solved issue of singular matrices. fully functional conduction

singular matrices were caused by junctions with no conduction path
to the source and drain nodes. fixed by only calculating conduction
on the spanning cluster

network.py

@@ -60,8 +60,6 @@ def make_A(self, G):
         BTD=np.append(B.T,D,axis=1)
         A=np.append(np.append(G,B,axis=1),BTD,axis=0)
         A=np.delete(np.delete(A,self.ground_nodes,0),self.ground_nodes,1)
-        plt.matshow(A,vmin=-1,vmax=1)
-        plt.show()
         return A
     def make_z(self):
         z = np.append(np.zeros((self.network_size-len(self.ground_nodes),1)), self.voltage_sources[:,1][:,None], axis=0)
@@ -104,7 +102,7 @@ def show_device(self,v=False,ax=False):
             ax=plt.subplot(111)
         self.plot_network(ax,v=v)
         self.plot_regions(ax)
-        ax.legend()
+        # ax.legend()
         if not(ax):
             plt.show()
     def plot_regions(self,ax):

percolation.py

@@ -75,9 +75,12 @@ def make_clusters(self, sticks):
                 intersection=self.check_intersect(sticks.iloc[i].endarray, sticks.iloc[j].endarray)
                 if intersection and 0<=intersection[0]<=1 and 0<=intersection[1]<=1:
                     sticks.loc[sticks.cluster==sticks.loc[j,'cluster'],'cluster'] = sticks.loc[i,'cluster']
-                    intersects.append([i,j,*intersection, sticks.iloc[i].kind+sticks.iloc[j].kind])
+                    intersects.append([i,j,*intersection, sticks.iloc[i].kind+sticks.iloc[j].kind],)
         self.percolating=sticks.loc[0,"cluster"]==sticks.loc[len(sticks)-1,"cluster"]
-        return sticks,pd.DataFrame(intersects, columns=["stick1",'stick2','x','y','kind'])
+        intersects=pd.DataFrame(intersects, columns=["stick1",'stick2','x','y','kind'])
+        intersects['cluster']=intersects['stick1'].apply(lambda x: sticks.iloc[x].cluster)
+        return sticks, intersects
+    def
     def show_system(self,clustering=True,junctions=True,conduction=True):
         fig = plt.figure(figsize=(15,5))
         axes=[fig.add_subplot(1,3,i+1) for i in range(3)]
@@ -86,7 +89,7 @@ def show_system(self,clustering=True,junctions=True,conduction=True):
         if junctions:
             self.show_sticks(ax=axes[1])
         if conduction and self.percolating:
-            self.solve_cnet()
+            self.make_cnet()
             self.cnet.show_device(ax=axes[2])
         plt.show()
     def show_clusters(self,intersects=True,ax=False):
@@ -140,7 +143,12 @@ def make_test_sticks(self):
         self.sticks, self.intersects  = self.make_clusters(sticks)
 
     def make_graph(self):
-        self.graph=nx.from_pandas_edgelist(self.intersects, source='stick1',target='stick2',edge_attr=True)
+        # only calculates the conduction through the spanning cluster of sticks
+        # to avoid the creation of a singular adjacency matrix caused by
+        # disconnected junctions becoming unconnected nodes in the cnet
+        dom_cluster=self.intersects[self.intersects.cluster==self.sticks.loc[0,'cluster']]
+
+        self.graph=nx.from_pandas_edgelist(dom_cluster, source='stick1',target='stick2',edge_attr=True)
 
         self.ground_nodes=[len(self.graph)-1]
         self.voltage_sources=[[0,0.1]]
@@ -153,16 +161,17 @@ def make_graph(self):
 
     def populate_graph(self):
         for edge in self.graph.edges():
+
             self.graph.edges[edge]['component']=Transistor()
 
 
-    def solve_cnet(self):
+    def make_cnet(self):
         assert self.percolating, "The network is not conducting!"
         self.cnet=ConductionNetwork(*self.make_graph())
         # print(self.cnet.make_G(),'\n')
         # print(self.cnet.make_A(self.cnet.make_G()))
         self.cnet.set_global_gate(0)
-        # self.cnet.set_local_gate([0.5,.7,0.4,1], 10)
+        # self.cnet.set_local_gate([0.5,0,0.4,1.2], 10)
         self.cnet.update()
         # print(self.cnet.source_currents)
 
@@ -182,9 +191,8 @@ def solve_cnet(self):
         collection=StickCollection(10,l=1,pm=args.pm,scaling=1)
         collection.make_test_sticks()
         collection.show_system(conduction=False)
-        collection.solve_cnet()
+        collection.make_cnet()
     else:
         collection=StickCollection(args.number,l=args.length,pm=args.pm,scaling=args.scaling)
-        collection.show_system(conduction=False)
-        collection.solve_cnet()
+        collection.show_system()
         # print(len(collection.sticks.cluster.drop_duplicates()))