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....@gmail.com> > *To:* Anders Logg <l...@simula.no> > *Cc:* dolfin-dev <dolfin@lists.launchpad.net> > *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 <l...@simula.no > <mailto:l...@simula.no>> 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@lists.launchpad.net <mailto:dolfin@lists.launchpad.net> > Unsubscribe : https://launchpad.net/~dolfin > More help : https://help.launchpad.net/ListHelp > > _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : dolfin@lists.launchpad.net Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
