diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
index fca4a8315b..c02e20b678 100644
--- a/.git-blame-ignore-revs
+++ b/.git-blame-ignore-revs
@@ -27,6 +27,7 @@ d866510188d26d51bcd6d37239283db690af7e82
 e096358c832ab292ddfd22dd5878826c7c788968
 475831f0fb0e31e97f630eac4e078c886558b61c
 fd5f177131d63d39e79a13918390bdfb642d781e
+a51816e0de380300b69db9fc3e2c7fa83b267b64
 # Ran SystemTests and python/ctsm through black python formatter
 5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
 8056ae649c1b37f5e10aaaac79005d6e3a8b2380
@@ -52,3 +53,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
 753fda3ff0147837231a73c9c728dd9ce47b5997
 f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c
+bd535c710db78420b8e8b9d71d88d8339e899c59
diff --git a/.gitmodules b/.gitmodules
index 87676223a0..9aeb7d4de0 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.79.3_api.37.0.0
+fxtag = sci.1.80.4_api.37.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
@@ -36,7 +36,7 @@ fxDONOTUSEurl = https://github.com/NCAR/fates-release
 [submodule "cism"]
 path = components/cism
 url = https://github.com/ESCOMP/CISM-wrapper
-fxtag = cismwrap_2_2_002
+fxtag = cismwrap_2_2_005
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
@@ -44,7 +44,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
 [submodule "rtm"]
 path = components/rtm
 url = https://github.com/ESCOMP/RTM
-fxtag = rtm1_0_80
+fxtag = rtm1_0_86
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/RTM
@@ -52,7 +52,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/RTM
 [submodule "mosart"]
 path = components/mosart
 url = https://github.com/ESCOMP/MOSART
-fxtag = mosart1.1.02
+fxtag = mosart1.1.07
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
@@ -60,7 +60,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
 [submodule "mizuRoute"]
 path = components/mizuRoute
 url = https://github.com/ESCOMP/mizuRoute
-fxtag = cesm-coupling.n02_v2.1.3
+fxtag = cesm-coupling.n03_v2.2.0
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
@@ -68,7 +68,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/ESMCI/ccs_config_cesm.git
-fxtag = ccs_config_cesm1.0.10
+fxtag = ccs_config_cesm1.0.16
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
@@ -76,7 +76,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
 [submodule "cime"]
 path = cime
 url = https://github.com/ESMCI/cime
-fxtag = cime6.1.37
+fxtag = cime6.1.59
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESMCI/cime
@@ -84,7 +84,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime
 [submodule "cmeps"]
 path = components/cmeps
 url = https://github.com/ESCOMP/CMEPS.git
-fxtag = cmeps1.0.16
+fxtag = cmeps1.0.33
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
@@ -92,7 +92,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
 [submodule "cdeps"]
 path = components/cdeps
 url = https://github.com/ESCOMP/CDEPS.git
-fxtag = cdeps1.0.53
+fxtag = cdeps1.0.61
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
@@ -100,7 +100,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
 [submodule "share"]
 path = share
 url = https://github.com/ESCOMP/CESM_share
-fxtag = share1.1.2
+fxtag = share1.1.7
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
diff --git a/README b/README
index c5c06daae7..af8f2cbaaa 100644
--- a/README
+++ b/README
@@ -126,9 +126,9 @@ cime_config/config_tests.xml ----- Define CTSM specific tests
 cime_config/config_pes.xml ------- Define Processor layouts for various CTSM grids and compsets
 cime_config/testdefs ------------- Directory for specification of CTSM testing
 cime_config/testdefs/ExpectedTestFails.xml -- List of tests that are expected to fail
-cime_config/usermods_dirs -------- Directories of sets of user-modification subdirs
+cime_config/usermods_dirs/clm ---- Directories of sets of user-modification subdirs
                                    (These are directories that add specific user modifications to
-                                    simulations created using "cime/scripts/create_newcase --user-mods-dir".)
+                                    simulations created using "cime/scripts/create_newcase --user-mods-dir clm/*)
 
 tools/mksurfdata_esmf --------- Directory to build program to create surface dataset 
                                 at any resolution.
diff --git a/WhatsNewInCTSM5.3.md b/WhatsNewInCTSM5.3.md
index b1f753081b..1fabfd1192 100644
--- a/WhatsNewInCTSM5.3.md
+++ b/WhatsNewInCTSM5.3.md
@@ -1,53 +1,48 @@
-Purpose and description of changes since ctsm5.2.005
-----------------------------------------------------
+# What's new in CTSM 5.3 (tag `ctsm5.3.0`)
 
-Bring in updates needed for the CESM3.0 science capability/functionality "chill". Most importantly bringing
-in: CN Matrix to speed up spinup for the BGC model, updated surface datasets, updated Leung 2023 dust emissions,
-explicit Air Conditioning for the Urban model, updates to crop calendars. For clm6_0 physics these options are now
-default turned on in addition to Sturm snow, and excess ice.
+## Purpose and description of changes since CTSM 5.2 (tag `ctsm5.2.005`)
+- Adds CN Matrix method to speed up spinup for the BGC model.
+- Updates surface datasets.
+- Brings in new Leung 2023 dust emissions.
+- Adds explicit air conditioning for the urban model.
+- Updates crop calendars.
+- Updates fire model with various improvements, including default parameterization against climate reanalysis from CRU-JRA instead of GSWP.
+- FATES compsets can now be run with transient land use.
 
-Changes to CTSM Infrastructure:
-===============================
+These changes were needed ahead of the CESM3 capability/functionality "chill". For `clm6_0` physics these options are now turned on by default, in addition to Sturm snow and excess ice.
 
- - manage_externals removed and replaced by git-fleximod
- - Ability to handle CAM7 in LND_TUNING_MODE
+## Changes to CTSM infrastructure
+ - `manage_externals` removed and replaced by `git-fleximod`
+ - Ability to handle CAM7 in `LND_TUNING_MODE`
 
-Changes to CTSM Answers:
-========================
+## Changes to CTSM answers
 
- Changes to defaults for clm6_0 physics:
+ Changes to defaults for `clm6_0` physics:
   - Urban explicit A/C turned on
-  - Snow thermal conductivity is now Sturm_1997
-  - New IC file for f09 1850
+  - Snow thermal conductivity method is now `Sturm_1997`
+  - New initial conditions file for f09 ("1-degree") 1850, with more in progress
   - New crop calendars
-  - Dust emissions is now Leung_2023
+  - Dust emissions method is now `Leung_2023`
   - Excess ice is turned on
-  - Updates to MEGAN for BVOC's
+  - Updates to MEGAN for BVOCs
   - Updates to BGC fire method
 
  Changes for all physics versions:
-
   - Parameter files updated
   - FATES parameter file updated
   - Glacier region 1 is now undefined
-  - Update in FATES transient Land use
+  - Update in FATES transient land use
   - Pass active glacier (CISM) runoff directly to river model (MOSART)
-  - Add the option for using matrix for Carbon/Nitrogen BGC spinup
+  - Add the option for using Matrix CN method for Carbon/Nitrogen BGC spinup
 
-New surface datasets:
-=====================
+## New surface datasets
 
-- With new surface datasets the following GLC fields have region "1" set to UNSET:
-     glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
+- With new surface datasets the following GLC fields have region "1" set to UNSET: glacier_region_behavior, glacier_region_melt_behavior, glacier_region_ice_runoff_behavior
 - Updates to allow creating transient landuse timeseries files going back to 1700.
-- Fix an important bug on soil fields that was there since ctsm5.2.0. This results in mksurfdata_esmf now giving identical answers with a change in number of processors, as it should.
-- Add in creation of ne0np4.POLARCAP.ne30x4 surface datasets.
-- Add version to the surface datasets.
-- Remove the --hires_pft option from mksurfdata_esmf as we don't have the datasets for it.
-- Remove VIC fields from surface datasets.
-
-New input datasets to mksurfdata_esmf:
-======================================
-
-- Updates in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (AG fire, peatland), and the glacier behavior dataset.
+- Fix an important bug on soil fields that was there since `ctsm5.2.0`. This has the side effect of `mksurfdata_esmf` now giving identical answers with a change in number of processors, as it should.
+- Surface datasets now provided for the `ne0np4.POLARCAP.ne30x4` grid.
+- Surface datasets now have their version number embedded to prevent mismatch of surface dataset and CTSM version.
+- Remove the `--hires_pft` option from `mksurfdata_esmf` as we don't have the datasets for it.
+- Remove `VIC` fields from surface datasets.
+- Updates to input datasets in PFT/LAI/soil-color raw datasets (now from the TRENDY2024 timeseries that ends in 2023), as well as two fire datasets (crop fire peak month, peatland fraction), and the glacier behavior dataset.
 
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
index 07e78952f9..ab0aab0cc5 100755
--- a/bld/CLMBuildNamelist.pm
+++ b/bld/CLMBuildNamelist.pm
@@ -3395,7 +3395,7 @@ sub setup_logic_mineral_nitrogen_dynamics {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  my @vars = ( "freelivfix_slope_wet", "freelivfix_intercept" );
+  my @vars = ( "freelivfix_slope_wet", "freelivfix_intercept", "nfix_method" );
   if (  &value_is_true($nl_flags->{'use_cn'}) && &value_is_true($nl->get_value('use_fun')) ) {
     foreach my $var ( @vars ) {
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
@@ -3408,6 +3408,7 @@ sub setup_logic_mineral_nitrogen_dynamics {
        }
     }
   }
+
 }
 
 
@@ -5208,6 +5209,7 @@ sub write_output_files {
   }
   push @groups, "clm_humanindex_inparm";
   push @groups, "cnmresp_inparm";
+  push @groups, "cnfun_inparm";
   push @groups, "photosyns_inparm";
   push @groups, "cnfire_inparm";
   push @groups, "cn_general";
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
index 18b9b0b9e9..21b92ba472 100644
--- a/bld/namelist_files/namelist_defaults_ctsm.xml
+++ b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -524,10 +524,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241017.nc</paramfile>
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c241017.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241017.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241017.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241119.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241119.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241119.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -1658,6 +1657,8 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa480_hist_2000_78pfts_c240908.nc</
 <fsurdat hgrid="mpasa120"  sim_year="2000">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_mpasa120_hist_2000_78pfts_c240908.nc</fsurdat>
 
+<fsurdat hgrid="ne3np4"                  sim_year="2000">
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4_hist_2000_78pfts_c240925.nc</fsurdat>
 <fsurdat hgrid="ne3np4.pg3"              sim_year="2000">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_2000_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne120np4.pg3"             sim_year="2000">
@@ -1712,6 +1713,8 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg2_hist_1850_78pfts_c240908.n
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne30np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne3np4.pg3"  sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
+<fsurdat hgrid="ne3np4"       sim_year="1850">
+lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4_hist_1850_78pfts_c240925.nc</fsurdat>
 
 <fsurdat hgrid="C96"  sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_C96_hist_1850_78pfts_c240908.nc</fsurdat>
@@ -1722,8 +1725,6 @@ lnd/clm2/surfdata_esmf/ctsm5.3.0/synthetic/surfdata_1x1_cidadinhoBR_synth_hist_2
 <fsurdat hgrid="1x1_brazil"       sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_1x1_brazil_hist_1850_78pfts_c240912.nc</fsurdat>
 
-<fsurdat hgrid="ne3np4.pg3"               sim_year="1850">
-lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne3np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne16np4.pg3"              sim_year="1850">
 lnd/clm2/surfdata_esmf/ctsm5.3.0/surfdata_ne16np4.pg3_hist_1850_78pfts_c240908.nc</fsurdat>
 <fsurdat hgrid="ne120np4.pg3"             sim_year="1850">
@@ -1794,6 +1795,8 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
+<flanduse_timeseries hgrid="ne3np4"        sim_year_range="1850-2000"
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4_SSP2-4.5_1850-2100_78pfts_c240926.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne3np4.pg3"    sim_year_range="1850-2000"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2000"
@@ -1840,6 +1843,8 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <flanduse_timeseries hgrid="mpasa120"      sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_mpasa120_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 
+<flanduse_timeseries hgrid="ne3np4"        sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
+>lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4_SSP2-4.5_1850-2100_78pfts_c240926.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne3np4.pg3"    sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
 >lnd/clm2/surfdata_esmf/ctsm5.3.0/landuse.timeseries_ne3np4.pg3_SSP2-4.5_1850-2100_78pfts_c240908.nc</flanduse_timeseries>
 <flanduse_timeseries hgrid="ne16np4.pg3"   sim_year_range="1850-2100" ssp_rcp="SSP2-4.5"
@@ -1900,6 +1905,8 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <freelivfix_intercept use_fun=".true." use_cn=".true.">0.0117d00</freelivfix_intercept>
 <freelivfix_slope_wet use_fun=".true." use_cn=".true.">0.0006d00</freelivfix_slope_wet>
 
+<nfix_method>Houlton</nfix_method>
+
 <br_root>0.83d-06</br_root>
 
 <!-- Scalar of leaf respiration to vcmax (used for SP mode and with luna) (could vary with physics version) -->
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
index 2d5ab0e4c7..ac61b86852 100644
--- a/bld/namelist_files/namelist_definition_ctsm.xml
+++ b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -388,6 +388,11 @@ Slope of free living Nitrogen fixation with annual ET
 Intercept of free living Nitrogen fixation with zero annual ET
 </entry>
 
+<entry id="nfix_method" type="char*25" category="cnfun_inparm"
+       group="cnfun_inparm" valid_values="Houlton,Bytnerowicz" value="Houlton" >
+Choice of nfix parameterization
+</entry>
+
 <entry id="use_undercanopy_stability" type="logical" category="clm_physics"
        group="canopyfluxes_inparm" valid_values="" >
 If TRUE use the undercanopy stability term used with CLM4.5 (Sakaguchi&amp;Zeng, 2008)
diff --git a/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl
index 9959632470..7480af82fb 100755
--- a/bld/unit_testers/build-namelist_test.pl
+++ b/bld/unit_testers/build-namelist_test.pl
@@ -368,7 +368,7 @@ sub cat_and_create_namelistinfile {
 my $phys = "clm6_0";
 $mode = "-phys $phys";
 &make_config_cache($phys);
-my $neondir      = "../../cime_config/usermods_dirs/NEON";
+my $neondir      = "../../cime_config/usermods_dirs/clm/NEON";
 foreach my $site ( "ABBY", "BLAN", "CPER", "DEJU", "GRSM", "HEAL", "KONA", "LENO", "NIWO",
                    "ONAQ", "PUUM", "SERC", "SRER", "TALL", "TREE", "WOOD", "BARR", "BONA",
                    "DCFS", "DELA", "GUAN", "JERC", "KONZ", "MLBS", "NOGP", "ORNL", "RMNP",
@@ -421,7 +421,7 @@ sub cat_and_create_namelistinfile {
 my $phys = "clm6_0";
 $mode = "-phys $phys";
 &make_config_cache($phys);
-my $plumdir      = "../../cime_config/usermods_dirs/PLUMBER2";
+my $plumdir      = "../../cime_config/usermods_dirs/clm/PLUMBER2";
 foreach my $site ( 
     "AR-SLu",  "AU-Emr",  "AU-TTE",  "CA-NS1",  "CA-SF3",  "CN-HaM",  "DE-Obe",  "ES-ES1",  "FR-Gri",  "IE-Dri",  "IT-LMa",  "IT-SRo",  "RU-Fyo",  "US-Aud",  "US-Ho1",  "US-Ne2",  "US-Syv",  "ZM-Mon",
     "AT-Neu",  "AU-Gin",  "AU-Tum",  "CA-NS2",  "CH-Cha",  "CN-Qia",  "DE-Seh",  "ES-ES2",  "FR-Hes",  "IT-Amp",  "IT-Mal",  "JP-SMF",  "RU-Zot",  "US-Bar",  "US-KS2",  "US-Ne3",  "US-Ton",
@@ -1490,7 +1490,7 @@ sub cat_and_create_namelistinfile {
 print "========================================================================\n";
 
