fix: reject start_file equal to restart_file on simple export

pqsetup/input_writer.py

@@ -294,6 +294,19 @@ def validate_setup(
         diagnostics.append(
             _error("input.restart_file", "Restart filename is too long.")
         )
+    if (
+        setup.start_file
+        and setup.start_file.casefold() == restart_filename(setup).casefold()
+    ):
+        diagnostics.append(
+            _error(
+                "input.restart_collision",
+                (
+                    "Start file and restart file must differ so PQ does not "
+                    "overwrite the starting structure."
+                ),
+            )
+        )
     if len(setup.file_prefix) > 128:
         diagnostics.append(_error("input.file_prefix", "Run name is too long."))
     if setup.ensemble != "OPT":

tests/test_presets_and_input.py

@@ -85,6 +85,8 @@ def test_mm_opt_with_md_ensemble_is_rejected() -> None:
 
     assert not result.valid
     assert "workflow.mm_opt_ensemble" in {item.code for item in result.diagnostics}
+
+
 def test_qm_rpmd_requires_bead_count() -> None:
     missing = render_input(
         SimulationSetup(
@@ -123,6 +125,29 @@ def test_qm_rpmd_requires_bead_count() -> None:
     assert "rpmd_n_replica = 32;" in ok.input_text
 
 
+def test_start_file_cannot_equal_restart_file() -> None:
+    result = render_input(
+        SimulationSetup(start_file="pq-run.rst", file_prefix="pq-run")
+    )
+
+    assert not result.valid
+    assert "input.restart_collision" in {
+        item.code for item in result.diagnostics
+    }
+
+    casefold_result = render_input(
+        SimulationSetup(
+            start_file="Structure.rst",
+            restart_file="structure.rst",
+            file_prefix="run",
+        )
+    )
+    assert not casefold_result.valid
+    assert "input.restart_collision" in {
+        item.code for item in casefold_result.diagnostics
+    }
+
+
 def test_unreleased_and_unknown_runners_fail_without_probing(
     monkeypatch,
 ) -> None: