dolfin team mailing list archive

[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())

> 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.

Where is speed needed other than during assembly? Will it for example be a 
problem when the function is plotted? 

Again note that the envelope design will potential only be applied in the 
compiled function approach.


Johan