[Dune-devel] Updates on psurface convert

Fri Jul 26 19:14:59 CEST 2013

Xiaoxue Gong <xiaoxue198912 at gmail.com> schrieb:
>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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>>

Hi,

Thanks that makes it a little clearer. Does this mean that the new repository is a dune-module created with the dunecontrol script?

Markus
--
Dr. Markus Blatt - HPC-Simulation-Software & Services
Hans-Bunte-Str. 8-10, 69123 Heidelberg, Germany
Tel. +49 (0)160 97590858 Fax +49 (0)322 1108991658