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*: [email protected] 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 <[email protected]> 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 <[email protected] >> <mailto:[email protected]>> 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 <[email protected] >> <mailto:[email protected]>> 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 <[email protected] >> <mailto:[email protected]>> 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 >> > _______________________________________________ >> > Powered by www.kitware.com <http://www.kitware.com> >> > >> > Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> > >> > Please keep messages on-topic and check the ParaView Wiki at: >> http://paraview.org/Wiki/ParaView >> > >> > Search the list archives at: >> http://markmail.org/search/?q=ParaView >> > >> > Follow this link to subscribe/unsubscribe: >> > http://public.kitware.com/mailman/listinfo/paraview >> >> >> >> _______________________________________________ >> Powered by www.kitware.com >> >> Visit other Kitware open-source projects at >> http://www.kitware.com/opensource/opensource.html >> >> Please keep messages on-topic and check the ParaView Wiki at: >> http://paraview.org/Wiki/ParaView >> >> Search the list archives at: http://markmail.org/search/?q=ParaView >> >> Follow this link to subscribe/unsubscribe: >> http://public.kitware.com/mailman/listinfo/paraview >> >> _______________________________________________ > Powered by www.kitware.com > > Visit other Kitware open-source projects at > http://www.kitware.com/opensource/opensource.html > > Please keep messages on-topic and check the ParaView Wiki at: > http://paraview.org/Wiki/ParaView > > Search the list archives at: http://markmail.org/search/?q=ParaView > > Follow this link to subscribe/unsubscribe: > http://public.kitware.com/mailman/listinfo/paraview >
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