Fixed bugs. Bois model limit works correctly

fixed_boundaries.json

+{
+    "morphogen" : true,
+
+    "resolution" : 64,
+    "system_size_by_2PI" : 1 ,
+
+    "elasticity" : 0.0,
+    "viscosity" : 1.0,
+    "friction" : 1.0,
+    "lamda": 1.75,
+
+    "diffusion_rho" : 1.0,
+    "turnover_rho" : 0.0,
+    "average_rho" : 1.0,
+    "saturation_rho" : 1.0,
+
+    "diffusion_c" : 1.0,
+    "turnover_c" : 0.0,
+    "average_c" : 1.0,
+
+    "noise_level": 0.1,
+
+    "timestep" : 0.05,
+    "maxtime" : 200.0
+
+}

fixed_boundaries.py

@@ -51,14 +51,14 @@ class FixedBoundaries(object):
     def reaction_rho(self, rho, trho):
     def reaction_rho(self, rho, trho):
         return self.turnover_rho * df.inner(rho - self.average_rho, trho)
         return self.turnover_rho * df.inner(rho - self.average_rho, trho)
 
 
-    def reaction_rho(self, c, tc):
+    def reaction_c(self, c, tc):
         return self.turnover_c * df.inner(c - self.average_c, tc)
         return self.turnover_c * df.inner(c - self.average_c, tc)
     
     
     def diffusion_reaction_rho(self, rho, trho):
     def diffusion_reaction_rho(self, rho, trho):
         return (self.diffusion_rho * df.inner(rho.dx(0), trho.dx(0)) + self.reaction_rho(rho, trho))
         return (self.diffusion_rho * df.inner(rho.dx(0), trho.dx(0)) + self.reaction_rho(rho, trho))
 
 
     def diffusion_reaction_c(self, c, tc):
     def diffusion_reaction_c(self, c, tc):
-        return (self.diffusion_c * df.inner(c.dx(0), tc.dx(0)) + self.reaction_rho(c, tc))
+        return (self.diffusion_c * df.inner(c.dx(0), tc.dx(0)) + self.reaction_c(c, tc))
 
 
     def setup_initial_conditions(self, u0=None, rho0=None, c0=None):
     def setup_initial_conditions(self, u0=None, rho0=None, c0=None):
         if u0==None and rho0==None and c0==None:
         if u0==None and rho0==None and c0==None:
@@ -168,7 +168,6 @@ class FixedBoundaries(object):
             
             
         # parse data
         # parse data
         data = np.array(data)
         data = np.array(data)
-        print(data.shape)
         if self.morphogen:
         if self.morphogen:
             # u, v, rho, c
             # u, v, rho, c
             return np.split(data, 4, axis=2)
             return np.split(data, 4, axis=2)
@@ -192,8 +191,6 @@ if __name__ == '__main__':
         u, v, rho, c = Z
         u, v, rho, c = Z
     else:
     else:
         u, v, rho = Z
         u, v, rho = Z
-        
-    print(u.shape, v.shape, rho.shape)
 
 
 
 
     x = fb.mesh.coordinates()
     x = fb.mesh.coordinates()