LJ cluster minimization (built-in potential)

Minimize a small Lennard-Jones cluster (ljcluster) from benchmarks/data/min_lj_cluster/. Movies are required for the modern plot stack.

Plotting conventions:

  • energy profile and convergence from the minimization trajectory

  • a single 2D landscape for this job (one endpoint → one RMSD frame), with title from --label and initial / minimized captions

  • relative energy on the landscape colorbar for readable ticks

Setup and run

Energy profile

out = plot_dir / "min_1d.png"
run_rgpycrumbs(
    "eon",
    "plt-min",
    "--job-dir",
    str(work),
    "--label",
    "lj cluster",
    "--plot-type",
    "profile",
    "--dpi",
    "150",
    "-o",
    str(out),
)
show_plot(out)

2D optimization landscape

One landscape for this trajectory only. The title becomes Lj cluster minimization; endpoints are labeled initial / minimized.

out = plot_dir / "min_2d.png"
run_rgpycrumbs(
    "eon",
    "plt-min",
    "--job-dir",
    str(work),
    "--label",
    "lj cluster",
    "--plot-type",
    "landscape",
    "--project-path",
    "--surface-type",
    "grad_imq",
    "--plot-structures",
    "endpoints",
    "--strip-renderer",
    "xyzrender",
    "--strip-dividers",
    "--xyzrender-config",
    "paton",
    "--rotation",
    "90x,0y,0z",
    "--dpi",
    "150",
    "-o",
    str(out),
)
show_plot(out)

Convergence

out = plot_dir / "min_conv.png"
run_rgpycrumbs(
    "eon",
    "plt-min",
    "--job-dir",
    str(work),
    "--label",
    "lj cluster",
    "--plot-type",
    "convergence",
    "--dpi",
    "150",
    "-o",
    str(out),
)
show_plot(out)

Multiple endpoints (reactant and product)

When both ends of a path are minimized, plot two landscapes (one job dir each). Overlay only the 1D profile / convergence panels:

# separate 2D frames
python -m rgpycrumbs.cli eon plt-min --job-dir min_reactant --label reactant \
  --plot-type landscape --project-path --plot-structures endpoints -o min_2D_reactant.png
python -m rgpycrumbs.cli eon plt-min --job-dir min_product --label product \
  --plot-type landscape --project-path --plot-structures endpoints -o min_2D_product.png

# shared 1D overlays
python -m rgpycrumbs.cli eon plt-min \
  --job-dir min_reactant --label reactant \
  --job-dir min_product --label product \
  --plot-type profile -o min_1D.png

See also