dolfin team mailing list archive

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

2008/10/22 Anders Logg <logg@xxxxxxxxx>:
> On Wed, Oct 22, 2008 at 07:27:06PM +0200, Martin Sandve Alnæs wrote:
>> 2008/10/22 Anders Logg <logg@xxxxxxxxx>:
>> > On Wed, Oct 22, 2008 at 11:55:10AM +0200, 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.
>> >> >> >> >> >> >> >> >
>> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> 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
>> >>
>> >>
>> >> >> The relation between UFL and UFC code is (at a certain level) simple:
>> >> >>
>> >> >>   ufc::* is generated by form compilers from ufl.* (equivalently ffc.*)
>> >> >>   once generated, ufc::* depends on nothing
>> >> >>
>> >> >> In DOLFIN (C++) it is also simple:
>> >> >>
>> >> >>   dolfin::* does not depend directly on ufl.* (equivalently ffc.*)
>> >> >>   dolfin::* depends on ufc::*
>> >> >>
>> >> >> PyDOLFIN could (should!) be kept simple. I've been using PyDOLFIN
>> >> >> without the FFC-dependent multiple inheritance stuff all the time
>> >> >> with the dolfin.cpp_* classes.
>> >> >
>> >> > Me too.
>> >> >
>> >> >> I believe that's also how it must be
>> >> >> done if you have external UFC code, e.g. precompiled in a library
>> >> >> or manually written.
>> >> >
>> >> > Agree.
>> >> >
>> >> >> So no matter what, it should at least be possible to avoid
>> >> >> relying on the multiple inheritance and JIT in PyDOLFIN.
>> >> >
>> >> > and more or less have the possibilities we have today. I agree.
>> >> >
>> >> > Johan
>> >>
>> >> Seems at least we're on the same page here.
>> >
>> > I've been in meetings the whole day and it took me a while to get
>> > through the discussion... :-)
>> >
>> > I agree that life would be easier if we did not need to worry about
>> > integrating UFL, UFC, and DOLFIN, but I think we should. I don't think
>> > a user should need to worry about the relations between all the
>> > different flavours of for example the finite element abstractions. We
>> > have quite a few:
>> >
>> >  ufl.FiniteElement
>> >  ufc::finite_element
>> >  dolfin::FiniteElement
>> >  dolfin.FiniteElement
>> >  FIAT.FiniteElement
>> >  (ffc.FiniteElement)
>> >  ...
>>
>> There are different kinds of "worry about" though. Beginners
>> might only want to copy literally what the manual and demos do.
>> But I believe semi-technical users who want to debug their
>> applications by looking into the underlying code would find
>> clear separation between these types easier to comprehend.
>>
>> In reality, they would only need to worry about:
>>   ufl.FiniteElement
>>   ufc::finite_element
>>   dolfin::FiniteElement == dolfin.FiniteElement
>>
>>
>> > DOLFIN plays two roles here:
>> >
>> > 1. It functions as a user interface/problem-solving environment and as
>> >   such should present a clean and simple interface where only one of the
>> >   above flavours should be visible.
>> >
>> > 2. It provides a general assembler, and as such should provide an
>> >   assembly algorithm that just works with ufc:: types (+ mesh and
>> >   linear algebra).
>> >
>> > So, we need to provide (1) for general use (and make it efficient) but
>> > also allow (2) for experts.
>> >
>> > So far, I like Martin's idea with dynamic inheritance to solve (1).
>> >
>>
>> Do you have a solution for the circular dependency problem when
>> reusing dofmaps?
>
> Do we really need the DofMapSet class? If all Functions are associated
> with a FunctionSpace, then they will automatically share the DofMap
> (if they are in the same space).

True. Maybe we can just drop it then.

--
Martin