Js runs (#187)

* sc locpot

* ccd bug

* volumetric data

* get_ediff first

* get_ediff first

* get_ediff first

* lint

* lint

* lint

* lint

* lint

* lint

* lint

* lint

* lint

* lint

* lint

* lint

* lint

* fixed serialzation error

* fix kwarg passing

* fix kwarg passing

* fix kwarg passing

Author: jmmshn

pymatgen/analysis/defects/core.py

@@ -512,7 +512,10 @@ def __init__(
         site: PeriodicSite,
         multiplicity: int | None = None,
         oxi_state: float | None = None,
-        **kwargs,
+        equivalent_sites: list[PeriodicSite] | None = None,
+        symprec: float = 0.01,
+        angle_tolerance: float = 5,
+        user_charges: list[int] | None = None,
     ) -> None:
         """Initialize a substitutional defect object.
 
@@ -525,9 +528,23 @@ def __init__(
             multiplicity: The multiplicity of the defect.
             oxi_state: The oxidation state of the defect, if not specified,
                 this will be determined automatically.
-            **kwargs: Additional kwargs to pass to the Defect constructor.
+            equivalent_sites: A list of equivalent sites for the defect in the structure.
+            symprec: Tolerance for symmetry finding.
+            angle_tolerance: Angle tolerance for symmetry finding.
+            user_charges: User specified charge states. If specified,
+                ``get_charge_states`` will return this list. If ``None`` or empty list
+                the charge states will be determined automatically.
         """
-        super().__init__(structure, site, multiplicity, oxi_state, **kwargs)
+        super().__init__(
+            structure=structure,
+            site=site,
+            multiplicity=multiplicity,
+            oxi_state=oxi_state,
+            equivalent_sites=equivalent_sites,
+            symprec=symprec,
+            angle_tolerance=angle_tolerance,
+            user_charges=user_charges,
+        )
 
     def get_multiplicity(self) -> int:
         """Returns the multiplicity of a defect site within the structure.
@@ -643,7 +660,9 @@ def __init__(
         multiplicity: int = 1,
         oxi_state: float | None = None,
         equivalent_sites: list[PeriodicSite] | None = None,
-        **kwargs,
+        symprec: float = 0.01,
+        angle_tolerance: float = 5,
+        user_charges: list[int] | None = None,
     ) -> None:
         """Initialize an interstitial defect object.
 
@@ -656,15 +675,19 @@ def __init__(
             oxi_state: The oxidation state of the defect, if not specified,
                 this will be determined automatically.
             equivalent_sites: A list of equivalent sites for the defect in the structure.
-            **kwargs: Additional kwargs to pass to the Defect constructor.
+            symprec: Tolerance for symmetry finding.
+            angle_tolerance: Angle tolerance for symmetry finding.
+            user_charges: User specified charge states. If specified,
         """
         super().__init__(
-            structure,
-            site,
-            multiplicity,
-            oxi_state,
-            equivalent_sites,
-            **kwargs,
+            structure=structure,
+            site=site,
+            multiplicity=multiplicity,
+            oxi_state=oxi_state,
+            equivalent_sites=equivalent_sites,
+            symprec=symprec,
+            angle_tolerance=angle_tolerance,
+            user_charges=user_charges,
         )
 
     def get_multiplicity(self) -> int:

pymatgen/analysis/defects/plotting/phases.py

@@ -1,6 +1,5 @@
 """Plotting functions for competing phases."""
 
-# %%
 from __future__ import annotations
 
 import logging

tests/test_core.py

@@ -110,6 +110,9 @@ def test_substitution(gan_struct):
     n_ga = Substitution(s, n_site)
     assert n_ga.get_charge_states() == [-7, -6, -5, -4, -3, -2, -1, 0, 1]
 
+    n_ga.user_charges = [-100, 102]
+    assert n_ga.get_charge_states() == [-100, 102]
+
 
 def test_interstitial(gan_struct):
     s = gan_struct.copy()
@@ -135,6 +138,10 @@ def test_interstitial(gan_struct):
     fpos = finder.get_defect_fpos(inter_sc_struct, inter.structure)
     assert np.allclose(fpos, [0.25, 0.5, 0.89809658])  # closest equivalent site
 
+    inter2 = Interstitial(s, n_site)
+    inter2.user_charges = [-100, 102]
+    assert inter2.get_charge_states() == [-100, 102]
+
 
 def test_adsorbate(gan_struct):
     s = gan_struct.copy()