dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Fri, Apr 29, 2011 at 10:31:07AM +0200, Martin Sandve Alnæs wrote:
> On 29 April 2011 10:20, Anders Logg <logg@xxxxxxxxx> wrote:
> > On Fri, Apr 29, 2011 at 09:15:51AM +0100, Garth N. Wells wrote:
> >>
> >>
> >> On 29/04/11 08:58, Martin Sandve Alnæs wrote:
> >> > On 29 April 2011 09:35, Anders Logg <logg@xxxxxxxxx> wrote:
> >> >> On Thu, Apr 28, 2011 at 10:48:28PM +0100, Garth N. Wells wrote:
> >> >>>
> >> >>>
> >> >>> On 28/04/11 22:17, Anders Logg wrote:
> >> >>>> On Thu, Apr 28, 2011 at 12:55:02PM +0200, Martin Sandve Alnæs wrote:
> >> >>>>> On 28 April 2011 11:45, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
> >> >>>>>>
> >> >>>>>>
> >> >>>>>> On 27/04/11 20:50, Johan Hake wrote:
> >> >>>>>>> On Wednesday April 27 2011 12:45:46 Martin Sandve Alnæs wrote:
> >> >>>>>>>> On 27 April 2011 21:34, Anders Logg <logg@xxxxxxxxx> wrote:
> >> >>>>>>>>> On Wed, Apr 27, 2011 at 09:30:08PM +0200, Martin Sandve Alnæs wrote:
> >> >>>>>>>>>> 2011/4/27 Johan Hake <johan.hake@xxxxxxxxx>
> >> >>>>>>>>>>
> >> >>>>>>>>>>     On Wednesday April 27 2011 12:03:56 Martin Sandve Aln s wrote:
> >> >>>>>>>>>>     > On 27 April 2011 19:07, Garth N. Wells <gnw20@xxxxxxxxx> wrote:
> >> >>>>>>>>>>     > > I'm starting here a new thread on how to deal with the recent
> >> >>>>>>>>>
> >> >>>>>>>>> change in
> >> >>>>>>>>>
> >> >>>>>>>>>>     > > UFL that has broken a good number of DOLFIN demos. The previous
> >> >>>>>>>>>
> >> >>>>>>>>> thread
> >> >>>>>>>>>
> >> >>>>>>>>>>     > > meandered and got side-tracked.
> >> >>>>>>>>>>     > >
> >> >>>>>>>>>>     > > The framework in we need to operate is:
> >> >>>>>>>>>>     > >
> >> >>>>>>>>>>     > > A. UFL will not allow forms to be modified post-construction.
> >> >>>>>>>>>>     > >
> >> >>>>>>>>>>     > > B. It should be relatively easy to replace ufl.Coefficients in
> >> >>>>>>>>>>     > > a
> >> >>>>>>>>>
> >> >>>>>>>>> form
> >> >>>>>>>>>
> >> >>>>>>>>>>     > > and return a new form.
> >> >>>>>>>>>>     > >
> >> >>>>>>>>>>     > > C. The issue with replacing ufl.Coefficients is that we lose
> >> >>>>>>>>>
> >> >>>>>>>>> DOLFIN
> >> >>>>>>>>>
> >> >>>>>>>>>>     data
> >> >>>>>>>>>>
> >> >>>>>>>>>>     > > (like the eval() functions) associated with the removed
> >> >>>>>>>>>
> >> >>>>>>>>> coefficients.
> >> >>>>>>>>>
> >> >>>>>>>>>>     > > I'll kick off with the obvious solution:
> >> >>>>>>>>>>     > >
> >> >>>>>>>>>>     > > 1. Require that all DOLFIN Expressions are associated with a
> >> >>>>>>>>>>     > > ufl.FiniteElement.
> >> >>>>>>>>>>     > >
> >> >>>>>>>>>>     > > Other solutions?
> >> >>>>>>>>>>     > >
> >> >>>>>>>>>>     > > Garth
> >> >>>>>>>>>>     >
> >> >>>>>>>>>>     > 2.  At the stage when ffc calls ufl.preprocess, or even in
> >> >>>>>>>>>>
> >> >>>>>>>>>>     ufl.preprocess,
> >> >>>>>>>>>>
> >> >>>>>>>>>>     > let the preprocessed form contain ufl Coefficients with new
> >> >>>>>>>>>
> >> >>>>>>>>> elements in
> >> >>>>>>>>>
> >> >>>>>>>>>>     > place of the dolfin.Expressions. This is similar to the
> >> >>>>>>>>>
> >> >>>>>>>>> replacements done
> >> >>>>>>>>>
> >> >>>>>>>>>>     > for renumbering of Coefficients, and could either be done
> >> >>>>>>>>>
> >> >>>>>>>>> simultaneously
> >> >>>>>>>>>
> >> >>>>>>>>>>     or
> >> >>>>>>>>>>
> >> >>>>>>>>>>     > as an additional step. The original Form and Expression objects
> >> >>>>>>>>>
> >> >>>>>>>>> will be
> >> >>>>>>>>>
> >> >>>>>>>>>>     > untouched, and the preprocessed form will be fine.
> >> >>>>>>>>>>
> >> >>>>>>>>>>     +
> >> >>>>>>>>>>
> >> >>>>>>>>>>     However, setting cell and degree is done during analysis and relies
> >> >>>>>>>>>
> >> >>>>>>>>> on
> >> >>>>>>>>>
> >> >>>>>>>>>>     form_data. The form is also preprocessed when the form_data is
> >> >>>>>>>>>
> >> >>>>>>>>> extracted.
> >> >>>>>>>>>
> >> >>>>>>>>>>     This
> >> >>>>>>>>>>     means that for the preprocessed form to get correct signature, cell
> >> >>>>>>>>>
> >> >>>>>>>>> and
> >> >>>>>>>>>
> >> >>>>>>>>>>     degrees being set, we need to break up the logic.
> >> >>>>>>>>>>
> >> >>>>>>>>>>      1) extract form_data
> >> >>>>>>>>>>      2) set degree and cell
> >> >>>>>>>>>>      3) genererate preprocessed form
> >> >>>>>>>>>>
> >> >>>>>>>>>> Lets figure out the exact algorithm if we need it. It could perhaps be
> >> >>>>>>>>>> integrated better with preprocess. Or it might be better to extract
> >> >>>>>>>>>> just
> >> >>>>>>>>>
> >> >>>>>>>>> the
> >> >>>>>>>>>
> >> >>>>>>>>>> information needed to determine degree and cell first, and pass the
> >> >>>>>>>>>
