Merge pull request #40 from cote3804/master

Merge pull request #1 from cote3804/jdftx-coords

src/pymatgen/io/jdftx/inputs.py

@@ -432,6 +432,7 @@ def to_pmg_structure(cls, jdftxinfile: JDFTXInfile, sort_structure: bool = False
         """
         # use dict representation so it's easy to get the right column for
         # moveScale, rather than checking for velocities
+        print(jdftxinfile.get_dict_representation(jdftxinfile), "INPUT DICT REP")
         jdftxstructure = JDFTXStructure.from_jdftxinfile(
             jdftxinfile.get_dict_representation(jdftxinfile),
             sort_structure=sort_structure,
@@ -765,6 +766,7 @@ def from_jdftxinfile(cls, jdftxinfile: JDFTXInfile, sort_structure: bool = False
 
         atomic_symbols = [x["species-id"] for x in jdftxinfile["ion"]]
         coords = np.array([[x["x0"], x["x1"], x["x2"]] for x in jdftxinfile["ion"]])
+        coords *= const.value("Bohr radius") * 10**10  # Bohr radius in Ang; convert to Ang
         selective_dynamics = np.array([x["moveScale"] for x in jdftxinfile["ion"]])
 
         coords_are_cartesian = False  # is default for JDFTx

src/pymatgen/io/jdftx/joutstructure.py

@@ -531,7 +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:
@@ -690,7 +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: