dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Tue, Jun 10, 2008 at 07:50:09PM +0200, Anne Voigt wrote:
> Am Dienstag, den 10.06.2008, 19:06 +0200 schrieb Anders Logg:
> > On Fri, Jun 06, 2008 at 10:28:54AM +0200, Anne Voigt wrote:
> > > Am Dienstag, den 03.06.2008, 22:02 +0200 schrieb Anders Logg:
> > > > On Fri, May 30, 2008 at 10:02:29AM +0200, Anne Voigt wrote:
> > > > > Hello all,
> > > > > 
> > > > > I'm working with FFC for quite a while and I like the easy way to
> > > handle
> > > > > multilinear forms with the help of FFC.
> > > > > 
> > > > > But now I have a problem where I'm not sure if it is possible to
> > > > > programme this with FFC.
> > > > > 
> > > > > I'm working on an optimal control problem where I have to solve an
> > > > > integral over just a part of the whole twodimensional domain (x,y)
> > > \in
> > > > > \Omega. So what I need is the bilinear form
> > > > > 
> > > > > \int_{y_0}^{y_1} u*v dy where [y_0,y_1] \in \Omega
> > > > > 
> > > > > Is it possible to implement something like that in FFC and how can I
> > > do
> > > > > that?  
> > > > > 
> > > > > Hope somebody can help me?!
> > > > 
> > > > Yes, that's easy (but not so well documented I admit).
> > > > 
> > > > The simplest way is to just supply a SubDomain as argument to the
> > > assembler:
> > > > 
> > > >   assemble(A, form, mesh, sub_domain);
> > > > 
> > > > Create a SubDomain which overloads the inside() function, returning
> > > > True when you are inside your subdomain, for example
> > > > 
> > > >   class MySubDomain : public SubDomain
> > > >   {
> > > >     bool inside(const real* x, bool on_boundary) const
> > > >     {
> > > >       return x[0] + x[1] > 1.0;
> > > >     }
> > > >   };  
> > > > 
> > > > If you can't specify your domain based on an expression, you need to
> > > > create a MeshFunction that labels which cells are included in your
> > > > domain.
> > > > 
> > > > It's also possible to have different integrals over different
> > > > subdomains, integrals over subsets of the boundary etc.
> > > > 
> > > 
> > > Thanks for your respond. But it seems like it would not work.
> > > 
> > > If I do
> > > 
> > > #include <iostream>
> > > #include <fstream>
> > > #include <sstream>
> > > #include <vector>
> > > 
> > > #include <dolfin.h>
> > > #include <dolfin/dolfin_mf.h>
> > > 
> > > 
> > > #include "MassMatrix2D.h"
> > > 
> > > using namespace dolfin;
> > > using namespace std;
> > > 
> > > 
> > > class MySubDomain : public SubDomain
> > > {
> > >         bool inside(const dolfin::real *x, bool on_boundary) const
> > >         {       
> > >         return true;    
> > >         }
> > > };
> > > 
> > > int main(int argc, char* argv[])
> > > {
> > >   dolfin_init(argc, argv);
> > >   Mesh mesh("cylinder_10.xml");
> > > 
> > >   int inode = mesh.numVertices();
> > >   PETScMatrix K;
> > >   MassMatrix2DBilinearForm a;
> > >   MySubDomain subDomain;
> > >   assemble(K, a, mesh, subDomain);
> > > }
> > > 
> > > I get there error message
> > > 
> > > | Assembling over cells                                           |
> > > |-----------------------------------------------------------------| 0.0%
> > > [0]PETSC ERROR:
> > > ------------------------------------------------------------------------
> > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
> > > probably memory access out of range
> > > [0]PETSC ERROR: Try option -start_in_debugger or
> > > -on_error_attach_debugger
> > > [0]PETSC ERROR: or see
> > > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors
> > > [0]PETSC ERROR: likely location of problem given in stack below
> > > [0]PETSC ERROR: ---------------------  Stack Frames
> > > ------------------------------------
> > > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not
> > > available,
> > > [0]PETSC ERROR:       INSTEAD the line number of the start of the
> > > function
> > > [0]PETSC ERROR:       is given.
> > > [0]PETSC ERROR: --------------------- Error Message
> > > ------------------------------------
> > > [0]PETSC ERROR: Signal received!
> > > [0]PETSC ERROR:
> > > ------------------------------------------------------------------------
> > > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 8, Fri Nov 16
> > > 17:03:40 CST 2007 HG revision:
> > > 414581156e67e55c761739b0deb119f7590d0f4b      
> > > ...
> > > 
> > > But I should get the same result as I would get if I woulde assemble
> > > over the whole domain or???
> > > It does also not work if would compile it with your little example. So
> > > is it possible that there is a bug in one of the functions?!
> > > 
> > > Anne                                                    
> > 
> > Works for me. Take a look in
> > 
> >   sandbox/misc/
> > 
> > Does this give you a segmentation fault?
> 
> I think there was a misunderstanding. I'm able to assemble the Stiffness
> and Mass Matrix over the whole domain. 
> But it doesn't work for any(!) subdomain.
> 
> I had a look in
> 
> sandbox/misc
> 
> but there the whole Stiffness Matrix is assembled (and not just a part).
> This works fine, but as soon as I use 
> 
>  assemble(K, a, mesh, subDomain);

But isn't this exactly the line which is in the sandbox?

  assemble(A, a, mesh, subDomain);

???

-- 
Anders


> I get a segmentation fault. So first I thought was that my
> implementation of the subDomain was wrong. So I tried 
> 
>  class MySubDomain : public SubDomain
> {         bool inside(const dolfin::real *x, bool on_boundary) const
>         {       
>          return true;    
>          }
>  };
> 
> Now I thought I would get the WHOLE Stiffness Matrix (or what ever I had
> as a ffc form). But I got a segmentation fault again. How is that
> possible?
> 
> If you like you can try it by yourself. Here is my main-program 
> 
> 
> #include <dolfin.h>
> 
> 
> #include "MassMatrix2D.h"
> 
> using namespace dolfin;
> 
> class MySubDomain : public SubDomain
> {
> 	bool inside(const dolfin::real *x, bool on_boundary) const
> 	{	
> 	return true;	
> 	}
> };
> 
> int main(int argc, char* argv[])
> {
>   dolfin_init(argc, argv);
>   UnitSquare mesh(10, 10);
> 
>   int inode = mesh.numVertices();
>   PETScMatrix K;
>   MassMatrix2DBilinearForm a;
>   MySubDomain subDomain;
>   assemble(K, a, mesh, subDomain);
> 
>   return 0;
> }
> 
> 
> You just have to include the MassMatrix2D.h ( src/kernel/mf/ffc-forms ).
> I think there is something wrong in the assemble function but of course
> I'm not sure...
> 
> It would be great if you would be able to help!
> 
> Thanks Anne
>

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