 # Check for ALL resolutions with CLM50SP
-my @resolutions = ( "360x720cru", "10x15", "4x5", "0.9x1.25", "1.9x2.5", "ne3np4.pg3", "ne16np4.pg3", "ne30np4", "ne30np4.pg2", "ne30np4.pg3", "ne120np4.pg3", "ne0np4CONUS.ne30x8", "ne0np4.ARCTIC.ne30x4", "ne0np4.ARCTICGRIS.ne30x8", "C96", "mpasa480", "mpasa120" );
+my @resolutions = ( "360x720cru", "10x15", "4x5", "0.9x1.25", "1.9x2.5", "ne3np4", "ne3np4.pg3", "ne16np4.pg3", "ne30np4", "ne30np4.pg2", "ne30np4.pg3", "ne120np4.pg3", "ne0np4CONUS.ne30x8", "ne0np4.ARCTIC.ne30x4", "ne0np4.ARCTICGRIS.ne30x8", "C96", "mpasa480", "mpasa120" );
 my @only2000_resolutions = ( "1x1_numaIA", "1x1_brazil", "1x1_mexicocityMEX", "1x1_vancouverCAN", "1x1_urbanc_alpha", "5x5_amazon", "0.125nldas2", "mpasa60", "mpasa15", "mpasa3p75" );
 my @regional;
 foreach my $res ( @resolutions ) {
@@ -1527,7 +1527,7 @@ sub cat_and_create_namelistinfile {
 print " Test important resolutions for BGC and historical\n";
 print "==================================================\n";
 
-my @resolutions = ( "4x5", "10x15", "360x720cru", "ne30np4.pg3", "ne3np4.pg3", "1.9x2.5", "0.9x1.25", "C96", "mpasa120" );
+my @resolutions = ( "4x5", "10x15", "360x720cru", "ne30np4.pg3", "ne3np4", "ne3np4.pg3", "1.9x2.5", "0.9x1.25", "C96", "mpasa120" );
 my @regional;
 my $nlbgcmode = "bgc";
 my $mode = "$phys-$nlbgcmode";
@@ -1754,7 +1754,7 @@ sub cat_and_create_namelistinfile {
    &cleanup();
 }
 
-my @crop_res = ( "1x1_numaIA", "4x5", "10x15", "0.9x1.25", "1.9x2.5", "ne3np4.pg3", "ne30np4", "ne30np4.pg3", "C96", "mpasa120" );
+my @crop_res = ( "1x1_numaIA", "4x5", "10x15", "0.9x1.25", "1.9x2.5", "ne3np4", "ne3np4.pg3", "ne30np4", "ne30np4.pg3", "C96", "mpasa120" );
 foreach my $res ( @crop_res ) {
    $options = "-bgc bgc -crop -res $res -envxml_dir .";
    &make_env_run();
@@ -1843,7 +1843,7 @@ sub cat_and_create_namelistinfile {
    &cleanup();
 }
 # Transient ssp_rcp scenarios that work
-my @tran_res = ( "4x5", "0.9x1.25", "1.9x2.5", "10x15", "360x720cru", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
+my @tran_res = ( "4x5", "0.9x1.25", "1.9x2.5", "10x15", "360x720cru", "ne3np4", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
 foreach my $usecase ( "1850-2100_SSP2-4.5_transient" ) {
    my $startymd = 20150101;
    foreach my $res ( @tran_res ) {
@@ -1880,7 +1880,7 @@ sub cat_and_create_namelistinfile {
                      "-bgc bgc -clm_demand flanduse_timeseries -sim_year 1850-2000 -namelist '&a start_ymd=18500101/'",
                      "-bgc bgc -envxml_dir . -namelist '&a use_c13=.true.,use_c14=.true.,use_c14_bombspike=.true./'" );
   foreach my $clmopts ( @clmoptions ) {
-     my @clmres = ( "10x15", "4x5", "360x720cru", "0.9x1.25", "1.9x2.5", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
+     my @clmres = ( "10x15", "4x5", "360x720cru", "0.9x1.25", "1.9x2.5", "ne3np4", "ne3np4.pg3", "ne16np4.pg3", "ne30np4.pg3", "C96", "mpasa120" );
      foreach my $res ( @clmres ) {
         $options = "-res $res -envxml_dir . ";
         &make_env_run( );
diff --git a/ccs_config b/ccs_config
index 6e77e7ee17..a712a92045 160000
--- a/ccs_config
+++ b/ccs_config
@@ -1 +1 @@
-Subproject commit 6e77e7ee1748a4d3b2497d7ad3943498a7cec2aa
+Subproject commit a712a920453dc0cb2831dce576e78c389b567f7e
diff --git a/cime b/cime
index a8a04e2d9d..addf9e67ce 160000
--- a/cime
+++ b/cime
@@ -1 +1 @@
-Subproject commit a8a04e2d9deac572e6f2222b4f893a575308db99
+Subproject commit addf9e67ceeb0e056de33ee793d67491176dd3a5
diff --git a/cime_config/config_component.xml b/cime_config/config_component.xml
index e7a644f7e2..55ca78f1f4 100644
--- a/cime_config/config_component.xml
+++ b/cime_config/config_component.xml
@@ -355,15 +355,15 @@
     <valid_values></valid_values>
     <default_value></default_value>
     <values match="last">
-      <value                  compset="_CLM60%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
-      <value                  compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
-      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
-      <value                  compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
-      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
-      <value                  compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
-      <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
-      <value                  compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
-      <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
+      <value                  compset="_CLM60%[^_]*FATES-SP[%_]"      >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/fates_sp</value>
+      <value                  compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_nociso_deck</value>
+      <value                  compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck</value>
+      <value                  compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]"     >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_nociso_deck</value>
+      <value                  compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_deck</value>
+      <value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck</value>
     </values>
     <group>run_component_ctsm</group>
     <file>env_case.xml</file>
diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
index f718582b60..9735c02f4c 100644
--- a/cime_config/testdefs/ExpectedTestFails.xml
+++ b/cime_config/testdefs/ExpectedTestFails.xml
@@ -84,21 +84,21 @@
     </phase>
   </test>
 
-  <test name="ERP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
+  <test name="ERP_P64x2_Ld396.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
     <phase name="BASELINE">
       <status>FAIL</status>
       <issue>#2619</issue>
       <comment>This failure relates to the following REP failure.</comment>
     </phase>
   </test>
-  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
+  <test name="REP_P64x2_Ld396.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
     <phase name="COMPARE_base_rep2">
       <status>FAIL</status>
       <issue>#2619</issue>
       <comment>This failure relates to the preceding ERP failure.</comment>
     </phase>
   </test>
-  <test name="REP_P64x2_Lm13.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
+  <test name="REP_P64x2_Ld396.f10_f10_mg37.IHistClm60Bgc.derecho_intel.clm-monthly--clm-matrixcnOn_ignore_warnings">
     <phase name="BASELINE">
       <status>FAIL</status>
       <issue>#2619</issue>
@@ -114,7 +114,7 @@
   </test>
 
   <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.derecho_nvhpc.clm-crop">
-    <phase name="RUN">
+    <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
       <issue>#1733</issue>
     </phase>
@@ -126,7 +126,7 @@
       <issue>#2310</issue>
     </phase>
   </test>
-  
+
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.derecho_gnu.clm-NEON-MOAB--clm-PRISM">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
@@ -138,6 +138,41 @@
     </phase>
   </test>
   
+  <test name="SSPMATRIXCN_Ly5_Mmpi-serial.1x1_numaIA.I2000Clm50BgcCropQianRs.izumi_intel.clm-ciso_monthly">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2913</issue>
+    </phase>
+  </test>
+
+  <test name="SSP_D_Ld10.f10_f10_mg37.I1850Clm60Bgc.derecho_intel.clm-rtmColdSSP">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2913</issue>
+    </phase>
+  </test>
+
+  <test name="SSP_D_Ld4.f10_f10_mg37.I1850Clm50BgcCrop.derecho_intel.clm-ciso_rtmColdSSP">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2913</issue>
+    </phase>
+  </test>
+
+  <test name="SSP_Ld10.f10_f10_mg37.I1850Clm50Bgc.derecho_gnu.clm-rtmColdSSP">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2913</issue>
+    </phase>
+  </test>
+
+  <test name="SSP_Ld4.f09_g17.I1850Clm50BgcCrop.derecho_intel.clm-ciso_rtmColdSSP">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2913</issue>
+    </phase>
+  </test>
+
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Bgc.izumi_nag.clm-default--clm-NEON-HARV--clm-matrixcnOn">
     <phase name="RUN">
       <status>FAIL</status>
@@ -155,7 +190,7 @@
       <issue>#2310</issue>
     </phase>
   </test>
-  
+
   <test name="SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm60Fates.derecho_gnu.clm-FatesPRISM--clm-NEON-FATES-YELL">
     <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
@@ -186,23 +221,12 @@
   </test>
 
   <test name="ERS_D_Ld20.f45_f45_mg37.I2000Clm50FatesRs.izumi_nag.clm-FatesColdTwoStream">
-    <phase name="CREATE_NEWCASE">
-      <status>FAIL</status>
-      <issue>#2454</issue>
-    </phase>
     <phase name="COMPARE_base_rest">
       <status>FAIL</status>
       <issue>#2325</issue>
     </phase>
   </test>
 
-  <test name="SMS_Lm3_D_Mmpi-serial.1x1_brazil.I2000Clm50FatesCruRsGs.izumi_intel.clm-FatesColdHydro">
-    <phase name="CREATE_NEWCASE">
-      <status>FAIL</status>
-      <issue>#2454</issue>
-    </phase>
-  </test>
-  
   <test name="ERS_Ld60.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesColdST3">
     <phase name="RUN">
       <status>FAIL</status>
@@ -319,6 +343,13 @@
     </phase>
   </test>
 
+  <test name="PVT_Lm3.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesLUPFT">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2919</issue>
+    </phase>
+  </test>
+
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 
   <test name="SMS_Lh3.f10_f10_mg37.I2000Clm60Sp.derecho_intel.mosart-clmAccelSpinupIgnoreWarn">
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
index 08a0951a3d..7a665444a2 100644
--- a/cime_config/testdefs/testlist_clm.xml
+++ b/cime_config/testdefs/testlist_clm.xml
@@ -12,6 +12,7 @@
         hillslope: Experimental test list used for the hillslope option of the model
         rxcropmaturity: Short tests to be run during development related to prescribed crop calendars
         matrixcn: Tests exercising the matrix-CN capability
+        aux_clm_mpi_serial: aux_clm tests using mpi-serial. Useful for redoing tests that failed due to https://github.com/ESCOMP/CTSM/issues/2916, after having replaced libraries/mpi-serial with a fresh copy.
 -->
 <testlist version="2.0">
   <test name="ERI_D_Ld9" grid="f10_f10_mg37" compset="I1850Clm60Bgc" testmods="clm/default">
@@ -905,6 +906,7 @@
   <test name="ERS_Ld1640_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCrop" testmods="clm/ciso_monthly_matrixcn_spinup">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
@@ -1149,6 +1151,7 @@
   <test name="SMS_Ld5_Mmpi-serial" grid="1x1_brazil" compset="IHistClm60Bgc" testmods="clm/mimics">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1158,6 +1161,7 @@
   <test name="SMS_Ly5_Mmpi-serial" grid="1x1_brazil" compset="IHistClm50BgcQianRs" testmods="clm/newton_krylov_spinup">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1317,6 +1321,15 @@
       <option name="comment"  >Science support for I1850Clm50BgcCropCru at f19</option>
     </options>
   </test>
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN_BNF">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
@@ -1524,7 +1537,7 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_P64x2_Ld762" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/monthly">
+  <test name="ERP_P64x2_Ld765" grid="f10_f10_mg37" compset="I2000Clm60BgcCrop" testmods="clm/monthly">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
     </machines>
@@ -1692,6 +1705,7 @@
   <test name="ERS_D_Ld7_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropRs" testmods="clm/decStart1851_noinitial">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -1709,6 +1723,7 @@
   <test name="ERS_Ld600_Mmpi-serial" grid="1x1_smallvilleIA" compset="I1850Clm50BgcCrop" testmods="clm/cropMonthlyNoinitial">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">01:20:00</option>
@@ -1718,6 +1733,7 @@
   <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1727,6 +1743,7 @@
   <test name="ERS_Ly5_Mmpi-serial" grid="1x1_smallvilleIA" compset="I1850Clm50BgcCrop" testmods="clm/ciso_monthly--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="izumi" compiler="gnu" category="matrixcn"/>
     </machines>
     <options>
@@ -1737,6 +1754,7 @@
   <test name="ERS_Ld1200_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1746,6 +1764,7 @@
   <test name="ERS_Ld1600_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1755,6 +1774,7 @@
   <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock"     >04:00:00</option>
@@ -1765,6 +1785,7 @@
   <test name="ERS_Ly20_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/cropMonthlyNoinitial--clm/matrixcnOn">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
       <machine name="izumi" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
@@ -1785,6 +1806,7 @@
   <test name="ERS_Ly3_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
@@ -1859,6 +1881,7 @@
   <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -1869,6 +1892,7 @@
   <test name="ERS_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/cropMonthOutput--clm/matrixcnOn_ignore_warnings">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
       <machine name="izumi" compiler="intel" category="matrixcn"/>
     </machines>
     <options>
@@ -1881,6 +1905,7 @@
     <machines>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">01:00:00</option>
@@ -2290,18 +2315,22 @@
   <test name="ERS_D_Ld5_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm50SpRs" testmods="clm/CLM1PTStartDate">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="aux_clm_mpi_serial"/>
       <machine name="izumi" compiler="nag" category="prealpha"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_Mmpi-serial" grid="f45_f45_mg37" compset="I2000Clm50SpRs" testmods="clm/ptsRLA">
+  <test name="SMS_D_Ld1_Mmpi-serial" grid="ne3_ne3_mg37" compset="I2000Clm50SpRs" testmods="clm/ptsRLA">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="intel" category="prealpha"/>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="aux_clm_mpi_serial"/>
       <machine name="izumi" compiler="gnu" category="prealpha"/>
       <machine name="izumi" compiler="nag" category="prealpha"/>
     </machines>
@@ -2399,6 +2428,7 @@
     <machines>
       <machine name="derecho" compiler="gnu" category="ctsm_sci"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
     </machines>
     <options>
@@ -2410,7 +2440,9 @@
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/HARV">
     <machines>
       <machine name="derecho"  compiler="gnu" category="aux_clm"/>
+      <machine name="derecho"  compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2421,8 +2453,10 @@
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/default--clm/NEON/HARV--clm/matrixcnOn">
     <machines>
       <machine name="derecho"  compiler="gnu" category="aux_clm"/>
+      <machine name="derecho"  compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="derecho"  compiler="gnu" category="matrixcn"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="aux_clm_mpi_serial"/>
       <machine name="izumi"    compiler="nag" category="matrixcn"/>
     </machines>
     <options>
@@ -2434,7 +2468,9 @@
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60SpRs" testmods="clm/default--clm/NEON/TOOL">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="aux_clm_mpi_serial"/>
       <machine name="derecho"  compiler="intel" category="aux_clm"/>
+      <machine name="derecho"  compiler="intel" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2445,7 +2481,9 @@
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Bgc" testmods="clm/NEON/MOAB--clm/PRISM">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="aux_clm_mpi_serial"/>
       <machine name="derecho"  compiler="gnu" category="aux_clm"/>
+      <machine name="derecho"  compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2454,7 +2492,7 @@
     </options>
   </test>
 
