Are there any control parameters in the namelist to control the output files in pressure or height coordinates?
You have to use the ocards when running the model to get these additional diagnostic outputs at pressure or height levels. Set the namelist variable npfil to be the name of the ocards file. The ocards file has to be located in the same run directory where you run your job. Also the format has to be correct (it is a formatted read from the model). Check your output.m… file and search for character string “reado”. You should see the print statements for fields that model read in from the ocards.