fix: honor job-local LAMMPS time settings

Fixes #1904

Coding-Agent: Codex

Codex-Version: codex-cli 0.149.0

Model: gpt-5.6-sol

Reasoning-Effort: xhigh

Author: njzjz-bot

dpgen/generator/arginfo.py

@@ -292,6 +292,7 @@ def model_devi_jobs_args() -> list[Argument]:
     doc_nsteps = "Running steps of MD. It is not optional when not using a template."
     doc_nbeads = "Number of beads in PIMD. If not given, classical MD will be performed. Only supported for LAMMPS version >= 20230615."
     doc_ensemble = "Determining which ensemble used in MD, options include “npt” and “nvt”. It is not optional when not using a template."
+    doc_dt = "Timestep for this MD job. Overrides the workflow-wide model_devi_dt."
     doc_neidelay = "delay building until this many steps since last build."
     doc_taut = "Coupling time of thermostat (ps)."
     doc_taup = "Coupling time of barostat (ps)."
@@ -311,6 +312,7 @@ def model_devi_jobs_args() -> list[Argument]:
         Argument("nsteps", int, optional=True, doc=doc_nsteps),
         Argument("nbeads", int, optional=True, doc=doc_nbeads),
         Argument("ensemble", str, optional=True, doc=doc_ensemble),
+        Argument("dt", float, optional=True, doc=doc_dt),
         Argument("neidelay", int, optional=True, doc=doc_neidelay),
         Argument("taut", float, optional=True, doc=doc_taut),
         Argument("taup", float, optional=True, doc=doc_taup),

dpgen/generator/run.py

@@ -995,6 +995,16 @@ def parse_cur_job(cur_job):
     return ensemble, nsteps, trj_freq, temps, press, pka_e, dt, nbeads
 
 
+def _get_lammps_job_settings(cur_job, jdata):
+    """Resolve per-job LAMMPS settings over workflow-wide defaults."""
+    return (
+        cur_job.get("dt", jdata["model_devi_dt"]),
+        cur_job.get("neidelay", jdata.get("model_devi_neidelay")),
+        cur_job.get("taut", jdata.get("model_devi_taut", 0.1)),
+        cur_job.get("taup", jdata.get("model_devi_taup", 0.5)),
+    )
+
+
 def expand_matrix_values(target_list, cur_idx=0):
     nvar = len(target_list)
     if cur_idx == nvar:
@@ -1667,7 +1677,9 @@ def _make_model_devi_native(iter_index, jdata, mdata, conf_systems):
     if iter_index >= len(model_devi_jobs):
         return False
     cur_job = model_devi_jobs[iter_index]
-    ensemble, nsteps, trj_freq, temps, press, pka_e, dt, nbeads = parse_cur_job(cur_job)
+    ensemble, nsteps, trj_freq, temps, press, pka_e, _dt, nbeads = parse_cur_job(
+        cur_job
+    )
     model_devi_f_avg_relative = jdata.get("model_devi_f_avg_relative", False)
     model_devi_merge_traj = jdata.get("model_devi_merge_traj", False)
     if (nbeads is not None) and model_devi_f_avg_relative:
@@ -1682,23 +1694,17 @@ def _make_model_devi_native(iter_index, jdata, mdata, conf_systems):
         raise RuntimeError(
             "trj_freq should be a factor of nsteps for pimd. Please check your input."
         )
-    if dt is not None:
-        model_devi_dt = dt
     sys_idx = expand_idx(cur_job["sys_idx"])
     if len(sys_idx) != len(list(set(sys_idx))):
         raise RuntimeError("system index should be uniq")
 
     use_ele_temp = jdata.get("use_ele_temp", 0)
-    model_devi_dt = jdata["model_devi_dt"]
-    model_devi_neidelay = None
-    if "model_devi_neidelay" in jdata:
-        model_devi_neidelay = jdata["model_devi_neidelay"]
-    model_devi_taut = 0.1
-    if "model_devi_taut" in jdata:
-        model_devi_taut = jdata["model_devi_taut"]
-    model_devi_taup = 0.5
-    if "model_devi_taup" in jdata:
-        model_devi_taup = jdata["model_devi_taup"]
+    (
+        model_devi_dt,
+        model_devi_neidelay,
+        model_devi_taut,
+        model_devi_taup,
+    ) = _get_lammps_job_settings(cur_job, jdata)
     mass_map = jdata["mass_map"]
     nopbc = jdata.get("model_devi_nopbc", False)
 

tests/generator/test_parse_cur_job.py

@@ -4,6 +4,9 @@
 
 sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
 __package__ = "generator"
+from dpgen.generator.arginfo import model_devi_jobs_args
+from dpgen.generator.run import _get_lammps_job_settings
+
 from .context import (
     parse_cur_job,
     setUpModule,  # noqa: F401
@@ -63,6 +66,31 @@ def test_pka(self):
         for ii, jj in zip(res, [ens, ns, tf, ts, [-1], pka, dt]):
             self.assertEqual(ii, jj)
 
+    def test_job_local_lammps_settings_override_global_defaults(self):
+        cur_job = {"dt": 0.001, "neidelay": 5, "taut": 0.2, "taup": 1.0}
+        jdata = {
+            "model_devi_dt": 0.002,
+            "model_devi_neidelay": 10,
+            "model_devi_taut": 0.1,
+            "model_devi_taup": 0.5,
+        }
+        self.assertEqual(_get_lammps_job_settings(cur_job, jdata), (0.001, 5, 0.2, 1.0))
+
+    def test_job_schema_accepts_local_timestep(self):
+        arginfo = model_devi_jobs_args()
+        jobs = [
+            {
+                "sys_idx": [0],
+                "ensemble": "nvt",
+                "temps": [300.0],
+                "nsteps": 100,
+                "trj_freq": 10,
+                "dt": 0.001,
+            }
+        ]
+        normalized = arginfo.normalize_value(jobs, trim_pattern="_*")
+        arginfo.check_value(normalized, strict=True)
+
 
 if __name__ == "__main__":
     unittest.main()