Merge branch 'master' into core-surface

Author: DanielYang59

docs/_config.yml

@@ -0,0 +1,7 @@
+All examples are housed at [matgenb]. Please consult this resource first.
+
+If there are questions that cannot be found in the examples, you may use the [pymatgen MatSci forum] or [GitHub discussion].
+
+[matgenb]: https://matgenb.materialsvirtuallab.org/
+[pymatgen MatSci forum]: https://matsci.org/pymatgen
+[github discussion]: https://github.com/materialsproject/pymatgen/discussions

docs/index.md

@@ -30,8 +30,7 @@
 
 
 class TransformedStructure(MSONable):
-    """Container object for new structures that include history of
-    transformations.
+    """Container for new structures that include history of transformations.
 
     Each transformed structure is made up of a sequence of structures with
     associated transformation history.

docs/pymatgen.md

@@ -1265,7 +1265,7 @@ def from_dict(cls, dct: dict) -> Self:
 
 
 class NbSetWeight(MSONable, abc.ABC):
-    """Abstract object for neighbors sets weights estimations."""
+    """Abstract base class for neighbor set weight estimations."""
 
     @abc.abstractmethod
     def as_dict(self):
@@ -1282,7 +1282,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
 
 
@@ -1313,7 +1313,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.aw(nb_set=nb_set)
 
@@ -1534,7 +1534,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         fda_list = self.fda(nb_set=nb_set)
         return self.eval(fda_list=fda_list)
@@ -1680,7 +1680,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         effective_csm = get_effective_csm(
             nb_set=nb_set,
@@ -1791,7 +1791,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         effcsm = get_effective_csm(
             nb_set=nb_set,
@@ -2006,7 +2006,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.cn_weights[len(nb_set)]
 
@@ -2186,7 +2186,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.area_weight(
             nb_set=nb_set,
@@ -2379,7 +2379,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.weight_rf.eval(nb_set.distance_plateau())
 
@@ -2446,7 +2446,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         return self.weight_rf.eval(nb_set.angle_plateau())
 
@@ -2509,7 +2509,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         cn = cn_map[0]
         isite = nb_set.isite
@@ -2590,7 +2590,7 @@ def weight(self, nb_set, structure_environments, cn_map=None, additional_info=No
             additional_info: Additional information.
 
         Returns:
-            Weight of the neighbors set.
+            float: Weight of the neighbors set.
         """
         cn = cn_map[0]
         isite = nb_set.isite

examples/README.md

@@ -112,7 +112,7 @@ def get_entries(self, chemsys):
 
 @singleton
 class CostDBElements(CostDBCSV):
-    """Singleton object that provides the cost data for elements."""
+    """Singleton that provides the cost data for elements."""
 
     def __init__(self):
         CostDBCSV.__init__(self, f"{module_dir}/costdb_elements.csv")

examples/aims_io/FHI-aims-example.ipynb

@@ -638,7 +638,7 @@ def _recurse(self, matrix, m_list, indices, output_m_list=None):
             indices: Set of indices which haven't had a permutation
                 performed on them.
         """
-        # check to see if we've found all the solutions that we need
+        # Check if we've found all the solutions that we need
         if self._finished:
             return
 

pymatgen/alchemy/materials.py

@@ -166,7 +166,7 @@ def _fragment_one_level(self, old_frag_dict: dict) -> dict:
         """
         Perform one step of iterative fragmentation on a list of molecule graphs. Loop through the graphs,
         then loop through each graph's edges and attempt to remove that edge in order to obtain two
-        disconnected subgraphs, aka two new fragments. If successful, check to see if the new fragments
+        disconnected subgraphs, aka two new fragments. If successful, check if the new fragments
         are already present in self.unique_fragments, and append them if not. If unsuccessful, we know
         that edge belongs to a ring. If we are opening rings, do so with that bond, and then again
         check if the resulting fragment is present in self.unique_fragments and add it if it is not.

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -161,7 +161,7 @@ def __init__(
             except ValueError:
                 warnings.warn(f"Could not assign valences for {structure.reduced_formula}")
 
-        # check to see if structure has magnetic moments
+        # Check if structure has magnetic moments
         # on site properties or species spin properties,
         # prioritize site properties
 

pymatgen/analysis/cost.py

@@ -36,7 +36,7 @@
 
 
 class BalancedReaction(MSONable):
-    """An object representing a complete chemical reaction."""
+    """Represent a complete chemical reaction."""
 
     # Tolerance for determining if a particular component fraction is > 0.
     TOLERANCE = 1e-6