Do a diff of the dmleung DUSTEMIS branch based off of release-clm5.0.34
to ctsm5.1.dev106 and apply the diff after updating the paths for
namelist_definition and lnd_import_export.F90 in the diff.

git apply -3 dust.diff

Diffs with conflicts:
	modified:   src/biogeochem/DUSTMod.F90
	modified:   src/biogeophys/SoilStateInitTimeConstMod.F90
	modified:   src/main/controlMod.F90
	modified:   src/cpl/mct/lnd_import_export.F90

The changes in lnd_import_export were to change a check for negative
LW that seems to be removed in the latest version.

…dataset

…abort, don't output USTAR as FV is already output in FrictionVelocity

…ybrid drag partitioning. (previous use of wt_lunit in DUSTMod was not working because wt_lunit was deallocated after CTSM initialization.)

…m the cesm2_3_beta09 tag

…orce the outgoing longwave radiation to be non-negative.

…to 5. (14 Nov 2022)

…to 5. (14 Nov 2022)

…on; code cleanup

dmleung 14 Nov 2022

Erik enabled outputting fv (FV) in FrictionVelocityMod.F90
14 Nov 2022

…rigent's roughness data

modified clm_instMod.F90. Now CTSM can compile successfully.
31 Jan 2023

…ct (25 Feb 2023).

…gh_fct) since the stream methods is here (dmleung 31 Mar 2023)

…exp is going to be large and thus end up with a very small term

 Conflicts:
	src/biogeochem/DUSTMod.F90

BFB merge tag dev166

2315 @TeaganKing Refactoring run_neon for PLUMBER2 part1
2326 @samsrabin run_sys_tests: Check Python environment for FatesColdTwoStream tests
2213 @samsrabin Automatically assign high priority items to project 25
2330 @samsrabin Add Izumi version of the aux_clm unit testing

 Conflicts:
	bld/CLMBuildNamelist.pm
	bld/namelist_files/namelist_definition_ctsm.xml

0f884bfec Merge pull request ESCOMP#205 from jedwards4b/sunset_svn_git_access
82a5edf79 merge in billsacks:svn_testing_no_github
17532c160 Use a local svn repo for testing
9c904341a different method to determine if in tests
539952ebd remove debug print statement
cc5434fa7 fix submodule testing
1d7f28840 remove broken tests
04e94a519 provide a meaningful error message
38bcc0a8c Merge pull request ESCOMP#201 from jedwards4b/partial_match
b4466a5aa remove debug print statement
c3cf3ec35 fix issue with partial branch match

git-subtree-dir: manage_externals
git-subtree-split: 0f884bfec8e43d0c02261de858d6ec3f6d855e51

…_dev

… commented out Zender code, remove unneeded markers by Danny Leung

…to be read in, this is important when we need to flip between Zender and Leung

…te that was missing, add underscore to a name for readability, always allocate, but allocate only 0th element if usestreams is false

…cking around making sure namelist is read in and stream initialization has been done, this builds and runs

…physical parameters, changing numbers into double precisions, and putting more comments into the code. 20 Feb 2024

…process in the DustEmission subroutine. 20 Feb 2024

… Feb 2024

@dmleung

…g. Also added precision in other defined parameters. 26 Feb 2024

…. Also set output for impact threshold. 27 Feb 2024

… partitioning, which worked much better than the patch level VAI. 1 Apr 2024

…n equation in Leung 2023 should be impact threshold instead of standardized fluid threshold. So, that was corrected in the code. dmleung 1 Apr 2024

… contribution to the subtimestep wind fluctuations, instead of assuming zero buoyancy contributions. dmleung 1 Apr 2024

…on dust emission calculation. 24 May 2024

…uation of dpfct_rock(p) = NaN, which likely causes the run to die when turning on debug mode

…on intermittency in DUSTMod.F90. 28 May 2024

…sions

Merge b4b-dev

 Conflicts:
	.github/workflows/assign-to-project.yml
	bld/CLMBuildNamelist.pm
	bld/namelist_files/namelist_definition_ctsm.xml
	bld/unit_testers/build-namelist_test.pl
	src/biogeochem/DUSTMod.F90

Add some log statements around this.

