dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

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.

> >> 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