From c094dfd7e3663e1f0b117fb3c66a57c5f4400c1e Mon Sep 17 00:00:00 2001
From: "Josef M. Gallmetzer" <64498081+galjos@users.noreply.github.com>
Date: Mon, 24 Aug 2026 09:13:06 +0200
Subject: [PATCH] fix: correct box file step indices for unequal trajectories

BoxWriter.write_box_file derived the step offset from the call count
multiplied by the current trajectory length, assuming all previously
written trajectories had the same number of frames. When traj2box was
given input files of unequal length, the box file silently contained
duplicated and skipped step indices. The writer now accumulates the
number of frames actually written and uses that as the offset.
---
 PQAnalysis/io/box_writer.py | 11 ++++++++---
 tests/io/test_boxWriter.py  | 24 ++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 3 deletions(-)

diff --git a/PQAnalysis/io/box_writer.py b/PQAnalysis/io/box_writer.py
index d6281f2f..fd6c7793 100644
--- a/PQAnalysis/io/box_writer.py
+++ b/PQAnalysis/io/box_writer.py
@@ -58,6 +58,7 @@ def __init__(
 
         super().__init__(filename, FileWritingMode(mode))
         self.output_format = BoxFileFormat(output_format)
+        self._n_frames_written = 0
 
     @runtime_type_checking
     def write(self, traj: Trajectory, reset_counter: bool = True) -> None:
@@ -117,7 +118,7 @@ def write_vmd(self, traj: Trajectory) -> None:
     def write_box_file(
         self,
         traj: Trajectory,
-        reset_counter: bool = True  # pylint: disable=unused-argument # is needed for the decorator
+        reset_counter: bool = True
     ) -> None:
         """
         Writes the given trajectory to the file in data file format.
@@ -141,8 +142,10 @@ def write_box_file(
         """
         self.__check_pbc__(traj)
 
-        counter = self.counter[BoxWriter.write_box_file.__name__]  # pylint: disable=no-member # is added via decorator
-        counter = len(traj) * (counter - 1)
+        if reset_counter:
+            self._n_frames_written = 0
+
+        counter = self._n_frames_written
 
         for i, frame in enumerate(traj):
             cell = frame.cell
@@ -155,6 +158,8 @@ def write_box_file(
                 file=self.file
             )
 
+        self._n_frames_written += len(traj)
+
     def __check_pbc__(self, traj: Trajectory) -> None:
         """
         Checks if the cell of the trajectory is not None.
diff --git a/tests/io/test_boxWriter.py b/tests/io/test_boxWriter.py
index 2844104b..e7c98d41 100644
--- a/tests/io/test_boxWriter.py
+++ b/tests/io/test_boxWriter.py
@@ -92,6 +92,30 @@ def test_write_box_file(self, capsys: CaptureFixture):
 
         assert captured.out == "1 10 10 10 90 90 90\n2 10 10 11 90 90 120\n"
 
+    def test_write_box_file_unequal_trajectories(self, capsys: CaptureFixture):
+        writer = BoxWriter()
+
+        cell = Cell(10, 10, 10, 90, 90, 90)
+        frame = AtomicSystem(atoms=self.atoms1, pos=self.pos1, cell=cell)
+
+        traj3 = Trajectory([frame, frame, frame])
+        traj2 = Trajectory([frame, frame])
+
+        writer.write_box_file(traj3, reset_counter=False)
+        writer.write_box_file(traj2, reset_counter=False)
+
+        captured = capsys.readouterr()
+        steps = [int(line.split()[0]) for line in captured.out.splitlines()]
+
+        assert steps == [1, 2, 3, 4, 5]
+
+        writer.write_box_file(traj2, reset_counter=True)
+
+        captured = capsys.readouterr()
+        steps = [int(line.split()[0]) for line in captured.out.splitlines()]
+
+        assert steps == [1, 2]
+
     def test_write_vmd(self, capsys: CaptureFixture):
         writer = BoxWriter()