old updates

src/pymatgen/io/jdftx/jdftxoutfileslice.py

@@ -39,6 +39,27 @@
 
 __author__ = "Ben Rich"
 
+_jofs_atr_from_jstrucs = [
+    "structure",
+    "eopt_type",
+    "elecmindata",
+    "stress",
+    "strain",
+    "forces",
+    "nstep",
+    "e",
+    "grad_k",
+    "alpha",
+    "linmin",
+    "abs_magneticmoment",
+    "tot_magneticmoment",
+    "elec_nstep",
+    "elec_e",
+    "elec_grad_k",
+    "elec_alpha",
+    "elec_linmin",
+]
+
 
 @dataclass
 class JDFTXOutfileSlice:
@@ -265,6 +286,7 @@ class JDFTXOutfileSlice:
     elecmindata: JElSteps | None = None
     stress: np.ndarray | None = None
     strain: np.ndarray | None = None
+    forces: np.ndarray | None = None
     nstep: int | None = None
     e: float | None = None
     grad_k: float | None = None
@@ -842,23 +864,8 @@ def _set_jstrucs(self, text: list[str]) -> None:
         if self.jstrucs is not None:
             self._set_trajectory()
             self.mu = self._get_mu()
-            self.structure = self.jstrucs[-1].structure
-            self.eopt_type = self.jstrucs.eopt_type
-            self.elecmindata = self.jstrucs.elecmindata
-            self.stress = self.jstrucs.stress
-            self.strain = self.jstrucs.strain
-            self.nstep = self.jstrucs.nstep
-            self.e = self.jstrucs.e
-            self.grad_k = self.jstrucs.grad_k
-            self.alpha = self.jstrucs.alpha
-            self.linmin = self.jstrucs.linmin
-            self.abs_magneticmoment = self.jstrucs.abs_magneticmoment
-            self.tot_magneticmoment = self.jstrucs.tot_magneticmoment
-            self.elec_nstep = self.jstrucs.elec_nstep
-            self.elec_e = self.jstrucs.elec_e
-            self.elec_grad_k = self.jstrucs.elec_grad_k
-            self.elec_alpha = self.jstrucs.elec_alpha
-            self.elec_linmin = self.jstrucs.elec_linmin
+            for var in _jofs_atr_from_jstrucs:
+                setattr(self, var, getattr(self.jstrucs, var))
 
     def _set_backup_vars(self, text: list[str]) -> None:
         """Set backups for important variables.

src/pymatgen/io/jdftx/joutstructure.py

@@ -76,6 +76,7 @@ class JOutStructure(Structure):
     elecmindata: JElSteps | None = None
     stress: np.ndarray | None = None
     strain: np.ndarray | None = None
+    forces: np.ndarray | None = None
     nstep: int | None = None
     e: float | None = None
     grad_k: float | None = None
@@ -530,7 +531,7 @@ def _parse_ecomp_lines(self, ecomp_lines: list[str]) -> None:
                 key = lsplit[0].strip()
                 val = float(lsplit[1].strip())
                 self.ecomponents[key] = val * Ha_to_eV
-        if key is not None and (self.etype is None) and (key in ["F", "G"]):
+        if key is not None and (self.etype is None) and (key in ["F", "G", "Etot"]):
             self.etype = key
 
     def _parse_lowdin_lines(self, lowdin_lines: list[str]) -> None:
@@ -689,7 +690,11 @@ def _collect_generic_line(self, line_text: str, generic_lines: list[str]) -> tup
     def _init_structure(self) -> None:
         """Initialize structure attribute."""
         self.structure = Structure(
-            lattice=self.lattice, species=self.species, coords=self.cart_coords, site_properties=self.site_properties
+            lattice=self.lattice,
+            species=self.species,
+            coords=self.cart_coords,
+            site_properties=self.site_properties,
+            coords_are_cartesian=True,
         )
 
     def to_dict(self) -> dict:

src/pymatgen/io/jdftx/joutstructures.py

@@ -30,6 +30,7 @@
     "elecmindata",
     "stress",
     "strain",
+    "forces",
     "nstep",
     "e",
     "grad_k",
@@ -47,6 +48,7 @@
     "charges",
     "magnetic_moments",
     "selective_dynamics",
+    "structure",
 ]
 
