dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Mon, May 02, 2011 at 10:05:26AM +0200, Anders Logg wrote:
> 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.

I've pushed the changes I made so far. It seems to mostly not break
anything (compared to the currently broken FFC/DOLFIN). Feel free to
jump in. Things to do:

1. Add reconstruct() to the element classes in UFL.

2. Handle the input element_mapping in reconstruct.py in UFL.

3. ?

4. Remove call to _adjust_elements in analysis.py in FFC.

--
Anders