…fied profile

2) Added a logical switch (reference_sounding) to specify whether the thermodynamic
variables are computed as a perturbation from a specified reference sounding. If false,
the full thermodynamic variables are used and the pressure gradients on the large
time steps are computed using log(p).

1) Code added to ../src/core_atmosphere/mpas_atm_core.F to compute
vertical profiles of epssm that vary with height at the start of the
time integration. These profiles are determined by the parameters
config_min_coeff, config_max_coeff, config_transition_lower_bound,
and config_transition_upper_bound, and are specified in namelist.atmosphere.

2) Code added to allow thermodynamic variables to be represented either
as perurbations from a specified reference state or as the full
variables without a reference state. This option is controlled by the
logical config_reference_sounding as specified in namelist.init_atmosphere.
When configured using the full variables, the horizontal and vertical
pressure gradients computed on the large time steps are written in terms
of log(p).

MPAS version 8 to include:
1) an option to use full thermodynamic variables instead of perturbations
from a reference profile and
2) a capability for specifying an epssm profile that is variable with
height.
These revisions include the changes suggested by Bill Skamarock in his
review of the pull request.