[Dune-devel] Updates on psurface convert

Fri Jul 26 18:04:50 CEST 2013

I make the new project file folder because I need to use the code in
dune-grid. And there are some instructions on how to make use of the code
in dune-grid by the tutorial "The DUNE Buildsystem HOWTO“.
I am not  very clear what should I do to the psurface make.in and
configure.ac so I can make use of the code in
/dune/grid/io/file/vtk/vtk/. Should I put the lib and folder name into
make.in?
 best,
 xiaoxue

On Fri, Jul 26, 2013 at 8:12 AM, Markus Blatt <markus at dr-blatt.de> wrote:

> Hi Xiaoxue,
>
> I must admit, I am totally confused now. The last time you reported
> about your changes to psurface, you did that as advised by
> cloning psurface, creating a branch, and comitting your changes. Oliver
> answered to your blog entry on this list and commented and requested
> some changes, see
> http://lists.dune-project.org/pipermail/dune-devel/2013-July/000383.html
> . Unfortunately, there was no response to his email (at
> least until your new report).
>
> On Thu, Jul 25, 2013 at 04:13:06PM -0400, Xiaoxue Gong wrote:
> > I have write a new psurface-convert code to convert the psurface into vtu
> > file format. The code (in new project dune-psurface-convert) is save is
> > git://gitorious.org/dune-psurface-convert/dune-psurface-convert.git
> > This is I have made use of  the vtu writer in /dune/grid/io/file/vtk/vtk
> > writer.hh, instead of  the third party code. It is written in a more
> > C++-like style.
>
> It seems like you did address the comments of Oliver in this new
> project. What I do not understand is why you did not apply these
> changes to the repository that you already created like advised
> (xiaoxueiriss-psurface).
>
> Instead, you create a brand new repository (dune-psurface-convert), which
> seems to include the
> code of psurface, but is not a clone of it. This means it does not
> have the commit history of psurface available. On my system the
> complete history looks like this:
>
> mblatt at legolas:~/src/dune/gsoc/iris/dune-psurface-convert$ git log
> commit 67b3982d6ee7d0f2074be5749cc5ef73da6dc7ca
> Author: irisxiaoxue <xiaoxue198912 at gmail.com>
> Date:   Thu Jul 25 15:42:01 2013 -0400
>
>     xi
>
> (Nice commit comment by the way ;) I think you should definitely read
> http://tbaggery.com/2008/04/19/a-note-about-git-commit-messages.html )
>
> Now this poses a serious problem for our collaboration as nobody will
> be able to easily apply your changes to the upstream psurface
> repository. The cause of this is that git has no way of knowing what
> part of your initial commit is made by you and what part is from the
> upstream psurface repository. Additionally there are many
> automatically created files in that commit, that should not be there
> (e.g the symbolic link am pointing to
> /home/xiaoxue/GCoS/0722/dune-common-2.2.1/am, autom4te.cache, etc.)
>
> If this is the way it was supposed to be, then please explain your
> reasoning for doing it this way. Otherwise you will have to transfer
> your changes manually to your original xiaoxueiriss-psurface
> repository. Please make sure that for a fresh checkout of the
> repository  the only additional files (compared to the upstream
> psurface repository) are really needed and not some automatically
> created ones. Please do this fast as we otherwise have no means to
> evaluate your changes.
>
> Additionally please comment on what of the points of the original work
> plan of Oliver
> http://lists.dune-project.org/pipermail/dune-devel/2013-June/000356.html
> you adressed until now.
>
> > The code could deal with the cube.par.am and sphere.par.am.
>
> What does could mean?
>
> > The out put is
> > shown in the attachment. I have trouble reading the trice.par.am, with
> an
> > error message of  "You're trying to read a file in the old-style
> AmiraMesh
> > format.
> > But the format is not supported anymore :-(".
>
> I am afraid you have to deal with this alone, as I am no AmiraMesh
> expert and Oliver is not available until August 11. Maybe a simple
> websearch for "amira User's Guide" might help? If it does not we have
> to postpone this issue until Oliver is back
> >
> > The amiramesh have the following information
> >  1) 'Patches'
> >   2) 'BaseGridVertexCoords
> >   3) 'BaseGridTriangles'
> >   4) 'NumNodesAndParameterEdgesPerTriangle'
> >   5) 'Nodes'
> >    For each node, five floats are stored containing first the local
> > position in
> >    barycentric coordinates on the respective triangle and x, y, and
> > z-coordinates of   the image position.
> >   6) 'ParameterEdges'
> >      All edges of the graphs on all triangles.  Each entry is a tuple of
> >      two integers storing the indices of the two endnodes of the edge.
> >      The counting starts anew for each triangle.  The three invented
> >      corner nodes always have the indices 0, 1, and 2, respectively.
> >   7) 'EdgePoints
> >
> > I stored the vertices (2) and nodes (5) (node positions) into point
> > coordinates. The Triangles (3) and Edges (6) are stored as cell in vtu.
> > Patches(1) is stored as cell data. The imagine position is stored as the
> > point data on nodes and vertices. I have not figure out how to store Edge
> > Points yet.
> > Do you think it is the right way to store the psurface information into
> vtu
> > file?
>
> Please add some more elaborate documentation on the format you used
> for storing psurface information into vtk files to the
> repository under directory doc. Additionally add documentation on how to
> replicate your results. Once that and merge of the two repositories as
> detailed above is done, I will evaluate it. Before that this is not
> possible. Please also note that this is mandatory for the approaching
> midterm evaluations.
>
> BTW you need to notify us once this is done.
>
>
> Best regards,
>
> Markus
>
> --
> Do you need more support with DUNE or HPC in general?
>
> Dr. Markus Blatt - HPC-Simulation-Software & Services
> http://www.dr-blatt.de
> Hans-Bunte-Str. 8-10, 69123 Heidelberg, Germany
> Tel.: +49 (0) 160 97590858  Fax: +49 (0)322 1108991658
>
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