Resurrect Insertion Workflow

atomate/utils/database.py

@@ -57,7 +57,6 @@ def __init__(
                         "compress" : Whether compression is used
                         "endpoint_url" : the url used to access the S3 store
             maggma_store_prefix: when using maggma stores, you can set the prefix string.
-
             **kwargs:
         """
         if maggma_store_kwargs is None:

atomate/vasp/firetasks/electrode_tasks.py

@@ -98,21 +98,12 @@ def run_task(self, fw_spec):
             chgcar = chgcar["aeccar0"] + chgcar["aeccar2"]
 
         cia = ChargeInsertionAnalyzer(chgcar, **cia_kwargs)
-        cia.get_labels()
+        avg_chg_groups = list(cia.filter_and_group())
 
         insert_sites = []
-        seent = set()
-
-        cia._extrema_df.sort_values(by=["avg_charge_den"], inplace=True)
-        for itr, li_site in cia._extrema_df.iterrows():
-            if len(insert_sites) >= attempt_insertions:
-                break
-            li_site = cia._extrema_df.iloc[itr]
-            lab = li_site["site_label"]
-            if lab not in seent:
-                insert_sites.append([li_site["a"], li_site["b"], li_site["c"]])
-                seent.add(lab)
-
+        for _, g in avg_chg_groups[:attempt_insertions]:
+            insert_sites.append(g[ 0])
+
         logger.info(
             f"Found {len(insert_sites)} insertion sites for task : {base_task_id}"
         )

setup.py

@@ -56,6 +56,7 @@
                 "moto>=4.1.14",
                 "pytest-cov>=4.1.0",
                 "pytest>=7.4.0",
+                "pymatgen-analysis-defects>=2022.8.18",
             ],
         },
         classifiers=[