dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Tue, Jun 23, 2009 at 09:25:19AM +0200, Kent Andre wrote:
> On ma., 2009-06-22 at 20:57 +0200, Anders Logg wrote:
> > On Mon, Jun 22, 2009 at 12:46:09PM -0600, Bartosz Sawicki wrote:
> > > Kent Andre wrote:
> > > > On ma., 2009-06-22 at 00:40 -0600, Bartosz Sawicki wrote:
> > > >> On 22/06/09 12:06 AM, Anders Logg wrote:
> > > >>> On Sun, Jun 21, 2009 at 11:36:29PM -0600, Bartosz Sawicki wrote:
> > > >>>> On 19/06/09 02:53 PM, kent-and@xxxxxxxxx wrote:
> > > >>>>> When using VMTK the boundary indicators are stored as a set of arrays
> > > >>>>> with names
> > > >>>>> boundary facet cells,
> > > >>>>> boundary facet numbers
> > > >>>>> boundary indicators
> > > >>>>> The two first arrays are used to find the global facet numbers.
> > > >>>>> The function computes a mesh function based on these arrays.
> > > >>>>>
> > > >>>>> This was what Anders prefered since VMTK does not now anything
> > > >>>>> about the global numbering of facets in Dolfin (without linking it into
> > > >>>>> Dolfin).
> > > >>>>>
> > > >>>>> This is not a VMTK specific problem, but I do think VMTK is the only
> > > >>>>> mesh-generator
> > > >>>>> that let you store boundary indicators at the moment. I guess we should add
> > > >>>>> this to NetGen as well, both Hans Petter Langtangen and Douglas Arnold has
> > > >>>>> bugged
> > > >>>>> me about this the last few days.
> > > >>>> I'm every day user of this functionality. I use Netgen generated models, 
> > > >>>> but also other software which add boundary indicators to existing 
> > > >>>> meshes. Netgen supports boundary indicators quite well, both by geo 
> > > >>>> files, and by GUI. I don't understand what you want to add?
> > > >>> Is it possible to set DOLFIN boundary indicators from Netgen? I didn't
> > > >>> know.
> > > >> It is definitely possible :) I don't have direct converter from Netgen 
> > > >> vol to Dolfin xml. Most of my old models were stored in Diffpack grid 
> > > >> format, so I'm using grid to xml converter.
> > > >> Netgen can export to the grid format, so this is not a big issue.
> > > > 
> > > > It is not possible to store the boundary indicators in Dolfin format
> > > > using Netgen, at  the current time. I wrote the Netgen -> dolfin filter
> > > > in Netgen so I should know :).  
> > > > 
> > > > But it should be possible to include support for that in a similar
> > > > fashion as we did in VMTK. 
> > > 
> > > You are right that Netgen doesn't support Dolfin XML mesh format. But it 
> > > doesn't mean that is not possible to use boundary indicators generated 
> > > by Netgen in Dolfin. Converterting via Diffpack grid file preserves 
> > > boundaries.
> > > 
> > > The algoritm is simple:
> > > 1. Generate mesh using Netgen.
> > > 2. Mark boundaries indicators.
> > > 3. Export to Diffpack format.
> > > 4. Convert Diffpack to XML.
> > > 5. Enjoy boundary indicators in Dolfin.
> > > 
> > > cheers,
> > 
> > Nice, but not optimal. At some point, we need an application that can
> > do all of these (and more). There seem to be a couple of different
> > options:
> > 
> >   1. Extend Netgen with full support for DOLFIN (and change the toolkit...) 
> >   2. Extend Gmsh with full support for DOLFIN (and change the toolkit...)
> >   3. Extend MeshBuilder to do mesh generation (using for example Netgen)
> >   4. ?
> > 
> > Any thoughts on these options?
> > 
> > The problem with (3) is that no one is really developing MeshBuilder,
> > except when we pay Kalkulo (http://simula.no/applications/kalkulo/) to
> > do it.
> > 
> 
> It should be fairly easy to include bc indicators in NetGen. I can look
> at it, I think I need to update the filter anyway to make sure the mesh
> is ordered correctly according to UFC. 
> 
> In general it is rather easy to write out the mesh and indicators
> compared to actually making it. I bet we can make Gmsh write Dolfin mesh
> in just a few hours (but I have not looked at Gmsh). 
> 
> The Dolfin XML file format needs to be documented. 

Yes, and there's some ongoing work on creating schemas and validating
against these schemas when parsing (Relax-NG using libxml2).

Ilmar has been working on it but I don't know the current
status. Ilmar? Ola?

-- 
Anders

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