[Paraview] paraview for a "new" application
Paul Anton Letnes
pa at letnes.com
Sat Jun 13 04:46:00 EDT 2015
Stefano (and others),
I’ve seen some of your efforts posted on github. I have to say I commend your efforts; the open source Fortran community is too small. I will investigate several of your libraries recently, especially after you modified the licensing terms to be very liberal.
Even though VTK is probably the “right” format to use, I am reluctant to introduce yet another file format into the fray (our code already has too many IMHO). That being said, it’s a relatively standard format that should stand the test of time. Your library appears to solve the issue of writing the data to disk, at least.
Best regards,
Paul
> On 8. jun. 2015, at 11.49, Stefano Zaghi <stefano.zaghi at gmail.com> wrote:
>
> Hi all,
>
> another possibility is to write your Fortran data directly into VTK files format.
>
> I develop a KISS library in pure Fortran for IO of Fortran data into VTK standard: see https://github.com/szaghi/Lib_VTK_IO
>
> The exporters are almost complete. The importers are under developing by a power collaborator https://github.com/victorsndvg/Lib_VTK_IO this work will be merged very soon into the main branch.
>
> Summarizing, Lib_VTK_IO is
>
> + Lib_VTK_IO is a pure Fortran library to write and read data conforming the VTK standard;
> + Lib_VTK_IO is Fortran 2003+ standard compliant;
> + Lib_VTK_IO supports parallel architectures by means OpenMP and MPI paradigms;
> + Lib_VTK_IO supports ascii, binary and base64 file formats;
> + Lib_VTK_IO is a Free, Open Source Project.
>
> My best regards
>
> Stefano Zaghi Ph.D. Aerospace Engineer
>
> Research Scientist, Dept. of Computational Hydrodynamics at CNR-INSEAN
> p: +39 0650299260 | m: +39 3497730036 | e: stefano.zaghi at gmail.com
>
> Codes Showcase
> OFF Open source Finite volumes Fluid dynamics code
> Lib_VTK_IO Fortran library to write and read data conforming the VTK standard
> FLAP Fortran command Line Arguments Parser for poor men
> BeFoR64 Base64 encoding/decoding library for FoRtran poor men
> FiNeR Fortran INI ParseR and generator for FoRtran poor men
> IR_Precision Fortran (standard 2003) module to develop portable codes
> FoBis.py Fortran Building System for poor men
> PreForM.py Preprocessor for Fortran poor men
> MaTiSSe.py Markdown To Impressive Scientific Slides
>
>
> On Mon, Jun 8, 2015 at 11:27 AM, Armin Wehrfritz <dkxls23 at gmail.com> wrote:
> Hi Paul,
>
> as you and Dan already stated, the HDF5 format is a very good choice to write out large datasets.
>
> I usually write the HDF5 files directly from my simulation codes and generate a XDMF file afterwards.
> The actual XDMF file contains just the meta data in XML format [1] and this can be tailored to your application/dataset (I use python with h5py and xml.etree to do this).
> Hence, my simulation codes (written in C++) only depend on the HDF5 libraries.
>
> Eventually, this will enable you to store your data in a robust, flexible and portable file format.
>
> For more complex setups I would also consider using the VTK libraries to handle the data IO as Dan suggested.
>
> -Armin
>
> [1] http://www.xdmf.org/index.php/XDMF_Model_and_Format
>
>
>
>
> On 06/07/2015 10:40 PM, Dan Lipsa wrote:
> You are right, ParaView does not read hdf5 directly but rather hdf5
> based formats (hdf5 + additional info): both netcdf and xdmf have readers.
> You can get a list of all readers supported by your ParaView
> installation using Help in ParaView. Additional readers can be enabled with
> compile time options.
>
> You can write Xdmf data using vtkXdmfWriter or vtkXdm3Writer (you'll
> have to link with the VTK library). These writers have tests which is a
> good way to see an example of how to use the class. You can also take a
> look at the VTK XML based formats: vtkXMLPolyDataWriter,
> vtkXMLImageDataWriter, vtkXMLUnstructuredGridWriter/Reader. Probably you
> could write data with a library that comes with that format and then
> read it with ParaView.
>
> Do you need parallel writing/reading?
>
> Dan
>
>
>
>
> On Sun, Jun 7, 2015 at 4:26 AM Paul Anton Letnes <pa at letnes.com
> <mailto:pa at letnes.com>> wrote:
>
> Hi Dan!
>
> I’m familiar with the HDF5 library and documentation, but thanks
> anyway for the link.
>
> I don’t see how I can have ParaView read and understand HDF5 files.
> That is, there are several readers (e.g. H5Nimrod) that use HDF5 as
> the underlying format, but I don’t see how to get paraview to
> understand which arrays are coordinates (nodes?), which are results,
> etc. for my application.
>
> Perhaps I should stress again that I have limited experience with
> ParaView, and since the supported file formats and possibilities
> seem endless, I have trouble getting an overview of sensible choices.
>
> My preference for hdf5 is partly due to other software in my
> organization supporting this format, and my own familiarity with it.
>
> Paul
>
> > On 7. jun. 2015, at 04.07, Dan Lipsa <dan.lipsa at kitware.com
> <mailto:dan.lipsa at kitware.com>> wrote:
> >
> > Hi Paul,
> > Indeed #2 makes sense, especially if you want to change the
> in-house format. To write the file (from the simulation) it seems to
> me you should checkout
> >
> > https://www.hdfgroup.org/HDF5/doc/fortran/index.html
> >
> > I don't see why ParaView would be used in that process. Am I
> missing something?
> > Dan
> >
> >
> >
> > On Sat, Jun 6, 2015 at 8:04 AM Paul Anton Letnes <pa at letnes.com
> <mailto:pa at letnes.com>> wrote:
> > Hi, fellow paraviewers!
> >
> > I’ve spent some time playing with tutorials and user manuals, and
> so far I’m impressed with what paraview can do.
> >
> > I am working on a specialized structural engineering program
> that, mainly, performs simulations of pipes with circular cross
> sections. Each pipe is split into nodes and 1D elements, and results
> are reported at points (or, less commonly, elements) along the pipe.
> >
> > Some results are reported once per cross section; e.g, the
> tension in the pipe has a single value for the entire cross section.
> Other results, e.g. plastic strain, is reported for a number of
> points along the circumference of the pipe (say, 5-50 points), for
> each of the cross sections. The results can be either “snapshots” or
> time series.
> >
> > After what I’ve seen from the paraview documentation, possible
> approaches include:
> > 1. Create a paraview plugin to read our current in-house file format.
> > 2. Directly write output files in an already supported format.
> > 3. Write pvpython scripts that perform the conversion on the fly.
> >
> > Approach 1 is probably a lot of work and the file format is not
> of interest to anyone else (optimally, I’d like to replace it), so
> this seems less attractive. Approach 3 is probably less
> user-friendly for our users.
> >
> > The second approach seems sensible, but the paraview
> documentation does not give many examples of how to do this.
> Optimally, I’d like to write a hdf5-based format (xdmf? netcdf? raw
> hdf5?) directly from Fortran, but I haven’t found documentation on
> how to do this. Using hdf5 seems attractive as it’s so widely
> supported by e.g. matlab, python, and other postprocessing tools
> used in the industry. Getting a single results database would
> simplify a lot of workflows!
> >
> > What would you guys do?
> >
> > Cheers
> > Paul
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