Backport fix from PR #50

src/loch/_sampler.py

@@ -259,8 +259,8 @@ def __init__(
             Whether to swap the end states of the alchemical systems.
 
         restart: bool
-            Whether this is a restart simulation. If True, then data will
-            be appended to existing log files.
+            Whether this is a restart simulation. If True, then ghost
+            residues will be appended to an existing 'ghost_file'.
 
         overwrite: bool
             Overwrite existing log files.
@@ -413,12 +413,11 @@ def __init__(
             if not isinstance(ghost_file, str):
                 raise ValueError("'ghost_file' must be of type 'str'")
             self._ghost_file = ghost_file
-            if not isinstance(ghost_file, str):
-                raise ValueError("'ghost_file' must be of type 'str'")
-            self._ghost_file = ghost_file
 
-            if _os.path.exists(self._ghost_file):
-                if not self._restart and not self._overwrite:
+            # On restart, keep the existing ghost residues so that they stay
+            # aligned with the trajectory frames written before the restart.
+            if _os.path.exists(self._ghost_file) and not self._restart:
+                if not self._overwrite:
                     raise ValueError(
                         "'ghost_file' already exists. Use 'overwrite=True' to overwrite it."
                     )

tests/test_ghost_file.py

@@ -0,0 +1,66 @@
+import os
+
+import pytest
+
+from loch import GCMCSampler
+
+
+def make_sampler(mols, ghost_file, restart=False, overwrite=False):
+    return GCMCSampler(
+        mols,
+        cutoff_type="rf",
+        cutoff="10 A",
+        ghost_file=str(ghost_file),
+        log_file=None,
+        restart=restart,
+        overwrite=overwrite,
+        test=True,
+        platform="cuda",
+        seed=42,
+    )
+
+
+@pytest.mark.skipif(
+    "CUDA_VISIBLE_DEVICES" not in os.environ,
+    reason="Requires CUDA enabled GPU.",
+)
+@pytest.mark.parametrize(
+    "restart, overwrite, expected",
+    [
+        (True, False, "1, 2, 3\n"),
+        (True, True, "1, 2, 3\n"),
+        (False, True, ""),
+    ],
+)
+def test_existing_ghost_file(water_box, tmp_path, restart, overwrite, expected):
+    """
+    An existing ghost file is kept on restart, so that it stays aligned with
+    the trajectory, and is only cleared when overwriting a fresh run.
+    """
+    mols, _ = water_box
+
+    ghost_file = tmp_path / "ghosts.txt"
+    ghost_file.write_text("1, 2, 3\n")
+
+    make_sampler(mols, ghost_file, restart=restart, overwrite=overwrite)
+
+    assert ghost_file.read_text() == expected
+
+
+@pytest.mark.skipif(
+    "CUDA_VISIBLE_DEVICES" not in os.environ,
+    reason="Requires CUDA enabled GPU.",
+)
+def test_existing_ghost_file_raises(water_box, tmp_path):
+    """
+    An existing ghost file can't be silently overwritten by a fresh run.
+    """
+    mols, _ = water_box
+
+    ghost_file = tmp_path / "ghosts.txt"
+    ghost_file.write_text("1, 2, 3\n")
+
+    with pytest.raises(ValueError, match="ghost_file"):
+        make_sampler(mols, ghost_file)
+
+    assert ghost_file.read_text() == "1, 2, 3\n"