Add options to core_init_atmosphere for P-X LSM

[jherwehe]

This EPA_init PR will add various options to the MPAS-A initialization
codes under src/core_init_atmosphere, with most of the additions
targeted for use by the Pleim-Xiu land-surface model (P-X LSM; a future
PR for MPAS-A). Several new features are detailed below.

A new "soilndg_update" package and a new case ("config_init_case = 10",
along with a new "soilndg" stream file template) have been added to
init_atmosphere_model to generate a soil nudging update file from
high-resolution analysis near-surface data (via a data path provided by
new option "config_sfc_prefix_hires"); the soil nudging file is used by
the P-X LSM at run time (Gilliam et al. 2021).

The 40-category NLCD land use option ("NLCD40") is now supported for the
CONUS (utilizing the nlcd2011_ll_9s geotile data), as is the option of
either fractional or dominant land use and soil type for each grid cell
(with MODIS land use from modis_landuse_20class_30s geotile data utilized
outside of CONUS). The original "soilcat_top" variable has now been
generalized to just "soilcat" because the two-layer P-X LSM soil model
uses data from the soiltype_bot_30s geotile set (enabled when specifying
the "NLCD40" option). Geotile set soiltype_top_30s is still used for the
USGS and MODIFIED_IGBP_MODIS_NOAH land use options.

Two new vertical grid discretization options have been added to
mpas_init_atm_cases.F for config_init_case = 7:
"config_EPA_vertical_grid", the original EPA vertical grid used to
improve vertical resolution in the PBL for air quality applications
(Bullock et al. 2018); and "config_spline_vertical_grid", a more
configurable vertical grid based on a cubic spline fit. These vertical
grid calculations predate the ability to specify vertical coordinate
levels as is now available in more recent MPAS-A releases (and also
require that config_tc_vertical_grid = false).

In addition, leaf area index (LAI) values are now interpolated from
available monthly geotile data set lai_modis_30s for use by the P-X LSM.

Note that the file needed for 3-D grid analysis nudging FDDA (Bullock et
al. 2018; also see related to PR #995) can be generated with these
EPA_init init_atmosphere_model codes. If available in the meteorological
analysis data, 3-D ozone mixing ratios, with tropopause level data, can
also be interpolated to the MPAS-A mesh as part of the FDDA file creation
process to provide time-dependent O₃ values for use by the
radiation schemes.

The streams.init_atmosphere and namelist.init_atmosphere files used for
each init_atmosphere_model step in tests of these EPA_init modifications,
along with the script used to generate the FDDA file, are attached to
this PR. Also refer to the descriptions in the WRF-ARW technical
document (available at
https://opensky.ucar.edu/islandora/object/opensky:2898) and in an
updated PX-ACM-WRFV4.4-MPASv7.3.pdf document (attached to this PR) for
additional information on the physics and methodology.

New stream file added to streams.init_atmosphere under <streams> to
create soil nudging file when config_init_case = 10 (and subsequently
used as input to the P-X LSM):
<immutable_stream name="soilndg"
                  type="output"
                  filename_template="x4.163842.US_fractional_nlcd40_soilndg.jul2016.nc"
                  filename_interval="none"
                  packages="soilndg_update"
                  output_interval="10800" />

New namelist.init_atmosphere options added under &dimensions:
   config_nsoillevels = 2
   config_nlandcat = 40

New namelist.init_atmosphere options added under &data_sources:
   config_sfc_prefix_hires = '/xxxxxx/mpas/MPASv7.3.EPA-modified.develop.EPA_init/run_init/data/NAM12.SFC.GLOBAL'
   config_landuse_data = 'NLCD40'
   config_frac_landuse = true

