Merge pull request #38 from mikibonacci/develop

Minor fixings
aiidateam · Aug 21, 2024 · 2621ce1 · 2621ce1
2 parents 254f381 + a6bc6d6
commit 2621ce1
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 8 deletions.
diff --git a/docs/01-structuredata.ipynb b/docs/01-structuredata.ipynb
@@ -228,7 +228,7 @@
       "text/plain": [
        "{'pbc': [True, True, True],\n",
        " 'cell': [[3.84, 0.0, 2.351321854362918e-16],\n",
-       "  [1.92, 2.7152900397563426, -1.9199999999999993],\n",
+       "  [1.92, 2.7152900397563426, -1.919999999999999],\n",
        "  [0.0, 0.0, 3.84]],\n",
        " 'tot_charge': None,\n",
        " 'tot_magnetization': None,\n",
@@ -242,7 +242,7 @@
        "   'weights': (1,)},\n",
        "  {'symbol': 'Si',\n",
        "   'kind_name': 'Si',\n",
-       "   'position': [3.84, 1.3576450198781713, 1.9200000000000004],\n",
+       "   'position': [3.84, 1.3576450198781713, 1.9200000000000006],\n",
        "   'mass': 28.0855,\n",
        "   'charge': 0.0,\n",
        "   'magmom': [0.0, 0.0, 0.0],\n",
@@ -255,7 +255,7 @@
        " 'kinds': ['Si', 'Si'],\n",
        " 'symbols': ['Si', 'Si'],\n",
        " 'positions': [[0.0, 0.0, 0.0],\n",
-       "  [3.84, 1.3576450198781713, 1.9200000000000004]],\n",
+       "  [3.84, 1.3576450198781713, 1.9200000000000006]],\n",
        " 'formula': 'Si2'}"
       ]
      },
@@ -297,7 +297,7 @@
     {
      "data": {
       "text/plain": [
-       "<aiida_atomistic.data.structure.structure.StructureDataMutable at 0x10402b910>"
+       "<aiida_atomistic.data.structure.structure.StructureDataMutable at 0x7383406166b0>"
       ]
      },
      "execution_count": 5,
@@ -374,7 +374,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/mbonacci/Documents/codes/aiida-atomistic/src/aiida_atomistic/data/structure/models.py:170: UserWarning: using default cell\n",
+      "/home/aiida/codes/aiida-atomistic/src/aiida_atomistic/data/structure/models.py:170: UserWarning: using default cell\n",
       "  warnings.warn(\"using default cell\")\n"
      ]
     },
@@ -646,8 +646,8 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "13\n",
-      "[<StructureData: uuid: e8f59708-2903-4382-b458-dcaa3dfc019b (pk: 13)>]\n"
+      "387\n",
+      "[<StructureData: uuid: aa1a31fc-7422-4d56-8c43-9529a3b8c4f9 (pk: 387)>]\n"
      ]
     }
    ],

diff --git a/src/aiida_atomistic/data/structure/mixin.py b/src/aiida_atomistic/data/structure/mixin.py
@@ -446,7 +446,7 @@ def get_composition(self, mode="full"):
             f"mode `{mode}` is invalid, choose from `full`, `reduced` or `fractional`."
         )
 
-    def get_kinds(self, kind_tags=[], exclude=["weight"], custom_thr={}, ready_to_use=False):
+    def get_kinds(self, kind_tags=[], exclude=["weights"], custom_thr={}, ready_to_use=False):
         """
         Get the list of kinds, taking into account all the properties.
         If the list of kinds is already provided--> len(kind_tags)>0, we check the consistency of it
@@ -533,6 +533,7 @@ def get_kinds(self, kind_tags=[], exclude=["weight"], custom_thr={}, ready_to_us
                 kinds_per_property = self._to_kinds(
                     property_name=single_property, symbols=symbols, thr=thr
                 )
+
                 kind_properties.append(kinds_per_property[0])
                 # I prefer to store again under the key 'value', may be useful in the future
                 kinds_dictionary[single_property] = kinds_per_property[1]
@@ -1131,6 +1132,8 @@ def _get_object_pymatgen_molecule(self, **kwargs):
             )
 
         species = []
+        additional_kwargs = {}
+
         for site in self.properties.sites:
             if hasattr(site, "weight"):
                 weight = site.weight