dolfin team mailing list archive

[Johan Hake <681415@xxxxxxxxxxxxxxxxxx>]

On Monday November 29 2010 10:23:43 Mikael Mortensen wrote:
> On 29 November 2010 17:06, Johan Hake <681415@xxxxxxxxxxxxxxxxxx> wrote:
> > On Monday November 29 2010 00:35:27 Mikael Mortensen wrote:
> > > Please don't.
> > > 
> > > The subspace functionality is used for example to compute the
> > > streamfunction, where the subspace of the velocity VectorFunctionSpace
> > > is used. I also use the subspace functionality to assemble into parts
> > > of the Navier-Stokes coefficient matrix componentwise. For example
> > > 
> > > uc = TrialFunction(V.sub(0))
> > > vc = TestFunction(V.sub(0))
> > > a = assemble(inner(grad(uc), grad(vc))*dx)
> > > 
> > > and then I can copy this 'small' matrix to the three diagonal slots of
> > > the 3*3 Laplacian matrix that makes up for the whole velocity
> > > vectorfield. I understand this is not the regular way of assembling,
> > > but it is much faster than switching V.sub(0) above to V and
> > > assembling the whole thing by itself.
> > 
> > What hinders you to do:
> >  Vs = FunctionSpace(mesh, "CG", 1)
> >  V  = MixedFunctionSpace([Vs]*3)
> >  ...
> >  uc = TrialFunction(Vs)
> >  vc = TestFunction(Vs)
> >  
> >   a = assemble(inner(grad(uc), grad(vc))*dx)
> 
> Nothing really. I used to do that. However, I want to be able to grab the
> velocity subpace when I'm computing the streamfunction as I want to use the
> same functionspace for the streamfunction as a velocity-component to avoid
> any interpolation. I understand that it's not strictly necessary, it's just
> a nice functionality the way I see it and I can use the same
> streamfunction-code for all velocity-functionspaces.

Ok.

What if we keep the original subspaces (without offset) in a protected
list.

  _spaces = [Vs0, Vs1, Vs2]

Then we add a kwarg: 'with_offset=True' to the 'sub' method. If 'with_offset' 
is False we just return the "original" subspace without offset. You then need 
to change your code to:

  uc = TrialFunction(V.sub(0, False))
  vc = TestFunction(V.sub(0, False))
  a = assemble(inner(grad(uc), grad(vc))*dx)

Then we make it impossible to instantiate a Function, TrialFunction, 
TestFunction with a FunctionSpace including an offset. 

How do I read out from a FunctionSpace that it includes a ufc offset?

This will diverge the C++ and Python implementation more...

