Merge pull request #14 from benrich37/liveshare

Liveshare edits

src/pymatgen/core/periodic_table.py

@@ -362,8 +362,7 @@ def electronic_structure(self) -> str:
             June 3]. National Institute of Standards and Technology, Gaithersburg,
             MD. DOI: https://doi.org/10.18434/T4W30F
         """
-        return Species(self.symbol, 0).electronic_structure
-        # return re.sub("</*sup>", "", self._data["Electronic structure"]["0"])
+        return re.sub("</*sup>", "", self._data["Electronic structure"]["0"])
 
     @property
     def average_ionic_radius(self) -> FloatWithUnit:
@@ -483,7 +482,6 @@ def valences(self) -> list[tuple[int | np.nan, int]]:
         obtained from full electron config, where L=0, 1, 2, or 3 for s, p, d,
         and f orbitals, respectively.
         """
-        # return Species(self.symbol, 0).valences
         if self.group == 18:
             return [(np.nan, 0)]  # The number of valence of noble gas is 0
 
@@ -1205,8 +1203,6 @@ def valences(self) -> list[tuple[int | np.nan, int]]:
         """List of valence subshell angular moment (L) and number of valence e- (v_e),
         obtained from full electron config, where L=0, 1, 2, or 3 for s, p, d,
         and f orbitals, respectively.
-
-
         """
         if self.group == 18:
             return [(np.nan, 0)]  # The number of valence of noble gas is 0
@@ -1222,20 +1218,6 @@ def valences(self) -> list[tuple[int | np.nan, int]]:
             ):  # check for full last shell (e.g. column 2)
                 valences.append((idx, ne))
         return valences
-        # if self.group == 18:
-        #     return [(np.nan, 0)]  # The number of valence of noble gas is 0
-
-        # L_symbols = "SPDFGHIKLMNOQRTUVWXYZ"
-        # valences: list[tuple[int, int]] = []
-        # full_electron_config = self.full_electronic_structure
-        # last_orbital = full_electron_config[-1]
-        # for n, l_symbol, ne in full_electron_config:
-        #     idx = L_symbols.lower().index(l_symbol)
-        #     if ne < (2 * idx + 1) * 2 or (
-        #         (n, l_symbol, ne) == last_orbital and ne == (2 * idx + 1) * 2 and len(valences) == 0
-        #     ):  # check for full last shell (e.g. column 2)
-        #         valences.append((idx, ne))
-        # return valences
 
     @property
     def valence(self) -> tuple[int | np.nan, int]:
@@ -1246,9 +1228,6 @@ def valence(self) -> tuple[int | np.nan, int]:
         if len(self.valences) > 1:
             raise ValueError(f"{self} has ambiguous valence")
         return self.valences[0]
-        # if len(self.valences) > 1:
-        #     raise ValueError(f"{self} has ambiguous valence")
-        # return self.valences[0]
 
     @property
     def ionic_radius(self) -> float | None:
@@ -1677,9 +1656,7 @@ def get_el_sp(obj: int | SpeciesLike) -> Element | Species | DummySpecies:
             of properties that can be determined.
     """
     # If obj is already an Element or Species, return as is
-    # Note: the below three if statements are functionally equivalent to the commented out
-    # code. They only exist due to a bug in mypy that doesn't allow the commented out code.
-    # This should be fixed once mypy fixes this
+    # TODO: Why do we need to check "_is_named_isotope"?
     if isinstance(obj, Element):
         if getattr(obj, "_is_named_isotope", None):
             return Element(obj.name)
@@ -1692,11 +1669,6 @@ def get_el_sp(obj: int | SpeciesLike) -> Element | Species | DummySpecies:
         if getattr(obj, "_is_named_isotope", None):
             return Species(str(obj))
         return obj
-    # if isinstance(obj, Element | Species | DummySpecies):
-    # if type(obj) in [Element, Species, DummySpecies]:
-    #     if getattr(obj, "_is_named_isotope", None):
-    #         return Element(obj.name) if isinstance(obj, Element) else Species(str(obj))
-    #     return obj
 
     # If obj is an integer, return the Element with atomic number obj
     try:

src/pymatgen/io/jdftx/__init__.py

@@ -4,13 +4,16 @@
 
 This includes:
 
-- JDFTXInfile:
-  - Initializable from pre-existing JDFTx in files or dictionaries
-  - Modifiable (acts as dictionary)
-  - Writes new in files
+- JDFTXInfile in jdfxinfile.py:
+  - Mutable, sub-classes dictionary
+  - Initializable from pre-existing JDFTx "in" files or dictionaries
+  - Writes new "in" files
   - Extracts Structure objects
-- JDFTXOutfile:
-  - Parses JDFTx out file
+  - Depends on:
+     - jdftxinfile_master_format.py which contains information on allowed keys
+     - jdftxinfile_ref_options.py which contains lists of valid options
+- JDFTXOutfile in jdftxoutfile.py:
+  - Parses JDFTx "out" file
   - Contains all typically relevant output variables from a JDFTx geometric optimization or single-point calculation.
   - Contains hierarchy of class objects (each contained by the former) for storing data at the following
     call frequencies.
@@ -27,7 +30,7 @@
       - JElSteps: Per geometric optimization update (same frequency as parent)
         - List of JElStep as well as convergence data relevant to electronic optimization.
       - JElStep: Per SCF update
-            - Contains all electronic data logged in out file at SCF update frequency.
+        - Contains all electronic data logged in out file at SCF update frequency.
 
 This folder is currently missing:
 

src/pymatgen/io/jdftx/jdftxoutfile.py

@@ -347,9 +347,7 @@ def from_file(cls, file_path: str | Path) -> JDFTXOutfile:
         """
         texts = read_outfile_slices(file_path)
         slices = [JDFTXOutfileSlice.from_out_slice(text) for text in texts]
-        instance = cls()
-        instance.slices = slices
-        return instance
+        return cls(slices=slices)
 
     ###########################################################################
     # Properties inherited from most recent JDFTXOutfileSlice
@@ -358,7 +356,7 @@ def from_file(cls, file_path: str | Path) -> JDFTXOutfile:
     @property
     def prefix(self) -> str:
         """
-        Return prefix from most recent JOutStructure.
+        The prefix of the most recent JDFTx call.
 
         Return prefix from most recent JOutStructure.
         """
@@ -369,7 +367,6 @@ def prefix(self) -> str:
     @property
     def jstrucs(self) -> JOutStructures:
         """
-        Return jstrucs from most recent JOutStructure.
 
         Return jstrucs from most recent JOutStructure.
         """