New namelist.init_atmosphere options added under &vertical_grid
(default values are shown for the cubic spline parameters):
   config_EPA_vertical_grid = false
   config_spline_vertical_grid = true
   config_spline_x1 = 0.0
   config_spline_y1 = 20.0
   config_spline_x2 = 350.0
   config_spline_y2 = 100.0
   config_spline_x3 = 800.0
   config_spline_y3 = 300.0
   config_spline_x4 = 2500.0
   config_spline_y4 = 600.0
   config_spline_x5 = 8000.0
   config_spline_y5 = 600.0
   config_spline_x6 = 16000.0
   config_spline_y6 = 700.0
   config_spline_x7 = 30000.0
   config_spline_y7 = 2000.0
   config_spline_x8 = 50000.0
   config_spline_y8 = 4000.0

New variables available for output from init_atmosphere_model:
   ismax_lu ; maximum number of land use categories (unitless)
   landusef ; grid cell fractional land use (unitless)
   soiltypf ; grid cell fractional soil type (unitless)
   lai12m ; monthly-mean climatological leaf area index (m² m^-2)
   lai_modis ; leaf area index (m² m^-2)
   t2anl ; 2-m temperature analysis (temporally interpolated during run) (K)
   rh2anl ; 2-m RH analysis (temporally interpolated during run) (%)
   snoanl ; snow water equivalent analysis (temporally interpolated during run) (kg m^-2)
   ptrop ; tropopause pressure (Pa)
   hgttrop ; tropopause height (m AMSL)
   ozone ; ozone mass mixing ratio (kg kg^-1)

NOTE: These EPA_init code changes to MPAS-A are based on the 21 November
2022 "develop" branch of MPAS v7.3.

References:
Bullock Jr., O. R., H. Foroutan, R. C. Gilliam, and J. A. Herwehe, 2018:
   Adding four-dimensional data assimilation by analysis nudging to the
   Model for Prediction Across Scales – Atmosphere (version 4.0).
   Geosci. Model Dev., 11, 2897–2922.
   https://doi.org/10.5194/gmd-11-2897-2018
Gilliam, R. C., J. A. Herwehe, O. R. Bullock Jr, J. E. Pleim, L. Ran, P.
   C. Campbell, and H. Foroutan, 2021: Establishing the suitability of
   the Model for Prediction Across Scales for global retrospective air
   quality modeling. J. Geophys. Res. Atmos., 126, e2020JD033588.
   https://doi.org/10.1029/2020JD033588

[jherwehe]

PX-ACM-WRFV4.4-MPASv7.3.pdf

Here are the related streams.init_atmosphere and namelist.init_atmosphere, and the script for creating the FDDA and O₃ files:

streams.init_atmosphere.fractional_nlcd40_static.92-25km.txt
namelist.init_atmosphere.fractional_nlcd40_static.92-25km.txt
streams.init_atmosphere.fractional_nlcd40_sfc_update.jul2016.92-25km.txt
namelist.init_atmosphere.fractional_nlcd40_sfc_update.jul2016.92-25km.txt
streams.init_atmosphere.fractional_nlcd40_soilndg.jul2016.92-25km.txt
namelist.init_atmosphere.fractional_nlcd40_soilndg.jul2016.92-25km.txt
streams.init_atmosphere.fractional_nlcd40_init.20160621.92-25km.txt
namelist.init_atmosphere.fractional_nlcd40_init.20160621.92-25km.txt
run_init_mpas73epa_develop_EPA_init_jul2016_92-25km_fdda.csh.txt

[jherwehe]

Evidently the recent (post-November 21) commits to the develop branch of the MPAS repo are causing at least one code conflict. Therefore, this PR may be replaced once I implement these EPA_init code changes into the latest develop branch codes.

[jherwehe]

The "Updates to resolve code conflicts" commit (dd39ea4) above for MPAS-A was based on the 12 December
2022 "develop" branch of MPAS v7.3. Then more code conflicts appeared for file src/core_init_atmosphere/Registry.xml, but those conflicts only referenced new variables and a vegfra units change, so the conflicts were manually resolved in GitHub and committed (ce81129).