…elease-clm5.0.14

… and resolving rejected differences by hand, make sure the build-namelist unit tester runs

…rcp, fix bgc_spinup tests for sp and suplnitro

…m array that is a 1D array, so you have to account for the number of levels in the index for it. Still need to get a 3D GSMAP to get this to work

…ture streams are turned on

…e file, and 3D grids don't allow mapping, so set mapping to none

…n without bounds errors, but dies with soil balance problem

dz --> dz_lake bug-fix in LakeTemperatureMod.F90 line 960

Bug-fix to prevent the model from aborting when running with fewer soil
layers than lake layers; not to imply that this was not a bug when the
model wasn't aborting. It was.

…n, add a couple more namelist tests for it, also check if streams are off, but streams namelist items are used

…nto prescribed_soil_moisture

…oticed on hobart_nag

…documentation on the new soilm streams

…lm grid to the grid running on

Fix rare soil color bug in mksurfdata_map

Under rare conditions, mksurfdata_map could put the default soil color
in an output cell where there is actually more information. This tag
fixes that issue. None of the out-of-the-box surface datasets are
impacted by this bug, so I have not recreated any surface datasets. (I
checked all out-of-the-box surface datasets except for
surfdata_0.125x0.125_mp24_simyr2000_c150114.nc, because it doesn't get
remade cleanly out of the box.)

Also:

- Add some unit tests for the creation of soil color in mksurfdata_map

- Point to correct (existing) surface dataset for year-1850 at f05
  resolution

…_3dglc that output them only when set

…t's correct

Modularize snow cover fraction method

This tag moves the calculation of frac_sno - and the related updates of
snow_depth - into a new set of classes, with one class for each
parameterization (Niu & Yang 2007 and Swenson & Lawrence 2012).

Previously, the code always calculated frac_sno the new way, but then
possibly overwrote it if using the older Niu & Yang method. The new code
cleans this up, only doing the calculations that are needed for each
method.

In addition, other code that is specific to one of the two methods is
now moved to a home that makes this dependence on method explicit. This
includes the addition of newsnow to int_snow: previously, int_snow was
always updated using an equation specific to the newer CLM5
parameterization of frac_sno, which was not appropriate if using the Niu
& Yang parameterization; this doesn't make a difference currently, since
int_snow is only referenced if using the Swenson & Lawrence
parameterization, but this clears up some confusion. Also, time-constant
parameters read from namelist or the netCDF parameter file now reside in
the appropriate class rather than being more global.

This tag also renames two namelist options to increase clarity:
- subgridflag is renamed to use_subgrid_fluxes, and is now a logical
- oldfflag is renamed to snow_cover_fraction_method, and is now a string

 Conflicts:
	bld/namelist_files/namelist_defaults_ctsm.xml
	bld/namelist_files/use_cases/1850-2100_rcp2.6_transient.xml
	bld/namelist_files/use_cases/1850-2100_rcp4.5_transient.xml
	bld/namelist_files/use_cases/1850-2100_rcp6_transient.xml
	bld/namelist_files/use_cases/1850-2100_rcp8.5_transient.xml
	bld/namelist_files/use_cases/2000-2100_rcp8.5_transient.xml
	bld/unit_testers/build-namelist_test.pl

User defined top-two snow layers

Instead of hardcoding, we now set:

dzmin(1) = snow_dzmin_1
dzmax_l(1) = snow_dzmax_l_1
dzmax_u(1) = snow_dzmax_u_1
dzmin(2) = snow_dzmin_2
dzmax_l(2) = snow_dzmax_l_2
dzmax_u(2) = snow_dzmax_u_2

where the right-hand-side variables get namelist-defined values and the
model calculates dzmin and dzmax_* for the remaining snow layers using
recursive formulas. The calculation is intended to match the previously
hardcoded values, except for the bottom snow layer when nlevsno < 12.
The bottom layer now always gets dzmax_* = huge(1._r8). The formulas
appear in a document titled "A firn model for CLM" that is linked to

User defined top-two snow layers

Instead of hardcoding, we now set:

dzmin(1) = snow_dzmin_1
dzmax_l(1) = snow_dzmax_l_1
dzmax_u(1) = snow_dzmax_u_1
dzmin(2) = snow_dzmin_2
dzmax_l(2) = snow_dzmax_l_2
dzmax_u(2) = snow_dzmax_u_2

where the right-hand-side variables get namelist-defined values and the
model calculates dzmin and dzmax_* for the remaining snow layers using
recursive formulas. The calculation is intended to match the previously
hardcoded values, except for the bottom snow layer when nlevsno < 12.
The bottom layer now always gets dzmax_* = huge(1._r8). The formulas
appear in a document titled "A firn model for CLM" that is linked to

… rel2master

…of a soilm set logic function and duplicate calls, and the argument list sent in wasn't correct, so I corrected it

Update externals, fixes to work with latest cime, get nuopc cap working

(1) Update to latest version of externals. This includes a significant
    cime update.

(2) Minor fixes to get things working with the latest version of cime.

(3) Fix from Mariana Vertenstein to get NUOPC cap working, fixes to
    externals cfg files to allow running NUOPC cases out of the box, and
    add a NUOPC test.

