(MISC) added a convenience function in misc for patching pymatgen's `…

…core/periodic_table.json` for exotic elements like Livermorium of Hessium

pysipfenn/misc/conveniences.py

@@ -0,0 +1,72 @@
+from importlib.resources import files
+
+def patchPymatgenForExoticElements(
+        x: bool = True,
+        iupacOrder: bool = True
+) -> None:
+    """Patches pymatgen's ``core/periodic_table.json`` with (selectable) electronegativities and IUPAC ordering values
+    needed to correctly handle some exotic chemical elements. The IUPAC rules are followed exactly per Table VI in the 
+    same reference. The electronegativity values are `not` Pauling ones but based on Oganov 2021 and are meant to be 
+    used primarily for providing trend information for ML model deployment (has to be included in training).
+
+    Args:
+        x: Patch electronegativities.
+        iupacOrder: Patch IUPAC ordering of elements in chemical formulas so that they can be handled at all.
+
+    Returns:
+        None. The ``core/periodic_table.json`` file in local install of ``pymatgen`` is patched. Reinstall or upgrade 
+        of ``pymatgen`` reverses the changes.
+
+    """
+
+    patchIUPAC = {
+        'Rf': 49.5,
+        'Db': 52.5,
+        'Sg': 55.5,
+        'Bh': 58.5,
+        'Hs': 61.5,
+        'Mt': 64.5,
+        'Ds': 67.5,
+        'Rg': 70.5,
+        'Cn': 73.5,
+        'Nh': 76.5,
+        'Fl': 81.5,
+        'Mc': 87.5,
+        'Lv': 92.5,
+        'Ts': 97.5,
+        'Og': -0.5
+    }
+
+    patchX = {
+        'Ar': 3.57,
+        'He': 4.42,
+        'Ne': 4.44,
+        'Rf': 2.27,
+        'Db': 2.38,
+        'Sg': 2.51,
+        'Bh': 2.48,
+        'Hs': 2.52,
+        'Mt': 2.66,
+        'Ds': 2.73,
+        'Rg': 2.83,
+        'Cn': 3.03,
+        'Nh': 2.49,
+        'Fl': 2.57,
+        'Mc': 2.21,
+        'Lv': 2.42,
+        'Ts': 2.61,
+        'Og': 2.59
+    }
+
+    with files("pymatgen").joinpath("core/periodic_table.json").open() as f:
+        pt = json.load(f)
+
+    # Patch periodic table
+    with files("pymatgen").joinpath("core/periodic_table.json").open("w") as f:
+        if x:
+            for el in patchX:
+                pt[el]["X"] = patchX[el]
+        if iupacOrder:        
+            for el in patchIUPAC:
+                pt[el]["IUPAC ordering"] = patchIUPAC[el]
+        json.dump(pt, f)