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'. Garth > -- > Anders _______________________________________________ Mailing list: https://launchpad.net/~dolfin Post to : dolfin@lists.launchpad.net Unsubscribe : https://launchpad.net/~dolfin More help : https://help.launchpad.net/ListHelp
