dolfin team mailing list archive

[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
> 
>> --
>> Anders
>>
> 
> 
> _______________________________________________
> Mailing list: https://launchpad.net/~dolfin
> Post to    : dolfin@xxxxxxxxxxxxxxxxxxx <mailto:dolfin@xxxxxxxxxxxxxxxxxxx>
> Unsubscribe : https://launchpad.net/~dolfin
> More help  : https://help.launchpad.net/ListHelp
> 
>