> >> >>>>>>>>> element
> >> >>>>>>>>>
> >> >>>>>>>>>> replacements to preprocess.
> >> >>>>>>>>>
> >> >>>>>>>>> That's what I suggested in an earlier mail. Preprocess already gets
> >> >>>>>>>>> common_cell. We could also figure out common_degree before calling
> >> >>>>>>>>> preprocess but that requires getting the data stored in
> >> >>>>>>>>> form_data.sub_elements.
> >> >>>>>>>>
> >> >>>>>>>> Extracting all sub elements from a form before preprocessing should be easy
> >> >>>>>>>> and efficient.
> >> >>>>>>>>
> >> >>>>>>>> I assume it's still possible to construct an Expression with a specific
> >> >>>>>>>> FunctionSpace?
> >> >>>>>>>
> >> >>>>>>> Yes.
> >> >>>>>>>
> >> >>>>>>
> >> >>>>>> So it seems we've reached a solution that won't require any changes to
> >> >>>>>> DOLFIN, and only minimal changes to FFC. The story is:
> >> >>>>>>
> >> >>>>>> 1. UFL will permit elements without a cell and without a degree. The
> >> >>>>>> will leads an error for some operations, like grad and div.
> >> >>>>>>
> >> >>>>>> 2. Add a function to UFL to extract all sub-elements from a form.
> >> >>>>
> >> >>>> The functionality is already there since this is already extracted in
> >> >>>> the preprocess function.
> >> >>>>
> >> >>>
> >> >>> We need a function to do this before preprocess in order to pass the
> >> >>> cell and element types to the preprocess function.
> >> >>
> >> >> Yes, but as I just said, we already do that inside preprocess (by
> >> >> calling extract_sub_elements) so the functionality is already there to
> >> >> be used.
> >> >>
> >> >>>>>> 3. Add 'unspecified_elements=[]' (perhaps a dict?) to the argument list
> >> >>>>>> of ufl.algorithms.preprocess.
> >> >>>>
> >> >>>> Not sure if this is needed.
> >> >>>>
> >> >>>>>> 4. For coefficients with incomplete elements, preprocess will replace
> >> >>>>>> these with coefficients based on elements from the list
> >> >>>>>> 'unspecified_elements'. The new form will be the 'preprocessed form'.
> >> >>>>>>
> >> >>>>>> Is that it? Anything else?
> >> >>>>>>
> >> >>>>>> Garth
> >> >>>>>
> >> >>>>> I think that should be all.
> >> >>>>
> >> >>>> I think all we need to do (in FFC) is to
> >> >>>>
> >> >>>> 1. extract the minimal amount of data we need to decide the undecided
> >> >>>> degree and cell (essentially building the list of elements)
> >> >>>>
> >> >>>> 2. select the degree and cell (as we do today)
> >> >>>>
> >> >>>> 3. pass the degree and cell to compute_form_data (and thus to
> >> >>>> preprocess)
> >> >>>>
> >> >>>
> >> >>> Related to my point 3, to keep UFL general, I think that the element
> >> >>> should be passed, and not just the degree. It is conceivable that
> >> >>> something other than continuous Lagrange elements could be used, which
> >> >>> is why an element rather than a degree should be supplied.
> >> >>
> >> >> I'd prefer if we just got the current functionality in place first
> >> >> (without using the now banned set_foo functions) before we make any
> >> >> such extensions. I can have a shot at this. If we want to extend it to
> >> >> other types of elements, we need to have a long discussion on how to
> >> >> choose the element type before we proceed.
> >> >
> >>
> >> I don't see the relevance of this. FFC can just create Lagrange elements
> >> of a given degree to pass to UFL. We don't need to discuss the element
> >> type at this stage.
> >
> > It's harder than that since we may have both scalar and vector-valued
> > elements.
>
> You have to deal with construction of scalar or vector-valued elements
> anyway. It's just a matter of whether this construction is done at the
> ffc or ufl side. The reconstruct pattern I mentioned in another mail
> is one way to implement the construction at the ufl side, but that can
> just as well be called from ffc.
>
> > Would it be enough for now to extract the following to send to UFL:
> >
> >  common_cell
> >  common_family
> >  common_degree
> >
> > ?
>
> Extract that and then do something like
>     element_mapping = {}
>     for oldelement in elements:
>         newelement = oldelement.reconstruct(family=common_family,
> cell=common_cell, degree=common_degree)
>         element_mapping[oldelement] = newelement
>     fd = preprocess(form, element_mapping=element_mapping)
> from ffc, then experimentation with other element types can be done
> later in ffc without updating ufl.

I've started some work on this but reconstruct is currently missing in
the finite element classes.

If anyone wants to continue, I can push what I have. Otherwise, I will
return to it later, tonight or tomorrow.

--
Anders