Abz update

update branch

merging 4/13

…ts324

…ange anything of substance

…e as well for the Kattge vs. Leuning switch

…nges froot_leaf and stem_leaf for arctic plants. So the file is identical to /glade/work/lbirch/devclm4gitfinal/clm5_params_abz_lbirch_update.nc

…irch_wkattge_jmaxb1-0.17_slatopA_leafcnA_stemleafA_frtlfA_sdt_hist, bring in source mod changes and paramsfile

…rch_wkattge_jmaxb1-0.17_slatopA_leafcnA_stemleafA_frtlfA_sdt_hist simulation, this changes it for clm5_0, but we should change it so that these changes only apply to ctsm5_1

Add LILAC

Add LILAC: The Lightweight Infrastructure for Land-Atmosphere
Coupling. This infrastructure consists of two major pieces:

(1) A lightweight coupling infrastructure built on top of ESMF that
    makes it easier for atmosphere models to call CTSM directly, rather
    than using the hub-and-spoke architecture that is used by CESM.

(2) A set of python-based tools for building CTSM and creating its
    runtime inputs when running in an atmosphere model via
    LILAC. Although these tools are built on top of cime, details of the
    create_newcase / case.setup / case.build process are hidden from the
    user, because many of the aspects of this workflow don't make sense
    in the LILAC context.

So far we have used LILAC to couple CTSM to WRF. There are plans to use
the same infrastructure to couple CTSM to other regional atmosphere
models.

Documentation of LILAC is provided in
https://escomp.github.io/ctsm-docs/versions/master/html/lilac/index.html
(though there are still some missing sections), as well as in various
presentations on the wiki
(https://github.com/ESCOMP/CTSM/wiki/Presentations).

There have been many contributors besides myself to the development,
testing and documentation of LILAC; chief among them being Mariana
Vertenstein, Negin Sobhani, Joe Hamman, Sam Levis, Mike Barlage and Dave
Lawrence.

…ds_on_veg, and min_crtical_dayl_depends_on_lat

…before

…d_temperate, so we can make sure clm45 and clm50 results are identical

… be the same as before

Some bit-for-bit changes needed for the Perturbed Parameter Ensemble work

 Conflicts:
	src/biogeophys/LunaMod.F90
	src/biogeophys/PhotosynthesisMod.F90

Fang Li's latest Fire version - includes allowing clm5.1 phys version. New physics option is added
called "clm5_1", with currently the new feature to use the latest fire changes. This has some
adjustments to the fire model and includes some changes to the parameter file. Other new features
will be added into clm5_1 in future tags.

Also bring in mksurfdata changes for the raw urban dataset change. This adds some changes to
mksurfdata for a new urban raw dataset, as well as preparation for new changes for some other
urban changes that will be a future part of clm5_1. Also use the half degree lightning dataset
by default for clm5_1.

Start adding a new test list ctsm_sci that tests all the scientifically supported compsets.
Some of those tests fail due to existing issues, that will be fixed later.

Some more work done to change clm to ctsm, and allow for ctsm as a component.

…o true for ctsm5.1

… get it to work

Call correct routine to calculate btran2 for CNFireLi2021

Due to a subtle code bug, CNFireLi2021 was using the btran2 calculating
routine from the base class rather than the new one that is specific to
this formulation.

Fix reading netcdf variable into a different data type

Main change is to fix the reading of a variable that is one type on a
NetCDF file but a different data type in memory. Previously, this could
lead to memory corruption (not just of the variable in question, but
other variables as well). This was not causing any problems in
out-of-the-box configurations, but it sometimes tripped up some
developers when they added new fields on datasets.

In addition, this adds new self-test code to test ncdio_pio. This module
is hard to get under unit test, but we want to have some tests of it, to
pick up problems like the one fixed in this tag. So as a compromise
solution for now, I have introduced unit test-like tests that are built
into a standard build of CTSM and run in a standard run if a given
namelist flag is set. A better long-term solution would be to integrate
these tests into the pFUnit-based unit testing framework, but that would
take some work. I have added tests of the new code, and a bit of testing
of other code in ncdio_pio, but there's still a lot in ncdio_pio that is
not tested. I figure we can gradually add tests as we make changes to
ncdio_pio.

Finally, an unrelated change to the unit test build: files generated by
genf90 now appear in the unit test build directory rather than the
source tree.

Resolves ESCOMP#1091 (Memory corruption when reading a netcdf
variable into a variable of a different type, at least with PIO1)

Resolves ESCOMP#1188 (In unit test build: files generated by
genf90 should go in build dir rather than source dir)

Refactor ozone code, and misc. small fixes

(1) Restructure ozone code (ESCOMP#1276) in
    preparation for new ozone parameterization.

(2) Fix non-standard hexadecimal constant
    (ESCOMP#1271), needed for gfortran 10

(3) Remove support for CISM1 (ESCOMP#1226)

(4) Move final WaterGridcellBalance call out to clm_driver (resolves
    ESCOMP#1286)

(5) Only add WA and QCHARGE history fields if use_aquifer_layer is true
    (resolves ESCOMP#1281)

(6) Consolidate conditional structures for VIC initialization (resolves
    ESCOMP#1287)

 Conflicts:
	bld/namelist_files/namelist_defaults_ctsm.xml
	bld/unit_testers/build-namelist_test.pl

Implemented new nuopc/cmeps single column functionality.

In config/cesm/config_files.xml - single point domains are only used
for mct/cpl7. For cmeps single point meshes are now generated on the
fly and component domains files are no longer needed.
env_run.xml variables PTS_LAT, PTS_LON and PTS_DOMAINFILE are used
to determine if there is a single point or single column run.
If PTS_LAT and PTS_LON are not -999 and PTS_DOMAINFILE is UNSET,
then you have a single point run and the exact values of PTS_LAT
and PTS_LON are used.  If PTS_LAT and PTS_LON are not -999 and
PTS_DOMAINFILE is not UNSET, then then the cmeps driver will recognize the nearest neighbor
values of PTS_LAT and PTS_LON in PTS_DOMAINFILE as the single column lat and lon to use.

Remove unnecessary settings of nextsw_cday

Remove setting of nextsw_cday in initialization: this hasn't been needed
ever since we stopped calculating albedos in initialization.

Also remove nextsw_cday from clm_time_manager: this was being set but
was never referenced from here: instead, nextsw_cday was being passed as
an argument to clm_drv.

Also, updates cime to a branch tag where I have fixed the --retry option
to create_test.

…t will work for different soil depths

…he upper_soil_layer was exactly 3 as ERS_Ly5_P144x1.f10_f10_mg37.IHistClm51BgcCrop.cheyenne_intel.clm-cropMonthOutput passes and with identical answers to previously