dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Wednesday 18 February 2009 21:22:15 A Navaei wrote:
> 2009/2/18 Johan Hake <hake@xxxxxxxxx>:
> > On Wednesday 18 February 2009 20:56:59 A Navaei wrote:
> >> 2009/2/18 Anders Logg <logg@xxxxxxxxx>:
> >> > On Wed, Feb 18, 2009 at 02:04:35PM +0000, A Navaei wrote:
> >> >> 2009/2/17 Anders Logg <logg@xxxxxxxxx>:
> >> >> > On Tue, Feb 17, 2009 at 03:28:08PM +0000, Garth N. Wells wrote:
> >> >> >> A Navaei wrote:
> >> >> >> > The following minimal test for Function in c++ reveals some
> >> >> >> > bugs. I guess this example can help me with dealing with the
> >> >> >> > current issues of ImageFunction.
> >> >> >> >
> >> >> >> > (1) interpolate.py does not work when a Function is created in
> >> >> >> > c++ and wrapped (see comment [2]). It seems that the bug is
> >> >> >> > originated from the copy constructor (see comment [3])
> >> >> >> >
> >> >> >> > (2) In order to perform the interpolation, why is it necessary
> >> >> >> > to create another Function and then copy it?
> >> >> >> >
> >> >> >> > (3) Signature checkes seem not working properly (see comment
> >> >> >> > [1]). The signature-based assignments are error-prone anyway,
> >> >> >> > why the object-oriented approach is not used?
> >> >> >>
> >> >> >> Signatures are used to permit reading/writing Functions to a file.
> >> >> >> They are indeed error prone, so I believe that we reached a
> >> >> >> consensus a short while ago that we would remove pre-compiled
> >> >> >> elements.
> >> >> >>
> >> >> >> Garth
> >> >> >
> >> >> > Instead of signatures, I'd recommend that you define a simple form
> >> >> > file for each of the different types of FunctionSpace you need, for
> >> >> > example:
> >> >> >
> >> >> >  element = FiniteElement("CG", "triangle", 1)
> >> >> >
> >> >> >  v = TestFunction(element)
> >> >> >  u = TrialFunction(element)
> >> >> >  a = v*u*dx
> >> >> >
> >> >> > If you put this in a file named My.form and compile it with FFC
> >> >> > using -l dolfin, you will get a class named MyFunctionSpace that
> >> >> > you can then instantiate using just a mesh:
> >> >> >
> >> >> >  MyFunctionSpace V(mesh);
> >> >> >
> >> >> > Create one form file for each of the different types of
> >> >> > FunctionSpace that you need, name the files to something suitable
> >> >> > and use the generated code. That way you won't need to worry about
> >> >> > signatures, dofmaps and finite elements.
> >> >>
> >> >> Effectively, I've been using the very same method all this time, it
> >> >> does not work.
> >> >
> >> > Yes, it does. It's used in about 20 of the demos.
> >> >
> >> >> The copy constructor fix never worked. I've been trying to explain
> >> >> this in many different ways, but the right attention was never paid
> >> >> to this. Let's see if the sandbox example can convince you this time.
> >> >>
> >> >> A Function instance still cannot be returned by reference (or value).
> >> >> Returning as shared_ptr seems to work initially, but eventually it
> >> >> generates segmentation fault -- see attached.
> >> >
> >> > Yes, it can. There's absolutely no problem to return a Function by
> >> > reference. See the updated sandbox demo.
> >> >
> >> > The only problem is when you want to copy a Function which is only
> >> > defined in terms of an eval() operator. In those cases the Function
> >> > cannot be copied.
> >> >
> >> > If you do the following:
> >> >
> >> > class MyFunction : public Function
> >> > {
> >> > public:
> >> >
> >> >  MyFunction(const FunctionSpace& V) : Function(V) {};
> >> >
> >> >  void eval(double* values, const double* x) const
> >> >  {
> >> >    values[0] = sin(x[0]);
> >> >  }
> >> > };
> >> >
> >> > MyFunction f(V);
> >> > Function g = f;
> >> >
> >> > Do you then expect g to return sin(x)? It would be possible to
> >> > implement this but it would require g to keep a pointer to f so that
> >> > the eval() in g may call the eval() in f.
> >>
> >> Yes, we eventually want to get the image data in eval() and obviously
> >> the work around:
> >>
> >>  Function g(V);
> >>  g.vector();
> >>  _f = g;
> >
> > I haven't fully followed the thread, so I might say somthing that has
> > already been mentioned, but shouldn't the approach used in interpolate.py
> > work?
>
> I initially used the approach in interpolate.py, which didn't work:
>
>  Function g(V);
>  _f = g;

Which interpolate.py are you talking about?

The c++(ish) equivalent of interpolate.py would be:

  Function interpolate(&Function g, V)
  {
     Function f(V);
     g.interpolate(f.vector(),V);
     return f;
  }

Here f is a discrete function which will be returned by value.

>  Then Anders added the, not so obvious, addition of initialising the
> vector:
>
>  Function g(V);
>  g.vector();
>  _f = g;
>
> But this doesn't help with eval().

Correct as no interpolation is done, just an initialization of the vector.

> Something is going on in the python code, or the wrapper, which c++
> lacks. 

No this is essentially what happens in interpolate.py

def interpolate(v, V):
    #...
    # Compute interpolation
    Pv = Function(V)
    v.interpolate(Pv.vector(), V)

    return Pv

which is exactly the same I suggest above for C++.

> How did you end up with using g instead of directly using f? 

I want to interpolate the function g, using its eval, to the _f's _vector, 
which defines the coefficients in the discrete function in the FunctionSpace 
V. This is just how you do it and which also interpolate.py does.

Johan

>
>
> -Ali
>
> >  class FunctionContainer
> >  {
> >  public:
> >    FunctionContainer(const FunctionSpace& V):_f(V)
> >    {
> >      message("assigning function");
> >      MyFunction g(V);
> >      g.interpolate(_f.vector(),V);
> >    };
> >
> >    const Function& get_function()
> >    {
> >      message("returning");
> >      return _f;
> >    };
> >  protected:
> >    Function _f;
> >  };
> >
> > Here g's vector is never initialized and the eval function is used to
> > interpolate to the vector of _f.
> >
> > Johan
> >
> >> does not call eval(). I don't think if it is possible to do this
> >> without amending the Function class? The denial of changing the
> >> visibility of the member variables to protected is making this
> >> unnecessarily more and more complicated. I am attaching the updated
> >> sandbox test.
> >>
> >>
> >> -Ali
> >>
> >> > --
> >> > Anders
> >> >
> >> >> -Ali
> >> >>
> >> >> > -----BEGIN PGP SIGNATURE-----
> >> >> > Version: GnuPG v1.4.9 (GNU/Linux)
> >> >> >
> >> >> > iEYEARECAAYFAkma2rQACgkQTuwUCDsYZdHp4ACfSbCXc2FAulzIdDsKvhz/6EGV
> >> >> > aY4An0eyftGV3hxR3L25M9LPu3X7KFg+
> >> >> > =z1cY
> >> >> > -----END PGP SIGNATURE-----
> >> >> >
> >> >> > _______________________________________________
> >> >> > DOLFIN-dev mailing list
> >> >> > DOLFIN-dev@xxxxxxxxxx
> >> >> > http://www.fenics.org/mailman/listinfo/dolfin-dev
> >> >>
> >> >> // Place for random tests
> >> >>
> >> >> #include <dolfin.h>
> >> >> #include "Poisson.h"
> >> >>
> >> >> using namespace dolfin;
> >> >>
> >> >> class MyFunction : public Function
> >> >> {
> >> >> public:
> >> >>
> >> >>   MyFunction(const FunctionSpace& V) : Function(V) {};
> >> >>
> >> >>   void eval(double* values, const double* x) const
> >> >>   {
> >> >>     message("Calling eval");
> >> >>     double dx = x[0] - 0.5;
> >> >>     double dy = x[1] - 0.5;
> >> >>     values[0] = 500.0*exp(-(dx*dx + dy*dy) / 0.02);
> >> >>   }
> >> >> };
> >> >>
> >> >> class FunctionContainer
> >> >> {
> >> >> public:
> >> >>   FunctionContainer(const FunctionSpace& V)
> >> >>   {
> >> >>     _f = Function(V);
> >> >>   };
> >> >>
> >> >>   const Function& get_function()
> >> >>   {
> >> >>     return _f;
> >> >>   };
> >> >> protected:
> >> >>   Function _f;
> >> >> };
> >> >>
> >> >>
> >> >> int main()
> >> >> {
> >> >>   UnitSquare mesh(2, 2);
> >> >>   PoissonFunctionSpace V(mesh);
> >> >>   MyFunction f(V);
> >> >>   Vector x;
> >> >>
> >> >>   message("Interpolating to another vector");
> >> >>   f.interpolate(x, f.function_space());
> >> >>   x.disp();
> >> >>
> >> >>   message("Interpolating to the function vector");
> >> >>   f.interpolate(f.vector(), f.function_space());
> >> >>   f.vector().disp();
> >> >>
> >> >>   message("Interpolating using initialising by an external
> >> >> function"); MyFunction f_(f);
> >> >>   f.interpolate(f_.vector(), f.function_space());
> >> >>   f.vector().disp();
> >> >>
> >> >>   message("Returning Function by reference");
> >> >>   FunctionContainer fc(V);
> >> >>   Function f2 = fc.get_function();
> >> >> }
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> DOLFIN-dev mailing list
> >> >> DOLFIN-dev@xxxxxxxxxx
> >> >> http://www.fenics.org/mailman/listinfo/dolfin-dev
> >> >
> >> > -----BEGIN PGP SIGNATURE-----
> >> > Version: GnuPG v1.4.9 (GNU/Linux)
> >> >
> >> > iEYEARECAAYFAkmcOUcACgkQTuwUCDsYZdE/tACghYR+pHvXwurxKi2rKdcAPrtr
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> >> > =8wBa
> >> > -----END PGP SIGNATURE-----
> >> >
> >> > _______________________________________________
> >> > DOLFIN-dev mailing list
> >> > DOLFIN-dev@xxxxxxxxxx
> >> > http://www.fenics.org/mailman/listinfo/dolfin-dev