dolfin team mailing list archive

["Martin Sandve Alnæs" <martinal@xxxxxxxxx>]

2008/10/22 Johan Hake <hake@xxxxxxxxx>:
> On Tuesday 21 October 2008 23:23:27 Martin Sandve Alnæs wrote:
>> 2008/10/21 Johan Hake <hake@xxxxxxxxx>:
>> > On Tuesday 21 October 2008 22:34:04 Martin Sandve Alnæs wrote:
>> >> 2008/10/21 Johan Hake <hake@xxxxxxxxx>:
>> >> > On Tuesday 21 October 2008 21:37:13 Martin Sandve Alnæs wrote:
>> >> >> 2008/10/21 Anders Logg <logg@xxxxxxxxx>:
>> >> >> > On Tue, Oct 21, 2008 at 06:01:53PM +0100, Garth N. Wells wrote:
>> >> >> >> Anders Logg wrote:
>> >> >> >> > On Tue, Oct 21, 2008 at 04:45:01PM +0100, Garth N. Wells wrote:
>> >> >> >> >> I have a few questions and thoughts regarding the new Function
>> >> >> >> >> design
>> >> >> >> >>
>> >> >> >> >> * It's not clear to me what the intention is with user-defined
>> >> >> >> >> functions. The functions Function::interpolate(...) never call
>> >> >> >> >> eval(..), so they can't pick up user-defined values. Should
>> >> >> >> >> Function::interpolate test for the presence of a GenericVector
>> >> >> >> >> to decide whether or not the Function is discrete or
>> >> >> >> >> user-defined?
>> >> >> >> >
>> >> >> >> > Yes, sorry. I've missed this. I'll fix it.
>> >> >> >> >
>> >> >> >> >> * It would be useful to declare user-defined functions without
>> >> >> >> >> associating a FunctionSpace. If we want to interpolate the
>> >> >> >> >> function, a FunctionSpace must then be provided. Anyone see any
>> >> >> >> >> problems with this?
>> >> >> >> >
>> >> >> >> > The reasoning here is that all Functions must always be
>> >> >> >> > associated with a FunctionSpace so that they may be correctly
>> >> >> >> > interpreted in forms and correctly plotted. When a Function is
>> >> >> >> > created in PyDOLFIN, it must always be associated with a certain
>> >> >> >> > FiniteElement (and in a while FunctionSpace). It would simplify
>> >> >> >> > the handling of Functions if they are always associated with a
>> >> >> >> > FunctionSpace.
>> >> >> >>
>> >> >> >> I agree that is makes life simple if every function has a space,
>> >> >> >> but it is a bit clunky for declaring user-defined functions. The
>> >> >> >> forms must be declared first to extract the finite element to
>> >> >> >> create the function space. Could look nasty when a lot of
>> >> >> >> functions are involved.
>> >> >> >>
>> >> >> >> We have a function Function::interpolate which takes a function
>> >> >> >> space V as an argument and it interpolates the function u in V.
>> >> >> >> What if we permit undefined function spaces (which perhaps only
>> >> >> >> have a domain)? We would then interpolate the user defined
>> >> >> >> function u in the provided space V.
>> >> >> >>
>> >> >> >> Garth
>> >> >> >
>> >> >> > Are user-defined functions ever used without being related to a
>> >> >> > particular element/function space?
>> >> >> >
>> >> >> > It don't think it will be very clumsy. The clumsy thing will be to
>> >> >> > (in C++) get from something compiled by a form compiler to a
>> >> >> > FunctionSpace.
>> >> >> >
>> >> >> > If we can make that operation smooth, then creating (user-defined)
>> >> >> > functions will be very simple and convenient. One just needs to
>> >> >> > supply the variable V holding the function space.
>> >> >> >
>> >> >> > The current way of extracting function space data from the form is
>> >> >> > not very nice (in C++). What would be the optimal way to initialize
>> >> >> > a FunctionSpace in C++? We could think of extending the code
>> >> >> > generation to generate code that makes this convenient.
>> >> >> >
>> >> >> > --
>> >> >> > Anders
>> >> >>
>> >> >> The current way of extracting function space data from the form is
>> >> >> not very nice in Python either, since it doesn't work with compiled
>> >> >> functions. (Never mind that the current code is FFC-specific, this
>> >> >> will be the same with UFL).
>> >> >>
>> >> >> Using Python functors can easily make the assembly slower than
>> >> >> solving the linear system, so it's not really interesting to do in
>> >> >> real applications...
>> >> >>
>> >> >> To make a function object that is both of a C++ subclass of
>> >> >> dolfin::Function and of the Python class ufl.Function, we can't use
>> >> >> the fixed multiple inheritance
>> >> >> solution in the current PyDOLFIN.
>> >> >>
>> >> >> We would have to define a new class dynamically in python, inheriting
>> >> >> from both ufl.Function and the freshly compiled C++ Function
>> >> >> subclass. After all this work cleaning up the Function class
>> >> >> hierarchy, is that really something you want?
>> >> >>
>> >> >> I'm not sure if that is even possible to do while maintaining
>> >> >> efficiency, with cross-language inheritance and SWIG directors and
>> >> >> all that.
>> >> >>
>> >> >> If anyone has another solution, I'm very interested in hearing it!
>> >> >> Otherwise, I'm all for keeping the ufl.Function objects used in form
>> >> >> definition separated from dolfin.Function objects used in assembly.
>> >> >
>> >> > I agree with Martin that we need to have a solution for PyDOLFIN users
>> >> > that does not depend on using python functors, as it will take forever
