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 <[email protected]> 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... :-) -- Anders _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : [email protected] Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
