On Sat, Aug 27, 2011 at 09:47:14AM +0200, Anders Logg wrote: > On Fri, Aug 26, 2011 at 06:54:31PM -0700, Garth N. Wells wrote: > > > > > > On 26/08/11 07:27, Anders Logg wrote: > > > On Fri, Aug 26, 2011 at 07:11:11AM -0400, Garth N. Wells wrote: > > >> > > >> > > >> On 26/08/11 02:39, Anders Logg wrote: > > >>> On Thu, Aug 25, 2011 at 05:57:51PM -0400, Garth N. Wells wrote: > > >>>> > > >>>> > > >>>> On 25/08/11 16:53, Anders Logg wrote: > > >>>>> On Thu, Aug 25, 2011 at 09:59:44AM -0400, Garth N. Wells wrote: > > >>>>> > > >>>>>>>>> How about using DOM everywherme and reserve the use of SAX for an > > >>>>>>>>> XML->HDF5 converter? > > >>>>>>>>> > > >>>>>>>> > > >>>>>>>> That could be OK, but if we have the to implement a SAX parser it's > > >>>>>>>> probably easiest to have it in DOLFIN anyway. I don't see the > > >>>>>>>> advantage > > >>>>>>>> over having the SAX parser with the io code. > > >>>>>>> > > >>>>>>> I agree we should keep it in DOLFIN, but if the only thing it needs > > >>>>>>> to > > >>>>>>> do is extract data and spit out HDF5, I imagine it can be simpler > > >>>>>>> than > > >>>>>>> the current parser since it doesn't need to be parallel. (?) > > >>>>>>> > > >>>>>> > > >>>>>> To make things clearer, I've just renamed the LocalMeshData parsers > > >>>>>> to > > >>>>>> > > >>>>>> XMLLocalMeshDOM (was XMLLocalMeshData) > > >>>>>> > > >>>>>> and > > >>>>>> > > >>>>>> XMLLocalMeshSAX (was XMLLocalMeshDataDistributed) > > >>>>> > > >>>>> That's good. > > >>>>> > > >>>>>> When XMLLocalMeshSAX is complete, it may be desirable to remove > > >>>>>> XMLLocalMeshDOM. > > >>>>> > > >>>>> Either way is fine for me, as long as we decide which one to use. I > > >>>>> initially wanted to use SAX (as before) but the DOM looks easier and > > >>>>> may be enough if we plan to use HDF5 for large-scale problems anyway. > > >>>>> Or is it the case that DOM is a limitation even for medium sized > > >>>>> problems? > > >>>>> > > >>>> > > >>>> It works for 'medium' (very arbitrary) size problems. > > >>>> > > >>>>>> I don't know what you mean by parallel - the XMLLocalMeshSAX works in > > >>>>>> the same way as the old parser (each process reading a chunk). I > > >>>>>> don't > > >>>>>> see how it can be made simpler by reading a XML file and then > > >>>>>> converting > > >>>>>> to HDF5. The steps that are there now will all still be required to > > >>>>>> read > > >>>>>> the XML mesh before writing a HDF file. > > >>>>> > > >>>>> I don't know HDF, but I imagine one could write one single file and > > >>>>> HDF will handle parallel parsing of that file later. Then the > > >>>>> conversion script we write does not need to do anything parallel, just > > >>>>> read line by line and convert from one format to another. > > >>>>> > > >>>> > > >>>> It may not be possible to do it line-by-line (I don't know, but I > > >>>> wouldn't want to bank on it). Even if line-by-line is technically > > >>>> possible, it could turn out to be terribly slow. We should support that > > >>>> a mesh can be read into memory (distributed), and written to HDF5. > > >>>> > > >>>> Since we'll have support for writing HDF5 meshes, if we can read a > > >>>> large > > >>>> XML mesh then we can re-use the HDF5 output code to make the > > >>>> conversion. > > >>>> > > >>>> I've removed the DOM-based LocalMeshData parser - there is no point to > > >>>> it since we can just read the mesh on one process using XMLMesh and use > > >>>> it to construct a dolfin::XMLLocalMeshData object. > > >>> > > >>> ok, looks good. > > >>> > > >>> How should we store boundary indicators? I'm not sure whether it needs > > >>> to be stored as part of ParallelData. Is it really "parallel data"? > > >>> ParallelData will for sure need to be used to compute it (convert > > >>> somehow from the input) but it seems it can then be stored > > >>> locally. > > >> > > >> OK. It's not really parallel data (but perhaps ParallelData should be > > >> renamed). > > >> > > >>> Each facet just needs to know its indicator value. > > >>> > > >>> The input is a list of triples: > > >>> > > >>> (indicator, facet_cell, facet_number) > > >>> > > >>> This indicates that local facet number `facet_number` of the cell > > >>> `facet_cell` should have the indicator value (sub domain number) > > >>> `indicator`. > > >>> > > >> > > >> Let's make it generic: > > >> > > >> (parent_cell_index, entity_dim, local_entity_index, indicator/value) > > > > > > Yes, that looks good. What about the XML format? It becomes unwieldy > > > to store it as 4 different MeshFunctions. Here's an initial sketch: > > > > > > <mesh> > > > # cells and vertices here as before > > > <data> > > > # user data here as before > > > </data> > > > <indicators dim="..."> > > > <indicator cell="..." local_entity_index="..." value="..."> > > > <indicator cell="..." local_entity_index="..." value="..."> > > > <indicator cell="..." local_entity_index="..." value="..."> > > > <indicator cell="..." local_entity_index="..." value="..."> > > > </indicators> > > > <indicators dim="..."> > > > <indicator cell="..." local_entity_index="..." value="..."> > > > <indicator cell="..." local_entity_index="..." value="..."> > > > <indicator cell="..." local_entity_index="..." value="..."> > > > <indicator cell="..." local_entity_index="..." value="..."> > > > </indicators> > > > ... > > > </mesh> > > > > > > > That looks OK, except for the name 'indicator(s)'. > > > > Essentially what it is is a MeshFunction that is defined only on a > > subset of entities of a given dimension. I think we should template it > > on the C++ side so that any data can be attached. We should then have > > > > <indicators dim="..." type="..."> > > > > (but with something other than 'indicators'). Internally, there may be > > no need to construct a MeshFunction. > > > > > > >> It could go into MeshData (possibly with what's in ParallelData), and > > >> the current MeshData could be renamed to something like 'UserMeshData'. > > > > > > I think it's better to keep the name MeshData for user-defined data > > > (and internal DOLFIN data stored there in waiting for a proper place > > > to store it). mesh.data() is used in many places in user code. > > > > > > It would be better to each time we decide to amend the Mesh class with > > > new data to add a proper class to hold it, like ParallelData (possibly > > > renamed). How about a new class called "MeshIndicators" to hold mesh > > > indicators. It would need to handle initialization from various > > > sources of input data, in particular MeshFunctions, which is then > > > converted to some proper internal representation. The MeshIndicator > > > class should be "parallel aware" and not need any special extras in > > > ParallelData. > > > > > > > All fine if we can find a more appropriate name than 'Indicator'. > > How about SubsetFunction and we template it the same way as we do > MeshFunctions? > > Or SubsetIndicators.
Or perhaps it's "markers"? So we add a class MeshMarkers that holds all markers and make it a member of the Mesh class. And the XML format would be <markers dim="..." type="..." size="..."> </markers> I've added "size" so we can preallocate when parse. -- Anders _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : [email protected] Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
