[petsc-users] human-readable examples and PETSc idioms

[Matthew Knepley]

On Fri, Jul 10, 2015 at 2:56 PM, Marco Zocca <zocca.marco at gmail.com> wrote:

> Thank you for the reply;
>
>   let me improve my question: in e.g. a FEM code, we need:
>
>
> *) a mesh table :: [element -> [face -> [edge -> [node] ] ] ]
>
> *) one or more reference elements with associated basis over elements
> and/or faces and Jacobians, or a quadrature rule to represent
> integration over the real-space elements, for each element
>
> *) one or more scalar/tensor coefficients per element
>
>
> Assembly (in the simplest case) of the global matrix is then a single
> loop over elements.
>
>
> I would like to use the highest-level primitives for this task (I am
> tackling a stochastic PDE-constrained optimization problem, so
> complexity control and modularity is paramount ), could you provide
> some hints ?
>

I try to organize things this way in SNES ex12, but there is a lot of
associated
infrastructure, so it might not be all that easy to read. However, I
orthogonalize
mesh topology from data layout from element specification from form
integration
from assembly from solvers, so that you can change them independently.

   Matt


> Thank you again and kind regards,
> Marco
>
>
>
>
>
>
> >>    I'm looking for some non-optimized PETSc code; namely, I struggle a
> >> bit with generalizing the provided examples. On one hand inlined
> >> elementary operations help keep track of the FLOPs but make for
> >> hard-to read code.
> >>
>
> >
> > You can use MatSetValuesStencil() as is done here:
> >
> >
> http://www.mcs.anl.gov/petsc/petsc-current/src/ksp/ksp/examples/tutorials/ex50.c.html
> >
> > on line 162.
> >
> >>
>
> >> , removed comments for space) we are interested in forming a matrix A
> >> from the values contained in a vector x; i.e. some 'map' operation
> >> that sweeps x and prepares rows of A at a time according to some fixed
> >> stencil, with separate treatment of boundary values .
> >>
> >> Isn't there an idiom to abstract out this functionality? It's one of
> >> the most common operations in numerical PDE codes:
> >
> >
> > Actually, this is only common is toy example. Almost no real PDEs have a
> > fixed stencil
> > because you have material coefficients, or nonlinearities, or
> constraints,
> > etc.
> >
> >    Matt
>



-- 
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
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