-  <test name="ERS_P128x1_Ld762" grid="f10_f10_mg37" compset="I2000Clm60Fates" testmods="clm/FatesColdNoComp">
+  <test name="ERS_P128x1_Ld765" grid="f10_f10_mg37" compset="I2000Clm60Fates" testmods="clm/FatesColdNoComp">
     <machines>
       <!-- no izumi tests since this has a pe layout specific for derecho -->
       <machine name="derecho" compiler="intel"   category="aux_clm"/>
@@ -2469,8 +2507,10 @@
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Fates" testmods="clm/FatesFireLightningPopDens--clm/NEON/FATES/NIWO">
     <machines>
       <machine name="derecho"  compiler="intel" category="aux_clm"/>
+      <machine name="derecho"  compiler="intel" category="aux_clm_mpi_serial"/>
       <machine name="derecho"  compiler="intel" category="fates"/>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="aux_clm_mpi_serial"/>
       <machine name="izumi"    compiler="nag"   category="fates"/>
     </machines>
     <options>
@@ -2482,8 +2522,10 @@
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Fates" testmods="clm/FatesPRISM--clm/NEON/FATES/YELL">
     <machines>
       <machine name="izumi"    compiler="nag"   category="aux_clm"/>
+      <machine name="izumi"    compiler="nag"   category="aux_clm_mpi_serial"/>
       <machine name="izumi"    compiler="nag"   category="fates"/>
       <machine name="derecho"  compiler="gnu" category="aux_clm"/>
+      <machine name="derecho"  compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="derecho"  compiler="gnu" category="fates"/>
     </machines>
     <options>
@@ -2514,6 +2556,7 @@
   <test name="SMS_D_Ly6_Mmpi-serial" grid="1x1_smallvilleIA" compset="IHistClm45BgcCropQianRs" testmods="clm/cropMonthOutput">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">02:00:00</option>
@@ -2529,7 +2572,7 @@
       <option name="comment">Include a test of transient lakes</option>
     </options>
   </test>
-  <test name="ERS_L761" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/smallville_dynurban_monthly">
+  <test name="ERS_Ld765" grid="1x1_smallvilleIA" compset="IHistClm50BgcCropQianRs" testmods="clm/smallville_dynurban_monthly">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
     </machines>
@@ -2556,9 +2599,10 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld1_Mmpi-serial" grid="f45_f45_mg37" compset="I2000Clm50SpRs" testmods="clm/ptsROA">
+  <test name="SMS_D_Ld1_Mmpi-serial" grid="ne3_ne3_mg37" compset="I2000Clm50SpRs" testmods="clm/ptsROA">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2705,6 +2749,7 @@
   <test name="SMS_Ly3_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcDvCropQianRs" testmods="clm/ignor_warn_cropMonthOutputColdStart">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>
+      <machine name="izumi" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">01:40:00</option>
@@ -2714,6 +2759,7 @@
   <test name="SSPMATRIXCN_Ly5_Mmpi-serial" grid="1x1_numaIA" compset="I2000Clm50BgcCropQianRs" testmods="clm/ciso_monthly">
     <machines>
       <machine name="izumi"    compiler="intel" category="aux_clm"/>
+      <machine name="izumi"    compiler="intel" category="aux_clm_mpi_serial"/>
       <machine name="izumi"    compiler="intel" category="matrixcn"/>
     </machines>
     <options>
@@ -2765,6 +2811,7 @@
   <test name="SMS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm60FatesRs" testmods="clm/FatesCold">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="gnu" category="ctsm_sci"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
     </machines>
@@ -2869,7 +2916,9 @@
   <test name="ERS_D_Mmpi-serial_Ld5" grid="1x1_brazil" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -2878,6 +2927,7 @@
   <test name="ERS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm50FatesRs" testmods="clm/FatesCold">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="gnu" category="prebeta"/>
     </machines>
     <options>
@@ -2896,6 +2946,7 @@
   <test name="ERS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm60FatesRs" testmods="clm/FatesCold">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm_mpi_serial"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
@@ -3208,6 +3259,7 @@
   <test name="SMS_Lm3_D_Mmpi-serial" grid="1x1_brazil" compset="I2000Clm50FatesCruRsGs" testmods="clm/FatesColdHydro">
     <machines>
       <machine name="izumi" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="intel" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="intel" category="fates"/>
       <machine name="izumi" compiler="nag" category="fates"/>
     </machines>
@@ -3450,6 +3502,7 @@
   <test name="SMS_Ly1_Mmpi-serial" grid="1x1_brazil" compset="IHistClm60BgcQianRs" testmods="clm/output_bgc_highfreq">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="derecho" compiler="intel" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
@@ -3460,6 +3513,7 @@
   <test name="SMS_Ld12_Mmpi-serial" grid="1x1_vancouverCAN" compset="I1PtClm60SpRs" testmods="clm/output_sp_highfreq">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="intel" category="ctsm_sci"/>
     </machines>
     <options>
@@ -3526,6 +3580,7 @@
   <test name="FSURDATMODIFYCTSM_D_Mmpi-serial_Ld1" grid="5x5_amazon" compset="I2000Clm50SpRs">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="gnu" category="clm_pymods"/>
     </machines>
     <options>
@@ -3670,6 +3725,7 @@
   <test name="SMS_D_Mmpi-serial_Ld5" grid="5x5_amazon" compset="I2000Clm60Bgc" testmods="clm/HillslopeC">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
+      <machine name="derecho" compiler="gnu" category="aux_clm_mpi_serial"/>
       <machine name="derecho" compiler="gnu" category="hillslope"/>
     </machines>
     <options>
diff --git a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods
index 6d8de3732a..142522f5b3 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/ExcessIceStartup_output_sp_exice/include_user_mods
@@ -1,2 +1,2 @@
 ../monthly
-../../../../usermods_dirs/output_sp_exice
+../../../../usermods_dirs/clm/output_sp_exice
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands
deleted file mode 100644
index e629e7ca34..0000000000
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/shell_commands
+++ /dev/null
@@ -1,8 +0,0 @@
-SRCDIR=`./xmlquery SRCROOT --value`
-CASEDIR=`./xmlquery CASEROOT --value`
-FATESDIR=$SRCDIR/src/fates
-FATESPARAMFILE=$CASEDIR/fates_params_hydrograsstempfix.nc
-
-ncgen -o $FATESPARAMFILE $FATESDIR/parameter_files/fates_params_default.cdl
-
-$FATESDIR/tools/modify_fates_paramfile.py --O --fin $FATESPARAMFILE --fout $FATESPARAMFILE --var fates_allom_smode --val 1 --allpfts
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
index 318a34dfec..f0bdb388eb 100644
--- a/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm
@@ -2,7 +2,6 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 use_fates_planthydro= .true.
-fates_paramfile = '$CASEROOT/fates_params_hydrograsstempfix.nc'
 hist_fincl1       = 'FATES_ERRH2O_SZPF', 'FATES_TRAN_SZPF',
 'FATES_SAPFLOW_SZPF', 'FATES_ITERH1_SZPF','FATES_ABSROOT_H2O_SZPF',
 'FATES_TRANSROOT_H2O_SZPF','FATES_STEM_H2O_SZPF','FATES_LEAF_H2O_SZPF',
diff --git a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
index edeb0fce21..8a1e5bb216 100644
--- a/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm
@@ -1,2 +1,2 @@
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c241017.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_ciso_cwd_hr_params.c241119.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm50cam7LndTuningMode/user_nl_datm b/cime_config/testdefs/testmods_dirs/clm/clm50cam7LndTuningMode/user_nl_datm
new file mode 100644
index 0000000000..c35d3fd9d4
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm50cam7LndTuningMode/user_nl_datm
@@ -0,0 +1,2 @@
+iradsw = -1
+nextsw_cday_calc = "cam7"
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
index b1d856797d..d982aea0f0 100644
--- a/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm
@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c241017.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c241119.nc'
diff --git a/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/user_nl_datm b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/user_nl_datm
new file mode 100644
index 0000000000..c35d3fd9d4
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/clm60cam7LndTuningMode/user_nl_datm
@@ -0,0 +1,2 @@
+iradsw = -1
+nextsw_cday_calc = "cam7"
diff --git a/cime_config/testdefs/testmods_dirs/clm/cmip6_deck/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/cmip6_deck/include_user_mods
index 45859d47f6..0f34cfe5cd 100644
--- a/cime_config/testdefs/testmods_dirs/clm/cmip6_deck/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/cmip6_deck/include_user_mods
@@ -1 +1 @@
-../../../../usermods_dirs/cmip6_deck
+../../../../usermods_dirs/clm/cmip6_deck
diff --git a/cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/include_user_mods
new file mode 100644
index 0000000000..4fbf11b334
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/include_user_mods
@@ -0,0 +1 @@
+../flexCN_FUN
diff --git a/cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/user_nl_clm
new file mode 100644
index 0000000000..8084f982e1
--- /dev/null
+++ b/cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/user_nl_clm
@@ -0,0 +1,2 @@
+ nfix_method = 'Bytnerowicz'
+
diff --git a/cime_config/testdefs/testmods_dirs/clm/lilac/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/lilac/include_user_mods
index 7b5f17cf20..6e978f6389 100644
--- a/cime_config/testdefs/testmods_dirs/clm/lilac/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/lilac/include_user_mods
@@ -1 +1 @@
-../../../../usermods_dirs/lilac
+../../../../usermods_dirs/clm/lilac
diff --git a/cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/README b/cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/README
index 1363ea696b..4c18c9d65a 100644
--- a/cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/README
+++ b/cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/README
@@ -1,6 +1,6 @@
 slevis 2022/2/1:
 This testmod tests the newton_krylov_spinup usermod found in
-cime_config/usermods_dirs/newton_krylov_spinup
+cime_config/usermods_dirs/clm/newton_krylov_spinup
 combined with the mimics testmod.
 
 By default this usermod runs for 20 yrs and writes a history file at that
diff --git a/cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/include_user_mods
index 192aa023a8..148f615059 100644
--- a/cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/newton_krylov_spinup/include_user_mods
@@ -1,2 +1,2 @@
 ../mimics
-../../../../usermods_dirs/newton_krylov_spinup
+../../../../usermods_dirs/clm/newton_krylov_spinup
diff --git a/cime_config/testdefs/testmods_dirs/clm/output_bgc_highfreq/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/output_bgc_highfreq/include_user_mods
index de8b9039c8..0336470fa8 100644
--- a/cime_config/testdefs/testmods_dirs/clm/output_bgc_highfreq/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/output_bgc_highfreq/include_user_mods
@@ -1,2 +1,2 @@
-../../../../usermods_dirs/output_bgc_highfreq
+../../../../usermods_dirs/clm/output_bgc_highfreq
 ../basic
diff --git a/cime_config/testdefs/testmods_dirs/clm/output_crop_highfreq/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/output_crop_highfreq/include_user_mods
index 770abf5cf9..bd3d4850fa 100644
--- a/cime_config/testdefs/testmods_dirs/clm/output_crop_highfreq/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/output_crop_highfreq/include_user_mods
@@ -1,2 +1,2 @@
-../../../../usermods_dirs/output_crop_highfreq
+../../../../usermods_dirs/clm/output_crop_highfreq
 ../basic
diff --git a/cime_config/testdefs/testmods_dirs/clm/output_sp_highfreq/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/output_sp_highfreq/include_user_mods
index 2df730d2d0..81287ac4c4 100644
--- a/cime_config/testdefs/testmods_dirs/clm/output_sp_highfreq/include_user_mods
+++ b/cime_config/testdefs/testmods_dirs/clm/output_sp_highfreq/include_user_mods
@@ -1,3 +1,3 @@
 ../CLM1PTStartDate
-../../../../usermods_dirs/output_sp_highfreq
+../../../../usermods_dirs/clm/output_sp_highfreq
 ../basic
diff --git a/cime_config/usermods_dirs/NEON/ABBY/include_user_mods b/cime_config/usermods_dirs/clm/NEON/ABBY/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/ABBY/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/ABBY/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/ABBY/shell_commands b/cime_config/usermods_dirs/clm/NEON/ABBY/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/ABBY/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/ABBY/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/BARR/include_user_mods b/cime_config/usermods_dirs/clm/NEON/BARR/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/BARR/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/BARR/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/BARR/shell_commands b/cime_config/usermods_dirs/clm/NEON/BARR/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/BARR/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/BARR/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/BART/include_user_mods b/cime_config/usermods_dirs/clm/NEON/BART/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/BART/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/BART/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/BART/shell_commands b/cime_config/usermods_dirs/clm/NEON/BART/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/BART/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/BART/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/BLAN/include_user_mods b/cime_config/usermods_dirs/clm/NEON/BLAN/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/BLAN/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/BLAN/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/BLAN/shell_commands b/cime_config/usermods_dirs/clm/NEON/BLAN/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/BLAN/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/BLAN/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/BONA/include_user_mods b/cime_config/usermods_dirs/clm/NEON/BONA/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/BONA/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/BONA/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/BONA/shell_commands b/cime_config/usermods_dirs/clm/NEON/BONA/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/BONA/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/BONA/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/CLBJ/include_user_mods b/cime_config/usermods_dirs/clm/NEON/CLBJ/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/CLBJ/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/CLBJ/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/CLBJ/shell_commands b/cime_config/usermods_dirs/clm/NEON/CLBJ/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/CLBJ/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/CLBJ/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/CPER/include_user_mods b/cime_config/usermods_dirs/clm/NEON/CPER/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/CPER/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/CPER/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/CPER/shell_commands b/cime_config/usermods_dirs/clm/NEON/CPER/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/CPER/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/CPER/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/DCFS/include_user_mods b/cime_config/usermods_dirs/clm/NEON/DCFS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/DCFS/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/DCFS/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/DCFS/shell_commands b/cime_config/usermods_dirs/clm/NEON/DCFS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/DCFS/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/DCFS/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/DEJU/include_user_mods b/cime_config/usermods_dirs/clm/NEON/DEJU/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/DEJU/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/DEJU/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/DEJU/shell_commands b/cime_config/usermods_dirs/clm/NEON/DEJU/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/DEJU/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/DEJU/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/DELA/include_user_mods b/cime_config/usermods_dirs/clm/NEON/DELA/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/DELA/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/DELA/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/DELA/shell_commands b/cime_config/usermods_dirs/clm/NEON/DELA/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/DELA/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/DELA/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/DSNY/include_user_mods b/cime_config/usermods_dirs/clm/NEON/DSNY/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/DSNY/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/DSNY/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/DSNY/shell_commands b/cime_config/usermods_dirs/clm/NEON/DSNY/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/DSNY/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/DSNY/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/ABBY/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/ABBY/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/ABBY/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/ABBY/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/ABBY/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/ABBY/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/ABBY/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/ABBY/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/BARR/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/BARR/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/BARR/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/BARR/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/BARR/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/BARR/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/BARR/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/BART/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/BART/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/BART/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/BART/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/BART/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/BART/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/BART/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/BART/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/BLAN/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/BLAN/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/BLAN/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/BLAN/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/BLAN/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/BLAN/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/BLAN/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/BONA/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/BONA/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/BONA/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/BONA/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/BONA/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/BONA/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/BONA/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/BONA/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/CLBJ/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/CLBJ/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/CLBJ/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/CLBJ/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/CLBJ/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/CLBJ/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/CLBJ/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/CLBJ/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/CPER/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/CPER/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/CPER/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/CPER/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/CPER/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/CPER/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/CPER/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/DCFS/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/DCFS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/DCFS/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/DCFS/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/DCFS/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/DCFS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/DCFS/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/DCFS/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/DEJU/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/DEJU/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/DEJU/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/DEJU/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/DEJU/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/DEJU/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/DEJU/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/DEJU/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/DELA/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/DELA/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/DELA/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/DELA/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/DELA/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/DELA/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/DELA/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/DELA/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/DSNY/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/DSNY/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/DSNY/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/DSNY/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/DSNY/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/DSNY/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/DSNY/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/DSNY/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/GRSM/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/GRSM/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/GRSM/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/GRSM/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/GRSM/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/GRSM/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/GRSM/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/GRSM/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/GUAN/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/GUAN/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/GUAN/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/GUAN/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/GUAN/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/GUAN/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/GUAN/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/HARV/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/HARV/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/HARV/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/HARV/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/HARV/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/HARV/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/HARV/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/HARV/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/HEAL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/HEAL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/HEAL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/HEAL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/HEAL/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/HEAL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/HEAL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/HEAL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/JERC/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/JERC/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/JERC/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/JERC/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/JERC/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/JERC/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/JERC/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/JERC/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/JORN/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/JORN/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/JORN/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/JORN/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/JORN/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/JORN/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/JORN/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/JORN/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/KONZ/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/KONZ/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/KONZ/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/KONZ/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/KONZ/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/KONZ/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/KONZ/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/KONZ/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/LAJA/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/LAJA/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/LAJA/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/LAJA/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/LAJA/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/LAJA/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/LAJA/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/LENO/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/LENO/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/LENO/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/LENO/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/LENO/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/LENO/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/LENO/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/MLBS/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/MLBS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/MLBS/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/MLBS/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/MLBS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/MLBS/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/MLBS/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/MOAB/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/MOAB/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/MOAB/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/MOAB/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/MOAB/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/MOAB/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/MOAB/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/NIWO/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/NIWO/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/NIWO/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/NIWO/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/NIWO/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/NIWO/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/NIWO/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/NOGP/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/NOGP/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/NOGP/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/NOGP/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/NOGP/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/NOGP/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/NOGP/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/NOGP/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/OAES/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/OAES/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/OAES/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/OAES/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/OAES/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/OAES/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/OAES/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/OAES/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/ONAQ/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/ONAQ/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/ONAQ/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/ONAQ/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/ONAQ/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/ONAQ/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/ONAQ/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/ORNL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/ORNL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/ORNL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/ORNL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/ORNL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/ORNL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/ORNL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/OSBS/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/OSBS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/OSBS/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/OSBS/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/OSBS/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/OSBS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/OSBS/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/OSBS/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/PUUM/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/PUUM/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/PUUM/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/PUUM/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/PUUM/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/PUUM/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/PUUM/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/PUUM/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/README.md b/cime_config/usermods_dirs/clm/NEON/FATES/README.md
similarity index 75%
rename from cime_config/usermods_dirs/NEON/FATES/README.md
rename to cime_config/usermods_dirs/clm/NEON/FATES/README.md
index 49cd2fc767..2d099771aa 100644
--- a/cime_config/usermods_dirs/NEON/FATES/README.md
+++ b/cime_config/usermods_dirs/clm/NEON/FATES/README.md
@@ -2,7 +2,7 @@
 
