Merge pull request #114 from pmrv/liquid

Update find_w call sites

calphy/alchemy.py

@@ -314,19 +314,15 @@ def thermodynamic_integration(self):
         Calculates the final work, energy dissipation; In alchemical mode, there is reference system,
         the calculated free energy is the same as the work.
         """
-        w, q, qerr = find_w(self.simfolder, nelements=self.calc.n_elements, 
-            concentration=[val['composition'] for key, val in self.calc._element_dict.items()], 
-            nsims=self.calc.n_iterations, 
+        w, q, qerr = find_w(self.simfolder, self.calc,
             full=True, solid=False, alchemy=True)
 
         self.w = w
         self.ferr = qerr
         self.fe = self.w
 
         if self.calc.mode == "composition_scaling":
-            w_arr, q_arr, qerr_arr, flambda_arr = find_w(self.simfolder, nelements=self.calc.n_elements, 
-                concentration=[val['composition'] for key, val in self.calc._element_dict.items()], 
-                nsims=self.calc.n_iterations, 
+            w_arr, q_arr, qerr_arr, flambda_arr = find_w(self.simfolder, self.calc,
                 full=True, solid=False, alchemy=True, composition_integration=True)
 
             #now we need to process the comp scaling

calphy/liquid.py

@@ -323,10 +323,9 @@ def thermodynamic_integration(self):
         Calculates the final work, energy dissipation and free energy by
         matching with UFM model
         """
-        w, q, qerr = find_w(self.simfolder, nsims=self.calc.n_iterations, 
-            full=True, solid=False)  
-
-        #TODO: Hardcoded UFM parameters - enable option to change          
+        w, q, qerr = find_w(self.simfolder, self.calc, full=True, solid=False)
+
+        #TODO: Hardcoded UFM parameters - enable option to change
         f1 = get_uhlenbeck_ford_fe(self.calc._temperature, 
             self.rho, 50, 1.5)