From 4869e2658faaf2871ba7525461235c44a615af84 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Fri, 9 Oct 2026 15:42:53 +0100
Subject: [PATCH 1/3] fix(trajectory): support non-periodic trajectories
 without box dimensions

---
 CodeEntropy/trajectory/mda.py | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/CodeEntropy/trajectory/mda.py b/CodeEntropy/trajectory/mda.py
index 1cdb6e75..1467fdc4 100644
--- a/CodeEntropy/trajectory/mda.py
+++ b/CodeEntropy/trajectory/mda.py
@@ -354,7 +354,10 @@ def merge_forces(
         select_atom_force = u_force.select_atoms("all")
 
         coordinates = self._extract_timeseries(select_atom, kind="positions")
-        dimensions = self._extract_timeseries(select_atom, kind="dimensions")
+        if u.dimensions is None:
+            dimensions = self._build_non_periodic_dimensions(coordinates)
+        else:
+            dimensions = self._extract_timeseries(select_atom, kind="dimensions")
 
         forces = self._extract_force_timeseries_with_fallback(
             select_atom_force,
@@ -374,6 +377,31 @@ def merge_forces(
 
         return new_universe
 
+    @staticmethod
+    def _build_non_periodic_dimensions(coordinates: np.ndarray) -> np.ndarray:
+        """Build a box large enough that periodic wrapping never acts.
+
+        Non-periodic trajectories (for example gas-phase simulations) carry no
+        box. The axes and covariance code applies the minimum image convention
+        and unwraps molecules, which requires a box. A cubic box more than
+        twice the largest interatomic distance makes both operations no-ops.
+
+        Args:
+            coordinates: Positions with shape ``(n_frames, n_atoms, 3)``.
+
+        Returns:
+            Array of shape ``(n_frames, 6)`` holding the box lengths and 90
+            degree angles for every frame.
+        """
+        span = float(np.max(np.ptp(coordinates, axis=1)))
+        length = max(10.0 * span, 100.0)
+        box = np.array([length, length, length, 90.0, 90.0, 90.0], dtype=np.float32)
+        logger.warning(
+            "Trajectory has no box dimensions; treating it as non-periodic "
+            f"using a {length:.1f} A cubic box."
+        )
+        return np.tile(box, (coordinates.shape[0], 1))
+
     def _extract_timeseries(self, atomgroup, *, kind: str) -> np.ndarray:
         """Extract a time series array using explicit frame indexing.
 

From 82d715b3cb0e977ff537aa307aefcdb22d634ade Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Fri, 9 Oct 2026 15:48:52 +0100
Subject: [PATCH 2/3] tests(unit): cover non-periodic trajectories in
 `merge_forces`

---
 .../levels/test_mda_universe_operations.py    | 36 +++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/tests/unit/CodeEntropy/levels/test_mda_universe_operations.py b/tests/unit/CodeEntropy/levels/test_mda_universe_operations.py
index d298c486..cbe2804a 100644
--- a/tests/unit/CodeEntropy/levels/test_mda_universe_operations.py
+++ b/tests/unit/CodeEntropy/levels/test_mda_universe_operations.py
@@ -424,3 +424,39 @@ def test_extract_fragment_atomgroup_returns_lightweight_range_selection() -> Non
         "index 10:13",
         updating=False,
     )
+
+
+def test_build_non_periodic_dimensions_box_exceeds_twice_largest_extent():
+    coordinates = np.zeros((3, 2, 3))
+    coordinates[:, 1] = [50.0, 0.0, 0.0]
+
+    out = UniverseOperations._build_non_periodic_dimensions(coordinates)
+
+    assert out.shape == (3, 6)
+    assert np.all(out[:, :3] > 2 * 50.0)
+    assert np.allclose(out[:, 3:], 90.0)
+
+
+def test_merge_forces_builds_box_for_non_periodic_trajectory(monkeypatch):
+    ops = UniverseOperations()
+
+    u = MagicMock()
+    u.dimensions = None
+    u_force = MagicMock()
+    monkeypatch.setattr(
+        "CodeEntropy.trajectory.mda.mda.Universe", MagicMock(side_effect=[u, u_force])
+    )
+    ops._extract_timeseries = MagicMock(return_value=np.zeros((2, 2, 3)))
+    ops._extract_force_timeseries_with_fallback = MagicMock(
+        return_value=np.ones((2, 2, 3))
+    )
+
+    merged = MagicMock()
+    monkeypatch.setattr("CodeEntropy.trajectory.mda.mda.Merge", lambda ag: merged)
+
+    ops.merge_forces(
+        tprfile="tpr", trrfile="trr", forcefile="f.trr", fileformat=None, kcal=False
+    )
+
+    dimensions = merged.load_new.call_args.kwargs["dimensions"]
+    assert dimensions.shape == (2, 6)

From 139b98e7ad90e959af62f0f99a4abad8342c1c20 Mon Sep 17 00:00:00 2001
From: harryswift01 <harry.swift@stfc.ac.uk>
Date: Fri, 9 Oct 2026 16:01:44 +0100
Subject: [PATCH 3/3] docs(trajectory): simplify non-periodic box docstring

---
 CodeEntropy/trajectory/mda.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/CodeEntropy/trajectory/mda.py b/CodeEntropy/trajectory/mda.py
index 1467fdc4..56118a3d 100644
--- a/CodeEntropy/trajectory/mda.py
+++ b/CodeEntropy/trajectory/mda.py
@@ -379,12 +379,11 @@ def merge_forces(
 
     @staticmethod
     def _build_non_periodic_dimensions(coordinates: np.ndarray) -> np.ndarray:
-        """Build a box large enough that periodic wrapping never acts.
+        """Build a box for a trajectory without box dimensions.
 
-        Non-periodic trajectories (for example gas-phase simulations) carry no
-        box. The axes and covariance code applies the minimum image convention
-        and unwraps molecules, which requires a box. A cubic box more than
-        twice the largest interatomic distance makes both operations no-ops.
+        The axes and covariance code needs a box for the minimum image
+        convention and unwrapping. The box is cubic and more than twice the
+        largest interatomic distance, so neither step changes the coordinates.
 
         Args:
             coordinates: Positions with shape ``(n_frames, n_atoms, 3)``.