dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Tue, Sep 13, 2011 at 11:25:00AM -0700, Johan Hake wrote:
> On Tuesday September 13 2011 11:15:06 Anders Logg wrote:
> > On Tue, Sep 13, 2011 at 10:51:28AM -0700, Johan Hake wrote:
> > > On Tuesday September 13 2011 10:21:24 Anders Logg wrote:
> > > > On Tue, Sep 13, 2011 at 10:18:58AM -0700, Johan Hake wrote:
> > > > > On Tuesday September 6 2011 14:01:10 Anders Logg wrote:
> > > > > > On Tue, Sep 06, 2011 at 01:57:20PM -0700, Johan Hake wrote:
> > > > > > > On Tuesday September 6 2011 13:47:02 Anders Logg wrote:
> > > > > > > > On Tue, Sep 06, 2011 at 12:21:03PM -0700, Johan Hake wrote:
> > > > > > > > > On Tuesday September 6 2011 12:18:33 Anders Logg wrote:
> > > > > > > > > > On Tue, Sep 06, 2011 at 11:31:03AM -0700, Johan Hake wrote:
> > > > > > > > > > > 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);
> > > > > > > > > >
> > > > > > > > > > Yes, that is the intention! Thanks for proofreading my code
> > > > > > > > > > before I've even had a chance to test it. :-)
> > > > > > > > > :
> > > > > > > > > :)
> > > > > > > > >
> > > > > > > > > You gave the impression that it was test when you asked me to
> > > > > > > > > wrap it to Python. Give me a ping when it is ready and I will
> > > > > > > > > have a bite at the SWIG code.
> > > > > > > >
> > > > > > > > I wanted the Python wrappers so that I could write the unit
> > > > > > > > tests for it (in Python) and then find the bugs... :-)
> > > > > > >
> > > > > > > Ahhh!
> > > > > > >
> > > > > > > You fix the backward compatability of the file format of the
> > > > > > > MeshFunction and I start on the SWIG code. Deal?
> > > > > >
> > > > > > Deal! But not until after tomorrow. I have a paper I need to
> > > > > > revise.
> > > > >
> > > > > Where should I push my fix? To
> > > > >
> > > > >   lp:~dolfin-core/dolfin/logg
> > > > >
> > > > > ?
> > > >
> > > > I've merged with trunk so you can just push there.
> > >
> > > Pushed it to trunk. You need to enable the unit test and fix some errors
> > > which is throwned from the C++ code. :) Also see a README in
> > > MeshValueCollection.h.
> >
> > Thanks! That was fast! I will look at it tomorrow.
>
> Ctrl-w Ctrl-y + Meta-% MeshFunction MeshValueCollection
>
> Is bleeding fast!

I thought about it but I didn't dare... :-)

--
Anders