Bring in CMIP6 compset modifiers, output usermods and bit-for-bit fixes from dev014 and dev015

Bring in all changes from ctsm1.0.dev014 and ctsm1.0.dev015:

From ctsm1.0.dev015:

(1) Support %BGC-CROP-CMIP6DECK and %BGC-CROP-CMIP6WACCMDECK compset
modifiers, so that we can turn on the necessary options
(output-related and others) via new CMIP6-specific compsets.

(2) Turn on carbon isotopes in CMIP6 runs (from Erik Kluzek)

(3) Remove setting of CCSM_BGC=CO2A in the cmip6 usermods

(4) Add usermods directories for getting typical extra output that's
wanted in many cases: output_crop, output_crop_highfreq, output_bgc,
output_bgc_highfreq, output_sp, and output_sp_highfreq. These can be
enabled by adding something like '--user-mods-dir output_crop' on
the create_newcase line (that short-hand works for an I compset; for
F or B compsets, you need to provide the full path to the usermod
directory).

(4) Allow holes in the number of history tapes. Holes are cases where,
for example, we have h0, h1 and h3 tapes, but no h2 tape (because
there are no fields on the h2 tape). (This is needed for (3).)

(5) Fix reading and writing of 1-d logical global arrays. This fixes
#24 for real (rather than just preventing an attempt to
read/write 1-d logical arrays, as was done in the previous 'fix').

(6) Add C13_NBP and C14_NBP diagnostic fields (from Keith Oleson)

(7) Make a bunch of carbon isotope diagnostic fields inactive by default

(8) Don't allow interpolation (use_init_interp) from a case without
carbon isotopes to a case with carbon isotopes: Due to
#67, interpolation from a case
without carbon isotopes to a case with carbon isotopes yields
incorrect initialization values for the carbon isotopes. Now that
we're turning carbon isotopes on via some semi-out-of-the-box
usermods (for cmip6), it is becoming more important to check to make
sure someone doesn't shoot themselves in the foot this way.

(9) Add tests of the new output usermods as well as of the CMIP6 compset
modifiers

From ctsm1.0.dev014: Four miscellaneous minor, bit-for-bit bug fixes:

(1) Py3 pylint check and address cime issue ESMCI/cime#2822 (from Jim
Edwards: #526)

(2) Change uppercase DEBUG variables to lowercase debug (requested by
Jim Edwards to avoid conflicting with the DEBUG CPP token)
(Fixes #534)

(3) Remove unnecessary line of code in LunaMod.F90 that was causing
problems with some compilers due to an uninitialized variable
(Fixes #322)

(4) Add r8 to 0 constant to fix build issue with XLF compiler (from Jim
Edwards: #531)

Bring in bit-for-bit changes from master up to ctsm1.0.dev012: AnnEt init, snowmip fields

Bring in new diagnostic fields added by Justin Perket, Sean Swenson and Mark Flanner
for Snow-MIP. Most of those are fields that represent "Snow Free" data.

Also bring in fixes for a list of issues. Add handling of the new CO2 which includes
both latitude-band and global average versions. Add some changes to make it easier
for input data processing including NOT doing the slow 1km map file creation. Have
the number of steps that are skipped at startup dependent on the time-step size. Add
a test for some requirements of WACCMX (time-step and use of ESMF). Calculations of
local time are now done in a global subroutine, that can handle negative longitudes.
Fix how FFIX_TO_SMINN is handled for history output. The namelist logical "calc_human_stress_indices"
changed from logical to a character string of three values: FAST, NONE, ALL. FAST
is the default so the less expensive ones are output, NONE turns them all off, and ]
ALL does all of them including the expensive ones.

InitAccVars was mistakenly setting qflx_evap_tot_col rather than
AnnET. This fix allows us to remove now-redundant cold start and restart
code for AnnET.

