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I have two solutions. Use MetPy to calculate the height from the geopotential height. Use the hypsometric equation, averaging the temperature below the level.


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If I understood the question right: CDO can interpolate from model level to height level with the operator ml2hl infile.nc outfile.nc additionally, for the lower atmospheric levels, you can add an extrapolation option. BUT I don't recommend it since its extrapolation performance is questionable.


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