 Use these user mods as you would any other user_mods, e.g.:
 
-`./create_newcase --case FATES_ABBY_test --res CLM_USRDAT --compset I1PtClm60Fates --run-unsupported --user-mods-dir /glade/work/$user/CTSM/cime_config/usermods_dirs/NEON/FATES/ABBY`
+`./create_newcase --case FATES_ABBY_test --res CLM_USRDAT --compset I1PtClm60Fates --run-unsupported --user-mods-dir clm/NEON/FATES/ABBY`
 
 ## Note on crop sites KONA and STER
 
diff --git a/cime_config/usermods_dirs/NEON/FATES/RMNP/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/RMNP/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/RMNP/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/RMNP/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/RMNP/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/RMNP/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/RMNP/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/RMNP/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/SCBI/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/SCBI/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SCBI/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/SCBI/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/SCBI/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/SCBI/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SCBI/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/SCBI/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/SERC/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/SERC/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SERC/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/SERC/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/SERC/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/SERC/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SERC/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/SERC/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/SJER/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/SJER/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SJER/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/SJER/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/SJER/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SJER/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/SJER/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/SOAP/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/SOAP/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SOAP/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/SOAP/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/SOAP/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/SOAP/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SOAP/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/SOAP/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/SRER/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/SRER/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SRER/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/SRER/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/SRER/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/SRER/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/SRER/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/SRER/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/STEI/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/STEI/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/STEI/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/STEI/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/STEI/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/STEI/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/STEI/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/STEI/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/TALL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/TALL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/TALL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/TALL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/TALL/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/TALL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/TALL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/TALL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/TEAK/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/TEAK/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/TEAK/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/TEAK/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/TEAK/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/TEAK/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/TEAK/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/TOOL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/TOOL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/TOOL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/TOOL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/TOOL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/TOOL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/TOOL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/TREE/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/TREE/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/TREE/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/TREE/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/TREE/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/TREE/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/TREE/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/TREE/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/UKFS/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/UKFS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/UKFS/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/UKFS/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/UKFS/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/UKFS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/UKFS/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/UKFS/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/UNDE/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/UNDE/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/UNDE/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/UNDE/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/UNDE/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/UNDE/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/UNDE/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/WOOD/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/WOOD/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/WOOD/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/WOOD/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/WOOD/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/WOOD/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/WOOD/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/WOOD/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/WREF/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/WREF/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/WREF/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/WREF/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/WREF/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/WREF/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/WREF/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/YELL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/FATES/YELL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/YELL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/FATES/YELL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/YELL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/YELL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/YELL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands b/cime_config/usermods_dirs/clm/NEON/FATES/defaults/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/defaults/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/FATES/defaults/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm b/cime_config/usermods_dirs/clm/NEON/FATES/defaults/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_clm
rename to cime_config/usermods_dirs/clm/NEON/FATES/defaults/user_nl_clm
diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_cpl b/cime_config/usermods_dirs/clm/NEON/FATES/defaults/user_nl_cpl
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_cpl
rename to cime_config/usermods_dirs/clm/NEON/FATES/defaults/user_nl_cpl
diff --git a/cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/clm/NEON/FATES/defaults/user_nl_datm_streams
similarity index 100%
rename from cime_config/usermods_dirs/NEON/FATES/defaults/user_nl_datm_streams
rename to cime_config/usermods_dirs/clm/NEON/FATES/defaults/user_nl_datm_streams
diff --git a/cime_config/usermods_dirs/NEON/GRSM/include_user_mods b/cime_config/usermods_dirs/clm/NEON/GRSM/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/GRSM/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/GRSM/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/GRSM/shell_commands b/cime_config/usermods_dirs/clm/NEON/GRSM/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/GRSM/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/GRSM/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/GUAN/include_user_mods b/cime_config/usermods_dirs/clm/NEON/GUAN/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/GUAN/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/GUAN/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/GUAN/shell_commands b/cime_config/usermods_dirs/clm/NEON/GUAN/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/GUAN/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/GUAN/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/HARV/include_user_mods b/cime_config/usermods_dirs/clm/NEON/HARV/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/HARV/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/HARV/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/HARV/shell_commands b/cime_config/usermods_dirs/clm/NEON/HARV/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/HARV/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/HARV/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/HEAL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/HEAL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/HEAL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/HEAL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/HEAL/shell_commands b/cime_config/usermods_dirs/clm/NEON/HEAL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/HEAL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/HEAL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/JERC/include_user_mods b/cime_config/usermods_dirs/clm/NEON/JERC/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/JERC/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/JERC/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/JERC/shell_commands b/cime_config/usermods_dirs/clm/NEON/JERC/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/JERC/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/JERC/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/JORN/include_user_mods b/cime_config/usermods_dirs/clm/NEON/JORN/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/JORN/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/JORN/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/JORN/shell_commands b/cime_config/usermods_dirs/clm/NEON/JORN/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/JORN/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/JORN/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/KONA/include_user_mods b/cime_config/usermods_dirs/clm/NEON/KONA/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/KONA/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/KONA/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/KONA/shell_commands b/cime_config/usermods_dirs/clm/NEON/KONA/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/KONA/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/KONA/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/KONZ/include_user_mods b/cime_config/usermods_dirs/clm/NEON/KONZ/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/KONZ/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/KONZ/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/KONZ/shell_commands b/cime_config/usermods_dirs/clm/NEON/KONZ/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/KONZ/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/KONZ/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/LAJA/include_user_mods b/cime_config/usermods_dirs/clm/NEON/LAJA/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/LAJA/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/LAJA/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/LAJA/shell_commands b/cime_config/usermods_dirs/clm/NEON/LAJA/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/LAJA/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/LAJA/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/LENO/include_user_mods b/cime_config/usermods_dirs/clm/NEON/LENO/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/LENO/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/LENO/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/LENO/shell_commands b/cime_config/usermods_dirs/clm/NEON/LENO/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/LENO/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/LENO/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/MLBS/include_user_mods b/cime_config/usermods_dirs/clm/NEON/MLBS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/MLBS/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/MLBS/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/MLBS/shell_commands b/cime_config/usermods_dirs/clm/NEON/MLBS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/MLBS/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/MLBS/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/MOAB/include_user_mods b/cime_config/usermods_dirs/clm/NEON/MOAB/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/MOAB/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/MOAB/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/MOAB/shell_commands b/cime_config/usermods_dirs/clm/NEON/MOAB/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/MOAB/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/MOAB/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/NIWO/include_user_mods b/cime_config/usermods_dirs/clm/NEON/NIWO/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/NIWO/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/NIWO/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/NIWO/shell_commands b/cime_config/usermods_dirs/clm/NEON/NIWO/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/NIWO/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/NIWO/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/NOGP/include_user_mods b/cime_config/usermods_dirs/clm/NEON/NOGP/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/NOGP/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/NOGP/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/NOGP/shell_commands b/cime_config/usermods_dirs/clm/NEON/NOGP/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/NOGP/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/NOGP/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/OAES/include_user_mods b/cime_config/usermods_dirs/clm/NEON/OAES/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/OAES/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/OAES/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/OAES/shell_commands b/cime_config/usermods_dirs/clm/NEON/OAES/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/OAES/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/OAES/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/ONAQ/include_user_mods b/cime_config/usermods_dirs/clm/NEON/ONAQ/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/ONAQ/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/ONAQ/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/ONAQ/shell_commands b/cime_config/usermods_dirs/clm/NEON/ONAQ/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/ONAQ/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/ONAQ/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/ORNL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/ORNL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/ORNL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/ORNL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/ORNL/shell_commands b/cime_config/usermods_dirs/clm/NEON/ORNL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/ORNL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/ORNL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/OSBS/include_user_mods b/cime_config/usermods_dirs/clm/NEON/OSBS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/OSBS/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/OSBS/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/OSBS/shell_commands b/cime_config/usermods_dirs/clm/NEON/OSBS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/OSBS/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/OSBS/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/PUUM/include_user_mods b/cime_config/usermods_dirs/clm/NEON/PUUM/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/PUUM/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/PUUM/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/PUUM/shell_commands b/cime_config/usermods_dirs/clm/NEON/PUUM/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/PUUM/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/PUUM/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/RMNP/include_user_mods b/cime_config/usermods_dirs/clm/NEON/RMNP/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/RMNP/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/RMNP/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/RMNP/shell_commands b/cime_config/usermods_dirs/clm/NEON/RMNP/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/RMNP/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/RMNP/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/SCBI/include_user_mods b/cime_config/usermods_dirs/clm/NEON/SCBI/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SCBI/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/SCBI/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/SCBI/shell_commands b/cime_config/usermods_dirs/clm/NEON/SCBI/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SCBI/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/SCBI/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/SERC/include_user_mods b/cime_config/usermods_dirs/clm/NEON/SERC/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SERC/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/SERC/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/SERC/shell_commands b/cime_config/usermods_dirs/clm/NEON/SERC/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SERC/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/SERC/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/SJER/include_user_mods b/cime_config/usermods_dirs/clm/NEON/SJER/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SJER/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/SJER/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/SJER/shell_commands b/cime_config/usermods_dirs/clm/NEON/SJER/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SJER/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/SJER/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/SOAP/include_user_mods b/cime_config/usermods_dirs/clm/NEON/SOAP/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SOAP/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/SOAP/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/SOAP/shell_commands b/cime_config/usermods_dirs/clm/NEON/SOAP/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SOAP/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/SOAP/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/SRER/include_user_mods b/cime_config/usermods_dirs/clm/NEON/SRER/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SRER/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/SRER/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/SRER/shell_commands b/cime_config/usermods_dirs/clm/NEON/SRER/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/SRER/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/SRER/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/STEI/include_user_mods b/cime_config/usermods_dirs/clm/NEON/STEI/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/STEI/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/STEI/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/STEI/shell_commands b/cime_config/usermods_dirs/clm/NEON/STEI/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/STEI/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/STEI/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/STER/include_user_mods b/cime_config/usermods_dirs/clm/NEON/STER/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/STER/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/STER/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/STER/shell_commands b/cime_config/usermods_dirs/clm/NEON/STER/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/STER/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/STER/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/TALL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/TALL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/TALL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/TALL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/TALL/shell_commands b/cime_config/usermods_dirs/clm/NEON/TALL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/TALL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/TALL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/TEAK/include_user_mods b/cime_config/usermods_dirs/clm/NEON/TEAK/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/TEAK/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/TEAK/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/TEAK/shell_commands b/cime_config/usermods_dirs/clm/NEON/TEAK/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/TEAK/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/TEAK/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/TOOL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/TOOL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/TOOL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/TOOL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/TOOL/shell_commands b/cime_config/usermods_dirs/clm/NEON/TOOL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/TOOL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/TOOL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/TREE/include_user_mods b/cime_config/usermods_dirs/clm/NEON/TREE/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/TREE/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/TREE/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/TREE/shell_commands b/cime_config/usermods_dirs/clm/NEON/TREE/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/TREE/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/TREE/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/UKFS/include_user_mods b/cime_config/usermods_dirs/clm/NEON/UKFS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/UKFS/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/UKFS/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/UKFS/shell_commands b/cime_config/usermods_dirs/clm/NEON/UKFS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/UKFS/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/UKFS/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/UNDE/include_user_mods b/cime_config/usermods_dirs/clm/NEON/UNDE/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/UNDE/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/UNDE/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/UNDE/shell_commands b/cime_config/usermods_dirs/clm/NEON/UNDE/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/UNDE/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/UNDE/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/WOOD/include_user_mods b/cime_config/usermods_dirs/clm/NEON/WOOD/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/WOOD/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/WOOD/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/WOOD/shell_commands b/cime_config/usermods_dirs/clm/NEON/WOOD/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/WOOD/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/WOOD/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/WREF/include_user_mods b/cime_config/usermods_dirs/clm/NEON/WREF/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/WREF/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/WREF/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/WREF/shell_commands b/cime_config/usermods_dirs/clm/NEON/WREF/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/WREF/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/WREF/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/YELL/include_user_mods b/cime_config/usermods_dirs/clm/NEON/YELL/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/NEON/YELL/include_user_mods
rename to cime_config/usermods_dirs/clm/NEON/YELL/include_user_mods
diff --git a/cime_config/usermods_dirs/NEON/YELL/shell_commands b/cime_config/usermods_dirs/clm/NEON/YELL/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/YELL/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/YELL/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/defaults/shell_commands b/cime_config/usermods_dirs/clm/NEON/defaults/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/NEON/defaults/shell_commands
rename to cime_config/usermods_dirs/clm/NEON/defaults/shell_commands
diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_clm b/cime_config/usermods_dirs/clm/NEON/defaults/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/NEON/defaults/user_nl_clm
rename to cime_config/usermods_dirs/clm/NEON/defaults/user_nl_clm
diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_cpl b/cime_config/usermods_dirs/clm/NEON/defaults/user_nl_cpl
similarity index 100%
rename from cime_config/usermods_dirs/NEON/defaults/user_nl_cpl
rename to cime_config/usermods_dirs/clm/NEON/defaults/user_nl_cpl
diff --git a/cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/clm/NEON/defaults/user_nl_datm_streams
similarity index 100%
rename from cime_config/usermods_dirs/NEON/defaults/user_nl_datm_streams
rename to cime_config/usermods_dirs/clm/NEON/defaults/user_nl_datm_streams
