From 175e914f6ba01ca0ece624d5831e4bd359f3908e Mon Sep 17 00:00:00 2001
From: Sean Kavanagh <s.kavanagh19@imperial.ac.uk>
Date: Mon, 13 May 2024 13:46:02 +0100
Subject: [PATCH] Update `Defect` initialisation code to match `pymatgen`
 update

---
 doped/analysis.py |  4 ++++
 doped/core.py     | 23 ++++++++++++++---------
 2 files changed, 18 insertions(+), 9 deletions(-)

diff --git a/doped/analysis.py b/doped/analysis.py
index 72470efc..b5f970ec 100644
--- a/doped/analysis.py
+++ b/doped/analysis.py
@@ -318,6 +318,10 @@ def defect_from_structures(
     }  # note that we now define the Defect in the bulk supercell, rather than the primitive structure
     # as done during generation. Future work could try mapping the relaxed defect site back to the
     # primitive cell, however interstitials will be very tricky for this...
+    if def_type == "interstitial":
+        for_monty_defect["multiplicity"] = 1  # multiplicity needed for interstitial initialisation with
+        # pymatgen-analysis-defects, so set to 1 here. Set later for interstitials during parsing anyway
+        # (see below)
     defect = MontyDecoder().process_decoded(for_monty_defect)
 
     if not return_all_info:
diff --git a/doped/core.py b/doped/core.py
index 561d41ca..ab84e5d1 100644
--- a/doped/core.py
+++ b/doped/core.py
@@ -48,7 +48,7 @@
 class DefectEntry(thermo.DefectEntry):
     """
     Subclass of ``pymatgen.analysis.defects.thermo.DefectEntry`` with
-    additional attributes used by doped.
+    additional attributes used by ``doped``.
 
     Core Attributes:
         defect:
@@ -1415,7 +1415,7 @@ def __init__(
     ):
         """
         Subclass of ``pymatgen.analysis.defects.core.Defect`` with additional
-        attributes and methods used by doped.
+        attributes and methods used by ``doped``.
 
         Args:
             structure (Structure):
@@ -1675,7 +1675,10 @@ def get_supercell_structure(
             )[0]
 
         sc_defect = self.__class__(
-            structure=self.structure * sc_mat, site=sc_site, oxi_state=self.oxi_state
+            structure=self.structure * sc_mat,
+            site=sc_site,
+            oxi_state=self.oxi_state,
+            multiplicity=1,  # so doesn't break for interstitials
         )
         sc_defect_struct = sc_defect.defect_structure
         sc_defect_struct.remove_oxidation_states()
@@ -1822,11 +1825,11 @@ def doped_defect_from_pmg_defect(defect: core.Defect, bulk_oxi_states=False, **d
     return defect_type._from_pmg_defect(defect, bulk_oxi_states=bulk_oxi_states, **doped_kwargs)
 
 
-class Vacancy(core.Vacancy, Defect):
+class Vacancy(Defect, core.Vacancy):
     def __init__(self, *args, **kwargs):
         """
         Subclass of ``pymatgen.analysis.defects.core.Vacancy`` with additional
-        attributes and methods used by doped.
+        attributes and methods used by ``doped``.
         """
         super().__init__(*args, **kwargs)
 
@@ -1838,11 +1841,11 @@ def __repr__(self) -> str:
         return f"{self.name} vacancy defect at site [{frac_coords_string}] in structure"
 
 
-class Substitution(core.Substitution, Defect):
+class Substitution(Defect, core.Substitution):
     def __init__(self, *args, **kwargs):
         """
         Subclass of ``pymatgen.analysis.defects.core.Substitution`` with
-        additional attributes and methods used by doped.
+        additional attributes and methods used by ``doped``.
         """
         super().__init__(*args, **kwargs)
 
@@ -1854,12 +1857,14 @@ def __repr__(self) -> str:
         return f"{self.name} substitution defect at site [{frac_coords_string}] in structure"
 
 
-class Interstitial(core.Interstitial, Defect):
+class Interstitial(Defect, core.Interstitial):
     def __init__(self, *args, **kwargs):
         """
         Subclass of ``pymatgen.analysis.defects.core.Interstitial`` with
-        additional attributes and methods used by doped.
+        additional attributes and methods used by ``doped``.
         """
+        if "multiplicity" not in kwargs:  # will break for Interstitials if not set
+            kwargs["multiplicity"] = 1
         super().__init__(*args, **kwargs)
 
     def __repr__(self) -> str: