On 11 Dec 2014 19:17, "Anna Kalogirou" <a.kalogirou@leeds.ac.uk> wrote:
>
> Thanks Andrew. About your comment 1), how can I fix this?

I think that requires a Firedrake (PyOP2) fix.  Lawrence?

>
> The two equations valid on one of the boundaries can actually be combined into one by paying the price of a higher time derivative. This is not a problem for this simple system, so if I use
>
> aphi = v*phi*ds(4) + g*dt**2*inner(grad(v),grad(phi))*dx
> Lphi = v*(2*phi1-phi0)*ds(4)
>  
> phi_problem = LinearVariationalProblem(aphi,Lphi,phi2)
> phi_solver = LinearVariationalSolver(phi_problem)
>
> is equivalent to what I had before, and this time the code works and gives a good result (compared to the exact solution).

Cool...

>
> However, I need to understand why the other case doesn't work because that will later be generalised to become nonlinear.
>
>
> Anna.
>
>
>
> On 11/12/14 13:04, Andrew McRae wrote:
>>
>> Four comments:
>>
>> 1)  If I understand correctly, PETSc insists that the diagonal entries of the sparse matrix are filled in.  Usually, the LHS form will cause this to happen; however, that obviously isn't the case for your form!
>>
>> 2)  It should be possible to build the nullspace you want, but I'm clueless on the actual syntax.  This wouldn't get around (1) without further fixes from our end.
>>
>> 3)  Could the equations given not be included in the weak form for the rest of the problem?
>>
>> 4)  If not, there might be a hacky "add-a-weighted-mass-matrix-to-the-LHS" fix you could use?....
>>
>> Andrew
>>
>> On 11 December 2014 at 12:46, Anna Kalogirou <a.kalogirou@leeds.ac.uk> wrote:
>>>
>>> Dear all,
>>>
>>> I am trying to solve a simple problem (linear water wave equations),
>>> where I have the Laplace equation in a square domain with Neumann
>>> boundary conditions on the three sides and on the top boundary two
>>> equations are satisfied.
>>>
>>> I have the following code:
>>> --------------------------------------
>>> V = FunctionSpace(mesh,"CG",1)
>>>
>>> eta0 = Function(V).interpolate(Expression("cos(2*pi*x[0])"))
>>> phi0 = Function(V)
>>> eta1 = Function(V)
>>> phi1 = Function(V)
>>> eta = TrialFunction(V)
>>> phi = TrialFunction(V)
>>> v = TestFunction(V)
>>>
>>> aeta = v*eta*ds(4)
>>> Leta = v*eta0*ds(4) + dt*inner(grad(v),grad(phi0))*dx
>>>
>>> eta_problem = LinearVariationalProblem(aeta,Leta,eta1)
>>> eta_solver = LinearVariationalSolver(eta_problem)
>>>
>>> aphi = v*phi*ds(4)
>>> Lphi = (v*phi0 - g*dt*v*eta1)*ds(4)
>>>
>>> phi_problem = LinearVariationalProblem(aphi,Lphi,phi1)
>>> phi_solver = LinearVariationalSolver(phi_problem)
>>> --------------------------------------
>>>
>>> The error I get tells me that Object is in wrong state, and Matrix is
>>> missing diagonal entry 39.
>>>
>>> I thought this had to do with the problem being singular, so I tried to
>>> build the nullspace but I don't know how to define the VectorSpaceBasis.
>>> Any help would be appreciated.
>>>
>>> Thank you very much.
>>>
>>> Regards, Anna.
>>>
>>> _______________________________________________
>>> firedrake mailing list
>>> firedrake@imperial.ac.uk
>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>>
>>
>
> --
> 
>  Dr Anna Kalogirou
>  Research Fellow
>  School of Mathematics
>  University of Leeds