Merge commit 'a65df14478f5907e2d87c5909199089c028a7656' into ctsm5.1.…

…dev176-noresm

.git-blame-ignore-revs

@@ -30,3 +30,5 @@ d866510188d26d51bcd6d37239283db690af7e82
 8a168bb0895f4f2421608dd2589398e13a6663e6
 183fc26a6691bbdf87f515dc47924a64be3ced9b
 6fccf682eaf718615407d9bacdd3903b8786a03d
+2500534eb0a83cc3aff94b30fb62e915054030bf
+78d05967c2b027dc9776a884716597db6ef7f57c

.gitignore

@@ -111,6 +111,7 @@ unit_test_build
 /tools/site_and_regional/????.ad/
 /tools/site_and_regional/????.postad/
 /tools/site_and_regional/????.transient/
+/tools/site_and_regional/archive/
 
 # build output
 *.o

Externals.cfg

@@ -8,22 +8,22 @@ required = True
 local_path = components/cism
 protocol = git
 repo_url = https://github.com/ESCOMP/CISM-wrapper
-tag = cismwrap_2_1_96
+tag = cismwrap_2_1_99
 externals = Externals_CISM.cfg
 required = True
 
 [rtm]
 local_path = components/rtm
 protocol = git
 repo_url = https://github.com/ESCOMP/RTM
-tag = rtm1_0_78
+tag = rtm1_0_79
 required = True
 
 [mosart]
 local_path = components/mosart
 protocol = git
 repo_url = https://github.com/ESCOMP/MOSART
-tag = mosart1_0_48
+tag = mosart1_0_49
 required = True
 
 [mizuRoute]
@@ -44,18 +44,18 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.175
+tag = cime6.0.217_httpsbranch03
 required = True
 
 [cmeps]
-tag = cmeps0.14.43
+tag = cmeps0.14.50
 protocol = git
 repo_url = https://github.com/ESCOMP/CMEPS.git
 local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.24
+tag = cdeps1.0.28
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -70,7 +70,7 @@ local_path = components/cpl7
 required = True
 
 [share]
-tag = share1.0.17
+tag = share1.0.18
 protocol = git
 repo_url = https://github.com/ESCOMP/CESM_share
 local_path = share

Externals_CLM.cfg

@@ -1,8 +1,8 @@
 [fates]
 local_path = src/fates
 protocol = git
-repo_url = https://github.com/NGEET/fates
-tag = sci.1.71.0_api.33.0.0
+repo_url = https://github.com/rgknox/fates
+tag = sci.1.72.2_api.34.0.0
 required = True
 
 [externals_description]

bld/namelist_files/namelist_defaults_overall.xml

@@ -22,6 +22,12 @@ determine default values for namelists.
 
 -->
 
+<clm_start_type phys="clm4_5" lnd_tuning_mode="clm4_5_cam5.0" >cold</clm_start_type>
+<clm_start_type phys="clm4_5" lnd_tuning_mode="clm4_5_cam4.0" >cold</clm_start_type>
+<clm_start_type phys="clm5_0" lnd_tuning_mode="clm5_0_cam5.0" >cold</clm_start_type>
+<clm_start_type phys="clm5_0" lnd_tuning_mode="clm5_0_cam4.0" >cold</clm_start_type>
+<clm_start_type phys="clm5_1" lnd_tuning_mode="clm5_1_cam5.0" >cold</clm_start_type>
+<clm_start_type phys="clm5_1" lnd_tuning_mode="clm5_1_cam4.0" >cold</clm_start_type>
 <clm_start_type phys="clm5_1"  use_cndv=".true." >arb_ic</clm_start_type>
 <clm_start_type phys="clm5_0"  use_cndv=".true." >arb_ic</clm_start_type>
 <clm_start_type phys="clm4_5"  use_cndv=".true." >arb_ic</clm_start_type>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -777,6 +777,19 @@ Full pathname to the inventory initialization control file.
 (Only relevant if FATES is on).
 </entry>
 
+<entry id="fates_history_dimlevel" type="integer(2)" category="physics"
+       group="clm_inparm" valid_values="0,1,2" >
+  Setting for what types of FATES history to be allocate and
+  calculated at the dynamics timestep (1st integer) and the
+  model timestep (2nd integer). This must be consistent with
+  hist_fincl*, ie output variables must not be listed if the
+  output level is not enabled.
+  0 = no fates history variables are calculated or allocated
+  1 = only time x space (3d) fates history variables allowed
+  2 = multiplexed dimensioned fates history is also allowed
+  (Only relevant if FATES is on)
+</entry>
+
 <!-- This may eventually migrate to the dynamic_subgrid group-->
 <entry id="use_fates_luh" type="logical" category="physics"
        group="clm_inparm" valid_values="" >
@@ -800,6 +813,41 @@ LUNA operates on C3 and non-crop vegetation (see vcmax_opt for how other veg is
 LUNA: Leaf Utilization of Nitrogen for Assimilation
 </entry>
 
