[petsc-users] PetscFE and TS

[Julian Andrej]

I'm getting the correct solution now, thanks! There are still a few
open questions.

1. The mass term is necessary _and_ using the u_tShift value if i
provide the jacobian. After reading the manual countless times, i
still don't get what the u_tShift value tells me in this context. Are
there any resources which you could point me to?

2. Is DMProjectFunction necessary _before_ TSSolve? This acts like an
initial condition if i'm not mistaken.

3. A more in depth question i guess. Where is the "mass action"
formed? As i could see by stepping through the debugger, there is just
a formed action for the residual equation. It seems way over my
understanding how this formulation works out. I'd also appreciate
resources on that if thats possible.

Thanks again.

Julian

On Wed, Nov 9, 2016 at 9:25 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Wed, Nov 9, 2016 at 8:14 AM, Matthew Knepley <knepley at gmail.com> wrote:
>>
>> On Wed, Nov 9, 2016 at 7:52 AM, Julian Andrej <juan at tf.uni-kiel.de> wrote:
>>>
>>> I tried the example with different signs for the forcing, so this
>>> might be a mistake by me, yes. it doesn't change anything though. I
>>> also have to correct myself, the time for the callback in
>>> PetscDSAddBoundary changes correctly! Although u_t in all other
>>> callbacks seems to remain zero.
>>>
>>> I am out of ideas on my side though :)
>>
>>
>> The bug is that the boundary conditions are not being properly enforced. I
>> am fixing it now.
>> Thanks for the simple example demonstrating this. It made it much much
>> easier to debug.
>
>
> I think this works. Let me know if you agree.
>
> There is the business of u_t on the boundary, which is not handled right
> now. I am putting that
> in, but the homogeneous values for that is still alright here.
>
>   Thanks,
>
>      Matt
>
>>
>>     Matt
>>
>>>
>>> On Wed, Nov 9, 2016 at 2:33 PM, Matthew Knepley <knepley at gmail.com>
>>> wrote:
>>> > On Wed, Nov 9, 2016 at 12:32 AM, Julian Andrej <juan at tf.uni-kiel.de>
>>> > wrote:
>>> >>
>>> >> I tested a few other things and it turned out that the function added
>>> >> as a dirichlet boundary condition via PetscDSAddBoundary doesn't
>>> >> receive the time values correctly (PetscReal time is always 0.0).
>>> >
>>> >
>>> > I will check out your example and fix this. However, I wonder if there
>>> > is a
>>> > bug in your implementation:
>>> >
>>> > void f0_temp(PetscInt dim, PetscInt Nf, PetscInt NfAux,
>>> >           const PetscInt uOff[], const PetscInt uOff_x[], const
>>> > PetscScalar
>>> > u[], const PetscScalar u_t[], const PetscScalar u_x[],
>>> >           const PetscInt aOff[], const PetscInt aOff_x[], const
>>> > PetscScalar
>>> > a[], const PetscScalar a_t[], const PetscScalar a_x[],
>>> >           PetscReal t, const PetscReal x[], PetscScalar f0[])
>>> > {
>>> >   f0[0] = u_t[0] - 2.0;
>>> > }
>>> >
>>> > I get
>>> >
>>> >   du/dt - \Delta u = -2
>>> >
>>> > so that if u = x^2 + y^2 + 2t, then
>>> >
>>> >   2 - (2 + 2) = -2
>>> >
>>> > so you would want u_t + 2.
>>> >
>>> > If you give the Laplacian the opposite sign, this is an unstable
>>> > formulation.
>>> >
>>> >   Thanks,
>>> >
>>> >      Matt
>>> >
>>> >>
>>> >> I also see no effect adding DMTSSetIJacobianLocal vs. not setting the
>>> >> jacobian function. The analytic solution i used in my attached example
>>> >> is the same as in the src/ts/examples/tutorials/ex32.c.
>>> >>
>>> >> Am i doing anything obviously wrong here? My next step would be to try
>>> >> if assembling the matrices myself and writing a custom
>>> >> IFunction/IJacobian which assembles the different parts of the matrix
>>> >> like M and J for the stiff ODE with nontrivial mass matrix (see manual
>>> >> section of TS -> F = M u' - f) but i think this should be obsolete
>>> >> right?
>>> >>
>>> >> Appreciate your help.
>>> >>
>>> >> Regards
>>> >> Julian
>>> >>
>>> >> On Mon, Nov 7, 2016 at 10:49 AM, Julian Andrej <juan at tf.uni-kiel.de>
>>> >> wrote:
>>> >> > Hello,
>>> >> >
>>> >> > i'm using PetscFE in combination with SNES and a hand written
>>> >> > backward
>>> >> > euler solver right now and like to hand that over to TS. I have been
>>> >> > fiddling quite a while getting TS to work with PetscFE and have
>>> >> > encountered a few unclarities.
>>> >> >
>>> >> > I have looked at examples which are outdated i guess
>>> >> > (src/ts/examples/tutorials/ex32.c) and i am confused on how i have
>>> >> > to
>>> >> > formulate the discretization of the jacobian and the residual. It
>>> >> > seems obvious to use the DMTSSetIFunctionLocal and
>>> >> > DMTSSetIJacobianLocal functions because there are prepared wrappers
>>> >> > from DMPlexTSComputeIFunctionFEM and DMPlexTSComputeIJacobianFEM.
>>> >> >
>>> >> > I need a Mass matrix for my problem, is that formed from the
>>> >> > function
>>> >> > space information or do i have to form it myself? Is there any
>>> >> > working
>>> >> > example which uses PetscFE and TS to form the DMTSSetIFunctionLocal
>>> >> > and DMTSSetIJacobianLocal? (grepping the tree tells me "no"
>>> >> > unfortunately).
>>> >> >
>>> >> > Regards
>>> >> > Julian
>>> >
>>> >
>>> >
>>> >
>>> > --
>>> > What most experimenters take for granted before they begin their
>>> > experiments
>>> > is infinitely more interesting than any results to which their
>>> > experiments
>>> > lead.
>>> > -- Norbert Wiener
>>
>>
>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>
>
>
>
> --
> What most experimenters take for granted before they begin their experiments
> is infinitely more interesting than any results to which their experiments
> lead.
> -- Norbert Wiener