some comments added about difference with and without remshing

u_v_rho/1D/tissue.py

@@ -43,7 +43,7 @@ class OneDimTissue(object):
         self.function  = df.Function(self.function_space)
 
     def advection(self, conc, vel, tconc):
-        return df.inner(df.div(vel * conc), tconc)
+        return df.inner(df.div(vel) * conc, tconc)
 
     def active_stress(self, rho):
         if self.active_death:
@@ -59,7 +59,7 @@ class OneDimTissue(object):
         cell_markers = df.MeshFunction("bool", mesh, mesh.topology().dim())
         cell_markers.set_all(False)
         for cell in df.cells(mesh):
-            if cell.h() > 0.05:  # if the width of the cell > threshold, refine
+            if cell.h() > 0.05:  
                 cell_markers[cell] = True
         mesh = df.refine(mesh, cell_markers)
         return mesh
@@ -115,8 +115,9 @@ class OneDimTissue(object):
         u,  v, rho    = df.split(self.function)
         tu, tv, trho  = df.TestFunctions(self.function_space)
                   
-        uform = (df.inner((u - u0)/self.timestep, tu)
-                - df.inner(v0, tu))
+        uform = (  df.inner((u - u0)/self.timestep, tu) 
+                  - df.inner(v0, tu)
+                )
         
         vform = (self.friction * df.inner(v, tv) 
                 + df.inner(self.stress(u, v, rho), 
@@ -128,7 +129,7 @@ class OneDimTissue(object):
         
         self.form = (uform + vform + rhoform) * df.dx
 
-    def solve(self, initu=None, initv=None, initrho=None, initTime=0, extend=False):
+    def solve(self, initu = None, initv = None, initrho = None, initTime = 0, extend = False):
 
         # create function space, functions, bc
         self.setup()
@@ -177,31 +178,34 @@ class OneDimTissue(object):
             df.solve(self.form == 0, self.function, self.bc)
 
             # save the fields
-            u, v, rho = self.function.split(deepcopy=True)
+            u, v, rho = self.function.split(deepcopy = True)
             if steps % savesteps == 0:
-
                 self.uFile.write_checkpoint(u, 'displacement', self.time, append=True)
                 self.vFile.write_checkpoint(v, 'velocity', self.time, append=True)
                 self.rhoFile.write_checkpoint(rho, 'density', self.time, append=True)
 
             # assign the calculated function to a newly-defined function, to be used later
+            #NOTE: If no remeshing, only do self.function0.assign(self.function), following not needed
             old_function = df.Function(self.function_space)
             old_function.assign(self.function)
+            
 
             # move the mesh
             dr = df.project(v * self.timestep, self.function_space.sub(0).collapse())
             df.ALE.move(self.mesh, dr)
 
-            # refine the mesh
+            # refine the mesh 
+            #NOTE: If no remeshing, following not needed
             self.mesh = self.refine_mesh(self.mesh)
 
-            # new function space, bc, functions
+            # # new function space, bc, functions
             self.setup()
 
             # new function0 should be the old function in the old function space projected on the new function space
             self.function0 = df.project(old_function, self.function_space) 
 
             # new weak form
+            #NOTE: If no remeshing, following still needed
             self.setup_weak_forms()
             
         self.uFile.close()