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 <[email protected]>: > >> 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 <[email protected]> > >>> *To:* Anders Logg <[email protected]> > >>> *Cc:* dolfin-dev <[email protected]> > >>> *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 <[email protected] > >>> <mailto:[email protected]>> 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 > >>> > >>>> > >>> > >>> > >>> _______________________________________________ > >>> Mailing list: https://launchpad.net/~dolfin > >>> Post to : [email protected] > >>> <mailto:[email protected]> > >>> Unsubscribe : https://launchpad.net/~dolfin > >>> More help : https://help.launchpad.net/ListHelp > >>> > >>> > >> > >> > >> _______________________________________________ > >> Mailing list: https://launchpad.net/~dolfin > >> Post to : [email protected] > >> Unsubscribe : https://launchpad.net/~dolfin > >> More help : https://help.launchpad.net/ListHelp > > > _______________________________________________ > Mailing list: https://launchpad.net/~dolfin > Post to : [email protected] > Unsubscribe : https://launchpad.net/~dolfin > More help : https://help.launchpad.net/ListHelp _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : [email protected] Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