diff --git a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AR-SLu/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AR-SLu/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AR-SLu/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AR-SLu/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AR-SLu/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AR-SLu/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AT-Neu/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AT-Neu/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AT-Neu/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AT-Neu/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AT-Neu/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AT-Neu/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-ASM/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-ASM/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-ASM/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-ASM/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-ASM/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-ASM/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Cow/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Cow/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Cow/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Cow/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Cow/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Cow/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Cpr/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Cpr/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Cpr/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Cpr/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Cpr/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Cpr/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Ctr/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Ctr/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Ctr/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Ctr/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Ctr/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Ctr/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Cum/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Cum/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Cum/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Cum/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Cum/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Cum/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-DaP/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-DaP/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-DaP/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-DaP/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-DaP/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-DaP/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-DaS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-DaS/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-DaS/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-DaS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-DaS/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-DaS/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Dry/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Dry/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Dry/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Dry/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Dry/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Dry/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Emr/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Emr/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Emr/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Emr/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Emr/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Emr/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-GWW/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-GWW/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-GWW/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-GWW/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-GWW/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-GWW/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Gin/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Gin/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Gin/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Gin/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Gin/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Gin/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-How/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-How/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-How/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-How/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-How/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-How/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-How/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Lit/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Lit/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Lit/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Lit/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Lit/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Lit/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Otw/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Otw/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Otw/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Otw/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Otw/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Otw/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Rig/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Rig/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Rig/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Rig/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Rig/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Rig/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Rob/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Rob/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Rob/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Rob/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Rob/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Rob/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Sam/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Sam/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Sam/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Sam/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Sam/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Sam/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Stp/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Stp/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Stp/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Stp/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Stp/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Stp/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-TTE/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-TTE/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-TTE/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-TTE/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-TTE/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-TTE/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Tum/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Tum/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Tum/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Tum/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Tum/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Tum/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Whr/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Whr/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Whr/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Whr/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Whr/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Whr/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Wrr/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Wrr/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Wrr/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Wrr/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Wrr/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Wrr/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Ync/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Ync/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Ync/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/AU-Ync/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/AU-Ync/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/AU-Ync/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/BE-Bra/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BE-Bra/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/BE-Bra/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/BE-Bra/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BE-Bra/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/BE-Bra/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/BE-Lon/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BE-Lon/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/BE-Lon/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/BE-Lon/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BE-Lon/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/BE-Lon/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/BE-Vie/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BE-Vie/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/BE-Vie/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/BE-Vie/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BE-Vie/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/BE-Vie/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/BR-Sa3/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BR-Sa3/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/BR-Sa3/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/BR-Sa3/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BR-Sa3/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/BR-Sa3/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/BW-Ma1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BW-Ma1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/BW-Ma1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/BW-Ma1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/BW-Ma1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/BW-Ma1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS4/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS4/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS4/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS4/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS4/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS4/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS5/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS5/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS5/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS5/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS5/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS5/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS6/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS6/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS6/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS6/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS6/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS6/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS7/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS7/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS7/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-NS7/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-NS7/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-NS7/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-Qcu/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-Qcu/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-Qcu/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-Qcu/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-Qcu/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-Qcu/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-Qfo/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-Qfo/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-Qfo/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-Qfo/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-Qfo/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-Qfo/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-SF1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-SF1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-SF1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-SF1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-SF1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-SF1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-SF2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-SF2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-SF2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-SF2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-SF2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-SF2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CA-SF3/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-SF3/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-SF3/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CA-SF3/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CA-SF3/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CA-SF3/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CH-Cha/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CH-Cha/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CH-Cha/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CH-Cha/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CH-Cha/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CH-Cha/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CH-Dav/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CH-Dav/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CH-Dav/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CH-Dav/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CH-Dav/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CH-Dav/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CH-Fru/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CH-Fru/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CH-Fru/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CH-Fru/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CH-Fru/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CH-Fru/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CH-Oe1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CH-Oe1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CH-Oe1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CH-Oe1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CH-Oe1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CH-Oe1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Cha/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Cha/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Cha/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Cha/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Cha/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Cha/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Cng/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Cng/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Cng/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Cng/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Cng/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Cng/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Dan/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Dan/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Dan/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Dan/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Dan/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Dan/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Din/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Din/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Din/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Din/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Din/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Din/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Din/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Du2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Du2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Du2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Du2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Du2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Du2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CN-HaM/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-HaM/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-HaM/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CN-HaM/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-HaM/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-HaM/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Qia/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Qia/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Qia/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CN-Qia/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CN-Qia/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CN-Qia/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/CZ-wet/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CZ-wet/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/CZ-wet/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/CZ-wet/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/CZ-wet/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/CZ-wet/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Bay/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Bay/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Bay/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Bay/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Bay/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Bay/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Geb/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Geb/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Geb/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Geb/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Geb/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Geb/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Gri/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Gri/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Gri/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Gri/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Gri/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Gri/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Hai/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Hai/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Hai/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Hai/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Hai/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Hai/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Kli/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Kli/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Kli/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Kli/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Kli/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Kli/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Meh/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Meh/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Meh/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Meh/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Meh/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Meh/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Obe/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Obe/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Obe/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Obe/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Obe/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Obe/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Seh/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Seh/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Seh/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Seh/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Seh/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Seh/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-SfN/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-SfN/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-SfN/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-SfN/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-SfN/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-SfN/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Tha/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Tha/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Tha/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Tha/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Tha/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Tha/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Wet/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Wet/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Wet/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DE-Wet/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DE-Wet/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DE-Wet/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DK-Fou/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-Fou/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-Fou/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DK-Fou/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-Fou/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-Fou/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DK-Lva/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-Lva/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-Lva/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DK-Lva/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-Lva/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-Lva/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DK-Ris/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-Ris/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-Ris/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DK-Ris/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-Ris/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-Ris/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DK-Sor/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-Sor/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-Sor/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DK-Sor/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-Sor/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-Sor/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/DK-ZaH/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-ZaH/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-ZaH/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/DK-ZaH/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/DK-ZaH/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/DK-ZaH/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/ES-ES1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-ES1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-ES1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/ES-ES1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-ES1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-ES1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/ES-ES2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-ES2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-ES2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/ES-ES2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-ES2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-ES2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/ES-LMa/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-LMa/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-LMa/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/ES-LMa/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-LMa/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-LMa/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/ES-LgS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-LgS/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-LgS/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/ES-LgS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-LgS/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-LgS/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/ES-VDA/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-VDA/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-VDA/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/ES-VDA/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ES-VDA/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/ES-VDA/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FI-Hyy/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FI-Hyy/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FI-Hyy/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FI-Hyy/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FI-Hyy/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FI-Hyy/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FI-Kaa/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FI-Kaa/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FI-Kaa/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FI-Kaa/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FI-Kaa/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FI-Kaa/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FI-Lom/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FI-Lom/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FI-Lom/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FI-Lom/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FI-Lom/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FI-Lom/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FI-Sod/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FI-Sod/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FI-Sod/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FI-Sod/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FI-Sod/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FI-Sod/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Fon/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Fon/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Fon/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Fon/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Fon/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Fon/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Gri/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Gri/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Gri/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Gri/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Gri/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Gri/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Hes/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Hes/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Hes/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Hes/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Hes/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Hes/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FR-LBr/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-LBr/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-LBr/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FR-LBr/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-LBr/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-LBr/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Lq1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Lq1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Lq1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Lq1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Lq1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Lq1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Lq2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Lq2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Lq2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Lq2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Lq2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Lq2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Pue/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Pue/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Pue/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/FR-Pue/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/FR-Pue/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/FR-Pue/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/GF-Guy/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/GF-Guy/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/GF-Guy/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/GF-Guy/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/GF-Guy/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/GF-Guy/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/HU-Bug/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/HU-Bug/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/HU-Bug/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/HU-Bug/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/HU-Bug/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/HU-Bug/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/ID-Pag/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ID-Pag/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/ID-Pag/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/ID-Pag/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ID-Pag/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/ID-Pag/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IE-Ca1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IE-Ca1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IE-Ca1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IE-Ca1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IE-Ca1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IE-Ca1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IE-Dri/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IE-Dri/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IE-Dri/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IE-Dri/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IE-Dri/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IE-Dri/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Amp/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Amp/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Amp/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Amp/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Amp/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Amp/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-BCi/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-BCi/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-BCi/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-BCi/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-BCi/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-BCi/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-CA1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-CA1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-CA1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-CA1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-CA1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-CA1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-CA2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-CA2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-CA2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-CA2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-CA2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-CA2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-CA3/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-CA3/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-CA3/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-CA3/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-CA3/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-CA3/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Col/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Col/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Col/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Col/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Col/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Col/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Col/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Cpz/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Cpz/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Cpz/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Cpz/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Cpz/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Cpz/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Isp/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Isp/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Isp/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Isp/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Isp/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Isp/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-LMa/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-LMa/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-LMa/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-LMa/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-LMa/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-LMa/