Hello I am creating my vector using DMDA, so the hdf file knows something about the grid. But it uses (i,j) indices as (x,y) coordinates to plot. Here is what I do
ierr = DMCreateGlobalVector(da, &ug); CHKERRQ(ierr); // set values into ug ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, "sol.h5",FILE_MODE_WRITE,&viewer); CHKERRQ(ierr); ierr = PetscViewerHDF5SetTimestep(viewer, 0); CHKERRQ(ierr); ierr = VecView(ug, viewer); CHKERRQ(ierr); // update ug and save it again ierr = PetscViewerHDF5IncrementTimestep(viewer); CHKERRQ(ierr); ierr = VecView(ug, viewer); CHKERRQ(ierr); I have not saved mesh coordinates, so I can understand that it uses (i,j) coordinates. How can I save x,y coordinates and time information so that VisIt will be able to know the mesh and time information ? I can save solution at different times into different .h5 files but is that really necessary ? What I understood is that the h5 file only contains some data, and one has to create a xdmf file that tells VisIt how to use the data in the h5 file. The h5 file should contain "geometry" and "topology" sections. I could add the "geometry" section by saving the mesh coordinates. But how to add the "topology" section which contains cell information ? Is there an easy way to add this o the hdf file when I use DMDA ? Thanks praveen On Thu, Sep 29, 2016 at 11:03 PM, Santiago Ospina De Los Rios < [email protected]> wrote: > > > 2016-09-29 18:57 GMT+02:00 Praveen C <[email protected]>: > >> Dear all >> >> Is there an example to save hdf5 file on cartesian mesh with time >> dependent solution, that I can visualize in VisIt ? >> >> > If you save the file with a successive numbering at the final of the name, > Visit will recognize it as a time-dependent. > > I am able to save in hdf5 and open in VisIt but I cannot get the actual >> mesh coordinates or time dependent data. >> >> > To get the mesh you have to save a vector associated to a DM object, > otherwise, you will get a row of values at the visualization. > > >> I have seen a script petsc_gen_xdmf.py but that needs lot of information >> in the hdf5 file which I do not know how to create. An example for 2d >> Cartesian mesh would be very useful to learn this. >> >> > Anyway, it's a good question: how to visualize time-dependent hdf5 files > in other viewers such as Paraview just using PETSc calls. Is there a way? > > Santiago O. > > >> Thanks >> praveen >> > > > > -- > > -- > Att: > > Santiago Ospina De Los Ríos > National University of Colombia >
