Plot blank with Ubuntu 14.04 Fenics1.6

Question

Hi! I'm new to Ubuntu and Fenics and got problems with the display of my plot. Is there any special Program I have to install to get the plot to show up with command plot()? It's mostly empty or sometimes filled with glibberish. I already tried ParaViewer but that didn't really worked out either. I want to plot u[0] and u[1] for different times.
Or is my code not working at all?

# Create mesh and define function space
nx = 120
xmax = 1
mesh = IntervalMesh(nx, 0, xmax)

V = FunctionSpace(mesh, 'Lagrange', degree=1)
W=V*V


# Define const
D= 0.0005
Dc= 0.45
lamb= 30.0
alpha= 0.1
h= 10.0
k= 0.01
cM= 40.0

# Define boundary condition n=c=1 on the right side for x=1
class BoundaryRight1(SubDomain):
    def inside(self, x, on_boundary):
        return on_boundary and \
            (near(x[0], 1.0))

boundaryRight = BoundaryRight()
bsc = DirichletBC(V, 1.0, boundaryRight)

# Initial condition for t=0 x<1
n0=0
c0=0
u0_function= Expression(("n0", "c0"), n0=n0, c0=c0, element = W.ufl_element())

u0= Function(W)
u0.interpolate(u0_function)

#Def functions
def g (n):
 return (n*(1.0+alpha**2.0))/(n**2.0+alpha**2.0)

B =(1.0+cM**2.0-2.0*h*cM)/((1.0-cM)**2.0)

def s (c):
    return ((2.0*cM*(h-B)*c)/(cM**2.0+c**2.0))+B

# Vectors for saving 
uk = Function(W)
uk.vector()[:]=u0.vector()
ut = Function(W)
ut.vector()[:]=ut.vector()

#saving time dependant solutions
f = File("solution/AK.pvd")
# timesteps
dt=0.3
t=0
T=50.0
while t <= T:   
    t = t + dt
    v = TestFunction(W)
    u = Function(W)
    du= TrialFunction(W)    


    F1 = (1.0/dt * (u[0] - ut[0])-s(u[1])*(2-u[0])*u[0]+u[0])*v[0]*dx \
        + D*inner(nabla_grad (u[0]), nabla_grad (v[0]))*dx



    F2 = (1.0/dt * (u[1] - ut[1]) -lamb*g(u[0]) +lamb*u[1])*v[1]*dx \
        +inner(Dc*nabla_grad (u[1]), nabla_grad (v[1]))*dx


    F=F1+F2

    u.vector()[:]=uk.vector()

    J=derivative(F,u,du)

    # Solver
    problem = NonlinearVariationalProblem(F, u, bsc, J)
    solver  = NonlinearVariationalSolver(problem)
    solver.solve()

    f << u

plot(u[0])
interactive()

Comments

Maybe you have problems with your graphic card drivers? Does glxgears work? It should display a set of rotating gears. You need to install the mesa-utils package to install glxgears.

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Thanks for the reply! glxgears is working fine, but I already had some issues with my graphic card. For matlab I have to use " -softwareopengl" to plot, is there anything similar to Fenics? I can't even plot the minimum examples..

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FEniCS uses VTK to plot. Can you try some of the examples from the vtk-examples package? For instance, try to run python /usr/share/vtk/Tutorial/Step5/Python/Cone5.py.

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I didn't find the exact folder you are describing, but I tried this example,
http://www.vtk.org/Wiki/VTK/Examples/Python/GeometricObjects/Display/Cone

and it failed. I installed VTK with "sudo apt-get install libvtk5-dev python-vtk"

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Try installing the vtk-examples package: sudo apt-get install vtk-examples. Then try to run python /usr/share/vtk/Tutorial/Step5/Python/Cone5.py.

How did you install FEniCS?

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Okay, the Cone5 example didn't worked either, just got an completely black box. I installed Fenics like described on the homepage with the ppa and "sudo apt-get install fenics"

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Ok, then there is clearly something wrong on your side. Have you installed additional drivers? Once you have the VTK examples working, then plotting in FEniCS should also work fine.

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I already checked for drivers but didn't find anything suitable. I got a out of the box Ubuntu notebook. Maybe there is a problem with my graphic card?
Thanks for your support!

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I am having the exact same problem. Are there any updates?

I am running Linux Mint 17.2 (Ubuntu 14.04.3 LTS) on a Lenovo X1 (gen3) with Intel HD5500 graphics; glxgears is working but vtk-examples (and FEniCS plotting) is not.

Answer 1

I am using paraview to view my vtk plots. When loading a .pvd file the name at Coloring is set to 'f_123'(f_random number). I sometimes get following problem, at the next time step the Coloring seems to have another name, for example 'f_146' but paraview selects 'solid color' at coloring and does not show any solution. maybe check if coloring is set correctly at different time steps?

I got this problem when using your example code

putting 'u = Function(W)' out of the while loop fixes this problem

u = Function(W)
while t <= T:
    .....

function stops resetting the name in paraview, maybe this helps anyone