Improve trajectory handling for MD

emmet-core/emmet/core/tasks.py

@@ -963,6 +963,8 @@ def _get_task_files(files, suffix=""):
                 vol_files.append(file_no_path)
             elif file.match(f"*POSCAR.T=*{suffix}*"):
                 elph_poscars.append(file_no_path)
+            elif file.match(f"*OSZICAR{suffix}*"):
+                vasp_files["oszicar_file"] = file_no_path
 
         if len(vol_files) > 0:
             # add volumetric files if some were found or other vasp files were found

emmet-core/emmet/core/vasp/calculation.py

@@ -21,6 +21,7 @@
     BSVasprun,
     Kpoints,
     Locpot,
+    Oszicar,
     Outcar,
     Poscar,
     Potcar,
@@ -422,7 +423,7 @@ def from_vasp_outputs(
         contcar: Optional[Poscar],
         locpot: Optional[Locpot] = None,
         elph_poscars: Optional[List[Path]] = None,
-        store_trajectory: bool = False,
+        store_trajectory: Union[bool, str] = False,
     ) -> "CalculationOutput":
         """
         Create a VASP output document from VASP outputs.
@@ -441,8 +442,10 @@ def from_vasp_outputs(
             Path to displaced electron-phonon coupling POSCAR files generated using
             ``PHON_LMC = True``.
         store_trajectory
-            Whether to store ionic steps as a pymatgen Trajectory object. If `True`,
-            the `ionic_steps` field is left as None.
+            Whether to store ionic steps as a pymatgen Trajectory object. Can be
+            True, False or "partial", tuning the amount of data from the ionic_steps
+            stored in the Trajectory.
+            If not `False`, the `ionic_steps` field is left as None.
 
         Returns
         -------
@@ -610,6 +613,7 @@ def from_vasp_files(
         contcar_file: Union[Path, str],
         volumetric_files: List[str] = None,
         elph_poscars: List[Path] = None,
+        oszicar_file: Optional[Union[Path, str]] = None,
         parse_dos: Union[str, bool] = False,
         parse_bandstructure: Union[str, bool] = False,
         average_locpot: bool = True,
@@ -618,7 +622,7 @@ def from_vasp_files(
         strip_bandstructure_projections: bool = False,
         strip_dos_projections: bool = False,
         store_volumetric_data: Optional[Tuple[str]] = None,
-        store_trajectory: bool = False,
+        store_trajectory: Union[bool, str] = False,
         vasprun_kwargs: Optional[Dict] = None,
     ) -> Tuple["Calculation", Dict[VaspObject, Dict]]:
         """
@@ -641,6 +645,8 @@ def from_vasp_files(
         elph_poscars
             Path to displaced electron-phonon coupling POSCAR files generated using
             ``PHON_LMC = True``, given relative to dir_name.
+        oszicar_file
+            Path to the OSZICAR file, relative to dir_name
         parse_dos
             Whether to parse the DOS. Can be:
 
@@ -680,9 +686,17 @@ def from_vasp_files(
         store_volumetric_data
             Which volumetric files to store.
         store_trajectory
-            Whether to store the ionic steps in a pymatgen Trajectory object. if `True`,
-            :obj:'.CalculationOutput.ionic_steps' is set to None to reduce duplicating
-            information.
+            Whether to store the ionic steps in a pymatgen Trajectory object and the
+            amount of data to store from the ionic_steps. Can be:
+            - True: Store the Trajectory. All the properties from the ionic_steps
+              are stored in the frame_properties except for the Structure, to
+              avoid redundancy.
+            - "partial": Store the Trajectory. All the properties from the ionic_steps
+              are stored in the frame_properties except from Structure and
+              ElectronicStep
+            - False: Trajectory is not Stored.
+            If not `False`, :obj:'.CalculationOutput.ionic_steps' is set to None
+            to reduce duplicating information.
         vasprun_kwargs
             Additional keyword arguments that will be passed to the Vasprun init.
 
@@ -728,7 +742,9 @@ def from_vasp_files(
         ddec6 = None
         if run_ddec6 and VaspObject.CHGCAR in output_file_paths:
             densities_path = run_ddec6 if isinstance(run_ddec6, (str, Path)) else None
-            ddec6 = ChargemolAnalysis(path=dir_name, atomic_densities_path=densities_path).summary
+            ddec6 = ChargemolAnalysis(
+                path=dir_name, atomic_densities_path=densities_path
+            ).summary
 
         locpot = None
         if average_locpot:
@@ -749,11 +765,28 @@ def from_vasp_files(
             store_trajectory=store_trajectory,
         )
         if store_trajectory:
+            exclude_from_trajectory = ["structure"]
+            if store_trajectory == "partial":
+                exclude_from_trajectory.append("electronic_steps")
+            frame_properties = [
+                IonicStep(**x).model_dump(exclude=exclude_from_trajectory)
+                for x in vasprun.ionic_steps
+            ]
+            if oszicar_file:
+                try:
+                    oszicar = Oszicar(oszicar_file)
+                    if "T" in oszicar.ionic_steps[0]:
+                        for frame_property, oszicar_is in zip(
+                            frame_properties, oszicar.ionic_steps
+                        ):
+                            frame_property["temperature"] = oszicar_is.get("T")
+                except ValueError:
+                    # there can be errors in parsing the floats from OSZICAR
+                    pass
+
             traj = Trajectory.from_structures(
                 [d["structure"] for d in vasprun.ionic_steps],
-                frame_properties=[
-                    IonicStep(**x).model_dump() for x in vasprun.ionic_steps
-                ],
+                frame_properties=frame_properties,
                 constant_lattice=False,
             )
             vasp_objects[VaspObject.TRAJECTORY] = traj  # type: ignore