>> >> > for a complex form together with a moderate mesh to just assemble the
>> >> > form.
>> >> >
>> >> > Is it possible to let compile_functions compile a cpp function, with a
>> >> > FunctionSpace and all, instead of a mesh as it is today. Then after
>> >> > doing
>> >>
>> >> If you have a dolfin::FunctionSpace object already, there's no reason
>> >> compile_functions can't take this instead of dolfin::Mesh.
>> >> That's exactly the same and no problem at all.
>> >>
>> >> > this compile_function extract the element, and instantiate a
>> >> > UFL/FFC/PyFunction-function, and "attach" the compiled version to it.
>> >> > This
>> >>
>> >> What I state above is that this "attachment" must be done with
>> >> dynamic creation of a new class with multiple inheritance.
>> >> And I am unsure whether this will work out properly with SWIG directors
>> >> etc. I believe it _may_ work, but I don't dare to keep my hopes up :-)
>> >
>> > Ok, I get it. For a moment I thought we could get away by defineing our
>> > own PyDOLFIN::Function class that could inherit from UFL/FFC, and then
>> > have a cpp_Function, but I realise this will not work.
>> >
>> >> See the attached python file for a prototype of dynamic class creation
>> >> with multiple inheritance using pure python classes.
>> >> (I think this is called "aspect oriented programming" by some people)
>> >>
>> >> > can be used to define forms, but more important it can be handed to
>> >> > the python assembly that check if the function has a compiled version
>> >> > attached to it and send this to the cpp_assembler?
>> >>
>> >> If the "attachment" is anything other than inheritance, it will have
>> >> to be checked with manually written python code _everywhere_
>> >> a dolfin::Function is expected... We can't have one kind of functions
>> >> for assembly and one for other stuff.
>> >
>> > Ok, I guess we have three different cases:
>> >
>> >  1) PyFunctions inherting from both UFL/FFC and cpp_Function as today,
>> >     taking a functionsspace in its constructor. This will work with both
>> >     user defined and discrete functions, more or less as we have it
>> > today.
>> >
>> >  2) The special functions, MeshSize, etc, can also be defined in the same
>> >     way as now, right?
>> >
>> >  3) Using compile_functions, that creates a multi inheritance object that
>> >     can be sent to any function expecting a cpp_Function, without
>> > manually extending the python interface.
>>
>> I'm with you up to this point.
>>
>> > Could the last be done by letting compile_function create a muliti
>> > inheritance Function. Instantiate the cpp_one with the function space and
>> > by that creating a dummy cpp_function. Then "attach" the compiled
>> > function to a protected attribute and define eval, by overloading it in
>> > python. This will then just call the attached and compiled cpp_functions
>> > eval.
>>
>> What you describe here sounds like the envelope-letter design
>> that was just _removed_ from dolfin.
>
> Yes, but only for compiled functions in Python. No other places.
>
>> What I'm suggesting is that
>> compile_functions dynamically creates a Python class that inherits
>> from ufl.Function and the freshly compiled C++ class, which is
>> a dolfin::Function subclass. Then it can construct an object of this
>> new class, passing a FunctionSpace object given by the user to
>> the dolfin::Function constructor, and an ufl.FiniteElement to the
>> ufl.Function constructor.
>
> This sounds doable. I realize now that this was what you were talking about in
> your previous emails, but I did not get it until now ;)
>
>> This of course requires that dolfin.FunctionSpace
>> is a Python subclass of dolfin::FunctionSpace with an additional
>> ufl.FiniteElement member variable. Using jit, dolfin.FunctionSpace
>> can compile the ufc::finite_element and ufc::dof_map classes it needs
>> from an ufl.FiniteElement. And then there's the issue of reusing
>> dofmaps, where DofMapSet enters the play...
>
> Do we need to jit compile ufc::finite_elements and ufc::dof_maps from the
> created ufl.FiniteElement? What about the one that follows from the
> FunctionSpace?

I was thinking about when _constructing_ the FunctionSpace.
Just like PyDOLFIN uses jit in Function.__init__ today.

Then there's the discussion of introducing FunctionSpace in UFL,
but lets leave that for another thread.

>> > This will hopefully work in all cases that expect a cpp_Function? In
>> > assembly where we need speed we extract the compiled function and send
>> > that one to cpp_assembly.
>>
>> I'm not sure what you mean by extracting.
>
> Well, we could define a function 'compiled_function', in the python interface,
> that returnes the compiled c++ function, and then in Py_assemble we could
> check each coeffisient function for hasattr('compiled_function'), but
> nevermind. Your approach is cleaner and should work.

Although, if we get problems with SWIG, your envelope approach
should work, at the cost of extra virtual function calls in eval etc.

>> > Neat? No... but could work!
>>
>> And it is pretty much guaranteed to blow the minds
>> of any non-experts who tries to understand it.
>
> Well, you almost blewed my mind out with your suggestion ;)
>
> Johan


-- 
Martin