[Paraview] paraview for a "new" application
Stefano Zaghi
stefano.zaghi at gmail.com
Mon Jun 8 05:49:30 EDT 2015
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*
<http://www.insean.cnr.it/en/content/cnr-insean>
*p*: +39 0650299260 | *m*: +39 3497730036 | *e*: stefano.zaghi at gmail.com
Codes Showcase
*OFF* <https://github.com/szaghi/OFF> Open source Finite volumes
Fluid dynamics code
*Lib_VTK_IO <https://github.com/szaghi/Lib_VTK_IO> * Fortran library to
write and read data conforming the VTK standard
*FLAP* <https://github.com/szaghi/FLAP> Fortran command Line
Arguments Parser for poor men
*BeFoR64 <https://github.com/szaghi/BeFoR64>* Base64 encoding/decoding
library for FoRtran poor men
*FiNeR <https://github.com/szaghi/FiNeR>* Fortran INI ParseR and
generator for FoRtran poor men
*IR_Precision <https://github.com/szaghi/IR_Precision>* Fortran (standard
2003) module to develop portable codes
*FoBis.py* <https://github.com/szaghi/FoBiS> Fortran Building System
for poor men
*PreForM.py <https://github.com/szaghi/PreForM> * Preprocessor for Fortran
poor men
*MaTiSSe.py* <https://github.com/szaghi/MaTiSSe> 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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>>
>>
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>
> Visit other Kitware open-source projects at
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>
> Please keep messages on-topic and check the ParaView Wiki at:
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>
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