Updated Site.charge() method.

pyscses/site.py

@@ -194,12 +194,12 @@ def probabilities_as_list(self,
             list(float): Probabilities of site occupation for each defect species.
 
         """
-        warnings.warn("Site.probabilities_as_list() is deprecated and targetted for removal. Please use Site.probabilities() instead.", DeprecationWarning)
+        warnings.warn("Site.probabilities_as_list() is deprecated and targeted for removal. Please use Site.probabilities() instead.", DeprecationWarning)
         probabilities_dict = self.probabilities(phi=phi, temp=temp)
         return [probabilities_dict[d.label] for d in self.defects]
 
     def defect_valences(self) -> np.ndarray:
-        """Returns an array of valences for each defect from self.defects """
+        """Returns an array of valences for each defect in `self.defects`"""
         return np.array([d.valence for d in self.defects])
 
     def charge(self,
@@ -216,7 +216,9 @@ def charge(self,
             float: The charge at this site.
 
         """
-        charge =  (self.valence + np.sum(self.probabilities(phi, temp)
-                                * self.defect_valences()
-                                * self.scaling)) * fundamental_charge
-        return charge
+        defect_probabilities = self.probabilities(phi=phi, temp=temp)
+        charge = sum([defect_probabilities[d.label] * d.valence
+                      for d in self.defects]) * self.scaling
+        charge += self.valence
+        charge *= fundamental_charge
+        return float(charge)

tests/test_site.py

@@ -4,6 +4,7 @@
 from pyscses.defect_at_site import DefectAtSite
 from pyscses.site import Site, LabelError
 from unittest.mock import Mock, patch
+from pyscses.constants import fundamental_charge
 import numpy as np
 
 def create_mock_defect_species(n):
@@ -183,9 +184,15 @@ def test_probabilities_two(self):
                                                  temp=298.0),
                          {'A': exp_A, 'B': exp_B})
 
-    def test_probabilites_as_list(self):
+    def test_charge(self):
         self.site.probabilities = Mock(return_value={'E': 0.1, 'D': 0.2})
-        self.site.probabilities_as_list(phi=1.0, temp=298.0)
+        self.site.defects[0].valence = 1.0
+        self.site.defects[1].valence = 2.0
+        self.site.scaling = 0.5
+        self.site.valence = 1.0
+        expected_value = ((1.0*0.1 + 2.0*0.2)*0.5 + 1.0) * fundamental_charge
+        self.assertEqual(self.site.charge(phi=1.0, temp=298.0),
+                         expected_value)
 
 
 if __name__ == '__main__':