Couple of documentation fixes and improvmenents

* Use torch-pme logo as default thumbnail in example gallery
* Fix typo in atomistic example
* Fix thumbnail for atomistic example
* Fix wrong timestep in atomsitic example plot

docs/generate_examples/conf.py

@@ -16,6 +16,7 @@
 sphinx_gallery_conf = {
     "backreferences_dir": "backreferences",
     "copyfile_regex": r".*\.(xyz)",
+    "default_thumb_file": os.path.join(ROOT, "docs/src/logo/torch-pme-512.png"),
     "doc_module": ("torchpme",),
     "examples_dirs": ["../../examples"],
     "filename_pattern": ".*",

examples/9-atomistic-model.py

@@ -19,8 +19,6 @@
 
 # %%
 
-# sphinx_gallery_thumbnail_number = 2
-
 from typing import Dict, List, Optional  # noqa
 
 # tools to run the simulation and visualization
@@ -158,7 +156,7 @@ def __init__(self, calculator: torchpme.metatensor.Calculator, cutoff: float):
 
         self.calculator = calculator
 
-        # We use as half neighborlist and allow to have pairs farther than cutoff
+        # We use a half neighborlist and allow to have pairs farther than cutoff
         # (`strict=False`) since this is not problematic for PME and may speed up the
         # computation of the neigbors.
         self.nl = NeighborListOptions(cutoff=cutoff, full_list=False, strict=False)
@@ -413,7 +411,7 @@ def forward(
 
 fig, ax = plt.subplots(3, figsize=(8, 5), sharex=True)
 
-time = 0.5 * np.arange(n_steps)
+time = 2.0 * np.arange(n_steps)
 
 ax[0].plot(time, potential_energy, label="potential energy")
 ax[0].plot(time, kinetic_energy, label="kinetic energy")