fix(eon,mlmm): papercuts (#242)

* fix(eon-pet-neb): update for rgpycrumbs v1.5.x CLI changes

- Rename --ase-rotation to --rotation (v1.5.0)
- Add --strip-renderer xyzrender, --strip-dividers, --show-legend
- Add --project-path for reaction valley coordinates
- Increase figsize to 7x7 and zoom-ratio to 0.4
- Bump rgpycrumbs>=1.5.1, chemparseplot>=1.5.2
- Add strict=True to zip()

* chore(ml-mm): add missing dependency

* fix(ml-mm): add openmpi dep for MPI gromacs-metatomic variant

* fix(ml-mm): switch to nompi variant (MPI variant segfaults on CI runner)

* fix(ml-mm): use mpirun for mdrun (bare gmx_mpi segfaults on CI)

* fix(ml-mm): pin CUDA MPI variant (non-CUDA MPI segfaults on CI)

* fix(ml-mm): use nompi variant (non-CUDA MPI segfaults, feedstock fix incoming)

* fix(ml-mm): add libopenblas for nompi gromacs-metatomic variant

The nompi variant dynamically links against libopenblas.so.0 but the
feedstock does not declare it as a run dependency. MKL gets pulled in
via pytorch-cpu, so libopenblas is never installed unless explicit.

* fix(ml-mm): drop pip torch pin (conda libtorch 2.9 vs pip torch 2.7 = segfault)

The noxfile DEPENCENCIES_UPDATES adds pytorch-cpu 2.9.1 from conda when
libtorch is detected. The pip torch>=2.7,<2.8 pin then overwrites it
with torch 2.7.1+cpu, causing an ABI mismatch with the C++ libtorch
2.9.1 that gromacs-metatomic links against. Result: SIGSEGV in mdrun.

Removing the pip torch pin lets conda's pytorch-cpu provide the matching
torch version.

* fix(ml-mm): pin CPU libtorch variant, revert to MPI gromacs

The conda solver started picking libtorch gpu_cuda130 (565 MB) instead
of cpu_generic (58 MB) around 2026-03-23, breaking ml-mm on CI runners
with missing libopenblas.so.0. Adding `libtorch =*=cpu*` constrains the
solver to the CPU variant which pulls in libopenblas automatically.

Reverts the nompi/gmx changes since the MPI variant with gmx_mpi works
correctly with CPU libtorch (confirmed via act on cosmolab).

Author: HaoZeke

examples/eon-pet-neb/environment.yml

@@ -15,5 +15,5 @@ dependencies:
     - matplotlib
     - metatrain>=2026.2.1,<2027
     - requests
-    - rgpycrumbs>=1.4.1,<2
-    - chemparseplot>=1.4.2,<2
+    - rgpycrumbs>=1.5.1,<2
+    - chemparseplot>=1.5.2,<2

examples/eon-pet-neb/eon-pet-neb.py

@@ -199,7 +199,7 @@
 
 output_files = [output_dir / f"{num:02d}.con" for num in range(TOTAL_IMGS)]
 
-for outfile, img in zip(output_files, images):
+for outfile, img in zip(output_files, images, strict=True):
     aseio.write(outfile, img)
 
 print(f"Wrote {len(output_files)} IDPP images to '{output_dir}/'.")
@@ -404,20 +404,24 @@ def run_neb_plot(
         con_file,
         "--output-file",
         output_file,
-        "--ase-rotation",
+        "--rotation",
         rotation,
         "--facecolor",
         "white",
         "--figsize",
-        "5.37",
-        "5.37",
+        "7",
+        "7",
         "--fontsize-base",
         "16",
         "--show-pts",
         "--zoom-ratio",
-        "0.25",
+        "0.4",
         "--plot-structures",
         "crit_points",
+        "--strip-renderer",
+        "xyzrender",
+        "--strip-dividers",
+        "--show-legend",
     ]
 
     if title:
@@ -443,6 +447,7 @@ def run_neb_plot(
                 "all",
                 "--surface-type",
                 "grad_imq",
+                "--project-path",
             ]
         )
     else:
@@ -465,7 +470,7 @@ def run_neb_plot(
 
 # Display the result
 img = mpimg.imread("1D_oxad.png")
-plt.figure(figsize=(5.37, 5.37))
+plt.figure(figsize=(8, 8))
 plt.imshow(img)
 plt.axis("off")
 plt.show()
@@ -484,7 +489,7 @@ def run_neb_plot(
 
 # Display the result
 img = mpimg.imread("2D_oxad.png")
-plt.figure(figsize=(5.37, 5.37))
+plt.figure(figsize=(8, 8))
 plt.imshow(img)
 plt.axis("off")
 plt.show()

examples/ml-mm/environment.yml

@@ -4,6 +4,8 @@ channels:
 dependencies:
   - chemiscope
   - metatensor::gromacs-metatomic=*=mpi_*
+  - libtorch =*=cpu*
+  - pytorch-cpu
   - matplotlib
   - mdanalysis
   - python=3.12