Merge pull request #412 from qchempku2017/main

Fix #411

requirements.txt

@@ -1,3 +1,3 @@
 numpy==1.24.4
 monty==2023.9.5
-pymatgen==2023.8.10
+pymatgen==2023.9.10

smol/cofe/space/cluster.py

@@ -287,9 +287,7 @@ def from_dict(cls, d):
                 {
                     spec
                     if spec.symbol not in symbols
-                    else Vacancy(
-                        spec.symbol, spec.oxidation_state, spec.properties
-                    ): val
+                    else Vacancy(spec.symbol, spec.oxidation_state, spec.spin): val
                     for spec, val in site.species.items()
                     if spec.symbol not in symbols
                 }

smol/cofe/space/domain.py

@@ -242,7 +242,6 @@ def __init__(
         self,
         symbol: str = "A",
         oxidation_state: float = 0,
-        properties: dict | None = None,
         spin: float | None = None,
     ):
         """Initialize a Vacancy.
@@ -256,13 +255,11 @@ def __init__(
                 because Vac contains V, a valid Element.
             oxidation_state (float): oxidation state for Vacancy. More like
                 the charge of a point defect. Defaults to zero.
-            properties (dict): Deprecated. See pymatgen 2023.6.28 release notes.
             spin: Spin associated with Species. Defaults to None.
         """
         super().__init__(
             symbol=symbol,
             oxidation_state=oxidation_state,
-            properties=properties,
             spin=spin,
         )
 
@@ -286,8 +283,8 @@ def __repr__(self):
 
     def __copy__(self):
         """Copy the vacancy object."""
-        return Vacancy(self.symbol, self._oxi_state)
+        return Vacancy(self.symbol, self._oxi_state, self.spin)
 
     def __deepcopy__(self, memo):
         """Deepcopy the vacancy object."""
-        return Vacancy(self.symbol, self._oxi_state)
+        return Vacancy(self.symbol, self._oxi_state, self.spin)