+<entry id="use_hillslope" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on the hillslope model
+</entry>
+
+<entry id="downscale_hillslope_meteorology" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on meteorological downscaling in hillslope model
+</entry>
+
+<entry id="use_hillslope_routing" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on surface water routing in the hillslope hydrology model
+</entry>
+
+<entry id="hillslope_head_gradient_method" type="char*256" category="physics"
+        group="hillslope_hydrology_inparm" valid_values="Kinematic,Darcy">
+Method for calculating hillslope saturated head gradient
+</entry>
+
+<entry id="hillslope_transmissivity_method" type="char*256" category="physics"
+        group="hillslope_hydrology_inparm" valid_values="LayerSum,Uniform">
+Method for calculating transmissivity of hillslope columns
+</entry>
+
+<entry id="hillslope_pft_distribution_method" type="char*256" category="physics"
+        group="hillslope_properties_inparm" valid_values="Standard,FromFile,DominantPftUniform,DominantPftLowland,PftLowlandUpland">
+Method for distributing pfts across hillslope columns
+</entry>
+
+<entry id="hillslope_soil_profile_method" type="char*256" category="physics"
+        group="hillslope_properties_inparm" valid_values="Uniform,FromFile,SetLowlandUpland,Linear">
+Method for distributing soil thickness across hillslope columns
+</entry>
+
 <entry id="use_hydrstress" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the plant hydraulic stress model
@@ -1784,6 +1832,49 @@ Mapping method from Nitrogen deposition input file to the model resolution
     copy     = copy using the same indices
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- Dust namelist and Zender soil erodibility stream                                          -->
+<!-- ========================================================================================  -->
+
+<entry id="dust_emis_method" type="char*12" category="physics"
+       group="clm_inparm" valid_values="Zender_2003,Leung_2023" >
+Which dust emission method is going to be used. Either the Zender 2003 scheme or the Leung 2023
+scheme.
+(NOTE: The Leung 2023 method is NOT currently available)
+</entry>
+
+<entry id="zender_soil_erod_source" type="char*3" category="physics"
+       group="zendersoilerod" valid_values="lnd,atm" >
+Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
+here in CTSM, or in the ATM model.
+(only used when dust_emis_method is Zender_2003)
+</entry>
+
+<entry id="zendersoilerod_mapalgo" type="char*256" category="physics"
+       group="zendersoilerod" valid_values="bilinear,nn,nnoni,nnonj,spval,copy" >
+Option only applying for the Zender_2003 method for whether the soil erodibility file is handled
+here in CTSM, or in the ATM model.
+(only used when dust_emis_method is Zender_2003)
+    bilinear = bilinear interpolation
+    nn       = nearest neighbor
+    nnoni    = nearest neighbor on the "i" (longitude) axis
+    nnonj    = nearest neighbor on the "j" (latitude) axis
+    spval    = set to special value
+    copy     = copy using the same indices
+</entry>
+
+<entry id="stream_fldfilename_zendersoilerod" type="char*256" category="datasets"
+       input_pathname="abs" group="zendersoilerod" valid_values="" >
+Filename of input stream data for Zender's soil erodibility source function
+(only used when dust_emis_method is Zender_2003, and zender_soil_erod_source is lnd)
+</entry>
+
+<entry id="stream_meshfile_zendersoilerod" type="char*256" category="datasets"
+       input_pathname="abs" group="zendersoilerod" valid_values="" >
+mesh filename of input stream data for Zender's soil erodibility source function
+(only used when dust_emis_method is Zender_2003, and zender_soil_erod_source is lnd)
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- finundated stream -->
 <!-- ========================================================================================  -->
@@ -2179,7 +2270,7 @@ Land mask description
 
 <entry id="lnd_tuning_mode" type="char*20" category="default_settings"
        group="default_settings"
-       valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm5_0_cam6.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_cam6.0">
+       valid_values="clm4_5_CRUv7,clm4_5_GSWP3v1,clm4_5_cam6.0,clm4_5_cam5.0,clm4_5_cam4.0,clm5_0_cam6.0,clm5_0_cam5.0,clm5_0_cam4.0,clm5_0_CRUv7,clm5_0_GSWP3v1,clm5_1_GSWP3v1,clm5_1_CRUv7,clm5_1_cam6.0,clm5_1_cam5.0,clm5_1_cam4.0">
 General configuration of model version and atmospheric forcing to tune the model to run under.
 This sets the model to run with constants and initial conditions that were set to run well under 
 the configuration of model version and atmospheric forcing. To run well constants would need to be changed
@@ -2499,12 +2590,6 @@ If surface water is active or not
 (deprecated -- will be removed)
 </entry>
 
-<entry id="origflag" type="integer" category="clm_physics"
-       group="clm_soilhydrology_inparm" valid_values="0,1" >
-Use original CLM4 soil hydraulic properties
-(deprecated -- will be removed)
-</entry>
-
 <!-- ========================================================================================  -->
 <!-- namelist elements associated with the CH4 Model                                           -->
 <!-- ========================================================================================  -->