Hello Vasilios,
sorry for the messages before, hopefully the mail is now small enough, but i thought that adding a plot might explain better what i mean..
Plots are welcome. EMail sizes is not terribly important, we all have fast connections :-)
IOHDF5::one_file_per_group = no IOHDF5::output_symmetry_points = no IOHDF5::out3D_ghosts = no IOHDF5::output_ghost_points = no IOHDF5::out3D_outer_ghosts = no IOHDF5::output_boundary_points = no IOHDF5::output_buffer_points = no
are the specific parameters for cell-centered hdf5 output or other thorns that could take care of that?
I will give you somewhat of the opposite advise that Erik just did. Certainly what Erik suggested is not a bad idea to get rid of some of th symmetry plane junk. The other option is to add a "Clip" operator (maybe with an origin of 1e-3 rather than 0) to the plot.
Also I would try to successively change the "no"s above to "yes", in particular the one for ghost zones since new versions of VisIt do indeed use ghost zones for smooth transitions between blocks. With vertex centering this might show up as a white line, with cell centering possibly as the offset in data that you see at around point (15,8).
Note that found the best way to get trustworthy plots for debugging out of VisIt is to add a "Threshold" operator selecting its point mesh option, then making the point size in a pseudocolor plot a bit larger. This gives you one dot per grid point with no strange interpolation in between.
Yours, Roland