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Lav/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Lav/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Lav/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Lav/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Lav/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Lav/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-MBo/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-MBo/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-MBo/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-MBo/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-MBo/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-MBo/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Mal/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Mal/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Mal/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Mal/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Mal/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Mal/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Noe/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Noe/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Noe/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Noe/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Noe/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Noe/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Non/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Non/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Non/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Non/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Non/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Non/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Non/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-PT1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-PT1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-PT1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-PT1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-PT1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-PT1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Ren/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Ren/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Ren/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Ren/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Ren/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Ren/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Ro1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Ro1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Ro1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Ro1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Ro1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Ro1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Ro2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Ro2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Ro2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-Ro2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-Ro2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-Ro2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-SR2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-SR2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-SR2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-SR2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-SR2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-SR2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/IT-SRo/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-SRo/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-SRo/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/IT-SRo/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/IT-SRo/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/IT-SRo/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/JP-SMF/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/JP-SMF/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/JP-SMF/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/JP-SMF/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/JP-SMF/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/JP-SMF/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/NL-Ca1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/NL-Ca1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/NL-Ca1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/NL-Ca1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/NL-Ca1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/NL-Ca1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/NL-Hor/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/NL-Hor/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/NL-Hor/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/NL-Hor/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/NL-Hor/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/NL-Hor/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/NL-Loo/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/NL-Loo/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/NL-Loo/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/NL-Loo/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/NL-Loo/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/NL-Loo/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/PL-wet/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/PL-wet/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/PL-wet/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/PL-wet/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/PL-wet/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/PL-wet/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/PL-wet/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/PT-Esp/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/PT-Esp/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/PT-Esp/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/PT-Esp/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/PT-Esp/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/PT-Esp/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/PT-Mi1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/PT-Mi1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/PT-Mi1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/PT-Mi1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/PT-Mi1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/PT-Mi1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/PT-Mi2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/PT-Mi2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/PT-Mi2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/PT-Mi2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/PT-Mi2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/PT-Mi2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Che/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/RU-Che/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/RU-Che/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/RU-Che/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/RU-Che/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/RU-Che/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/RU-Che/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/RU-Fyo/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/RU-Fyo/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/RU-Fyo/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/RU-Fyo/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/RU-Fyo/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/RU-Fyo/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/RU-Zot/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/RU-Zot/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/RU-Zot/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/RU-Zot/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/RU-Zot/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/RU-Zot/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/SD-Dem/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/SD-Dem/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/SD-Dem/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/SD-Dem/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/SD-Dem/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/SD-Dem/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/SE-Deg/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/SE-Deg/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/SE-Deg/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/SE-Deg/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/SE-Deg/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/SE-Deg/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/UK-Gri/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/UK-Gri/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/UK-Gri/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/UK-Gri/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/UK-Gri/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/UK-Gri/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/UK-Ham/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/UK-Ham/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/UK-Ham/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/UK-Ham/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/UK-Ham/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/UK-Ham/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/UK-PL3/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/UK-PL3/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/UK-PL3/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/UK-PL3/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/UK-PL3/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/UK-PL3/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-AR1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-AR1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-AR1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-AR1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-AR1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-AR1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-AR2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-AR2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-AR2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-AR2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-AR2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-AR2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-ARM/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-ARM/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-ARM/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-ARM/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-ARM/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-ARM/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-ARM/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Aud/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Aud/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Aud/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Aud/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Aud/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Aud/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Aud/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bar/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Bar/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Bar/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Bar/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Bar/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Bar/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Bar/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Bkg/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Bkg/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Bkg/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Bkg/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Bkg/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Bkg/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Blo/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Blo/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Blo/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Blo/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Blo/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Blo/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Blo/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Bo1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Bo1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Bo1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Bo1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Bo1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Bo1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Cop/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Cop/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Cop/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Cop/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Cop/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Cop/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Cop/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-FPe/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-FPe/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-FPe/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-FPe/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-FPe/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-FPe/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-FPe/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-GLE/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-GLE/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-GLE/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-GLE/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-GLE/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-GLE/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-GLE/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Goo/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Goo/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Goo/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Goo/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Goo/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Goo/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Goo/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ha1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ha1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ha1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ha1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ha1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ha1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ho1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ho1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ho1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ho1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ho1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ho1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-KS2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-KS2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-KS2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-KS2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-KS2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-KS2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-KS2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Los/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Los/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Los/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Los/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Los/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Los/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Los/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MMS/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-MMS/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-MMS/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-MMS/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-MMS/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-MMS/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-MMS/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MOz/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-MOz/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-MOz/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-MOz/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-MOz/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-MOz/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-MOz/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Me2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Me2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Me2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Me2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Me2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Me2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me4/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Me4/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Me4/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Me4/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Me4/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Me4/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Me4/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me6/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Me6/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Me6/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Me6/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Me6/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Me6/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Me6/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Myb/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Myb/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Myb/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Myb/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Myb/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Myb/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Myb/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-NR1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-NR1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-NR1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-NR1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-NR1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-NR1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-NR1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ne1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ne1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ne1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ne1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ne1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ne1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ne2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ne2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ne2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ne2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ne2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ne2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ne3/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ne3/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ne3/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ne3/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ne3/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ne3/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-PFa/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-PFa/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-PFa/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-PFa/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-PFa/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-PFa/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-PFa/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Prr/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Prr/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Prr/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Prr/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Prr/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Prr/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Prr/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP1/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-SP1/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SP1/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SP1/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-SP1/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SP1/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SP1/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP2/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-SP2/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SP2/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SP2/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-SP2/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SP2/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SP2/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP3/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-SP3/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SP3/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SP3/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-SP3/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SP3/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SP3/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRG/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-SRG/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SRG/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SRG/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-SRG/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SRG/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SRG/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRM/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-SRM/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SRM/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SRM/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-SRM/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-SRM/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-SRM/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Syv/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Syv/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Syv/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Syv/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Syv/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Syv/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Syv/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ton/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ton/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ton/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ton/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Ton/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Ton/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Ton/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Tw4/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Tw4/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Tw4/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Tw4/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Tw4/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Tw4/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Twt/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Twt/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Twt/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Twt/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Twt/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Twt/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Twt/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-UMB/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-UMB/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-UMB/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-UMB/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-UMB/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-UMB/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-UMB/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Var/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Var/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Var/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Var/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Var/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Var/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Var/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-WCr/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-WCr/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-WCr/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-WCr/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-WCr/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-WCr/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-WCr/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Whs/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Whs/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Whs/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Whs/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Whs/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Whs/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Whs/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/US-Wkg/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Wkg/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Wkg/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/US-Wkg/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/US-Wkg/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/US-Wkg/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/ZA-Kru/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ZA-Kru/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/ZA-Kru/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/ZA-Kru/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ZA-Kru/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/ZA-Kru/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/include_user_mods b/cime_config/usermods_dirs/clm/PLUMBER2/ZM-Mon/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ZM-Mon/include_user_mods
rename to cime_config/usermods_dirs/clm/PLUMBER2/ZM-Mon/include_user_mods
diff --git a/cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/ZM-Mon/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/ZM-Mon/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/ZM-Mon/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/shell_commands b/cime_config/usermods_dirs/clm/PLUMBER2/defaults/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/defaults/shell_commands
rename to cime_config/usermods_dirs/clm/PLUMBER2/defaults/shell_commands
diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm b/cime_config/usermods_dirs/clm/PLUMBER2/defaults/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_clm
rename to cime_config/usermods_dirs/clm/PLUMBER2/defaults/user_nl_clm
diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_cpl b/cime_config/usermods_dirs/clm/PLUMBER2/defaults/user_nl_cpl
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_cpl
rename to cime_config/usermods_dirs/clm/PLUMBER2/defaults/user_nl_cpl
diff --git a/cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams b/cime_config/usermods_dirs/clm/PLUMBER2/defaults/user_nl_datm_streams
similarity index 100%
rename from cime_config/usermods_dirs/PLUMBER2/defaults/user_nl_datm_streams
rename to cime_config/usermods_dirs/clm/PLUMBER2/defaults/user_nl_datm_streams
diff --git a/cime_config/usermods_dirs/_includes/README b/cime_config/usermods_dirs/clm/_includes/README
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rename from cime_config/usermods_dirs/_includes/README
rename to cime_config/usermods_dirs/clm/_includes/README
diff --git a/cime_config/usermods_dirs/_includes/cmip6_carbon_isotopes/user_nl_clm b/cime_config/usermods_dirs/clm/_includes/cmip6_carbon_isotopes/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/_includes/cmip6_carbon_isotopes/user_nl_clm
rename to cime_config/usermods_dirs/clm/_includes/cmip6_carbon_isotopes/user_nl_clm
diff --git a/cime_config/usermods_dirs/_includes/cmip6_glaciers_cplhist/user_nl_cpl b/cime_config/usermods_dirs/clm/_includes/cmip6_glaciers_cplhist/user_nl_cpl
similarity index 100%
rename from cime_config/usermods_dirs/_includes/cmip6_glaciers_cplhist/user_nl_cpl
rename to cime_config/usermods_dirs/clm/_includes/cmip6_glaciers_cplhist/user_nl_cpl
diff --git a/cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm b/cime_config/usermods_dirs/clm/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
rename to cime_config/usermods_dirs/clm/_includes/cmip6_glaciers_virtual_antarctica/user_nl_clm
diff --git a/cime_config/usermods_dirs/_includes/output_base/README b/cime_config/usermods_dirs/clm/_includes/output_base/README
similarity index 100%
rename from cime_config/usermods_dirs/_includes/output_base/README
rename to cime_config/usermods_dirs/clm/_includes/output_base/README
diff --git a/cime_config/usermods_dirs/_includes/output_base/user_nl_clm b/cime_config/usermods_dirs/clm/_includes/output_base/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/_includes/output_base/user_nl_clm
rename to cime_config/usermods_dirs/clm/_includes/output_base/user_nl_clm
diff --git a/cime_config/usermods_dirs/_includes/output_base_highfreq/README b/cime_config/usermods_dirs/clm/_includes/output_base_highfreq/README
similarity index 100%
rename from cime_config/usermods_dirs/_includes/output_base_highfreq/README
rename to cime_config/usermods_dirs/clm/_includes/output_base_highfreq/README
diff --git a/cime_config/usermods_dirs/_includes/output_base_highfreq/include_user_mods b/cime_config/usermods_dirs/clm/_includes/output_base_highfreq/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/_includes/output_base_highfreq/include_user_mods
rename to cime_config/usermods_dirs/clm/_includes/output_base_highfreq/include_user_mods
