The variable GNDALT (altitude in libRadtran) sets the bottom level in the selected model atmosphere at the given altitude above sea level (in [km]), which varies from 0 km (sea-level, default value) to 9 km.
The profiles of pressure, temperature, molecular absorbers, ice and water clouds are cut at the specified altitude. The aerosol profile is not affected by altitude but starts right from the model surface. As such, GNDALT controls the length of the sun-target-sensor optical path, which increases/decreases the effects of absorption and scattering caused by gasses and aerosols. This is a convenient way for the user to calculate the radiation at other altitudes than sea level. Note that the ground altitude GNDALT is very different from sensot altitude ZOUT where the radiation is calculated at an altitude of ZOUT above the surface. E.g., to calculate the radiation field 1 km above the surface at a location at 0.73 km above sea level, one would specify GNDALT=0.73 and ZOUT=1.0. If an altitude is specified which is below the lowest level in the atmospheric profile, the atmospheric profiles are extrapolated assuming a constant gradient for temperature and mixing ratios.
In libRadtran, a second optional argument may be given to altitude as e.g. altitude 0.73 0.5. Here the bottom level will be at 0.73 km and the vertical resolution of the model atmosphere will be redistributed to have a spacing between levels specified by the second number, here 0.5 km, starting however from 0km. However, this option is not implemented in ALG.