Update externals to cesm2_3_beta17, remove mct, retire /test/tools

Changes unrelated to the tag's title:

Rm manage_externals and update documentation accordingly

Fixes ESCOMP#2537 Remove manage_externals stuff from run_sys_tests
Fixes ESCOMP#2536 Update documentation for git-fleximod
Fixes ESCOMP#2467 Remove references to cheyenne from the testlist

NOTE: Also
Add cam and cice to the .gitmodules file

 Conflicts:
	Externals.cfg

Update git fleximod to resolve some issues we found with it

Just update the gitfleximod subtree to v0.7.8. This fixes an issue in identifying that a tag is out of sync in a submodule.
An issue about recursion on a submodule. Allows untracked files, and fixes a MS Window Memory error. And
also git-fleximod status marks optional submodules, which helps explain why they are marked as not-checked out.

Get unit testing working for both Leung and Zender dust emissions. Leung
DuetEmission right now is just the Zender version. Only ran unit-testing
at this point. Added a clean method to PrigentStreams as well as a new
one for unit-testing.

 Conflicts:
	src/biogeochem/DustEmisBase.F90

 	new file:   biogeochem/DustEmisLeung2023.F90
 	new file:   biogeochem/test/DustEmis_test/test_DustEmisLeung2023.pf
 	new file:   unit_test_stubs/share_esmf/PrigentRoughnessStreamType.F90

…n to clay fraction. dmleung also corrected the output of soil surface friction velocity (wnd_frc_slt). Coded on 5 Jul 2024 and committed on 8 Jul 2024

dmleung reduced the sensitivity of dust emission to clay fraction, and corrected the output of soil surface friction velocity (wnd_frc_soil). Plus other updates from the CTSM side. dmleung coded 5 Jul 2024 and committed 8 Jul 2024

…n Derecho

 Conflicts:
	src/biogeochem/DUSTMod.F90
	src/biogeophys/SoilStateInitTimeConstMod.F90

Also get unit tests working.

… dust unit tests to use the appropriate ones for Zender and Leung tests, add tests for the new MassFracClayLeung2023 function, get the unit tests all working again

… because of change in answers

…, still two fail

…k through initialization, otherwise it fails thinking stremas are off

… doing on inside the Leung 2023 code

…t variables for DustEmission, remove begc/endc

Bring tmp-branch to master

Bring in changes that came in on the tmp-240620 branch to master now that cesm3_0_beta01 has been made.

The changes are documented in tags and the ChangeLog but include the following tags:

  tmp-240620.n03.ctsm5.2.007 samrabin -- upland hillslope column fsat values to zero
  tmp-240620.n02.ctsm5.2.007 erik ------ Another update of git-fleximod
  tmp-240620.n01.ctsm5.2.007 slevis ---- Merge b4b-dev

Fix/excess ice cold start

Changed the way soil temperature is initialized when excess ice is on and the model starts from cold.

Specific notes

TemperatureType now has a private ReadNL subroutine that reads two new namelist options: excess_ice_coldstart_depth and excess_ice_coldstart_temp which control top depth (higher layers get default initial temperature) and soil temperature for soil layers ONLY in columns where excess ice is present. Other columns get their default soil temperature.

New namelist options belong to a new group "clm_temperature_inparm" with its own logic routine. This is done so in the future hardcoded cold start temperatures can be moved to the namelists. Two namelist tests have been added to check for invalid values logic as well as a test for use_excess_ice_streams logic. use_excess_ice_streams has no default value (due to options for restart) and default value set in the CLMBuildNamelist.pm.

excessicestream_type has been taken out of waterstate_type and its routines are called directly in clm_inst%Init. Checks for UseExcessIceStreams() are still in place in WaterStateType.F90 for double-checking. clm_inst%Init now has a new local variable with excess ice concentration that are read from streams (or zeros if use_excess_ice is false). Arguments for temperature_type%Init and water_type%Init (and children types) have been changed to include this new variable. Fortran unit tests are also updated to account for these new arguments.

Get the namelist and PF unit src unit tests working again

Conflicts:
	bld/CLMBuildNamelist.pm
	bld/namelist_files/namelist_defaults_ctsm.xml
	bld/unit_testers/build-namelist_test.pl
	src/biogeochem/DustEmisFactory.F90
	src/biogeochem/test/DustEmis_test/test_DustEmisZender2003.pf

…mod problem in updating to this CAM version

Add a testmod for running Leung_2023 dust emission explicitly.
And change some existing aux_clm tests over to it (but not all).

… that's the default and it's not needed

…nd Leung dust tests

…ssFracClayLeung2023 function

… default inactive

…mbl_thr