dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Wed, Jan 30, 2013 at 08:24:20PM +0100, Johan Hake wrote:
> The fix is not released. So you need to check out the 1.1.x branch.
>
>   bzr branch lp:dolfin/1.1.x dolfin-1.1.x
>
> and compiled from source.
>
> An alternative would be to make a point release from the 1.1.x branch.
> Then that could propagate into an updated ppa package.
>
> What do the other developer says?

Yes, we should feel free to make releases from the 1.1.x branch
whenever we have fixed bugs or added useful features.

--
Anders



> Johan
>
> On 01/30/2013 07:10 PM, Maximilian Albert wrote:
> > Hi Johan,
> >
> > thanks for this recipe, that's exactly what I have been searching for
> > a while because we're having similar problems to Pietro. When you say
> > you will backport this change to 1.1, does that mean there will be an
> > updated package in the PPA available sometime soon? Also, until then
> > is there a similar recipe for how to achieve this with the current (=
> > 1.1.0) version of dolfin?
> >
> > Many thanks,
> > Max
> >
> > 2013/1/29 Johan Hake <hake.dev@xxxxxxxxx>:
> >> On 01/29/2013 10:00 PM, Pietro Maximoff wrote:
> >>> Hi
> >>>
> >>> Johan, thanks for adding this.
> >>>
> >>> This function is particularly important for me as currently, all my code
> >>> is broken in Fenics 1.1.
> >>>
> >>> I need to be able to associate each component of a 'solution' vector
> >>> with a coordinate value, carry out some processing and store data back
> >>> in exactly the same order in the 'same' or similar solution vector.
> >>>   compute_vertex_values() doesn't give this functionality but
> >>> tabulate_vertex_map() does this!?!
> >>
> >> Yes. I will soon rename the method to vertex_to_dof_map, however. Then
> >> it will be:
> >>
> >>   vertex_to_dof = V.dofmap().vertex_to_dof_map(mesh)
> >>
> >>   # Use num coordinates to work in parallel
> >>   data = np.zero(len(mesh.num_coordinates()))
> >>   data[vertex_to_dof] = u.vector().array()
> >>
> >>   # Do stuff on data
> >>
> >>   # Put data back
> >>   u.vector().set_local(data[vertex_to_dof])
> >>
> >>> How can I get my hands on it? Do I just use dorsal with stable_build set
> >>> to false?
> >>
> >> I guess so. Once I have changed the name I will back port it to 1.1. It
> >> might be safer to work with that instead of trunk right now, as trunk is
> >> undergoing heavy development.
> >>
> >> I am not sure how to install the latest revision of the lp:dolfin/1.1.x
> >> branch using dorsal. You can get the latest 1.1.x code by:
> >>
> >>   bzr branch lp:dolfin/1.1.x dolfin-1.1.x
> >>
> >> It might be just to copy the dorsal_configure and dorsal_build scripts
> >> to the dolfin-1.1.x dir and run them, as they should contain all
> >> information required to build and configure dolfin.
> >>
> >> Johan
> >>
> >>> Pietro
> >>>
> >>> ------------------------------------------------------------------------
> >>> *From:* Johan Hake <hake.dev@xxxxxxxxx>
> >>> *To:* Anders Logg <logg@xxxxxxxxx>
> >>> *Cc:* dolfin-dev <dolfin@xxxxxxxxxxxxxxxxxxx>
> >>> *Sent:* Monday, January 28, 2013 10:52 PM
> >>> *Subject:* Re: [Dolfin] DofMap.tabulate_vertex_map
> >>>
> >>> On 01/28/2013 11:36 PM, Anders Logg wrote:
> >>>> On Mon, Jan 28, 2013 at 10:33:15PM +0000, Garth N. Wells wrote:
> >>>>> On 28 January 2013 22:27, Anders Logg <logg@xxxxxxxxx
> >>> <mailto:logg@xxxxxxxxx>> wrote:
> >>>>>> On Mon, Jan 28, 2013 at 11:19:13PM +0100, Johan Hake wrote:
> >>>>>>> On 01/28/2013 11:08 PM, Anders Logg wrote:
> >>>>>>>> On Mon, Jan 28, 2013 at 10:37:46PM +0100, Johan Hake wrote:
> >>>>>>>>> On 01/28/2013 10:22 PM, Anders Logg wrote:
> >>>>>>>>>> On Mon, Jan 28, 2013 at 10:10:40PM +0100, Johan Hake wrote:
> >>>>>>>>>>> Hello!
> >>>>>>>>>>>
> >>>>>>>>>>> I have now added a method to DofMap, which tabulate a map between
> >>>>>>>>>>> vertices and dofs. It will only work for DofMaps with dofs on
> >>> vertices.
> >>>>>>>>>>> So basically for any CG 1 FunctionSpaces and will raise error