Johan

> Mikael
> 
> > Johan
> > 
> > --
> > Problem using sub-spaces
> > https://bugs.launchpad.net/bugs/681415
> > You received this bug notification because you are a member of DOLFIN
> > Team, which is subscribed to DOLFIN.
> > 
> > Status in DOLFIN: Confirmed
> > 
> > Bug description:
> > Hi,
> > 
> > I have trouble using MixedFunctionSpace. Basically I want to project a
> > 
> > function to a subspace of a MixedFunctionSpace:
> >   from dolfin import *
> >   mesh=UnitInterval(10)
> >   U = FunctionSpace(mesh, "CG", 1)
> >   V = FunctionSpace(mesh, "CG", 1)
> >   W=U*V
> >   f1=Function(W.sub(0))
> >   f1.vector()[:]=1.0
> >   #f2=project(f1, V)   # This works!
> >   f2=project(f1, W.sub(1))  # This doesn't!
> > 
> > The output of that script is attached to the end of this question. Now,
> > the confusing thing is that the projection works fine if one projects to
> > V instead of W.sub(1), although they are mathematically the same spaces.
> > 
> > I hope I haven't missed a similar question already reported.
> > 
> > Best wishes,
> > 
> > Simon
> > 
> > 
> > [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]PETSCERROR: or try http://valgrind.org on GNU/linux and Apple
> > Mac OS X to find memory corruption errors
> > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link,
> > and run
> > [0]PETSC ERROR: to get more information on the crash.
> > [0]PETSC ERROR: --------------------- Error Message
> > ------------------------------------
> > [0]PETSC ERROR: Signal received!
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun  4 15:34:52
> > CDT 2010
> > [0]PETSC ERROR: See docs/changes/index.html for recent updates.
> > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
> > [0]PETSC ERROR: See docs/index.html for manual pages.
> > [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: Unknown Name on a linux-gnu named doodson by sf1409 Thu
> > Nov 25 13:17:44 2010
> > [0]PETSC ERROR: Libraries linked from
> > /build/buildd/petsc-3.1.dfsg/linux-gnu-c-opt/lib
> > [0]PETSC ERROR: Configure run at Fri Sep 10 04:57:14 2010
> > [0]PETSC ERROR: Configure options --with-shared --with-debugging=0
> > --useThreads 0 --with-clanguage=C++ --with-c-support
> > --with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi
> > --with-mpi-shared=1 --with-blas-lib=-lblas --with-lapack-lib=-llapack
> > --with-umfpack=1 --with-umfpack-include=/usr/include/suitesparse
> > --with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]"
> > --with-spooles=1 --with-spooles-include=/usr/include/spooles
> > --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1
> > --with-hypre-dir=/usr --with-scotch=1
> > --with-scotch-include=/usr/include/scotch
> > --with-scotch-lib=/usr/lib/libscotch.so --with-hdf5=1
> > --with-hdf5-dir=/usr [0]PETSC ERROR:
> > ------------------------------------------------------------------------
> > [0]PETSC ERROR: User provided function() line 0 in unknown directory
> > unknown file
> > -------------------------------------------------------------------------
> > - MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> > with errorcode 59.
> > 
> > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> > You may or may not see output from other processes, depending on
> > exactly when Open MPI kills them.
> > -------------------------------------------------------------------------
> > -
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Mailing list:
> > https://launchpad.net/~dolfin<https://launchpad.net/%7Edolfin> Post to  
> >   : dolfin@xxxxxxxxxxxxxxxxxxx
> > Unsubscribe :
> > https://launchpad.net/~dolfin<https://launchpad.net/%7Edolfin> More help
> >   : https://help.launchpad.net/ListHelp

-- 
Problem using sub-spaces
https://bugs.launchpad.net/bugs/681415
You received this bug notification because you are a member of DOLFIN
Team, which is subscribed to DOLFIN.

Status in DOLFIN: Confirmed

Bug description:
Hi,

I have trouble using MixedFunctionSpace. Basically I want to project a function to a subspace of a MixedFunctionSpace:

   from dolfin import *
   mesh=UnitInterval(10)
   U = FunctionSpace(mesh, "CG", 1)
   V = FunctionSpace(mesh, "CG", 1)
   W=U*V
   f1=Function(W.sub(0))
   f1.vector()[:]=1.0
   #f2=project(f1, V)   # This works!
   f2=project(f1, W.sub(1))  # This doesn't!


The output of that script is attached to the end of this question. Now, the confusing thing is that the projection works fine if one projects to V instead of W.sub(1), although they are mathematically the same spaces. 

I hope I haven't missed a similar question already reported. 

Best wishes,

Simon


[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 GNU/linux and Apple Mac OS X to find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run 
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: --------------------- Error Message ------------------------------------
[0]PETSC ERROR: Signal received!
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.1.0, Patch 3, Fri Jun  4 15:34:52 CDT 2010
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Unknown Name on a linux-gnu named doodson by sf1409 Thu Nov 25 13:17:44 2010
[0]PETSC ERROR: Libraries linked from /build/buildd/petsc-3.1.dfsg/linux-gnu-c-opt/lib
[0]PETSC ERROR: Configure run at Fri Sep 10 04:57:14 2010
[0]PETSC ERROR: Configure options --with-shared --with-debugging=0 --useThreads 0 --with-clanguage=C++ --with-c-support --with-fortran-interfaces=1 --with-mpi-dir=/usr/lib/openmpi --with-mpi-shared=1 --with-blas-lib=-lblas --with-lapack-lib=-llapack --with-umfpack=1 --with-umfpack-include=/usr/include/suitesparse --with-umfpack-lib="[/usr/lib/libumfpack.so,/usr/lib/libamd.so]" --with-spooles=1 --with-spooles-include=/usr/include/spooles --with-spooles-lib=/usr/lib/libspooles.so --with-hypre=1 --with-hypre-dir=/usr --with-scotch=1 --with-scotch-include=/usr/include/scotch --with-scotch-lib=/usr/lib/libscotch.so --with-hdf5=1 --with-hdf5-dir=/usr
[0]PETSC ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD 
with errorcode 59.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------