Morse Pt NEB (built-in potential)

A compact Pt surface / adatom NEB using the built-in morse_pt potential. Geometries match benchmarks/data/neb_morse_pt/. The system is small, uses only a built-in potential, and is suitable for docs CI.

Workflow:

  1. write config.ini and copy endpoints

  2. run eonclient

  3. plot 1D profiles and a 2D reaction-valley landscape with the current rgpycrumbs eon plt-neb conventions (full history, 1:1 Å panel, structure strip)

Prerequisites

which eonclient
python -c "import rgpycrumbs, chemparseplot, readcon"

Setup and run

1D energy profiles (full history)

Plot every optimization step, mark the final band, and attach a structure strip for all images on the path (--plot-structures all). The saddle is marked with a gold star on the final profile.

neb_profile = plot_dir / "neb_1d.png"
run_rgpycrumbs(
    "eon",
    "plt-neb",
    "--con-file",
    str(work / "neb.con"),
    "--input-dat-pattern",
    str(work / "neb_*.dat"),
    "--plot-type",
    "profile",
    "--highlight-last",
    "--show-pts",
    "--plot-structures",
    "all",
    "--strip-renderer",
    "xyzrender",
    "--strip-dividers",
    "--xyzrender-config",
    "paton",
    "--rotation",
    "90x,0y,0z",
    "--show-legend",
    "--title",
    "Morse Pt NEB path optimization",
    "--dpi",
    "150",
    "--output-file",
    str(neb_profile),
    cwd=work,
)
show_plot(neb_profile)

$ /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 -m rgpycrumbs.cli eon plt-neb --con-file /tmp/eon_morse_pt_neb_cj0t4nxe/neb.con --input-dat-pattern /tmp/eon_morse_pt_neb_cj0t4nxe/neb_*.dat --plot-type profile --highlight-last --show-pts --plot-structures all --strip-renderer xyzrender --strip-dividers --xyzrender-config paton --rotation 90x,0y,0z --show-legend --title Morse Pt NEB path optimization --dpi 150 --output-file /tmp/eon_morse_pt_neb_cj0t4nxe/plots/neb_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_neb.py --con-file /tmp/eon_morse_pt_neb_cj0t4nxe/neb.con --input-dat-pattern /tmp/eon_morse_pt_neb_cj0t4nxe/neb_*.dat --plot-type profile --highlight-last --show-pts --plot-structures all --strip-renderer xyzrender --strip-dividers --xyzrender-config paton --rotation 90x,0y,0z --show-legend --title Morse Pt NEB path optimization --dpi 150 --output-file /tmp/eon_morse_pt_neb_cj0t4nxe/plots/neb_1d.png
[08/25/26 09:58:04] INFO     INFO - Setting global rcParams for ruhi theme      
                    WARNING  WARNING - Font 'Atkinson Hyperlegible' not found.  
                             Falling back to 'sans-serif'.                      
[08/25/26 09:58:05] INFO     INFO - Reading structures from                     
                             /tmp/eon_morse_pt_neb_cj0t4nxe/neb.con             
                    INFO     INFO - Loaded 9 structures.                        
                    INFO     INFO - Loading explicit saddle point from sp.con   
[08/25/26 09:58:09] INFO     INFO - Searching for files with pattern:           
                             '/tmp/eon_morse_pt_neb_cj0t4nxe/neb_*.dat'         
                    INFO     INFO - Found 25 file(s).                           
                    INFO     INFO - rgpycrumbs: installing xyzrender>=0.1.3 via 
                             uv                                                 
[08/25/26 09:58:12] INFO     INFO - Loading /tmp/tmpithr65ji.xyz                
[08/25/26 09:58:13] INFO     INFO - Built graph: 343 atoms, 1626 bonds          
[08/25/26 09:58:14] INFO     INFO - Loading /tmp/tmp38en3pe0.xyz                
                    INFO     INFO - Built graph: 343 atoms, 1626 bonds          
[08/25/26 09:58:15] INFO     INFO - Loading /tmp/tmp1dfk7jy6.xyz                
                    INFO     INFO - Built graph: 343 atoms, 1626 bonds          
[08/25/26 09:58:17] INFO     INFO - Loading /tmp/tmpnb4994ow.xyz                
                    INFO     INFO - Built graph: 343 atoms, 1628 bonds          
[08/25/26 09:58:18] INFO     INFO - Loading /tmp/tmpc6wahto1.xyz                
                    INFO     INFO - Built graph: 343 atoms, 1629 bonds          
[08/25/26 09:58:19] INFO     INFO - Loading /tmp/tmpoontnj_t.xyz                
                    INFO     INFO - Built graph: 343 atoms, 1628 bonds          
[08/25/26 09:58:21] INFO     INFO - Loading /tmp/tmpafk68yaj.xyz                
                    INFO     INFO - Built graph: 343 atoms, 1626 bonds          
[08/25/26 09:58:22] INFO     INFO - Loading /tmp/tmprs1oh3ri.xyz                
                    INFO     INFO - Built graph: 343 atoms, 1626 bonds          
[08/25/26 09:58:23] INFO     INFO - Loading /tmp/tmpclmfoo86.xyz                
[08/25/26 09:58:24] INFO     INFO - Built graph: 343 atoms, 1626 bonds          
[08/25/26 09:58:25] INFO     INFO - Profile content layout: main=3.55 in,       
                             strip=1.95 in, figsize=(6.40, 6.91)                

--> Using active interpreter (readcon/plot stack present or --dev)
../../_images/f50c070faf41da694343739ab2f0c6f2263404cdf8df69357bf24860e5fc1383.png

