Hi Christian,
Run "sigma2p" (found in the PostProc directory) on one ATM file at a time like so:
./sigma2p [output_path]/[sim_name]_ATM.[yyyymmddhh].nc
This creates a new file (same file name, but with "_pressure" appended) in pressure coordinates at standard pressure levels. Note that anywhere the surface pressure is less than 1000 hPa, the surface value is used.
If you are just looking for the values at the standard pressure levels, sigma2p works. If, however, you want to calculate a vertical gradient with pressure (i.e. d/dp) of a variable, do not use sigma2p, otherwise dp will give you missing values at the surface where surface pressure is less than 1000 hPa. Instead, compute pressure yourself using the surface pressure (ps) and top of atmosphere pressure (ptop) variables, where:
p = sigma * (ps - ptop) + ptop
Alex