Atmosphere: Added doxygen comments to the top of physics modules.
Atmosphere: Remove deprecated preprocessor directives and code in physics for hydrostatic dynamical core.
Atmosphere: Minor cleanup to physics code.
Atmosphere: Added initialization of the sea-surface skin temperature sstsk when computing the diurnal cycle of the sea-surface temperature.
Make an if-statement in mpas_atmphys_update_surface.F consistent with other code and remove a couple of print statements.
Atmosphere: Update code comments to reflect status of physics in released code.
Atmosphere: Minor fixes to preprocessor directives in mpas_atmphys_initialize_real.F,
and cleanup of comment lines in physics modules.
Changed the declaration of variable RV to "private" to avoid conflicts with the same
named variable RV already declared in ./src/framework/mpas_constants.F. Results are
not changed.
Atmosphere: have the initialization core more robustly handle
an incorrect specifications for config_nfglevels:

 - if too many levels are specified, the code will only use those
   that were filled with valid data

 - if too few levels are specified, the code aborts with a helpful
   error message
In the CAM radiation codes, now checks the value of variable mxaerl to ensure that
it is correctly initialized. If mxaerl equals zero, MPAS will abort with a warning
message.
In the CAM radiation codes, added initialization of variable mxaerl which is the number
of layers below 900 hPa in which background aerosols are present. mxaerl is computed
using the pressure-base array.
adding ifort-gcc compile option.

compiled with ifort-gcc in optimized and debug mode on OS X, Intel 13.0.2, gcc 4.2.1
Atmosphere: remove unnecessary rename of 'cp' in mpas_atmphys_constants.F.
Merge hotfix branch v1.1.

This hotfix was merged onto master already, and includes commit 0cb307c.

* mark-petersen/MPAS/ocean/fix_displacedDensity:
  Change displacedDensity to be relative displacement of one level. Add potentialDensity for displacement to top level.
Added subroutine compute_relhum to calculate the relative humidity using the functions
rslf and rsif from the Thompson cloud microphysics scheme.
Added interpolation of the temperature, height, zonal wind, meridional wind,
vertical velocity, and relative vorticity at 700 hPa.

Added interpolation of the relative humidity at 850 hPa, 700 hPa, 500 hPa, and
200 hPa.
Merge hotfix v1.2 branch into develop.

Included in this merge are commits d7e9127a0e and 337a78f72c.
Merge hotfix v1.3 branch into develop.

This merge includes commits fb67b5783 and 89a9e0aa8.
- in Registry.xml, added structure atm_input (pin,ozmixm), and arrays o3clim and
  o3vmr for the implementation of the monthly-varying ozone climatology in the RRTMG
  longwave and shortwave radiation codes.

- in mpas_atm_mpas_core.F, modified call to subroutine physics_init to add structure
  atm_input.

- in mpas_atmphys_manager.F, added call to subroutine o3climatology_from_MPAS to
  interpolate the monthly-varying ozone volume mixing ratios to the current julian day.
added module mpas_atmphys_o3climatology. This module contains the subroutines needed
to initialize, interpolate, and update the monthly-varying ozone climatology that can
be used in the RRTMG longwave and shortwave radiation codes if config_o3climatology
is true. This monthly-varying ozone climatology is the same as the one used in the
CAM radiation code.

added logical config_o3climatology in Registry.xml. If set to true, the RRTMG longwave
and shortwave radiation codes use monthly-varying climatological ozone instead of the
default annual mean ozone sounding.