diff --git a/cime_config/usermods_dirs/_includes/output_base_highfreq/user_nl_clm b/cime_config/usermods_dirs/clm/_includes/output_base_highfreq/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/_includes/output_base_highfreq/user_nl_clm
rename to cime_config/usermods_dirs/clm/_includes/output_base_highfreq/user_nl_clm
diff --git a/cime_config/usermods_dirs/cmip6_deck/include_user_mods b/cime_config/usermods_dirs/clm/cmip6_deck/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/cmip6_deck/include_user_mods
rename to cime_config/usermods_dirs/clm/cmip6_deck/include_user_mods
diff --git a/cime_config/usermods_dirs/cmip6_evolving_icesheet/include_user_mods b/cime_config/usermods_dirs/clm/cmip6_evolving_icesheet/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/cmip6_evolving_icesheet/include_user_mods
rename to cime_config/usermods_dirs/clm/cmip6_evolving_icesheet/include_user_mods
diff --git a/cime_config/usermods_dirs/cmip6_evolving_icesheet/user_nl_clm b/cime_config/usermods_dirs/clm/cmip6_evolving_icesheet/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/cmip6_evolving_icesheet/user_nl_clm
rename to cime_config/usermods_dirs/clm/cmip6_evolving_icesheet/user_nl_clm
diff --git a/cime_config/usermods_dirs/cmip6_waccm_deck/README b/cime_config/usermods_dirs/clm/cmip6_waccm_deck/README
similarity index 100%
rename from cime_config/usermods_dirs/cmip6_waccm_deck/README
rename to cime_config/usermods_dirs/clm/cmip6_waccm_deck/README
diff --git a/cime_config/usermods_dirs/cmip6_waccm_deck/include_user_mods b/cime_config/usermods_dirs/clm/cmip6_waccm_deck/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/cmip6_waccm_deck/include_user_mods
rename to cime_config/usermods_dirs/clm/cmip6_waccm_deck/include_user_mods
diff --git a/cime_config/usermods_dirs/cmip6_waccm_deck/shell_commands b/cime_config/usermods_dirs/clm/cmip6_waccm_deck/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/cmip6_waccm_deck/shell_commands
rename to cime_config/usermods_dirs/clm/cmip6_waccm_deck/shell_commands
diff --git a/cime_config/usermods_dirs/cmip6_waccm_nociso_deck/README b/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck/README
similarity index 100%
rename from cime_config/usermods_dirs/cmip6_waccm_nociso_deck/README
rename to cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck/README
diff --git a/cime_config/usermods_dirs/cmip6_waccm_nociso_deck/include_user_mods b/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/cmip6_waccm_nociso_deck/include_user_mods
rename to cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck/include_user_mods
diff --git a/cime_config/usermods_dirs/f09_37x288pt_PanBoreal/shell_commands b/cime_config/usermods_dirs/clm/f09_37x288pt_PanBoreal/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/f09_37x288pt_PanBoreal/shell_commands
rename to cime_config/usermods_dirs/clm/f09_37x288pt_PanBoreal/shell_commands
diff --git a/cime_config/usermods_dirs/f09_37x288pt_PanBoreal/user_nl_clm b/cime_config/usermods_dirs/clm/f09_37x288pt_PanBoreal/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/f09_37x288pt_PanBoreal/user_nl_clm
rename to cime_config/usermods_dirs/clm/f09_37x288pt_PanBoreal/user_nl_clm
diff --git a/cime_config/usermods_dirs/fates_sp/user_nl_clm b/cime_config/usermods_dirs/clm/fates_sp/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/fates_sp/user_nl_clm
rename to cime_config/usermods_dirs/clm/fates_sp/user_nl_clm
diff --git a/cime_config/usermods_dirs/lilac/README b/cime_config/usermods_dirs/clm/lilac/README
similarity index 100%
rename from cime_config/usermods_dirs/lilac/README
rename to cime_config/usermods_dirs/clm/lilac/README
diff --git a/cime_config/usermods_dirs/lilac/user_nl_ctsm b/cime_config/usermods_dirs/clm/lilac/user_nl_ctsm
similarity index 100%
rename from cime_config/usermods_dirs/lilac/user_nl_ctsm
rename to cime_config/usermods_dirs/clm/lilac/user_nl_ctsm
diff --git a/cime_config/usermods_dirs/newton_krylov_spinup/README b/cime_config/usermods_dirs/clm/newton_krylov_spinup/README
similarity index 100%
rename from cime_config/usermods_dirs/newton_krylov_spinup/README
rename to cime_config/usermods_dirs/clm/newton_krylov_spinup/README
diff --git a/cime_config/usermods_dirs/newton_krylov_spinup/shell_commands b/cime_config/usermods_dirs/clm/newton_krylov_spinup/shell_commands
similarity index 100%
rename from cime_config/usermods_dirs/newton_krylov_spinup/shell_commands
rename to cime_config/usermods_dirs/clm/newton_krylov_spinup/shell_commands
diff --git a/cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm b/cime_config/usermods_dirs/clm/newton_krylov_spinup/user_nl_clm
similarity index 100%
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rename to cime_config/usermods_dirs/clm/newton_krylov_spinup/user_nl_clm
diff --git a/cime_config/usermods_dirs/output_bgc/include_user_mods b/cime_config/usermods_dirs/clm/output_bgc/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/output_bgc/include_user_mods
rename to cime_config/usermods_dirs/clm/output_bgc/include_user_mods
diff --git a/cime_config/usermods_dirs/output_bgc/user_nl_clm b/cime_config/usermods_dirs/clm/output_bgc/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/output_bgc/user_nl_clm
rename to cime_config/usermods_dirs/clm/output_bgc/user_nl_clm
diff --git a/cime_config/usermods_dirs/output_bgc_highfreq/include_user_mods b/cime_config/usermods_dirs/clm/output_bgc_highfreq/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/output_bgc_highfreq/include_user_mods
rename to cime_config/usermods_dirs/clm/output_bgc_highfreq/include_user_mods
diff --git a/cime_config/usermods_dirs/output_bgc_highfreq/user_nl_clm b/cime_config/usermods_dirs/clm/output_bgc_highfreq/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/output_bgc_highfreq/user_nl_clm
rename to cime_config/usermods_dirs/clm/output_bgc_highfreq/user_nl_clm
diff --git a/cime_config/usermods_dirs/output_crop/include_user_mods b/cime_config/usermods_dirs/clm/output_crop/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/output_crop/include_user_mods
rename to cime_config/usermods_dirs/clm/output_crop/include_user_mods
diff --git a/cime_config/usermods_dirs/output_crop/user_nl_clm b/cime_config/usermods_dirs/clm/output_crop/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/output_crop/user_nl_clm
rename to cime_config/usermods_dirs/clm/output_crop/user_nl_clm
diff --git a/cime_config/usermods_dirs/output_crop_highfreq/include_user_mods b/cime_config/usermods_dirs/clm/output_crop_highfreq/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/output_crop_highfreq/include_user_mods
rename to cime_config/usermods_dirs/clm/output_crop_highfreq/include_user_mods
diff --git a/cime_config/usermods_dirs/output_sp/include_user_mods b/cime_config/usermods_dirs/clm/output_sp/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/output_sp/include_user_mods
rename to cime_config/usermods_dirs/clm/output_sp/include_user_mods
diff --git a/cime_config/usermods_dirs/output_sp/user_nl_clm b/cime_config/usermods_dirs/clm/output_sp/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/output_sp/user_nl_clm
rename to cime_config/usermods_dirs/clm/output_sp/user_nl_clm
diff --git a/cime_config/usermods_dirs/output_sp_exice/include_user_mods b/cime_config/usermods_dirs/clm/output_sp_exice/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/output_sp_exice/include_user_mods
rename to cime_config/usermods_dirs/clm/output_sp_exice/include_user_mods
diff --git a/cime_config/usermods_dirs/output_sp_exice/user_nl_clm b/cime_config/usermods_dirs/clm/output_sp_exice/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/output_sp_exice/user_nl_clm
rename to cime_config/usermods_dirs/clm/output_sp_exice/user_nl_clm
diff --git a/cime_config/usermods_dirs/output_sp_highfreq/include_user_mods b/cime_config/usermods_dirs/clm/output_sp_highfreq/include_user_mods
similarity index 100%
rename from cime_config/usermods_dirs/output_sp_highfreq/include_user_mods
rename to cime_config/usermods_dirs/clm/output_sp_highfreq/include_user_mods
diff --git a/cime_config/usermods_dirs/output_sp_highfreq/user_nl_clm b/cime_config/usermods_dirs/clm/output_sp_highfreq/user_nl_clm
similarity index 100%
rename from cime_config/usermods_dirs/output_sp_highfreq/user_nl_clm
rename to cime_config/usermods_dirs/clm/output_sp_highfreq/user_nl_clm
diff --git a/components/cdeps b/components/cdeps
index f6bc97483a..0750c91753 160000
--- a/components/cdeps
+++ b/components/cdeps
@@ -1 +1 @@
-Subproject commit f6bc97483a1bfb7352c6c5610a13ed898a86990b
+Subproject commit 0750c9175395d3ba3bf8eba65703dee230d08572
diff --git a/components/cism b/components/cism
index c84cc9f5b3..41843ef8fe 160000
--- a/components/cism
+++ b/components/cism
@@ -1 +1 @@
-Subproject commit c84cc9f5b3103766a35d0a7ddd5e9dbd7deae762
+Subproject commit 41843ef8fed91fcf60e2ea217c4f6f2ee5133c5d
diff --git a/components/cmeps b/components/cmeps
index 5b7d76978e..4b636c6f79 160000
--- a/components/cmeps
+++ b/components/cmeps
@@ -1 +1 @@
-Subproject commit 5b7d76978e2fdc661ec2de4ba9834b985decadc6
+Subproject commit 4b636c6f794ca02d854d15c620e26644751b449b
diff --git a/components/mizuRoute b/components/mizuRoute
index 2ff305a029..362bee329b 160000
--- a/components/mizuRoute
+++ b/components/mizuRoute
@@ -1 +1 @@
-Subproject commit 2ff305a0292cb06789de6cfea7ad3cc0d6173493
+Subproject commit 362bee329bd6bf1fd45c8f36e006b9c4294bb8ca
diff --git a/components/mosart b/components/mosart
index e2ffe00004..330574fbd8 160000
--- a/components/mosart
+++ b/components/mosart
@@ -1 +1 @@
-Subproject commit e2ffe00004cc416cfc8bcfae2a949474075c1d1f
+Subproject commit 330574fbd8a4810b7a168175690cbf7e1a7f6dab
diff --git a/components/rtm b/components/rtm
index b3dfcfbba5..26e96f500b 160000
--- a/components/rtm
+++ b/components/rtm
@@ -1 +1 @@
-Subproject commit b3dfcfbba58c151ac5a6ab513b3515ef3deff798
+Subproject commit 26e96f500b9500b32a870db20eed6b1bd37587ea
diff --git a/doc/ChangeLog b/doc/ChangeLog
index 5c0c6ba058..2c08950b2d 100644
--- a/doc/ChangeLog
+++ b/doc/ChangeLog
@@ -1,4 +1,802 @@
 ===============================================================
+Tag name: ctsm5.3.020
+Originator(s): samrabin (Sam Rabin, UCAR/TSS, samrabin@ucar.edu)
+Date: Fri Jan 17 12:21:24 MST 2025
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+Merging b4b-dev and ctsm5.3.019. Includes some improvements to test list / expected failures.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:
+- New test suite: Useful for redoing tests that failed due to https://github.com/ESCOMP/CTSM/issues/2916, after having replaced libraries/mpi-serial with a fresh copy.
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Other details
+-------------
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+
+Pull Requests that document the changes (include PR ids):
+- ESCOMP/CTSM#2938: ctsm5.3.020: Merge b4b-dev 2025-01-16 (https://github.com/ESCOMP/CTSM/pull/2938)
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.019
+Originator(s): olyson (Keith Oleson, UCAR/TSS)
+Date: Tue 14 Jan 2025 02:46:11 PM MST
+One-line Summary: Stop running 0th time step
+
+Purpose and description of changes
+----------------------------------
+ As with the last tag, this is also for consistency with CAM.
+
+Contributors
+------------
+ Bill Sacks. In the final steps, also slevis.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #925
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+ Same or similar changes needed separately in clm, in mosart, and in rtm.
+
+Changes to tests or testing:
+ FAIL RXCROPMATURITYSKIPGEN_Ld1097.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-cropMonthOutput RUN
+ I did not label this failure EXPECTED because the fix is planned for the next tag, ctsm5.3.020.
+
+ I resolved the izumi nag tests that failed to build (due to a bug in rtm and mosart) by introducing the bug-fix manually, as explained here:
+https://github.com/ESCOMP/CTSM/pull/2084#issuecomment-2584164690
+ In ctsm5.3.020 we plan to update to the rtm/mosart tags that include the fix.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  mosart
+    derecho ----- OK
+    izumi ------- OK
+
+  rtm
+    derecho ----- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+ I repeated the rtm & mosart test-suites with mosart1.1.04 instead of 06 and rtm1_0_82 instead of 84 (all else the same) and compared against the new baselines mosart1.1.06-ctsm5.3.019 and rtm1_0_84-ctsm5.3.019. These gave b4b identical answers.
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: All
+    - what platforms/compilers: All
+    - nature of change: larger than roundoff/same climate
+
+ Caveat: We see diffs in mosart and cpl output that will be eliminated in ctsm5.3.020. They are discussed here:
+https://github.com/ESCOMP/CTSM/pull/2838#issuecomment-2477608383
+https://github.com/ESCOMP/MOSART/issues/103#issuecomment-2479679014
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ rtm and mosart were already updated in the previous tag (ctsm5.3.018) to include the corresponding rtm and mosart tags
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2084
+ https://github.com/ESCOMP/MOSART/pull/67
+ https://github.com/ESCOMP/RTM/pull/37
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.018
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 10 Jan 2025 05:37:08 PM MST
+One-line Summary: Change history time to be the middle of the time bounds
+
+Purpose and description of changes
+----------------------------------
+ Making the change to be consistent with CAM and to make history output more intuitive.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Partly addresses issue #1059
+
+Notes of particular relevance for users
+---------------------------------------
+Caveats for users (e.g., need to interpolate initial conditions):
+ The history time variable now equals the middle of the time bounds.
+ Instantaneous history tapes now do not include time bounds.
+ Mixed history tapes do not change the treatment of instantaneous fields or move them to separate tapes, yet.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+ Same changes are needed separately in clm, in mosart, and in rtm.
+
+Changes to tests or testing:
+ This tag introduces changes to the mosart/rtm testlists.
+
+ FAIL RXCROPMATURITYSKIPGEN_Ld1097.f10_f10_mg37.IHistClm60BgcCrop.derecho_intel.clm-cropMonthOutput RUN
+ I did not label this failure EXPECTED because the fix comes in later in this series of "history" tags, in particular ctsm5.3.020.
+
+ I resolved the izumi nag tests that failed to build (due to a bug in rtm and mosart) by introducing the bug-fix manually, as explained here:
+https://github.com/ESCOMP/CTSM/pull/2084#issuecomment-2584164690
+ In the next tag we expect to update to the rtm/mosart tags that include the fix.
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests
+
+    derecho - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  mosart
+    derecho ----- OK
+    izumi ------- OK
+
+  rtm
+    derecho ----- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Only time variable, plus read caveat
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: all
+    - what platforms/compilers: all
+    - nature of change: only the time variable
+
+ Caveat: We see diffs in mosart and cpl output that will be eliminated later in this series of "history" tags, in particular ctsm5.3.020. They are discussed here:
+https://github.com/ESCOMP/CTSM/pull/2838#issuecomment-2477608383
+https://github.com/ESCOMP/MOSART/issues/103#issuecomment-2479679014
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ rtm, mosart (see related note in ctsm5.3.019)
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2838
+ https://github.com/ESCOMP/MOSART/pull/70
+ https://github.com/ESCOMP/RTM/issues/54
+ https://github.com/ESCOMP/MOSART/pull/106
+ https://github.com/ESCOMP/RTM/pull/39
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.017
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 09 Jan 2025 11:56:43 AM MST
+One-line Summary: Merge tmp-241219 branch to master
+
+Purpose and description of changes
+----------------------------------
+
+Includes three tmp-241219 tags:
+ tmp-241219.n01.ctsm5.3.016 Merge b4b-dev:
+    nfix_method options Houlton (default), Bytnerowicz (option)
+ tmp-241219.n02.ctsm5.3.016 FATES hydro test update
+ tmp-241219.n03.ctsm5.3.016 Bug fix for izumi nag tests to pass (b4b unless using Bytnerowicz)
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Each separate tag documents this information below.
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ nfix_method as explained in tmp-241219.n01.ctsm5.3.016 tag below.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ New tests as documented in tmp-241219.n03.ctsm5.3.016 tag below.
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK (baseline linked to tmp-241219.n03.ctsm5.3.016)
+    izumi ------- OK (baseline linked to tmp-241219.n03.ctsm5.3.016)
+
+  fates tests:
+    derecho ----- No new testing; last baseline is fates-sci.1.80.4_api.37.0.0-tmp-241219.n02.ctsm5.3.016
+    izumi ------- No new testing; see tmp-241219.n02.ctsm5.3.016 tag below
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, only for aux_clm fates testmods
+
+  Same comment as in tmp-241219.n02.ctsm5.3.016 tag:
+  The FATES tag update includes a number of science and bug fix updates since the
+  last fates tag update, which results in non-B4B changes.  These have been reviewed
+  and differ as expected.
+
+  Also, see caveat in Answer changes for tag tmp-241219.n01.ctsm5.3.016.
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ fates updated to sci.1.80.4_api.37.0.0
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2928
+
+===============================================================
+===============================================================
+Tag name: tmp-241219.n03.ctsm5.3.016
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Thu 09 Jan 2025 11:39:37 AM MST
+One-line Summary: Bug fix for izumi nag tests to pass
+
+Purpose and description of changes
+----------------------------------
+ Allocation statements should have been (0:mxpft) instead of (mxpft).
+ I introduced the bug in a small refactor requested in #2917.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Fixes #2924
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+ Added tests that I should have added in the tmp-241219.n01.ctsm5.3.016 tag:
+ ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-flexCN_FUN_BNF
+ ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.derecho_intel.clm-flexCN_FUN_BNF
+
+Testing summary:
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+ derecho used tmp-241219.n02.ctsm5.3.016 (i.e. the previous tag)
+ izumi used ctsm5.3.016 because it was the best available baseline
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No but read caveat.
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: a few Fates cases
+    - what platforms/compilers: izumi; only because I compared to ctsm5.3.016
+    - nature of change: same as in the tmp-241219.n02.ctsm5.3.016 tag
+
+ Note: Also on izumi I see the following failure in all the tests that 'failed to initialize'
+       that I had to go back to build and run, whether with ./case.build or ./create_test. For example:
+       FAIL ERP_D_Ld5_P48x1.f10_f10_mg37.I2000Clm50BgcCru.izumi_nag.clm-noFUN_flexCN BASELINE ctsm5.3.016: ERROR CPRNC failed to open files
+       I am aware that others have also seen this behavior.
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2925
+
+===============================================================
+===============================================================
+Tag name: tmp-241219.n02.ctsm5.3.016
+Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Date: Wed 08 Jan 2025 10:52:49 AM MST
+One-line Summary: FATES hydro test update
+
+Purpose and description of changes
+----------------------------------
+
+This minor update reverts a temporary work around for FATES hydro system tests.
+The FATES tag is updated to capture the FATES-side fix to the issue that predicated
+the temporary testing workaround.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+
+  #2878 - Remove fates_allom_smode shell_command update in FatesColdHydro testmod
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+  FATES hydro tests will no long build a custom parameter file on the fly
+  The one FATES PVT test has been added to expected failure per #2919
+
+Testing summary: regular + fates
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK (see #2924)
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+    izumi ------- OK
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, but only for aux_clm fates testmods
+
+  The FATES tag update includes a number of science and bug fix updates since the
+  last fates tag update, which results in non-B4B changes.  These have been reviewed
+  and differ as expected.
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+   fates: sci.1.79.3_api.37.0.0 -> sci.1.80.4_api.37.0.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+  https://github.com/ESCOMP/CTSM/pull/2882
+
+===============================================================
+===============================================================
+Tag name: tmp-241219.n01.ctsm5.3.016
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Tue 24 Dec 2024 03:43:01 PM MST
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+ #2869 Update temperature cost function for symbiotic Nfix in FUN
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Resolves #2869
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ New namelist variable: nfix_method
+
+Changes made to namelist defaults (e.g., changed parameter values):
+ nfix_method default: Houlton
+ other available option: Bytnerowicz
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- machine seems problematic at the moment
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No, but read caveat.
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: tests with ciso_cwd_hr testmods
+    - what platforms/compilers: all
+    - nature of change: irrelevant
+
+ Explanation:
+ "diff ctsm60_ciso_cwd_hr_params.c241119.asc ctsm60_params.c241119.asc"
+ differ ONLY in the value of ceta. The previous paramfile for ciso_cwd_hr
+ showed additional diffs, likely due to problems that we have seen before
+ when generating new paramfiles. The ciso_cwd_hr tests would not have shown
+ diffs had the previous paramfile been correct, so I only mention the diffs
+ here for the record.
+
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2869
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.016
+Originator(s): jedwards and erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Thu 19 Dec 2024 04:23:39 PM MST
+One-line Summary: Rpointer files for restart now have the simulation timestamp in the filename
+
+Purpose and description of changes
+----------------------------------
+
+Add the simulation timestamp to the rpointer files. Also update submodules with this change
+in CMEPS and CDEPS as well as updated cime to handle it. See the notes below for an explaination
+about this.
+
+Add a "clm" level directory under usermods_dirs so that the component where user-mods reside
+is declared and to make them function the same as test-mods.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+   There are text files that CESM uses to keep track of how far simulations
+   have progressed. They are simple text files that point to the filename of the latest
+   restart file for that component. There is such a file for each component. So for CTSM I cases
+   that's: lnd, cpl, and atm (and rof if it's active). Normally for just extending the length
+   of a simulations -- the user doesn't have to worry about these files.
+
+   However, if there was a problem when a simulation shut down, it's possible that
+   different components will have mismatched restarts and rpointer files. In the past this
+   meant figuring out what restart file should be pointed to in each component rpointer file
+   and correcting it by hand in an editor. There was only the final set of rpointer files that
+   was kept for a case.
+
+   Now, with this update the lnd, cpl, and atm rpointer files have the simulation date in the filenames.
+   So it's easy to spot if the restarts are mismatched for one of the components. Also since
+   there are matching rpointer files for each time restarts are created it's now easier to make
+   sure restarts and rpointer files are all correctly matched. And for a user to take a set of restarts
+   and matching rpointer files to start up from for any part of an existing simulation to start from.
+   This means you don't have to hand edit the rpointer files and make sure you don't make a mistake
+   when you do.
+
+   Old rpointer filenames:
+      rpointer.atm
+      rpointer.cpl
+      rpointer.lnd
+
+   New names:
+      rpointer.atm.YYYY-MM-DD-SSSSS
+      rpointer.cpl.YYYY-MM-DD-SSSSS
+      rpointer.lnd.YYYY-MM-DD-SSSSS
+
+   Where YYYY-MM-DD-SSSSS is the year month day and seconds into the day for the simulation timestamp
+   For example rpointer.lnd.2000-01-01-00000 for a rpointer file for starting at Jan/1st/2000 at midnight
+
+
+  NOTE: BACKWARDS COMPATIBLE
+     For all the components you can use both the new format or old format for the rpointer filenames.
+     So if you are restarting from an existing case before ctsm5.3.016 you CAN use those rpointer filenames
+     that don't have the timestamps in the name.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+  There's a lot of testing that failed with this tag, that we'll need to fix soonish.
+  There are issues on the problems and they are marked as expected fails
+
+  On Izumi I had to rebuild a bunch of tests as they failed with run_sys_tests submitted under ctsm_pylib.
+
+  Note, also that MOSART and RTM were NOT updated to use the new format.
+
+Testing summary:  regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS (inventoryfileDNE fails as expected)
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No bit-for-bit
+
+Other details
+-------------
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): cime, cmeps, cdeps
+    cime to cime6.1.49
+    cmeps to cmeps1.0.32
+    cdeps to cdeps1.0.61
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+   #2757 -- add timestamp to rpointer file
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.015
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Wed 18 Dec 2024 02:09:40 PM MST
+One-line Summary: Update cdeps with cam7 nextsw cday changes
+
+Purpose and description of changes
+----------------------------------
+
+Update CDEPS with changes for CAM7 nextsw_cday handling. This changes answers
+for CPLHIST cases. We also changed the cam7LndTuningMode tests to turn this on
+for DATM to more closely match what CAM7 does.
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+   Fixes: #2897 Update CDEPS to bring in DATM change regarding nextsw_cday changing answers in CPLHIST cases
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   New namelist parameter for DATM: nextsw_cday_calc
+      defaults to cam6, set to cam7 for CPLHIST and specific tests
+      Only applies if iradsw is NOT 0 or 1
+
+       Here is the documention on this in the namelist_definitial XML for DATM:
++      For CPLHIST cases, this should agree with the version of CAM (or other atmosphere
++      model) used to generate the CPLHIST forcings; the valid values for this variable are
++      based on this: 'cam6' is appropriate for cases generated with the driver ordering in
++      CAM6 and earlier, and 'cam7' is appropriate for cases generated with the driver
++      ordering in CAM7 and later.
++
++      For 'cam6', the next radiation timestep is set to the present time plus 2 timesteps
++      when mod(tod+dtime,delta_radsw)==0. For 'cam7', the next radiation timestep is set
++      to the present time plus 1 timestep when mod(tod,delta_radsw)==0.
+
+Notes of particular relevance for developers:
+---------------------------------------------
+
+Changes to tests or testing:
+    cam7LndTuningMode testmods changed so that iradsw==-1 (hourly) , and nextsw_cday_calc='cam7'
+
+Testing summary: regular
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Only for CPLHIST cases, otherwise bit-for-bit
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: Compsets with DATM^CPLHIST
+    - what platforms/compilers: All
+    - nature of change; larger than roundoff/same climate
+
+Other details
+-------------
+
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.): cdeps share
+   cdeps to cdeps1.0.57
+   share to share1.1.6
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+   #2900 -- Update cdeps with cam7 nextsw cday changes
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.014
 Originator(s): multiple (see contributors below)
 Date: Tue 03 Dec 2024 04:31:03 PM MST
diff --git a/doc/ChangeSum b/doc/ChangeSum
index 1ac751ea03..98739639a4 100644
--- a/doc/ChangeSum
+++ b/doc/ChangeSum
@@ -1,5 +1,14 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.020 samrabin 01/17/2025 Merge b4b-dev
+       ctsm5.3.019   olyson 01/14/2025 Stop running 0th time step
+       ctsm5.3.018   slevis 01/10/2025 Change history time to be the middle of the time bounds
+       ctsm5.3.017   slevis 01/09/2025 Merge tmp-241219 branch to master
+tmp-241219.n03.ctsm5.3.016  01/09/2025 Bug fix for izumi nag tests to pass (slevis)
+tmp-241219.n02.ctsm5.3.016  01/08/2025 FATES hydro test update (glemieux)
+tmp-241219.n01.ctsm5.3.016  12/24/2024 Merge b4b-dev (slevis)
+       ctsm5.3.016     erik 12/19/2024 Rpointer files for restart now have the simulation date in the filename
+       ctsm5.3.015     erik 12/18/2024 Update cdeps with cam7 nextsw cday changes
        ctsm5.3.014     erik 12/03/2024 Bring in several fixes for testing in the previous cesm3_0_beta03/04 tags
        ctsm5.3.013     erik 11/26/2024 Merge b4b-dev
        ctsm5.3.012  afoster 11/13/2024 update fates tag
diff --git a/python/ctsm/crop_calendars/cropcal_module.py b/python/ctsm/crop_calendars/cropcal_module.py
index 719d352665..3ea084e1d2 100644
--- a/python/ctsm/crop_calendars/cropcal_module.py
+++ b/python/ctsm/crop_calendars/cropcal_module.py
@@ -443,10 +443,7 @@ def import_output(
         )
 
