Add tests for edge cases

pyproject.toml

@@ -74,9 +74,6 @@ ignore_missing_imports = true
 disable_error_code = ["union-attr"]
 
 [tool.pytest.ini_options]
-markers = [
-    "slow: marks tests as slow (deselect with '-m \"not slow\"')",
-]
 filterwarnings = [
     "error",
     "ignore:custom data:UserWarning",

tests/test_edge_cases.py

@@ -0,0 +1,43 @@
+import ase.build
+import ase.io
+import ase.units
+import torch
+from ase.md import VelocityVerlet
+
+from flashmd import get_pretrained
+from flashmd.ase import EnergyCalculator
+
+
+def test_isolated_atom(monkeypatch, tmp_path):
+    """Test that a short MD run completes without errors on an isolated atom."""
+    monkeypatch.chdir(tmp_path)
+
+    atoms = ase.Atoms("O", positions=[[0, 0, 0]])
+
+    time_step = 64
+    device = "cuda" if torch.cuda.is_available() else "cpu"
+    energy_model, _ = get_pretrained("pet-omatpes-v2", time_step)
+    calculator = EnergyCalculator(energy_model, device=device)
+    atoms.calc = calculator
+
+    dyn = VelocityVerlet(atoms=atoms, timestep=time_step * ase.units.fs)
+    dyn.run(10)
+
+
+def test_slab_plus_isolated_atom(monkeypatch, tmp_path):
+    """Test that a short MD run completes without errors on a slab plus an isolated atom."""
+    monkeypatch.chdir(tmp_path)
+
+    # Create a slab and an isolated atom
+    slab = ase.build.fcc111("Al", size=(2, 2, 3), vacuum=10)
+    isolated_atom = ase.Atoms("O", positions=[[0, 0, 24]])
+    atoms = slab + isolated_atom
+
+    time_step = 64
+    device = "cuda" if torch.cuda.is_available() else "cpu"
+    energy_model, _ = get_pretrained("pet-omatpes-v2", time_step)
+    calculator = EnergyCalculator(energy_model, device=device)
+    atoms.calc = calculator
+
+    dyn = VelocityVerlet(atoms=atoms, timestep=time_step * ase.units.fs)
+    dyn.run(10)