Morse Pt saddle search (built-in potential)¶

A small dimer saddle search on morse_pt using the geometries from benchmarks/data/one_pt_saddle_search/. After the client finishes, plot the trajectory with rgpycrumbs eon plt-saddle (same single-ended landscape stack as minimization).

Setup and run¶

Profile and landscape¶

# Profile (energy / eigenvalue vs iteration when available)
out_p = plot_dir / "saddle_profile.png"
try:
    run_rgpycrumbs(
        "eon",
        "plt-saddle",
        "--job-dir",
        str(work),
        "--label",
        "pt saddle",
        "--plot-type",
        "profile",
        "--dpi",
        "150",
        "-o",
        str(out_p),
    )
    show_plot(out_p)
except Exception as exc:
    print("plt-saddle profile skipped:", exc)

$ /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 -m rgpycrumbs.cli eon plt-saddle --job-dir /tmp/eon_pt_saddle_rgtlwppu --label pt saddle --plot-type profile --dpi 150 -o /tmp/eon_pt_saddle_rgtlwppu/plots/saddle_profile.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_saddle.py --job-dir /tmp/eon_pt_saddle_rgtlwppu --label pt saddle --plot-type profile --dpi 150 -o /tmp/eon_pt_saddle_rgtlwppu/plots/saddle_profile.png
[08/19/26 09:49:54] INFO     INFO - Loading dimer trajectory from               
                             /tmp/eon_pt_saddle_rgtlwppu                        
                    INFO     INFO - Using dimer metrics from frame metadata (11 
                             rows)                                              
                    INFO     INFO - Loaded 11 frames, 11 data rows              
                    INFO     INFO - Loaded trajectory from                      
                             /tmp/eon_pt_saddle_rgtlwppu (11 frames, saddle=yes)
                    INFO     INFO - Setting global rcParams for ruhi theme      
                    WARNING  WARNING - Font 'Atkinson Hyperlegible' not found.  
                             Falling back to 'sans-serif'.                      
                    INFO     INFO - Saved                                       
                             /tmp/eon_pt_saddle_rgtlwppu/plots/saddle_profile.pn
                             g                                                  

--> Using active interpreter (readcon/plot stack present or --dev)

out_l = plot_dir / "saddle_2d.png"
try:
    run_rgpycrumbs(
        "eon",
        "plt-saddle",
        "--job-dir",
        str(work),
        "--label",
        "pt saddle",
        "--plot-type",
        "landscape",
        "--project-path",
        "--surface-type",
        "grad_imq",
        "--plot-structures",
        "endpoints",
        "--strip-renderer",
        "xyzrender",
        "--strip-dividers",
        "--dpi",
        "150",
        "-o",
        str(out_l),
    )
    show_plot(out_l)
except Exception as exc:
    print("plt-saddle landscape skipped:", exc)

$ /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 -m rgpycrumbs.cli eon plt-saddle --job-dir /tmp/eon_pt_saddle_rgtlwppu --label pt saddle --plot-type landscape --project-path --surface-type grad_imq --plot-structures endpoints --strip-renderer xyzrender --strip-dividers --dpi 150 -o /tmp/eon_pt_saddle_rgtlwppu/plots/saddle_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_saddle.py --job-dir /tmp/eon_pt_saddle_rgtlwppu --label pt saddle --plot-type landscape --project-path --surface-type grad_imq --plot-structures endpoints --strip-renderer xyzrender --strip-dividers --dpi 150 -o /tmp/eon_pt_saddle_rgtlwppu/plots/saddle_2d.png
[08/19/26 09:49:56] INFO     INFO - Loading dimer trajectory from               
                             /tmp/eon_pt_saddle_rgtlwppu                        
                    INFO     INFO - Using dimer metrics from frame metadata (11 
                             rows)                                              
                    INFO     INFO - Loaded 11 frames, 11 data rows              
                    INFO     INFO - Loaded trajectory from                      
                             /tmp/eon_pt_saddle_rgtlwppu (11 frames, saddle=yes)
                    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)...                                         
[08/19/26 09:50:13] INFO     INFO - Generating 2D surface using grad_imq        
                             (Projected: True)...                               
                    INFO     INFO - rgpycrumbs: installing jax>=0.4 via uv      
[08/19/26 09:50:16] 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                                          
[08/19/26 09:50:23] INFO     INFO - Calculating landscape coordinates (RMSD-A,  
                             RMSD-B)...                                         
[08/19/26 09:50:40] INFO     INFO - Loading /tmp/tmp8k59mmmx.xyz                
                    INFO     INFO - Built graph: 336 atoms, 1607 bonds          
[08/19/26 09:50:42] INFO     INFO - Loading /tmp/tmpcewzv7n4.xyz                
                    INFO     INFO - Built graph: 336 atoms, 1606 bonds          
[08/19/26 09:50:44] INFO     INFO - Saved                                       
                             /tmp/eon_pt_saddle_rgtlwppu/plots/saddle_2d.png    

--> Using active interpreter (readcon/plot stack present or --dev)

See also¶

Saddle search and Dimer method
LJ cluster minimization (built-in potential) for the shared single-ended plot conventions