fix problems with pymatgen radii

moldocker/samplers/voronoi.py

@@ -17,6 +17,7 @@
 MIN_VORONOI_RADIUS = 3.0
 REMOVE_SPECIES = []
 NUM_CLUSTERS = 10
+PYMATGEN_RADII = False
 
 
 class VoronoiSampler(Sampler):
@@ -29,11 +30,13 @@ def __init__(
         probe_radius=PROBE_RADIUS,
         remove_species=REMOVE_SPECIES,
         min_radius=MIN_VORONOI_RADIUS,
+        pymatgen_radii=PYMATGEN_RADII,
         **kwargs
     ):
         self.probe_radius = probe_radius
         self.remove_species = remove_species
         self.min_radius = min_radius
+        self.pymatgen_radii = pymatgen_radii
 
     @staticmethod
     def add_arguments(parser):
@@ -62,10 +65,7 @@ def remove_species_from_structure(self):
             self._structure.remove_species(species)
 
     def get_voronoi_structures(self):
-        try:
-            radii = self.get_atomic_radii()
-        except (ValueError, TypeError) as e:
-            radii = None
+        radii = self.get_atomic_radii()
 
         with suppress_stdout():
             nodes, edge_center, face_center = zeopp.get_voronoi_nodes(
@@ -75,14 +75,21 @@ def get_voronoi_structures(self):
         return nodes, edge_center, face_center
 
     def get_atomic_radii(self):
-        bv = BVAnalyzer()
-        valences = bv.get_valences(self._structure)
-        elements = [site.species_string for site in self._structure.sites]
-
-        valence_dict = dict(zip(elements, valences))
-        radii = {}
-        for k, v in valence_dict.items():
-            radii[k] = float(Specie(k, v).ionic_radius)
+        if not self.pymatgen_radii:
+            return None
+
+        try:
+            bv = BVAnalyzer()
+            valences = bv.get_valences(self._structure)
+            elements = [site.species_string for site in self._structure.sites]
+
+            valence_dict = dict(zip(elements, valences))
+            radii = {}
+            for k, v in valence_dict.items():
+                radii[k] = float(Specie(k, v).ionic_radius)
+
+        except (ValueError, TypeError) as e:
+            radii = None
 
         return radii
 

moldocker/utils/timing.py

@@ -1,5 +1,6 @@
 from timeit import default_timer as timer
 
+
 def time_fn(fn):
     def wrapped(*args, **kwargs):
         start = timer()