dolfin team mailing list archive

[Anders Logg <logg@xxxxxxxxx>]

On Fri, Sep 26, 2008 at 05:35:56PM +0200, Niclas Jansson wrote:
> Anders Logg wrote:
> > On Fri, Sep 26, 2008 at 11:35:38AM +0200, Niclas Jansson wrote:
> >> Anders Logg wrote:
> >>> On Mon, Sep 22, 2008 at 06:17:49PM +0200, Anders Logg wrote:
> >>>> On Mon, Sep 22, 2008 at 06:13:34PM +0200, Niclas Jansson wrote:
> >>>>> Anders Logg wrote:
> >>>>>> On Mon, Sep 22, 2008 at 05:03:59PM +0200, Niclas Jansson wrote:
> >>>>>>> Anders Logg wrote:
> >>>>>>>> I'm slowly working my way through PXMLMesh.cpp and I need some
> >>>>>>>> assistance (from Niclas).
> >>>>>>>>
> >>>>>>>> It all looks very good and I'm sure it works perfectly, but some work
> >>>>>>>> is needed to make it possible to read/understand:
> >>>>>>>>
> >>>>>>>> 1. PXMLMesh::closeMesh really needs some commenting. It's a large
> >>>>>>>> chunk of nontrivial and quite complex code so a whole lot of
> >>>>>>>> commenting is needed.
> >>>>>>> I'm working on it.
> >>>>>> ok, nice.
> >>>>>>
> >>>>>>>> 2. Why is the mesh editor closed in PXMLMesh::readCells and then
> >>>>>>>> opened again later in PXMLMesh::closeMesh?
> >>>>>>>>
> >>>>>>>> If we can't write to the mesh until everything is read in, then maybe
> >>>>>>>> we should wait with initializing anything until closeMesh() and at
> >>>>>>>> that point start editing the mesh?
> >>>>>>>>
> >>>>>>> It's a (ugly) workaround due to the static nature of the MeshEditor
> >>>>>>> (number of vertices must be specified a priori). It could of course be
> >>>>>>> fixed by moving the geometric partitioner inside the parser, and only
> >>>>>>> opening the editor inside closeMesh().
> >>>>>>>
> >>>>>>> However the nice solution would be to make the MeshEditor more dynamic.
> >>>>>>> That would also make life easier when implementing a better refinement
> >>>>>>> algorithm (for example, the recursive longest edge bisection (Rivara)
> >>>>>>> from unicorn)
> >>>>>> I agree it would be better to make MeshEditor dynamic. The problem is
> >>>>>> that this is not always needed. Perhaps we should add a new class
> >>>>>> DynamicMeshEditor that can be used when one does not know the number
> >>>>>> of vertices and cells a priori.
> >>>>>>
> >>>>>> It could be very simple, just storing the dynamic data in suitable STL
> >>>>>> containers and then calling MeshEditor in close().
> >>>>>>
> >>>>>>>> 3. I don't understand the logic in readTriangle/readTetrahedron.
> >>>>>>>> What does the following code do?
> >>>>>>>>
> >>>>>>>>   if (!(is_local(v2) || is_local(v1) || is_local(v0)) || !is_local(v0))
> >>>>>>>>     return;
> >>>>>>>>
> >>>>>>>>   used_vertex.insert(v0);
> >>>>>>>>   if (is_local(v1))
> >>>>>>>>     used_vertex.insert(v1);
> >>>>>>>>   if (is_local(v2))
> >>>>>>>>     used_vertex.insert(v2);
> >>>>>>>>
> >>>>>>>>   if (!(is_local(v1) && is_local(v2) && is_local(v0)))
> >>>>>>>>   {
> >>>>>>>>     if (!is_local(v1))
> >>>>>>>>       shared_vertex.insert(v1);
> >>>>>>>>     if (!is_local(v2))
> >>>>>>>>       shared_vertex.insert(v2);
> >>>>>>>>   }
> >>>>>>>>
> >>>>>>> The idea is to assign the triangle/tetrahedron to the processor who owns
> >>>>>>>   vertex v0. And, yes the logical could probably be more clearer.
> >>>>>> ok, I see.
> >>>>>>
> >>>>>> It seems that
> >>>>>>
> >>>>>>   !(is_local(v2) || is_local(v1) || is_local(v0)) || !is_local(v0)
> >>>>>>
> >>>>>> is equivalent to
> >>>>>>
> >>>>>>   (!is_local(v2) && !is_local(v1) && !is_local(v0)) || !is_local(v0)
> >>>>>>
> >>>>>> which is equivalent to
> >>>>>>
> >>>>>>   !is_local(v0)
> >>>>>>
> >>>>>> Is this correct, and is this what you have in mind?
> >>>>> It looks correct to me. Seems like I should refresh my logic, that was a
> >>>>> really simple reduction :)
> >>>>>
> >>>>> Niclas
> >>>> It wasn't very obvious that it could be so much simplified, but it
> >>>> should help to clear up the logic.
> >>>>
> >>>> I'll wait for you to do some more work on PXMLMesh.cpp before I
> >>>> continue reading it.
> >>>>
> >>>> If possible, I'll add DynamicMeshEditor later tonight so you can use
> >>>> that to simplify PXMLMesh.cpp further.
> >>> I've added DynamicMeshEditor. Try to use this in PXMLMesh.cpp. It may
> >>> simplify it a bit.
> >>>
> >>>
> >>>
> >> Commenting and bug fixes in PXMLMesh.
> > 
> > Thanks, it looks much better! I'll make a new attempt to get through
> > the code (after the suggested changes below).
> > 
> >> I couldn't use DynamicMeshEditor to get rid of the opening and closing
> >> of the mesh editor. The problem is that each processor parse (and
> >> receive from partitioning) vertices which are not used in the local
> >> cells. These must be removed before the final mesh is returned, and this
> >> is not supported by the editor.
> >>
> >> I think the easiest solution to this problem is to move the geometric
> >> partitioner inside the XML parser. Since it's produces rather bad
> >> partitions I don't see why anyone would like to use it in an application.
> > 
> > That sounds good, especially since you now call the partitionGeom()
> > before the mesh is even a mesh (it has only vertices).
> > 
> > Can you make an attempt to do the geometric partitioning inside
> > PXMLMesh?
> > 
> > I also suggest that you don't open the mesh editor until you get to
> > the closemMesh() function. Just store the vertices in an Array<>
> > (which is the same as an std::vector). You don't call editor.addCell()
> > until closeMesh() so it's not really a Mesh before then anyway.
> > 
> > It also fits well with how you treat the cells. You already have a
> > cell_buffer. You could store a vertex_buffer similarly.
> > 
> > So it would be something like this:
> > 
> > 1. Read vertex coordinates into a simple Array (or similar).
> > 
> > 2. Partition the vertices.
> > 
> > 3. Build the Mesh in closeMesh() using MeshEditor.
> > 
> > Would that work?
> > 
> 
> I think so. I'll try fix this and insert the geometric partitioner as 
> soon as possible.
> 
> Niclas

Any progress on the patch?

-- 
Anders

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