 Conflicts:
	Externals.cfg
	bld/namelist_files/namelist_defaults_ctsm.xml
	src/main/clm_initializeMod.F90
	src/main/clm_instMod.F90
	src/main/decompInitMod.F90
	src/main/ndepStreamMod.F90
	src/utils/clmfates_interfaceMod.F90

…d, this will compile/link

…user_nl_clm for prescribed test-mod

Use patch to apply the difference and move it to the branch.

Conflicts on the files:

./cime_config/testdefs/ExpectedTestFails.xml
./bld/unit_testers/build-namelist_test.pl
./bld/namelist_files/use_cases/1850_control.xml
./bld/namelist_files/namelist_defaults_ctsm.xml
./bld/CLMBuildNamelist.pm
./doc/ChangeSum
./src/main/clm_driver.F90
./src/biogeophys/SoilMoistureStreamMod.F90
./src/biogeophys/WaterStateType.F90
./src/biogeophys/UrbanTimeVarType.F90

…0BgcCrop.cheyenne_intel.clm-defau to build/link/run

…10_musgs.I1850Clm50BgcCrop.cheyenne_intel.clm-default

…under the src directory

… fix the pointer for prescribed soilm history term

… it in

…ewer variable name

Bounds assertion for C isotopes when threading is on

Previously, the bounds of c13 and c14 in subroutines TruncateCStates and
TruncateCandNStates were not checked when threading was on. This PR allows us
to handle c13 and c14 arrays like everything else in CTSM including (bounds
checking).

This PR resolves issue ESCOMP#811

… already being handled in a more sophisticated way on master

… file than the new ones

…ly interpolated dataset

… patch, this was causing the 2D Fates variables to die

This reverts commit 338be7b.

Bring documentation source to master

1. Bring documentation source to master: Pulls in the source from
   https://github.com/escomp/ctsm-docs. This is important so that
   documentation can remain in sync with changes in the model
   code. Images are stored here using git-lfs (Git Large File
   Storage). I also made some minor fixes to get the pdf build of the
   tech note working.

2. Use a different documentation theme that supports a version dropdown
   menu, and add the code needed to support this versioning on the
   documentation web pages. At a high level, the way the versioned
   documentation works is to have separate subdirectories in the
   gh-pages branch of the ctsm-docs repository for each version of the
   documentation we want to support. There is then a bit of JavaScript
   code which uses a json file in the gh-pages branch to determine which
   versions exist and how these should be named in the dropdown
   menu. Most of these changes were borrowed from ESMCI/cime#3439, which
   in turn borrowed from ESCOMP/CISM-wrapper#23, which in turn was a
   slight modification of an implementation provided by @mnlevy1981 for
   the MARBL documentation, which in turn borrowed from an
   implementation put together by Unidata (credit where credit is due).

   I am not aware of out-of-the-box support for a version pull-down in
   out-of-the-box sphinx themes (though the last time I looked was in
   Fall, 2018, so there may be something available now). However,
   support for a version dropdown exists in an open PR in the sphinx
   readthedocs theme repository: readthedocs/sphinx_rtd_theme#438. I
   have pushed this branch to a new repository in ESMCI
   (https://github.com/ESMCI/sphinx_rtd_theme) to facilitate long-term
   maintenance of this branch in case it disappears from the official
   sphinx_rtd_theme repository. I have also cherry-picked a commit onto
   that branch, which is needed to fix search functionality in sphinx1.8
   (from readthedocs/sphinx_rtd_theme#672) (which is another reason for
   maintaining our own copy of this branch). The branch in this
   repository is now named version-dropdown-with-fixes (branching off of
   the version-dropdown branch in the sphinx_rtd_theme repository). In
   the long-term, I am a little concerned about using this theme that
   isn't showing any signs of being merged to the main branch of the
   readthedocs theme, but this has been working for us in other projects
   for the last 2 years, so I feel this is a reasonable approach in the
   short-medium term.

The new process for building the documentation is given here:
https://github.com/ESCOMP/CTSM/wiki/Directions-for-editing-CLM-documentation-on-github-and-sphinx

Resolves ESCOMP#239

Update cime to latest in cesm2.2 beta tag (cesm2_2_beta04)
Fix two small issues that had gone on the release-clm5.0 branch.
Update manage_externals (to manic-v1.1.8)

NOTE: Part of the reason for updating cime, was because of some problems
Mike Mills was having on cheyenne with inputdata files being deleted out
from under him before setting up his cases. We think system issues were
interacting with issues with cime putting in place zero length
missing files for the version of cime he was using. Those issues went
away with a cime update, so we hope updating to a newer cime version here
will help prevent those issues for CTSM users.

cime updates:

some cleanup from the last maint-5.6 update
Add ne5np4.pg4 grid.
case.setup: Add --keep option
Add omip as option to DATM_CO2_TSERIES

…s now can, fix a difference that didn't get in from the release branch that wasn't allowing the code to compile in mkglcmecMod

…s and was missing off of master

…nial as well as PtVg and high resolution PFT raw datasets

…changed on master

…to work

…proposed in ESCOMP#673 for master didn't work

…2master