> >>> else wise.
> >>>>>>>>>>>
> >>>>>>>>>>> Usage:
> >>>>>>>>>>>
> >>>>>>>>>>>  from dolfin import *
> >>>>>>>>>>>  import numpy as np
> >>>>>>>>>>>  mesh = UnitSquareMesh(10,10)
> >>>>>>>>>>>  V = VectorFunctionSpace(mesh, "CG", 1)
> >>>>>>>>>>>  u = Function(V)
> >>>>>>>>>>>  u.interpolate(Constant((1,2)))
> >>>>>>>>>>>  vert_values = np.zeros(mesh.num_vertices()*2)
> >>>>>>>>>>>  vert_values[V.dofmap().tabulate_vertex_map(mesh)] = \
> >>>>>>>>>>>  u.vector().array()
> >>>>>>>>>>>  print vert_values
> >>>>>>>>>>>
> >>>>>>>>>>> In parallel the map will follow the local dofs. This means that
> >>> some
> >>>>>>>>>>> values in vert_values above will still be 0. The 0 values will then
> >>>>>>>>>>> correspond to vertex values which are owned by another process.
> >>>>>>>>>>>
> >>>>>>>>>>> In C++ the method returns a std::vector<std::size_t>.
> >>>>>>>>>>>
> >>>>>>>>>>> Questions:
> >>>>>>>>>>> Does the name "tabulate_vertex_map" work?
> >>>>>>>>>>
> >>>>>>>>>> Sounds ok.
> >>>>>>>>>>
> >>>>>>>>>>> Should a version of this method exist in other classes.
> >>> FunctionSpace,
> >>>>>>>>>>> Function (without the mesh argument of course)?
> >>>>>>>>>>
> >>>>>>>>>> Yes, would be good to have for convenience.
> >>>>>>>>>>
> >>>>>>>>>> What is the relation to Function::compute_vertex_values?
> >>>>>>>>>
> >>>>>>>>> compute_vertex_values works on any GenericFunction. However, for all
> >>>>>>>>> Functions from CG 1 families I guess one could use this map to just
> >>>>>>>>> tabulate the entries.
> >>>>>>>>
> >>>>>>>> What does the tabulate_vertex_map method do which
> >>>>>>>> compute_vertex_values doesn't? Enable writing to dofs?
> >>>>>>>
> >>>>>>> RTFC! ;)
> >>>>>>>
> >>>>>>> tabulate_vertex_map only computes a map based on the prior knowledge of
> >>>>>>> the dofs coinciding with the vertices. compute_vertex_values are much
> >>>>>>> more general and used
> >>>>>>>
> >>>>>>>  element.interpolate_vertex_values
> >>>>>>>
> >>>>>>> to do the heavy lifting.
> >>>>>>
> >>>>>> Yes, so why is tabulate_vertex_map needed, if compute_vertex_values
> >>>>>> already computes the vertex values and is much more general?
> >>>>>>
> >>>>>>> I see tabulate_vertex_map as a convenience mapping for users who want
> >>>>>>> their data on a vertex based format, or users who want data which
> >>>>>>> resides on vertices into dolfin la structures.
> >>>>>>
> >>>>>> What is the use case? If it is for plotting or postprocessing, then
> >>>>>> compute_vertex_values should be enough.
> >>>>>>
> >>>>>> Or is the intention to use it for modifying values of CG1 functions
> >>>>>> from the outside?
> >>>>>>
> >>>>>
> >>>>> I don't think that it's required, but I guess Johan is adding it by
> >>>>> popular demand.
> >>>
> >>> ;)
> >>>
> >>> Well I have a similar mapping in my own tools, and instead of giving
> >>> that code away all the freaking time I pushed it to DOLFIN. My code was
> >>> also Python only and recently we got some C++ request.
> >>>
> >>>> I'm not objecting to it. I just came to think about the
> >>>> compute_vertex_values function and it should be enough to cover most
> >>>> of the use cases that are the background for the popular demand: users
> >>>> of Hans Petter's tutorial who want to get the vertex values on a
> >>>> regular grid for postprocessing in external software like MATLAB.
> >>>
> >>> I think the compute_vertex_values could fill the purpose of most use
> >>> cases, but I think having the mapping available could be nice and
> >>> convenient.
> >>>
> >>> Even if we discourage indexing into vectors, people tend to ignore it,
> >>> because it is often just the natural way to do stuff. Especially for
> >>> Functions in CG1 family spaces. By forcing a user to use local process
> >>> data for all things numpy, we can be useful for both numpy and HPC folks.
> >>>
> >>> Johan
> >>>
> >>>>
> >>>
> >>>
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> >>>
> >>
> >>
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