 
@@ -97,6 +99,7 @@ class JOutStructures:
         charges (np.ndarray[float] | None): The most recent Lowdin-charges.
         magnetic_moments (np.ndarray[float] | None): The most recent Lowdin-magnetic moments.
         selective_dynamics (list[int] | None): The selective dynamics flags for the most recent JDFTx call.
+        structure (Structure | None): Cleaned pymatgen Structure object of final JOutStructure
     """
 
     out_slice_start_flag = "-------- Electronic minimization -----------"
@@ -114,6 +117,7 @@ class JOutStructures:
     elecmindata: JElSteps = None
     stress: np.ndarray | None = None
     strain: np.ndarray | None = None
+    forces: np.ndarray | None = None
     nstep: int | None = None
     e: float | None = None
     grad_k: float | None = None
@@ -131,6 +135,7 @@ class JOutStructures:
     charges: np.ndarray[float] | None = None
     magnetic_moments: np.ndarray[float] | None = None
     selective_dynamics: list[int] | None = None
+    structure: Structure | None = None
 
     @classmethod
     def _from_out_slice(cls, out_slice: list[str], opt_type: str = "IonicMinimize") -> JOutStructures:
@@ -399,6 +404,8 @@ def _get_initial_coords(pre_out_slice: list[str]) -> np.ndarray:
         coords_type = pre_out_slice[coords_type_lines[0]].strip().split()[1]
         if coords_type.lower() != "cartesian":
             coords = np.dot(coords, _get_initial_lattice(pre_out_slice))
+        else:
+            coords *= bohr_to_ang
     return coords
 
 

src/pymatgen/io/jdftx/outputs.py

@@ -248,6 +248,7 @@ def _store_eigenvals(self):
     "elecmindata",
     "stress",
     "strain",
+    "forces",
     "nstep",
     "e",
     "grad_k",
@@ -468,6 +469,7 @@ class JDFTXOutfile:
     elecmindata: JElSteps = field(init=False)
     stress: np.ndarray = field(init=False)
     strain: np.ndarray = field(init=False)
+    forces: np.ndarray = field(init=False)
     nstep: int = field(init=False)
     e: float = field(init=False)
     grad_k: float = field(init=False)
@@ -509,24 +511,32 @@ def from_calc_dir(
         return cls(slices=slices)
 
     @classmethod
-    def from_file(cls, file_path: str | Path, is_bgw: bool = False, none_slice_on_error: bool = False) -> JDFTXOutfile:
+    def from_file(
+        cls, file_path: str | Path, is_bgw: bool = False, none_slice_on_error: bool | None = None
+    ) -> JDFTXOutfile:
         """
         Create a JDFTXOutfile object from a JDFTx out file.
 
         Args:
             file_path (str | Path): The path to the JDFTx out file.
             is_bgw (bool): Mark True if data must be usable for BGW calculations. This will change the behavior of the
                 parser to be stricter with certain criteria.
-            none_slice_on_error (bool): If True, will return None if an error occurs while parsing a slice instead of
-                halting the parsing process. This can be useful for parsing files with multiple slices where some slices
-                may be incomplete or corrupted.
+            none_slice_on_error (bool | None): If True, will return None if an error occurs while parsing a slice
+                instead of halting the parsing process. This can be useful for parsing files with multiple slices where
+                some slices may be incomplete or corrupted. If False, all slices may raise errors. If None, only the
+                final slice can raise an error upon parsing (default behavior)
 
         Returns:
             JDFTXOutfile: The JDFTXOutfile object.
         """
         texts = read_outfile_slices(file_path)
+        if none_slice_on_error is None:
+            none_slice_bools = [i != len(texts) - 1 for i in range(len(texts))]
+        else:
+            none_slice_bools = [none_slice_on_error for i in range(len(texts))]
         slices = [
-            JDFTXOutfileSlice._from_out_slice(text, is_bgw=is_bgw, none_on_error=none_slice_on_error) for text in texts
+            JDFTXOutfileSlice._from_out_slice(text, is_bgw=is_bgw, none_on_error=none_slice_bools[i])
+            for i, text in enumerate(texts)
         ]
         return cls(slices=slices)