Add ModeInspector.plot_ppation_base which serves as the base plotting…

… function for participation ratios

Should be used by the other ppation plotting method.

kappa/conductivity.py

@@ -156,17 +156,31 @@ def tcond(self):
     def plot_mode(self, evec_index):
 
         from .plot import normal_modes
-        normal_modes(self.mol, self.evec[:self.N, evec_index])
+        normal_modes(self.mol, self.evec[1][:self.N, evec_index])
+
+    def plot_ppation_base(self, indices):
+
+        val = self.evec[0][indices]
+        vec = self.evec[1][:self.N,indices]
+
+        num = np.sum((vec**2), axis=0)**2
+        den = len(vec)*np.sum(vec**4, axis=0)
+
+        fig = plt.figure()        
+
+        plt.plot(val, num/den, 'bo')
+
+        fig.suptitle("Val vs p-ratio of selected modes")
+
+        plt.show()
 
     def plot_ppation(self):
 
         kappa, kappaList, val, vec = self.tcond()
 
         pprint.pprint(kappaList)
 
-        N = len(self.mol.posList)
-
-        vec = vec[:N,:]
+        vec = vec[:self.N,:]
 
         num = np.sum((vec**2), axis=0)**2
         den = len(vec)*np.sum(vec**4, axis=0)
@@ -233,6 +247,7 @@ def plot_contrib_mode(self, kappa_index):
 
         dict_ = self.kappaList[kappa_index]
         sigma, tau = dict_['sigma'], dict_['tau']
+        print(sigma, tau)
 
         self.plot_mode(sigma)
         self.plot_mode(tau)