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