From 7bb11650181e0fcbabaaf48d490232d5c3187aa3 Mon Sep 17 00:00:00 2001
From: swf1996120 <1247155045@qq.com>
Date: Fri, 30 Oct 2026 05:38:06 +0800
Subject: [PATCH 1/3] Reject invalid unit cell angles

---
 package/MDAnalysis/coordinates/timestep.pyx              | 9 +++++++++
 .../MDAnalysisTests/coordinates/test_timestep_api.py     | 5 +++++
 2 files changed, 14 insertions(+)

diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx
index 09e44c0f551..1f71ce09f62 100644
--- a/package/MDAnalysis/coordinates/timestep.pyx
+++ b/package/MDAnalysis/coordinates/timestep.pyx
@@ -468,6 +468,15 @@ cdef class Timestep:
         if new_dimensions is None:
             self._unitcell[:] = 0
         else:
+            new_dimensions = np.asarray(new_dimensions, dtype=np.float32)
+            if new_dimensions.ndim == 0 and new_dimensions < 0:
+                raise ValueError("Unit cell lengths must be non-negative")
+            if new_dimensions.size == 6:
+                values = new_dimensions.reshape(-1)
+                if (values[:3] < 0).any():
+                    raise ValueError("Unit cell lengths must be non-negative")
+                if not np.isfinite(values[3:]).all() or not ((values[3:] > 0) & (values[3:] < 180)).all():
+                    raise ValueError("Unit cell angles must be finite and strictly between 0 and 180 degrees")
             self._unitcell[:] = new_dimensions
 
     @property
diff --git a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
index 1b2bc468b3e..5cdbb81cbd4 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
@@ -170,6 +170,11 @@ def test_dimensions_set_box(self, ts, dtype):
         assert ts.dimensions.dtype == np.float32
         assert_allclose(ts.dimensions, self.newbox)
 
+    @pytest.mark.parametrize("angles", ([0, 90, 90], [180, 90, 90], [-1, 90, 90], [np.nan, 90, 90], [np.inf, 90, 90]))
+    def test_dimensions_reject_invalid_angles(self, ts, angles):
+        with pytest.raises(ValueError, match="angles"):
+            ts.dimensions = [10, 10, 10, *angles]
+
     def test_volume(self, ts):
         ts.dimensions = self.newbox
         assert_equal(ts.volume, self.ref_volume)

From 1387f05af7db7206e91921f63d9eb006bc652410 Mon Sep 17 00:00:00 2001
From: swf1996120 <1247155045@qq.com>
Date: Fri, 30 Oct 2026 05:38:43 +0800
Subject: [PATCH 2/3] Reject scalar unit cell dimensions

---
 package/MDAnalysis/coordinates/timestep.pyx                | 7 +++++--
 testsuite/MDAnalysisTests/coordinates/test_timestep_api.py | 6 ++++++
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/coordinates/timestep.pyx b/package/MDAnalysis/coordinates/timestep.pyx
index 1f71ce09f62..55c0d1e1745 100644
--- a/package/MDAnalysis/coordinates/timestep.pyx
+++ b/package/MDAnalysis/coordinates/timestep.pyx
@@ -469,8 +469,11 @@ cdef class Timestep:
             self._unitcell[:] = 0
         else:
             new_dimensions = np.asarray(new_dimensions, dtype=np.float32)
-            if new_dimensions.ndim == 0 and new_dimensions < 0:
-                raise ValueError("Unit cell lengths must be non-negative")
+            if new_dimensions.ndim == 0:
+                if new_dimensions != 0:
+                    raise ValueError("Unit cell dimensions must contain six values")
+                self._unitcell[:] = 0
+                return
             if new_dimensions.size == 6:
                 values = new_dimensions.reshape(-1)
                 if (values[:3] < 0).any():
diff --git a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
index 5cdbb81cbd4..5afef13e557 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
@@ -170,6 +170,12 @@ def test_dimensions_set_box(self, ts, dtype):
         assert ts.dimensions.dtype == np.float32
         assert_allclose(ts.dimensions, self.newbox)
 
+    def test_dimensions_reject_scalar_broadcast(self, ts):
+        with pytest.raises(ValueError, match="six values"):
+            ts.dimensions = 5
+        ts.dimensions = 0
+        assert ts.dimensions is None
+
     @pytest.mark.parametrize("angles", ([0, 90, 90], [180, 90, 90], [-1, 90, 90], [np.nan, 90, 90], [np.inf, 90, 90]))
     def test_dimensions_reject_invalid_angles(self, ts, angles):
         with pytest.raises(ValueError, match="angles"):

From 66488f8399cd644079dc28faea259f96568437f0 Mon Sep 17 00:00:00 2001
From: swf1996120 <1247155045@qq.com>
Date: Fri, 30 Oct 2026 05:41:45 +0800
Subject: [PATCH 3/3] Format unit-cell angle tests

---
 testsuite/MDAnalysisTests/coordinates/test_timestep_api.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
index 5afef13e557..780f7451cd9 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py
@@ -176,7 +176,10 @@ def test_dimensions_reject_scalar_broadcast(self, ts):
         ts.dimensions = 0
         assert ts.dimensions is None
 
-    @pytest.mark.parametrize("angles", ([0, 90, 90], [180, 90, 90], [-1, 90, 90], [np.nan, 90, 90], [np.inf, 90, 90]))
+    @pytest.mark.parametrize(
+        "angles",
+        ([0, 90, 90], [180, 90, 90], [-1, 90, 90], [np.nan, 90, 90], [np.inf, 90, 90]),
+    )
     def test_dimensions_reject_invalid_angles(self, ts, angles):
         with pytest.raises(ValueError, match="angles"):
             ts.dimensions = [10, 10, 10, *angles]