From 0979870f0670396bf44881ede0d026ab246c33d5 Mon Sep 17 00:00:00 2001
From: "Josef M. Gallmetzer" <64498081+galjos@users.noreply.github.com>
Date: Mon, 24 Aug 2026 09:12:27 +0200
Subject: [PATCH] fix: make AtomicSystem.copy deep-copy arrays and all fields

copy() forwarded only pos, vel, forces, charges, cell and topology by
reference, so the copy aliased the source arrays and silently dropped
energy, virial and stress. Mutating the copy, for example via center()
or randomize_positions(), therefore corrupted the original system. The
arrays are now copied and every field is carried over.
---
 PQAnalysis/atomic_system/atomic_system.py | 11 +++--
 tests/atomicSystem/test_atomic_system.py  | 56 +++++++++++++++++++++++
 2 files changed, 63 insertions(+), 4 deletions(-)

diff --git a/PQAnalysis/atomic_system/atomic_system.py b/PQAnalysis/atomic_system/atomic_system.py
index 43257633..d5d32d44 100644
--- a/PQAnalysis/atomic_system/atomic_system.py
+++ b/PQAnalysis/atomic_system/atomic_system.py
@@ -561,10 +561,13 @@ def copy(self) -> "AtomicSystem":
             A copy of the AtomicSystem.
         """
         return AtomicSystem(
-            pos=self.pos,
-            vel=self.vel,
-            forces=self.forces,
-            charges=self.charges,
+            pos=self.pos.copy(),
+            vel=self.vel.copy(),
+            forces=self.forces.copy(),
+            charges=self.charges.copy(),
+            energy=self.energy,
+            virial=None if self.virial is None else self.virial.copy(),
+            stress=None if self.stress is None else self.stress.copy(),
             cell=self.cell,
             topology=self.topology
         )
diff --git a/tests/atomicSystem/test_atomic_system.py b/tests/atomicSystem/test_atomic_system.py
index 5022ff5e..96e89607 100644
--- a/tests/atomicSystem/test_atomic_system.py
+++ b/tests/atomicSystem/test_atomic_system.py
@@ -758,6 +758,62 @@ def test_stress(self):
         assert not system.has_stress
         assert system.stress is None
 
+    def test_copy(self):
+        """
+        Test that copy carries all fields and does not alias the arrays.
+        """
+        system = AtomicSystem(
+            atoms=[Atom('C'), Atom('H')],
+            pos=np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]]),
+            vel=np.array([[0.1, 0.0, 0.0], [0.2, 0.0, 0.0]]),
+            forces=np.array([[1.0, 0.0, 0.0], [2.0, 0.0, 0.0]]),
+            charges=np.array([-1.0, 1.0]),
+            energy=-123.456,
+            virial=np.eye(3),
+            stress=2 * np.eye(3),
+            cell=Cell(10, 10, 10),
+        )
+
+        copy = system.copy()
+
+        assert np.isclose(copy.energy, -123.456)
+        assert np.allclose(copy.virial, np.eye(3))
+        assert np.allclose(copy.stress, 2 * np.eye(3))
+        assert copy.cell == system.cell
+        assert copy.topology == system.topology
+
+        assert copy.pos is not system.pos
+        assert copy.vel is not system.vel
+        assert copy.forces is not system.forces
+        assert copy.charges is not system.charges
+        assert copy.virial is not system.virial
+        assert copy.stress is not system.stress
+
+        copy.center(np.array([5.0, 0.0, 0.0]), image=False)
+        copy.vel[0] = [9.0, 9.0, 9.0]
+        copy.forces[0] = [9.0, 9.0, 9.0]
+        copy.charges[0] = 9.0
+        copy.virial[0, 0] = 9.0
+        copy.stress[0, 0] = 9.0
+
+        assert np.allclose(
+            system.pos, np.array([[0.0, 0.0, 0.0], [1.0, 0.0, 0.0]])
+        )
+        assert np.allclose(
+            system.vel, np.array([[0.1, 0.0, 0.0], [0.2, 0.0, 0.0]])
+        )
+        assert np.allclose(
+            system.forces, np.array([[1.0, 0.0, 0.0], [2.0, 0.0, 0.0]])
+        )
+        assert np.allclose(system.charges, np.array([-1.0, 1.0]))
+        assert np.allclose(system.virial, np.eye(3))
+        assert np.allclose(system.stress, 2 * np.eye(3))
+
+        empty_copy = AtomicSystem().copy()
+        assert empty_copy.energy is None
+        assert empty_copy.virial is None
+        assert empty_copy.stress is None
+
     def test_center_of_mass_resiudes(self):
         system = AtomicSystem()