dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Wednesday 22 October 2008 11:55:10 Martin Sandve Alnæs wrote:
> 2008/10/22 Johan Hake <hake@xxxxxxxxx>:
> > On Wednesday 22 October 2008 11:12:02 Martin Sandve Alnæs wrote:
> >> 2008/10/22 Johan Hake <hake@xxxxxxxxx>:
> >> > On Wednesday 22 October 2008 10:17:43 Martin Sandve Alnæs wrote:
> >> >> 2008/10/22 Johan Hake <hake@xxxxxxxxx>:
> >> >> > On Wednesday 22 October 2008 09:32:31 Martin Sandve Alnæs wrote:
> >> >> >> 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.
> >> >> >
> >> >> > Ok, something like:
> >> >> >
> >> >> > # Note pseudo code...
> >> >> > class FunctionSpace(cpp_FunctionSpace):
> >> >> >    def __init__(self,ufl_finite_element,mesh):
> >> >> >        ufc_finit_element = jit(ufl_finite_element)
> >> >> >        form = ufl.FiniteElement*ufl.TestFunction*ufl.dx
> >> >> >        dof_map = jit(form)
> >> >> >        cpp_FucntionSpace.__init__(mesh,ufc_FinitElement,dof_map)
> >> >> >        self._UFL_FiniteElement = ufl_finite_element
> >> >> >
> >> >> >    def UFL_FiniteElement(self):
> >> >> >        return self._UFL_FiniteElement
> >> >> >
> >> >> > By this the the ufc_element, ufl_element, the dofmaps and the mesh,
> >> >> > are cached in the FunctionSpace.
> >> >> >
> >> >> > The Function would then be something like:
> >> >> >
> >> >> > class Function(cpp_Function,ufl.Function):
> >> >> >    def __init__(self,function_space):
> >> >> >        cpp_Function.__init__(function_space):
> >> >> >        ufl.Function.__init__(function_space.UFL_FiniteElement())
> >> >> >
> >> >> > and dynamical created code in compile_functions()
> >> >> >
> >> >> > class MyFunction(MyCompiledFunction,ufl.Function):
> >> >> >    def __init__(self,function_space):
> >> >> >        MyCompiledFunction.__init__(function_space):
> >> >> >        ufl.Function.__init__(function_space.UFL_FiniteElement())
> >> >>
> >> >> Something like that, yes. This is close to the current PyDOLFIN.
> >> >>
> >> >> But FunctionSpace might become a subclass of ufl.FunctionSpace
> >> >> if we introduce that in UFL, and it should be possible to get
> >> >> cached initialized and renumbered DofMaps from a DofMapSet.
> >> >>
> >> >> Since a DofMapSet will typically be initialized with a Form,
> >> >> a Form depends on a Function, and a Function depends on
> >> >> a FunctionSpace which should be initialized by the DofMapSet,
> >> >> we have a cirular dependency right there.
> >> >
> >> > But won't you have this circular dependency in UFL already?
> >>
> >> In UFL this is simple:
> >>
> >>   FiniteElement depends on nothing
> >>   Function depends on FiniteElement
> >>   Form depends on Function
> >
> > I ment for a potential FunctionSpace class in UFL.
>
> Then it is simply:
>
>    FiniteElement depends on nothing
>    FunctionSpace depends on FiniteElement
>    Function depends on FunctionSpace
>    Form depends on Function

Ok, and FunctionSpace then compile/create a dofmap to be included in it, or 
will a possible UFLFunctionSpace not include that?

Johan