CTSM Master Tag This Corresponds To: ctsm1.0.dev012

Updated CMIP6 ndep file for historical transient Bgc cases, 1850_control same as before

Update the ndep file for transient cases for CLM50 to the CMIP6 version that has identical
data for 1849-1850 to the previous CMIP6 1850_control (with different mid-month times however), and
new 3-member ensemble average/5-year smoothing from the WACCM case: b.e21.BWHIST.f09_g17.CMIP6-historical-WACCM.00[123].
The new data is monthly rather than yearly, which means there will be a seasonal cycle to nitrogen deposition
for transient cases now. The midmonth times/dates are different for the multi-year file from
the previous file, so answers change when using it for 1850_control cases even though the data is exactly the same.
Because, of that we are still pointing to the previous 1850 CMIP6 ndep file.

CLM4.5 is still using the previous CMIP5 ndep dataset.

Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007

Bring in a list of simple fixes that came to CTSM master. Also change so glacier initialization is ALWAYS done
at startup (time step zero) even if it isn't cold or interpolated initial conditions. Also synchronize some of the
files in the doc directory with the files in ctsm/master.

This is a duplicate of the release-clm5.0.06 tag, but properly on the release-clm5.0 branch. The previous tag was stand-alone.

Bring in some simple fixes from ctsm1.0.dev006 and avoid glacier adjustment at startup from ctsm1.0.dev007

Bring in a list of simple fixes that came to CTSM master. Also change so glacier initialization is ALWAYS done
at startup (time step zero) even if it isn't cold or interpolated initial conditions. Also synchronize some of the
files in the doc directory with the files in ctsm/master.

Update 1850 ndep file, and last year for transient streams

Update to latest Nitrogen Deposition file from simulations with WACCM for 1850.
Also fix an issue with the last year for historical transient cases.

Fix some NFIX variables, update cime/cism for upgraded hobart new glade, new diagnostic fields, update cmip6 output

Add some new diagnostic fields. Some needed for CMIP6. Update the CMIP6 user-mods output.
Fix a couple issues. Get full list of history tapes working correctly. Check for valid range
of CO2. New IC file interpolated from the previous one for f19_g17_gl4 for 2000 Clm50BgcCrop

Update cime and cism so can work on upgraded hobart. Also fix an issue that the Nag6.2 compiler found
in CTSM. Also get working with glade changes that happened on cheyenne, DIN_LOC_ROOT_CLMFORC was
changed to a new directory.

Nitrogen Fixation flux arrays were being set to missing value over non-vegetated landunits. This sets them to zero everywhere
and averages in the zero's at the gridcell level for history output. It also reads in restarts with missing values and converts
them to zero's.

There are also some tools updates, getting the tools working on the new upgraded hobart.cgd.ucar.edu.

And mksurfdata_map is updated to add some *_MAX files on the landuse.timeseries files that will allow us to conserve memory
for transient cases.

Second release branch tag for CESM2.0 release, fixing DA and tools and README files, identical to clm5.0.dev013

Update cime and cism to newer versions used in release. These bring in some answer
changes. The cime version updates the orbit for 2000 compsets. The cism version
changes answers for two fields with NO_EVOLVE and more fields for EVOLVE.

Fixes an important bug needed for use with Data Assimulation. Several changes
to testing. Adding wallclock as needed, changing a few compsets so science
supported compsets are used, added tput_tolerance to some tests known to be
variable.

Many changes to the clm tools for creating input files. Added the version by
querying "git describe" and adding it as an attribute to NetCDF files. Changes
to get tools working, and tested. Also changed so that tools can be run in either
a CTSM checkout or a CESM checkout.

Updated README files so they are accurate.

Mistake tag identical to previous version

Mistake that was intended to point to clm5.0.dev013, but really points to clm5.0.dev012.

CTSM Master Tag This Corresponds To: clm5.0.dev012

First release branch tag for CESM2.0 release, identical to clm5.0.dev012

This is the first release branch tag for the CESM2.0 release for CTSM. There are many changes
to software mostly to fix a list of issues. There are some changes to the science that change
answers to fix some small problems, but don't have a large effect on simulations. Externals are
updated to new versions, fixing issues, and