Solving issues #145 and #144

src/dynsight/_internal/lens/lens.py

@@ -265,7 +265,7 @@ def compute_lens(
         universe.trajectory[t1]
         pos_env1 = ag_env.positions.astype(np.float64)
         pos_cent1 = ag_cent.positions.astype(np.float64)
-        if respect_pbc and universe.trajectory.ts.dimensions is not None:
+        if universe.trajectory.ts.dimensions is not None:
             box = universe.trajectory.ts.dimensions[:3]
         else:
             coords = universe.atoms.positions
@@ -284,7 +284,7 @@ def compute_lens(
         universe.trajectory[t2]
         pos_env2 = ag_env.positions.astype(np.float64)
         pos_cent2 = ag_cent.positions.astype(np.float64)
-        if respect_pbc and universe.trajectory.ts.dimensions is not None:
+        if universe.trajectory.ts.dimensions is not None:
             box = universe.trajectory.ts.dimensions[:3]
         else:
             coords = universe.atoms.positions
@@ -362,7 +362,7 @@ def _compute_frame_neighbors(frame_idx: int) -> list[AtomGroup]:
         pos_env = ag_env.positions.astype(np.float64)
         pos_cent = ag_centers.positions.astype(np.float64)
 
-        if respect_pbc and universe.trajectory.ts.dimensions is not None:
+        if universe.trajectory.ts.dimensions is not None:
             box = universe.trajectory.ts.dimensions[:3]
         else:
             coords = universe.atoms.positions

src/dynsight/_internal/trajectory/trajectory.py

@@ -21,7 +21,12 @@
 from dynsight.trajectory import Insight
 
 UNIVAR_DIM = 2
-logging.getLogger("MDAnalysis").setLevel(logging.ERROR)
+# Silence MDAnalysis INFO messages by default
+logging.getLogger("MDAnalysis").setLevel(logging.WARNING)
+
+# Prevent log propagation unless user configures logging
+logging.getLogger("MDAnalysis").addHandler(logging.NullHandler())
+logging.getLogger(__name__).addHandler(logging.NullHandler())
 
 
 @dataclass(frozen=True)

tests/lens/test_lens.py

@@ -7,9 +7,35 @@
 import pytest
 
 from dynsight.trajectory import Trj
+from dynsight.utilities import save_xyz_from_ndarray
 
 from .case_data import LENSCaseData
 
+# ---------------- Fixtures ----------------
+
+
+@pytest.fixture
+def trj_2d(tmp_path: Path) -> Trj:
+    """Return a Trj for a bidimensional system."""
+    rng = np.random.default_rng(42)
+    coords = rng.random((100, 100, 3))
+    coords[..., 2] = 0.0  # system is 2D
+    traj_path = tmp_path / "random_2d.xyz"
+    save_xyz_from_ndarray(traj_path, coords)
+
+    trj = Trj.init_from_xyz(traj_path, dt=1.0)
+    for ts in trj.universe.trajectory:  # Add box with thickness along z
+        coords = trj.universe.atoms.positions
+        mins = coords.min(axis=0)
+        maxs = coords.max(axis=0)
+        lengths = maxs - mins  # Lx, Ly, Lz
+        lengths[2] = 0.5
+        ts.dimensions = np.concatenate([lengths, np.array([90, 90, 90])])
+    return trj
+
+
+# ---------------- Tests ----------------
+
 
 def test_lens(case_data: LENSCaseData) -> None:
     original_dir = Path(__file__).resolve().parent
@@ -35,3 +61,30 @@ def test_lens(case_data: LENSCaseData) -> None:
         )
     exp_lens = np.load(expected_lens)
     assert np.allclose(exp_lens, test_lens.dataset, atol=1e-6)
+
+
+def test_lens_2d(trj_2d: Trj) -> None:
+    """Test LENS and number of neighbors on a 2D system."""
+    original_dir = Path(__file__).resolve().parent
+
+    test_lens_pbc = trj_2d.get_lens(r_cut=0.1, respect_pbc=True)
+    _ = trj_2d.get_coord_number(r_cut=0.1, respect_pbc=True)
+    pbc_path = original_dir / "../systems/lens_2d_pbc.npy"
+    if not pbc_path.exists():
+        np.save(pbc_path, test_lens_pbc.dataset)
+        pytest.fail(
+            "LENS test files were not present. They have been created."
+        )
+    exp_lens = np.load(pbc_path)
+    assert np.allclose(exp_lens, test_lens_pbc.dataset)
+
+    test_lens_fbc = trj_2d.get_lens(r_cut=0.1, respect_pbc=False)
+    _ = trj_2d.get_coord_number(r_cut=0.1, respect_pbc=False)
+    fbc_path = original_dir / "../systems/lens_2d_fbc.npy"
+    if not fbc_path.exists():
+        np.save(fbc_path, test_lens_fbc.dataset)
+        pytest.fail(
+            "LENS test files were not present. They have been created."
+        )
+    exp_lens = np.load(fbc_path)
+    assert np.allclose(exp_lens, test_lens_fbc.dataset)