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 <[email protected]> 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: [email protected] > > 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 <[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 > > _______________________________________________ > 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
