Ensure sorting in output dataframes is consistent

Author: kavanase

doped/thermodynamics.py

@@ -3601,7 +3601,8 @@ def _add_effective_dopant_concentration(
 def _group_defect_charge_state_concentrations(
     conc_df: pd.DataFrame, per_site: bool = False, skip_formatting: bool = False
 ):
-    summed_df = conc_df.groupby("Defect").sum(numeric_only=True)
+    original_order = {k: i for i, k in enumerate(conc_df["Defect"].unique())}  # preserve order
+    summed_df = conc_df.groupby("Defect").sum(numeric_only=True)  # auto-reordered by groupby sum
     conc_column = next(k for k in conc_df.columns if k.startswith("Concentration"))
     raw_concentrations = (
         summed_df["Raw Concentration"]
@@ -3611,6 +3612,9 @@ def _group_defect_charge_state_concentrations(
     summed_df[conc_column] = raw_concentrations.apply(
         lambda x: _format_concentration(x, per_site=per_site, skip_formatting=skip_formatting)
     )
+    # Group and sort by original order
+    summed_df["order"] = summed_df.index.map(original_order)
+    summed_df = summed_df.sort_values(by="order").drop(columns="order")
     return summed_df.drop(
         columns=[
             i