Fix Vasprun.get_potcars search method; tweak fake POTCARs (#3587)

* Fix Vasprun Potcar search in cases where no leading  is specified

* change potcar scrambling to not affect titel, update test files

* Update  and test comments to cite issue

* fix tests

* fix str | Path | bool type anno, remove debug print

* requirements.txt fix bad merge conflict resolution

* maybe fix failing TestPhaseDiagram.test_read_json

* revert monty==2024.1.23

see materialsvirtuallab/monty#610

* setup.py monty<=2024.1.26

---------

Co-authored-by: Janosh Riebesell <[email protected]>

Author: esoteric-ephemera

dev_scripts/potcar_scrambler.py

@@ -114,7 +114,7 @@ def scramble_single_potcar(self, potcar: PotcarSingle):
 
             aux_str = ""
             if "TITEL" in line:
-                aux_str = " FAKE"
+                aux_str = " ; FAKE"
             scrambled_potcar_str += f"{cline}{aux_str}\n"
 
         if needs_sha256:

pymatgen/core/__init__.py

@@ -35,7 +35,7 @@
 __maintainer__ = "Shyue Ping Ong, Matthew Horton, Janosh Riebesell"
 __maintainer_email__ = "[email protected]"
 try:
-    __version__ = "2024.1.27"
+    __version__ = version("pymatgen")
 except PackageNotFoundError:  # pragma: no cover
     # package is not installed
     pass

pymatgen/core/libxcfunc.py

@@ -482,16 +482,12 @@ def is_hyb_mgga_family(self) -> bool:
         return self.family == "HYB_MGGA"
 
     def as_dict(self):
-        """Makes LibxcFunc obey the general json interface used in pymatgen for
-        easier serialization.
-        """
+        """Serialize to MSONable dict representation e.g. to write to disk as JSON."""
         return {"name": self.name, "@module": type(self).__module__, "@class": type(self).__name__}
 
     @classmethod
-    def from_dict(cls, dct):
-        """Makes LibxcFunc obey the general json interface used in pymatgen for
-        easier serialization.
-        """
+    def from_dict(cls, dct: dict) -> LibxcFunc:
+        """Deserialize from MSONable dict representation."""
         return cls[dct["name"]]
 
     def to_json(self):

pymatgen/core/periodic_table.py

@@ -747,22 +747,14 @@ def iupac_ordering(self):
     def __deepcopy__(self, memo):
         return Element(self.symbol)
 
-    @staticmethod
-    def from_dict(d) -> Element:
-        """Makes Element obey the general json interface used in pymatgen for
-        easier serialization.
-        """
-        return Element(d["element"])
-
     def as_dict(self) -> dict[Literal["element", "@module", "@class"], str]:
-        """Makes Element obey the general json interface used in pymatgen for
-        easier serialization.
-        """
-        return {
-            "@module": type(self).__module__,
-            "@class": type(self).__name__,
-            "element": self.symbol,
-        }
+        """Serialize to MSONable dict representation e.g. to write to disk as JSON."""
+        return {"@module": type(self).__module__, "@class": type(self).__name__, "element": self.symbol}
+
+    @staticmethod
+    def from_dict(dct: dict) -> Element:
+        """Deserialize from MSONable dict representation."""
+        return Element(dct["element"])
 
     @staticmethod
     def print_periodic_table(filter_function: Callable | None = None) -> None:

pymatgen/core/xcfunc.py

@@ -173,13 +173,8 @@ def from_type_name(cls, typ, name):
         xc = LibxcFunc[name]
         return cls(xc=xc)
 
-    @classmethod
-    def from_dict(cls, d):
-        """Makes XcFunc obey the general json interface used in pymatgen for easier serialization."""
-        return cls(xc=d.get("xc"), x=d.get("x"), c=d.get("c"))
-
     def as_dict(self):
-        """Makes XcFunc obey the general json interface used in pymatgen for easier serialization."""
+        """Serialize to MSONable dict representation e.g. to write to disk as JSON."""
         dct = {"@module": type(self).__module__, "@class": type(self).__name__}
         if self.x is not None:
             dct["x"] = self.x.as_dict()
@@ -189,6 +184,11 @@ def as_dict(self):
             dct["xc"] = self.xc.as_dict()
         return dct
 
+    @classmethod
+    def from_dict(cls, dct):
+        """Deserialize from MSONable dict representation."""
+        return cls(xc=dct.get("xc"), x=dct.get("x"), c=dct.get("c"))
+
     def __init__(self, xc=None, x=None, c=None) -> None:
         """
         Args:

pymatgen/io/vasp/outputs.py

@@ -988,12 +988,12 @@ def get_vbm_cbm(fermi):
         # it is actually a metal
         return self.efermi
 
-    def get_potcars(self, path: str | Path) -> Potcar | None:
-        """
-        Returns the POTCAR from the specified path.
+    def get_potcars(self, path: str | Path | bool) -> Potcar | None:
+        """Returns the POTCAR from the specified path.
 
         Args:
-            path (str | Path): The path to search for POTCARs.
+            path (str | Path | bool): If a str or Path, the path to search for POTCARs.
+                If a bool, whether to take the search path from the specified vasprun.xml
 
         Returns:
             Potcar | None: The POTCAR from the specified path or None if not found/no path specified.
@@ -1005,7 +1005,10 @@ def get_potcars(self, path: str | Path) -> Potcar | None:
         if isinstance(path, (str, Path)) and "POTCAR" in str(path):
             potcar_paths = [str(path)]
         else:
-            search_path = os.path.split(self.filename)[0] if path is True else str(path)
+            # the abspath is needed here in cases where no leading directory is specified,
+            # e.g., Vasprun("vasprun.xml"). see gh-3586:
+            search_path = os.path.dirname(os.path.abspath(self.filename)) if path is True else str(path)
+
             potcar_paths = [
                 f"{search_path}/{fn}" for fn in os.listdir(search_path) if fn.startswith("POTCAR") and ".spec" not in fn
             ]

requirements.txt

@@ -1,8 +1,7 @@
 numpy==1.25.2
 sympy==1.11.1
 requests==2.31.0
-monty==2024.1.26
->>>>>>> bee080171 (Fix monty version.)
+monty==2024.1.23
 ruamel.yaml==0.17.32
 scipy==1.11.2
 tabulate==0.9.0

setup.py

@@ -29,7 +29,7 @@
     python_requires=">=3.9",
     install_requires=[
         "matplotlib>=1.5",
-        "monty>=3.0.2",
+        "monty<=2024.1.26",  # https://github.com/materialsvirtuallab/monty/issues/610
         "networkx>=2.2",
         "numpy>=1.25.0",
         "palettable>=3.1.1",

tests/analysis/test_phase_diagram.py

@@ -614,6 +614,7 @@ def test_read_json(self):
         dumpfn(self.pd, f"{self.tmp_path}/pd.json")
         pd = loadfn(f"{self.tmp_path}/pd.json")
         assert isinstance(pd, PhaseDiagram)
+        assert pd.elements == self.pd.elements
         assert {*pd.as_dict()} == {*self.pd.as_dict()}
 
     def test_el_refs(self):