eOn
LJ cluster minimization (built-in potential)¶
Minimize the 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
--labeland initial / minimized captionsrelative energy on the landscape colorbar for readable ticks
The benchmark geometry is under the force tolerance, so the client would write one frame.
The setup cell moves the first atom by 0.001 angstroms along x, and the minimizer then takes a real step.
The landscape cell passes --ira-kmax 1.8.
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)
$ /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 -m rgpycrumbs.cli eon plt-min --job-dir /tmp/eon_lj_min_g5xic0ji --label lj cluster --plot-type profile --dpi 150 -o /tmp/eon_lj_min_g5xic0ji/plots/min_1d.png
--> Dispatching to: /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/lib/python3.12/site-packages/rgpycrumbs/eon/plt_min.py --job-dir /tmp/eon_lj_min_g5xic0ji --label lj cluster --plot-type profile --dpi 150 -o /tmp/eon_lj_min_g5xic0ji/plots/min_1d.png
[10/21/26 13:46:33] INFO INFO - Loading minimization trajectory from
/tmp/eon_lj_min_g5xic0ji
INFO INFO - Using minimization metrics from frame
metadata (7 rows)
INFO INFO - Loaded 7 frames, 7 data rows
INFO INFO - Loaded minimization trajectory from
/tmp/eon_lj_min_g5xic0ji (7 frames)
INFO INFO - Setting global rcParams for ruhi theme
WARNING WARNING - Font 'Atkinson Hyperlegible' not found.
Falling back to 'sans-serif'.
[10/21/26 13:46:34] INFO INFO - Saved
/tmp/eon_lj_min_g5xic0ji/plots/min_1d.png
--> Using active interpreter (readcon/plot stack present or --dev)
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",
"--ira-kmax",
"1.8",
"--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)
$ /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 -m rgpycrumbs.cli eon plt-min --job-dir /tmp/eon_lj_min_g5xic0ji --label lj cluster --ira-kmax 1.8 --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 /tmp/eon_lj_min_g5xic0ji/plots/min_2d.png
--> Dispatching to: /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/lib/python3.12/site-packages/rgpycrumbs/eon/plt_min.py --job-dir /tmp/eon_lj_min_g5xic0ji --label lj cluster --ira-kmax 1.8 --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 /tmp/eon_lj_min_g5xic0ji/plots/min_2d.png
[10/21/26 13:46:36] INFO INFO - Loading minimization trajectory from
/tmp/eon_lj_min_g5xic0ji
INFO INFO - Using minimization metrics from frame
metadata (7 rows)
INFO INFO - Loaded 7 frames, 7 data rows
INFO INFO - Loaded minimization trajectory from
/tmp/eon_lj_min_g5xic0ji (7 frames)
INFO INFO - Setting global rcParams for ruhi theme
WARNING WARNING - Font 'Atkinson Hyperlegible' not found.
Falling back to 'sans-serif'.
INFO INFO - Calculating landscape coordinates (RMSD-A,
RMSD-B)...
INFO INFO - Generating 2D surface using grad_imq
(Projected: True)...
[10/21/26 13:46:37] INFO INFO - Unable to initialize backend 'tpu':
INTERNAL: Failed to open libtpu.so: libtpu.so:
cannot open shared object file: No such file or
directory
INFO INFO - Unable to initialize backend 'proxy': The
'proxy' backend requires the address of an IFRT
Proxy server. Set it via the JAX_BACKEND_TARGET
environment variable or the jax_backend_target
config option, e.g.
JAX_BACKEND_TARGET=grpc://localhost:29000.
[10/21/26 13:46:44] INFO INFO - Loading /tmp/tmpv3ala34n.xyz
[10/21/26 13:46:48] WARNING WARNING - Stated charge +0, but the bond orders
give -6594; formal charges follow the structure
INFO INFO - Built graph: 997 atoms, 5291 bonds
[10/21/26 13:46:51] INFO INFO - Loading /tmp/tmpt4d7r8cw.xyz
[10/21/26 13:46:55] WARNING WARNING - Stated charge +0, but the bond orders
give -6594; formal charges follow the structure
INFO INFO - Built graph: 997 atoms, 5291 bonds
[10/21/26 13:46:58] INFO INFO - Saved
/tmp/eon_lj_min_g5xic0ji/plots/min_2d.png
--> Using active interpreter (readcon/plot stack present or --dev)
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)
$ /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 -m rgpycrumbs.cli eon plt-min --job-dir /tmp/eon_lj_min_g5xic0ji --label lj cluster --plot-type convergence --dpi 150 -o /tmp/eon_lj_min_g5xic0ji/plots/min_conv.png
--> Dispatching to: /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/lib/python3.12/site-packages/rgpycrumbs/eon/plt_min.py --job-dir /tmp/eon_lj_min_g5xic0ji --label lj cluster --plot-type convergence --dpi 150 -o /tmp/eon_lj_min_g5xic0ji/plots/min_conv.png
[10/21/26 13:47:00] INFO INFO - Loading minimization trajectory from
/tmp/eon_lj_min_g5xic0ji
INFO INFO - Using minimization metrics from frame
metadata (7 rows)
INFO INFO - Loaded 7 frames, 7 data rows
INFO INFO - Loaded minimization trajectory from
/tmp/eon_lj_min_g5xic0ji (7 frames)
INFO INFO - Setting global rcParams for ruhi theme
WARNING WARNING - Font 'Atkinson Hyperlegible' not found.
Falling back to 'sans-serif'.
[10/21/26 13:47:01] INFO INFO - Saved
/tmp/eon_lj_min_g5xic0ji/plots/min_conv.png
--> Using active interpreter (readcon/plot stack present or --dev)
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¶
Morse Pt NEB (built-in potential): built-in NEB +
plt-nebVisualizing optimization trajectories: PET-MAD vinyl alcohol visualization