dolfin team mailing list archive

[Johan Hake <johan.hake@xxxxxxxxx>]

On Tuesday September 6 2011 11:04:23 Anders Logg wrote:
> On Tue, Sep 06, 2011 at 05:45:33PM +0100, Garth N. Wells wrote:
> > On 6 September 2011 17:31, Johan Hake <johan.hake@xxxxxxxxx> wrote:
> > > On Monday September 5 2011 00:09:58 Anders Logg wrote:
> > >> On Sun, Sep 04, 2011 at 11:23:04PM -0700, Johan Hake wrote:
> > >> > On Friday September 2 2011 23:19:22 Anders Logg wrote:
> > >> > > On Fri, Sep 02, 2011 at 02:35:57PM -0700, Johan Hake wrote:
> > >> > > > What is the different between a MeshMarker and a MeshFunction?
> > >> > > > Is MeshMarker a MeshFunction but instead of storing the values
> > >> > > > in line with its global entity index it stores it wrt the
> > >> > > > global cell entity index together with its local entity index?
> > >> > > 
> > >> > > Yes, that and values don't need to be stored on the entire mesh,
> > >> > > only for a subset, so you can mark just 3 facets without needing
> > >> > > to store markers for a million facets.
> > >> > 
> > >> > ok, I will see what I can do.
> > >> 
> > >> Thanks!
> > >> 
> > >> > > Copy paste from the MeshMarker docstring:
> > >> > >   /// The MeshMarkers class can be used to store data associated
> > >> > > with /// a subset of the entities of a mesh of a given
> > >> > > topological /// dimension. It differs from the MeshFunction class
> > >> > > in two ways. /// First, data does not need to be associated with
> > >> > > all entities /// (only a subset). Second, data is associated with
> > >> > > entities /// through the corresponding cell index and local
> > >> > > entity number /// (relative to the cell), not by global entity
> > >> > > index, which means /// that data may be stored robustly to file.
> > >> > > 
> > >> > > > Also, will this take over for the way we use MeshFunctions in
> > >> > > > the assembler, or will a MeshFunction be generated by a
> > >> > > > MeshMarker before assemble gets called?
> > >> > > 
> > >> > > I think we will do that as a first step (convert from MeshMarker
> > >> > > to MeshFunction) since then we don't need to touch the assembler.
> > >> > > Then later we can think about using MeshMarkers directly.
> > >> > 
> > >> > Ok.
> > >> > 
> > >> > > > I think I also get confused with the naming here. If my
> > >> > > > explaination of what MeshMarker is doing is correct, a
> > >> > > > MeshMarker and a MeshFunction are essentially doing the same
> > >> > > > thing. What differs is the way the data is stored. This is not
> > >> > > > reflected in the naming of the classes
> > >> > > 
> > >> > > It was the best I could come up with. Feel free to suggest
> > >> > > something else. SubsetMeshFunction would also be confusing since
> > >> > > it's not really a MeshFunction.
> > >> > > 
> > >> > > Either way, I expect the MeshMarkers class to be used mostly
> > >> > > internally by the MeshDomains class.
> > >> > 
> > >> > Ok.
> > >> > 
> > >> > Not sure these are better, but they might reflect the difference
> > >> > between this guy and a MeshFunction in a slightly more intuitive
> > >> > way.
> > >> > 
> > >> >   MeshEntityFunction, LocalMeshEntityFunction, LocalMeshFunction,
> > >> >   SubMeshFunction
> > >> 
> > >> I'm not sure those are much better, and I don't think it would be
> > >> correct to call them something containing "Function" since they are
> > >> not really functions. With a MeshFunction, one can input x (a mesh
> > >> entity) and get y = f(x) (the value of the MeshFunction at that
> > >> entity). That's not possible with MeshMarkers; they are just a
> > >> collection of markers, not really a function since the value is only
> > >> defined on a subset and one would need to loop through the list of
> > >> values to get the value at any entity where the value is actually
> > >> defined.
> > > 
> > > What with MeshValueCollection? As it is a templated class I do not
> > > think Marker is an appropriated name.
> > 
> > Agree.
> > 
> > > 'Collection' says that the class is not
> > > defined over the whole Mesh.
> 
> I don't see what the templating has to do with the name "markers" but
> MeshValueCollection sounds good.
> 
> > > Two questions:
> > > 
> > > How can the following code work:
> > > 
> > >      // Get marker data
> > >      const std::vector<uint>& marker = _markers[i];
> > >      const uint cell_index   = marker[0];
> > >      const uint local_entity = marker[1];
> > >      const T marker_value    = marker[2];
> > > 
> > > when _markers is declared as:
> > > 
> > >    // The markers
> > >    std::vector<std::pair<std::pair<uint, uint>, T> > _markers;
> 
> The above code doesn't work. I suspect the code hasn't yet been
> instantiated so it wasn't detected by the compiler.
> 
> The markers need to be accessed as follows (from XMLMeshMarkers.h):
> 
>   for (uint i = 0; i < mesh_markers.size(); ++i)
>   {
>     pugi::xml_node entity_node = mf_node.append_child("marker");
>     const std::pair<std::pair<uint, uint>, T>& marker =
>       mesh_markers.get_marker(i);
>     entity_node.append_attribute("cell_index") = marker.first.first;
>     entity_node.append_attribute("local_entity") = marker.first.second;
>     entity_node.append_attribute("marker_value") = marker.second;
>   }
> 
> > The above also permits multiple entries. Perhaps we want
> > 
> >     boost::unordered_map<std::pair<std::pair<uint, uint>, T> > _markers;
> 
> Yes, maybe but I'm not sure what the cost would be for the lookup on
> each cell during assembly.
> 
> > > What is the logic behind:
> > > 
> > >    // Set all value of mesh function to maximum value (not all will
> > >    // be set) by markers below
> > >    mesh_function.set_all(maxval);
> > > 
> > > Isn't it more natural to initiate the values to zero? Also it makes no
> > > sense in conjunction with boundary markers. Then all boundary faces
> > > gets marked with the largest marker value. I cannot see how that could
> > > be correct.
> > 
> > I don't get ' mesh_function.set_all(maxval);' or the code comment.
> 
> The point is that one should be able to define a form with domains say
> dx(0), dx(1) and dx(2) and then have a mesh file that marks a subset
> of the cells with '0', '1' and '2'.
> 
> Then the conversion to MeshFunction inserts '3' for all other
> (unmarked) cells. This allows a user to specify only the interesting
> cells and no need to mark the rest with -1 or None or similar.

That would make sense if the code would be:

  mesh_function.set_all(maxval+1);

Johan

> > >> So MeshMarkers may not be that bad. I'm starting to get used to
> > >> it... :-)
> > > 
> > > That's what worries me :)
> > 
> > Me too (worried, that is).
> 
> Don't worry.
> 
> --
> Anders