2D reaction-valley landscape

Use the full optimization history for the surface (--landscape-path all), project into progress / orthogonal deviation (--project-path), and keep a true 1:1 Å panel (Δs = Δd). The strip under the map shows every band image in two rows when there are many structures.

neb_land = plot_dir / "neb_2d.png"
run_rgpycrumbs(
    "eon",
    "plt-neb",
    "--con-file",
    str(work / "neb.con"),
    "--input-dat-pattern",
    str(work / "neb_*.dat"),
    "--input-path-pattern",
    str(work / "neb_path_*.con"),
    "--plot-type",
    "landscape",
    "--rc-mode",
    "path",
    "--landscape-mode",
    "surface",
    "--landscape-path",
    "all",
    "--surface-type",
    "grad_imq",
    "--project-path",
    "--show-pts",
    "--highlight-last",
    "--plot-structures",
    "all",
    "--strip-renderer",
    "xyzrender",
    "--strip-dividers",
    "--xyzrender-config",
    "paton",
    "--rotation",
    "90x,0y,0z",
    "--show-legend",
    "--title",
    "Morse Pt NEB-RMSD surface",
    "--dpi",
    "150",
    "--output-file",
    str(neb_land),
    cwd=work,
)
show_plot(neb_land)

$ /home/runner/work/eOn/eOn/.pixi/envs/docs-mta/bin/python3.12 -m rgpycrumbs.cli eon plt-neb --con-file /tmp/eon_morse_pt_neb_cj0t4nxe/neb.con --input-dat-pattern /tmp/eon_morse_pt_neb_cj0t4nxe/neb_*.dat --input-path-pattern /tmp/eon_morse_pt_neb_cj0t4nxe/neb_path_*.con --plot-type landscape --rc-mode path --landscape-mode surface --landscape-path all --surface-type grad_imq --project-path --show-pts --highlight-last --plot-structures all --strip-renderer xyzrender --strip-dividers --xyzrender-config paton --rotation 90x,0y,0z --show-legend --title Morse Pt NEB-RMSD surface --dpi 150 --output-file /tmp/eon_morse_pt_neb_cj0t4nxe/plots/neb_2d.png

---------------------------------------------------------------------------
KeyboardInterrupt                         Traceback (most recent call last)
Cell In[3], line 2
      1 neb_land = plot_dir / "neb_2d.png"
----> 2 run_rgpycrumbs(
      3     "eon",
      4     "plt-neb",
      5     "--con-file",
      6     str(work / "neb.con"),
      7     "--input-dat-pattern",
      8     str(work / "neb_*.dat"),
      9     "--input-path-pattern",
     10     str(work / "neb_path_*.con"),
     11     "--plot-type",
     12     "landscape",
     13     "--rc-mode",
     14     "path",
     15     "--landscape-mode",
     16     "surface",
     17     "--landscape-path",
     18     "all",
     19     "--surface-type",
     20     "grad_imq",
     21     "--project-path",
     22     "--show-pts",
     23     "--highlight-last",
     24     "--plot-structures",
     25     "all",
     26     "--strip-renderer",
     27     "xyzrender",
     28     "--strip-dividers",
     29     "--xyzrender-config",
     30     "paton",
     31     "--rotation",
     32     "90x,0y,0z",
     33     "--show-legend",
     34     "--title",
     35     "Morse Pt NEB-RMSD surface",
     36     "--dpi",
     37     "150",
     38     "--output-file",
     39     str(neb_land),
     40     cwd=work,
     41 )
     42 show_plot(neb_land)

Cell In[1], line 67, in run_rgpycrumbs(cwd, timeout, *args)
     65 cmd = [sys.executable, "-m", "rgpycrumbs.cli", *args]
     66 print("$", " ".join(cmd))
---> 67 r = subprocess.run(cmd, cwd=cwd, capture_output=True, text=True, timeout=timeout)
     68 if r.stdout:
     69     print(r.stdout)

File ~/work/eOn/eOn/.pixi/envs/docs-mta/lib/python3.12/subprocess.py:550, in run(input, capture_output, timeout, check, *popenargs, **kwargs)
    548 with Popen(*popenargs, **kwargs) as process:
    549     try:
--> 550         stdout, stderr = process.communicate(input, timeout=timeout)
    551     except TimeoutExpired as exc:
    552         process.kill()

File ~/work/eOn/eOn/.pixi/envs/docs-mta/lib/python3.12/subprocess.py:1209, in Popen.communicate(self, input, timeout)
   1206     endtime = None
   1208 try:
-> 1209     stdout, stderr = self._communicate(input, endtime, timeout)
   1210 except KeyboardInterrupt:
   1211     # https://bugs.python.org/issue25942
   1212     # See the detailed comment in .wait().
   1213     if timeout is not None:

File ~/work/eOn/eOn/.pixi/envs/docs-mta/lib/python3.12/subprocess.py:2115, in Popen._communicate(self, input, endtime, orig_timeout)
   2108     self._check_timeout(endtime, orig_timeout,
   2109                         stdout, stderr,
   2110                         skip_check_and_raise=True)
   2111     raise RuntimeError(  # Impossible :)
   2112         '_check_timeout(..., skip_check_and_raise=True) '
   2113         'failed to raise TimeoutExpired.')
-> 2115 ready = selector.select(timeout)
   2116 self._check_timeout(endtime, orig_timeout, stdout, stderr)
   2118 # XXX Rewrite these to use non-blocking I/O on the file
   2119 # objects; they are no longer using C stdio!

File ~/work/eOn/eOn/.pixi/envs/docs-mta/lib/python3.12/selectors.py:415, in _PollLikeSelector.select(self, timeout)
    413 ready = []
    414 try:
--> 415     fd_event_list = self._selector.poll(timeout)
    416 except InterruptedError:
    417     return ready

KeyboardInterrupt:

See also