dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On 6 September 2011 19:04, Anders Logg <logg@xxxxxxxxx> 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.
>

Because 'markers' leads one to believe that it's a boolean or integer.

>> > 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.
>

No need for a look up, just iterate over the map.

>> > 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.
>

Could you be precise about which class functions belong to and the
argument types for the above point?

Garth

>> >> 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
>