Hello Dumsani,
there are two different things you may want to do. If you have files
rho.file_0.h5 eps.file_0.h5 rho.file_1.h5 and eps.file_1.h5 and would
like to combine the variables you can use:
hdf5_merge rho.file_0.h5 eps.file_0.h5 vars.file_0.h5
hdf5_merge rho.file_1.h5 eps.file_1.h5 vars.file_1.h5
ie when you want to keep the file_X structure intact. If not then you
must use the hdf5 slicer:
hdf5_slicer --out3d-cube rho.file_*.h5 eps.file_*.h5 vars.h5
Also note that (as far as I know) this simply copies the datasets from one file to the other. It does not coalesce the individual rectangular components into a single one, suitable for viewing with a generic visualisation tool. This would not in general be possible for a mesh-refined grid.