fix: avoid staging GROMACS output names

Coding-Agent: Codex
Codex-Version: codex-cli 0.151.0
Model: gpt-5.6-sol
Reasoning-Effort: xhigh

Author: njzjz-bot

dpgen/generator/run.py

@@ -1806,6 +1806,20 @@ def _make_model_devi_native(iter_index, jdata, mdata, conf_systems):
         sys_counter += 1
 
 
+def _gromacs_input_files(gromacs_settings):
+    """Return only settings whose values name files staged for a GROMACS task."""
+    non_input_settings = {
+        "traj_filename",
+        "mdp_filename",
+        "group_name",
+        "maxwarn",
+        "deffnm",
+    }
+    return [
+        file for key, file in gromacs_settings.items() if key not in non_input_settings
+    ]
+
+
 def _make_model_devi_native_gromacs(iter_index, jdata, mdata, conf_systems):
     try:
         from gromacs.fileformats.mdp import MDP
@@ -1868,16 +1882,10 @@ def _make_model_devi_native_gromacs(iter_index, jdata, mdata, conf_systems):
                     task_path = os.path.join(work_path, task_name)
                     create_path(task_path)
                     gromacs_settings = jdata.get("gromacs_settings", "")
-                    for key, file in gromacs_settings.items():
-                        if (
-                            key != "traj_filename"
-                            and key != "mdp_filename"
-                            and key != "group_name"
-                            and key != "maxwarn"
-                        ):
-                            os.symlink(
-                                os.path.join(cc, file), os.path.join(task_path, file)
-                            )
+                    for file in _gromacs_input_files(gromacs_settings):
+                        os.symlink(
+                            os.path.join(cc, file), os.path.join(task_path, file)
+                        )
                     # input.json for DP-Gromacs
                     with open(os.path.join(cc, "input.json")) as f:
                         input_json = json.load(f)

tests/generator/test_gromacs_engine.py

@@ -6,6 +6,8 @@
 
 import numpy as np
 
+from dpgen.generator.run import _gromacs_input_files
+
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
 __package__ = "generator"
 dirname = os.path.join(os.path.abspath(os.path.dirname(__file__)), "gromacs")
@@ -43,6 +45,7 @@ def setUp(self):
                 "ref_filename": "em.tpr",
                 "model_devi_script": "model_devi.py",
                 "traj_filename": "deepmd_traj.gro",
+                "deffnm": "deepmd",
             },
             "model_devi_dt": 0.001,
             "model_devi_f_trust_lo": 0.05,
@@ -80,7 +83,10 @@ def setUp(self):
 
     def _check_dir(self, wdir, post=True):
         for key in self.jdata["gromacs_settings"].keys():
-            if key != "traj_filename":
+            if key == "deffnm":
+                # deffnm names generated outputs and must not be staged as input.
+                self.assertFalse(os.path.exists(os.path.join(wdir, "deepmd")))
+            elif key != "traj_filename":
                 self.assertTrue(
                     os.path.exists(
                         os.path.join(wdir, self.jdata["gromacs_settings"][key])
@@ -105,6 +111,13 @@ def _copy_outputs(self, path_1, path_2):
         )
         shutil.copytree(os.path.join(path_1, "traj"), os.path.join(path_2, "traj"))
 
+    def test_deffnm_is_not_an_input_file(self):
+        """Command/output settings must not be symlinked from the source system."""
+        input_files = _gromacs_input_files(self.jdata["gromacs_settings"])
+
+        self.assertNotIn("deepmd", input_files)
+        self.assertIn("processed.top", input_files)
+
     @unittest.skipIf(
         importlib.util.find_spec("openbabel") is not None,
         "when openbabel is found, this test will be skipped. ",