fixes for trajectory

Author: benrich37

src/pymatgen/io/jdftx/jdftxoutfileslice.py

@@ -179,6 +179,7 @@ class JDFTXOutfileSlice:
     jsettings_electronic: JMinSettings | None = None
     jsettings_lattice: JMinSettings | None = None
     jsettings_ionic: JMinSettings | None = None
+    constant_lattice: bool | None = None
 
     xc_func: str | None = None
 
@@ -391,13 +392,9 @@ def _set_trajectory(self) -> Trajectory:
         Returns:
             Trajectory: pymatgen Trajectory object containing intermediate Structure's of outfile slice calculation.
         """
-        constant_lattice = False
-        if self.jsettings_lattice is not None:
-            if "niterations" in self.jsettings_lattice.params:
-                constant_lattice = int(self.jsettings_lattice.params["niterations"]) == 0
-            else:
-                raise ValueError("Unknown issue due to partial initialization of settings objects.")
-        self.trajectory = Trajectory.from_structures(structures=self.jstrucs, constant_lattice=constant_lattice)
+        if self.jstrucs is not None:
+            structures = [slc.structure for slc in self.jstrucs.slices]
+            self.trajectory = Trajectory.from_structures(structures=structures, constant_lattice=self.constant_lattice)
 
     def _set_electronic_output(self) -> None:
         """Return a dictionary with all relevant electronic information.
@@ -806,6 +803,8 @@ def _set_min_settings(self, text: list[str]) -> None:
         self.jsettings_electronic = self._get_settings_object(text, JMinSettingsElectronic)
         self.jsettings_lattice = self._get_settings_object(text, JMinSettingsLattice)
         self.jsettings_ionic = self._get_settings_object(text, JMinSettingsIonic)
+        if self.jsettings_lattice is not None and "niterations" in self.jsettings_lattice.params:
+            self.constant_lattice = int(self.jsettings_lattice.params["niterations"]) != 0
 
     def _set_geomopt_vars(self, text: list[str]) -> None:
         """Set the geom_opt and geom_opt_type class variables.

src/pymatgen/io/jdftx/outputs.py

@@ -15,7 +15,6 @@ class is written.
 
 import numpy as np
 
-from pymatgen.core.trajectory import Trajectory
 from pymatgen.io.jdftx._output_utils import (
     _get_atom_orb_labels_dict,
     _get_nbands_from_bandfile_filepath,
@@ -26,6 +25,7 @@ class is written.
 
 if TYPE_CHECKING:
     from pymatgen.core.structure import Structure
+    from pymatgen.core.trajectory import Trajectory
     from pymatgen.io.jdftx.jelstep import JElSteps
     from pymatgen.io.jdftx.jminsettings import (
         JMinSettingsElectronic,
@@ -536,20 +536,16 @@ def __post_init__(self):
                 setattr(self, var, getattr(self.slices[-1], var))
             self.trajectory = self._get_trajectory()
 
-    def _get_trajectory(self) -> Trajectory:
+    def _get_trajectory(self) -> Trajectory | None:
         """Set the trajectory attribute of the JDFTXOutfile object."""
-        constant_lattice = True
-        structures = []
-        for _i, slc in enumerate(self.slices):
-            structures += slc.jstrucs.slices
-            if constant_lattice and (slc.jsettings_lattice is not None):
-                if "niterations" in slc.jsettings_lattice.params:
-                    if int(slc.jsettings_lattice.params["niterations"]) > 1:
-                        constant_lattice = False
+        traj = None
+        for outfile_slice in self.slices:
+            if outfile_slice is not None:
+                if traj is None:
+                    traj = outfile_slice.trajectory
                 else:
-                    constant_lattice = False
-
-        return Trajectory.from_structures(structures=structures, constant_lattice=constant_lattice)
+                    traj.extend(outfile_slice.trajectory)
+        return traj
 
     def to_dict(self) -> dict:
         """

tests/io/jdftx/test_jdftxoutfileslice.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import math
-import re
 
 import numpy as np
 import pytest
@@ -29,9 +28,7 @@ def test_jdftxoutfileslice_trajectory():
     joutslice = JDFTXOutfileSlice._from_out_slice(ex_slice1)
     traj = joutslice.trajectory
     assert isinstance(traj, Trajectory)
-    del joutslice.jsettings_lattice.params["niterations"]
-    with pytest.raises(ValueError, match=re.escape("Unknown issue due to partial initialization of settings objects.")):
-        joutslice._set_trajectory()
+    assert len(traj) == len(joutslice.jstrucs)
 
 
 def test_get_broadeningvars():