Shared viewing rotation control
`--perspective-tilt`	0.0	Small off-axis tilt to reveal occluded atoms
`-o`	`saddle_{type}.pdf`	Output file path
`--dpi`	200	Resolution

Using a Product Reference¶

By default, the landscape uses (initial, saddle) as the two references. To use (initial, product) instead (showing the full reaction path context):

rgpycrumbs eon plt-saddle --job-dir results/ --plot-type landscape --ref-product product.con

Structure Rendering¶

Landscape plots can render the endpoint strip below the axes:

rgpycrumbs eon plt-saddle \
  --job-dir results/ \
  --plot-type landscape \
  --plot-structures endpoints \
  --strip-renderer xyzrender \
  --rotation auto \
  --perspective-tilt 6

This shared renderer contract is identical to plt-min and plt-neb.

Prefer --config plot.toml for surface-fit knobs (auto_thin, default off); see eOn plot TOML config.

Required eOn Output Files¶

File	Required	Description
`climb`	Yes	Concatenated structure movie
`climb.dat`	Fallback	Compatibility/export TSV when the movie does not carry full per-frame metadata
`reactant.con` or `pos.con`	Yes	Initial structure
`saddle.con`	No	Final saddle point
`mode.dat`	No	Eigenvector at saddle

plt-saddle¶