     # Convert time axis to integer year, saving original as 'cftime'
-    this_ds_gs = this_ds_gs.assign_coords(
-        {"cftime": this_ds["time_bounds"].isel({"hist_interval": 0})}
-    )
-    this_ds_gs = this_ds_gs.assign_coords({"time": [t.year for t in this_ds_gs["cftime"].values]})
+    this_ds_gs = convert_time_to_int_year(filename, this_ds, this_ds_gs)
 
     # Get number of harvests
     this_ds_gs["NHARVESTS"] = (this_ds_gs["GDDHARV_PERHARV"] > 0).sum(dim="mxharvests")
@@ -458,6 +455,35 @@ def import_output(
     return this_ds_gs, any_bad
 
 
+def convert_time_to_int_year(filename, this_ds, this_ds_gs):
+    """
+    Convert time axis to integer year, saving original as 'cftime'
+    """
+    if "time_bounds" in this_ds:
+        # Always true before PR #2838, when even files with all instantaneous variables got
+        # time_bounds saved. After that PR (and before the segregation of instantaneous and other
+        # variables onto separate files), files with an instantaneous variable first in their list
+        # do not get time_bounds saved.
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"cftime": this_ds["time_bounds"].isel({"hist_interval": 0})}
+        )
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"time": [t.year for t in this_ds_gs["cftime"].values]}
+        )
+    elif this_ds["time"].attrs["long_name"] == "time at end of time step":
+        # This is an "instantaneous file."
+        this_ds_gs = this_ds_gs.assign_coords({"cftime": this_ds["time"]})
+        this_ds_gs = this_ds_gs.assign_coords(
+            {"time": [t.year - 1 for t in this_ds_gs["cftime"].values]}
+        )
+    else:
+        raise RuntimeError(
+            f"{filename} is neither an instantaneous nor a combined/non-instantaneous file."
+        )
+
+    return this_ds_gs
+
+
 def handle_zombie_crops(this_ds):
     """
     When doing transient runs, it's somehow possible for crops in newly-active patches to be
diff --git a/python/ctsm/crop_calendars/generate_gdds_functions.py b/python/ctsm/crop_calendars/generate_gdds_functions.py
index 81c71e2a51..e83eb7bb50 100644
--- a/python/ctsm/crop_calendars/generate_gdds_functions.py
+++ b/python/ctsm/crop_calendars/generate_gdds_functions.py
@@ -60,6 +60,7 @@ def error(logger, string):
     """
     Simultaneously print ERROR messages to console and to log file
     """
+    print(string)
     logger.error(string)
     raise RuntimeError(string)
 
@@ -271,7 +272,7 @@ def import_and_process_1yr(
     else:
         chunks = None
 
-    # Get h2 file (list)
+    # Get h1 file (list)
     h1_pattern = os.path.join(indir, "*h1.*.nc")
     h1_filelist = glob.glob(h1_pattern)
     if not h1_filelist:
@@ -551,13 +552,14 @@ def import_and_process_1yr(
     log(logger, "   Importing accumulated GDDs...")
     clm_gdd_var = "GDDACCUM"
     my_vars = [clm_gdd_var, "GDDHARV"]
-    pattern = os.path.join(indir, f"*h2.{this_year-1}-01-01*.nc")
-    h2_files = glob.glob(pattern)
-    if not h2_files:
-        pattern = os.path.join(indir, f"*h2.{this_year-1}-01-01*.nc.base")
+    patterns = [f"*h2.{this_year-1}-01*.nc", f"*h2.{this_year-1}-01*.nc.base"]
+    for p in patterns:
+        pattern = os.path.join(indir, p)
         h2_files = glob.glob(pattern)
-        if not h2_files:
-            error(logger, f"No files found matching pattern '*h2.{this_year-1}-01-01*.nc(.base)'")
+        if h2_files:
+            break
+    if not h2_files:
+        error(logger, f"No files found matching patterns: {patterns}")
     h2_ds = import_ds(
         h2_files,
         my_vars=my_vars,
diff --git a/python/ctsm/lilac_build_ctsm.py b/python/ctsm/lilac_build_ctsm.py
index d7b92517c5..c1350005a8 100644
--- a/python/ctsm/lilac_build_ctsm.py
+++ b/python/ctsm/lilac_build_ctsm.py
@@ -830,7 +830,7 @@ def _stage_runtime_inputs(build_dir, no_pnetcdf):
 
     shutil.copyfile(
         src=os.path.join(
-            path_to_ctsm_root(), "cime_config", "usermods_dirs", "lilac", "user_nl_ctsm"
+            path_to_ctsm_root(), "cime_config", "usermods_dirs", "clm", "lilac", "user_nl_ctsm"
         ),
         dst=os.path.join(build_dir, _RUNTIME_INPUTS_DIRNAME, "user_nl_ctsm"),
     )
diff --git a/python/ctsm/site_and_regional/modify_singlept_site_neon.py b/python/ctsm/site_and_regional/modify_singlept_site_neon.py
index 5c28bd3582..d0a86a9e3c 100755
--- a/python/ctsm/site_and_regional/modify_singlept_site_neon.py
+++ b/python/ctsm/site_and_regional/modify_singlept_site_neon.py
@@ -60,7 +60,7 @@
 
 # -- valid neon sites
 valid = glob.glob(
-    os.path.join(path_to_ctsm_root(), "cime_config", "usermods_dirs", "NEON", "[!d]*")
+    os.path.join(path_to_ctsm_root(), "cime_config", "usermods_dirs", "clm", "NEON", "[!d]*")
 )
 valid_neon_sites = [x[-4:] for x in valid]  # last 4 letters in each string
 
diff --git a/python/ctsm/site_and_regional/neon_site.py b/python/ctsm/site_and_regional/neon_site.py
index 70414d9e5c..73264719ae 100755
--- a/python/ctsm/site_and_regional/neon_site.py
+++ b/python/ctsm/site_and_regional/neon_site.py
@@ -45,7 +45,9 @@ def build_base_case(
     ):
         if user_mods_dirs is None:
             user_mods_dirs = [
-                os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)
+                os.path.join(
+                    self.cesmroot, "cime_config", "usermods_dirs", "clm", "NEON", self.name
+                )
             ]
         case_path = super().build_base_case(cesmroot, output_root, res, compset, user_mods_dirs)
 
@@ -94,7 +96,7 @@ def run_case(
             name of experiment, default False
         """
         user_mods_dirs = [
-            os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "NEON", self.name)
+            os.path.join(self.cesmroot, "cime_config", "usermods_dirs", "clm", "NEON", self.name)
         ]
         tower_type = "NEON"
 
diff --git a/python/ctsm/site_and_regional/plumber2_usermods.py b/python/ctsm/site_and_regional/plumber2_usermods.py
index d98899771b..aba6dfa336 100644
--- a/python/ctsm/site_and_regional/plumber2_usermods.py
+++ b/python/ctsm/site_and_regional/plumber2_usermods.py
@@ -24,7 +24,7 @@ def write_usermods(
     Write information to be added to user mods
     """
 
-    site_dir = os.path.join("../../cime_config/usermods_dirs/PLUMBER2/", site)
+    site_dir = os.path.join("../../cime_config/usermods_dirs/clm/PLUMBER2/", site)
 
     if not os.path.isdir(site_dir):
         os.makedirs(site_dir, exist_ok=True)
diff --git a/python/ctsm/site_and_regional/run_neon.py b/python/ctsm/site_and_regional/run_neon.py
index 3acbf435b1..ac72554d46 100755
--- a/python/ctsm/site_and_regional/run_neon.py
+++ b/python/ctsm/site_and_regional/run_neon.py
@@ -177,7 +177,7 @@ def main(description):
     # The [!Fd]* portion means that we won't retrieve cases that start with:
     # F (FATES) or d (default). We should be aware of adding cases that start with these.
     valid_neon_sites = glob.glob(
-        os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", "[!Fd]*")
+        os.path.join(cesmroot, "cime_config", "usermods_dirs", "clm", "NEON", "[!Fd]*")
     )
     valid_neon_sites = sorted([v.split("/")[-1] for v in valid_neon_sites])
 
diff --git a/python/ctsm/site_and_regional/tower_site.py b/python/ctsm/site_and_regional/tower_site.py
index 31c959cac7..2ff8999408 100644
--- a/python/ctsm/site_and_regional/tower_site.py
+++ b/python/ctsm/site_and_regional/tower_site.py
@@ -79,21 +79,50 @@ def build_base_case(
         Args:
         self:
             The NeonSite object
-        base_root (str):
-            root of the base_case CIME
+        cesmroot (str):
+            root of the CESM code to run
+        output_root (str):
+            root of the output directory to write to
         res (str):
             base_case resolution or gridname
         compset (str):
             base case compset
+        user_mods_dirs (str):
+            path to the user-mod-directory to use
         overwrite (bool) :
             Flag to overwrite the case if exists
+        setup_only (bool) :
+            Flag to only do the setup phase
         """
+        #
+        # Error checking on the input
+        #
+        if not os.path.isdir(cesmroot):
+            abort("Input cesmroot directory does NOT exist: " + str(cesmroot))
+        if not isinstance(res, str):
+            abort("Input res is NOT a string as expected: " + str(res))
+        if not isinstance(compset, str):
+            abort("Input compset is NOT a string as expected: " + str(compset))
+        if not isinstance(overwrite, bool):
+            abort("Input compset is NOT a boolean as expected: " + str(compset))
+        if not isinstance(setup_only, bool):
+            abort("Input setup_only is NOT a boolean as expected: " + str(setup_only))
+        if not isinstance(user_mods_dirs, list):
+            abort("Input user_mods_dirs is NOT a list as expected: " + str(user_mods_dirs))
+        for dir in user_mods_dirs:
+            if not os.path.isdir(dir):
+                abort("Input user_mods_dirs directory does NOT exist: " + str(dir))
+
         print("---- building a base case -------")
         # pylint: disable=attribute-defined-outside-init
         self.base_case_root = output_root
         # pylint: enable=attribute-defined-outside-init
         if not output_root:
             output_root = os.getcwd()
+
+        if not os.path.isdir(output_root):
+            abort("Input output_root directory does NOT exist: " + str(output_root))
+
         case_path = os.path.join(output_root, self.name)
 
         logger.info("base_case_name : %s", self.name)
diff --git a/python/ctsm/test/test_sys_modify_singlept_site_neon.py b/python/ctsm/test/test_sys_modify_singlept_site_neon.py
index 76a78c3db5..ed7e52ed38 100755
--- a/python/ctsm/test/test_sys_modify_singlept_site_neon.py
+++ b/python/ctsm/test/test_sys_modify_singlept_site_neon.py
@@ -55,7 +55,7 @@ def test_modify_site(self):
         sys.argv = [
             "modify_singlept_site_neon",
             "--neon_site",
-            path_to_ctsm_root() + "/ctsm/cime_config/usermods_dirs/NEON/ABBY",
+            path_to_ctsm_root() + "/ctsm/cime_config/usermods_dirs/clm/NEON/ABBY",
         ]
         # TODO: the above requires a full path instead of site name
         #       because of how run_neon is configured.
diff --git a/python/ctsm/test/test_unit_neon_arg_parse.py b/python/ctsm/test/test_unit_neon_arg_parse.py
index 4a5b0b9e6c..141b41fbc7 100755
--- a/python/ctsm/test/test_unit_neon_arg_parse.py
+++ b/python/ctsm/test/test_unit_neon_arg_parse.py
@@ -60,7 +60,7 @@ def test_function(self):
         description = ""
         cesmroot = path_to_ctsm_root()
         valid_neon_sites = glob.glob(
-            os.path.join(cesmroot, "cime_config", "usermods_dirs", "NEON", "[!d]*")
+            os.path.join(cesmroot, "cime_config", "usermods_dirs", "clm", "NEON", "[!d]*")
         )
         valid_neon_sites = sorted([v.split("/")[-1] for v in valid_neon_sites])
         parsed_arguments = get_parser(sys.argv, description, valid_neon_sites)
diff --git a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
index fdf9466763..bde92fcf18 100755
--- a/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
+++ b/python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py
@@ -202,11 +202,11 @@ def main():
         "ultra_hi_res_no_crop": ["mpasa15", "mpasa3p75"],
         "standard_res": ["360x720cru", "0.9x1.25", "1.9x2.5", "C96", "mpasa120"],
         "standard_res_no_f09": ["360x720cru", "1.9x2.5", "C96", "mpasa120"],
-        "low_res": ["4x5", "10x15", "ne3np4.pg3"],
+        "low_res": ["4x5", "10x15", "ne3np4.pg3", "ne3np4"],
         "mpasa480": ["mpasa480"],
         "nldas_res": ["0.125nldas2"],
         "5x5_amazon": ["5x5_amazon"],
-        "ne3": ["ne3np4.pg3"],
+        "ne3": ["ne3np4", "ne3np4.pg3"],
         "ne16": ["ne16np4.pg3"],
         "ne30": ["ne30np4.pg3", "ne30np4.pg2", "ne30np4"],
         "ne0np4": [
diff --git a/share b/share
index f6f31fd61c..c5e7603c29 160000
--- a/share
+++ b/share
@@ -1 +1 @@
-Subproject commit f6f31fd61cb8f80aee97311fcca64b3e26b0202c
+Subproject commit c5e7603c29ea5e2fe93ca16d88bc9c7f16175bcd
diff --git a/src/biogeochem/CNFUNMod.F90 b/src/biogeochem/CNFUNMod.F90
index a6614fe4b9..0af5efe580 100644
--- a/src/biogeochem/CNFUNMod.F90
+++ b/src/biogeochem/CNFUNMod.F90
@@ -26,7 +26,7 @@ module CNFUNMod
   use pftconMod                       , only : pftcon, npcropmin
   use decompMod                       , only : bounds_type
   use clm_varctl                      , only : use_nitrif_denitrif,use_flexiblecn
-    use CNSharedParamsMod               , only : use_matrixcn
+  use CNSharedParamsMod               , only : use_matrixcn
   use abortutils                      , only : endrun
   use CNVegstateType                  , only : cnveg_state_type
   use CNVegCarbonStateType            , only : cnveg_carbonstate_type
@@ -48,12 +48,18 @@ module CNFUNMod
   private
 !
 ! !PUBLIC MEMBER FUNCTIONS:
+  public :: CNFUNReadNML  ! Read in namelist variables
   public:: readParams            ! Read in parameters needed for FUN
   public:: CNFUNInit             ! FUN calculation initialization
   public:: CNFUN                 ! Run FUN
   
+  character(len=25) :: nfix_method  ! choice of nfix parameterization
+
   type, private :: params_type
      real(r8) :: ndays_off       ! number of days to complete leaf offset
+     real(r8), allocatable :: nfix_tmin(:)  ! A BNF parameter
+     real(r8), allocatable :: nfix_topt(:)  ! A BNF parameter
+     real(r8), allocatable :: nfix_tmax(:)  ! A BNF parameter
   end type params_type   
  
   !
@@ -82,17 +88,73 @@ module CNFUNMod
  contains
 !--------------------------------------------------------------------
    !---
+ subroutine CNFUNReadNML(NLFilename)
+    !
+    ! !DESCRIPTION:
+    ! Read in namelist variables
+    !
+    ! !USES:
+    use fileutils  , only : getavu, relavu, opnfil
+    use shr_nl_mod , only : shr_nl_find_group_name
+    use spmdMod    , only : masterproc, mpicom
+    use shr_mpi_mod, only : shr_mpi_bcast
+    use clm_varctl , only : iulog
+    use spmdMod    , only : MPI_CHARACTER
+    !
+    ! !ARGUMENTS:
+    character(len=*), intent(in) :: NLFilename  ! Namelist filename
+    !
+    ! !LOCAL VARIABLES:
+    integer :: ierr   ! error code
+    integer :: unitn  ! unit for namelist file
+
+    character(len=*), parameter :: nmlname = 'cnfun_inparm'
+    !-----------------------------------------------------------------------
+
+    namelist /cnfun_inparm/ nfix_method
+
+    ! Initialize options to default values, in case they are not specified in
+    ! the namelist
+
+    if (masterproc) then
+       unitn = getavu()
+       write(iulog,*) 'Read in '//nmlname//' namelist'
+       call opnfil (NLFilename, unitn, 'F')
+       call shr_nl_find_group_name(unitn, nmlname, status=ierr)
+       if (ierr == 0) then
+          read(unitn, nml=cnfun_inparm, iostat=ierr)
+          if (ierr /= 0) then
+             call endrun(msg="ERROR reading "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
+          end if
+       else
+          call endrun(msg="ERROR finding "//nmlname//"namelist"//errmsg(sourcefile, __LINE__))
+       end if
+       call relavu( unitn )
+    end if
+
+    call mpi_bcast (nfix_method, len(nfix_method), MPI_CHARACTER, 0, mpicom, ierr)
+
+    if (masterproc) then
+       write(iulog,*) ' '
+       write(iulog,*) nmlname//' settings:'
+       write(iulog,nml=cnfun_inparm)
+       write(iulog,*) ' '
+    end if
+
+ end subroutine CNFUNReadNML
+
+  !-----------------------------------------------------------------------
  subroutine readParams ( ncid )
   !
   ! !USES:
   use ncdio_pio , only : file_desc_t,ncd_io
+  use clm_varpar, only : mxpft
 
   ! !ARGUMENTS:
   implicit none
   type(file_desc_t),intent(inout) :: ncid   ! pio netCDF file id
   !
   ! !LOCAL VARIABLES:
-  character(len=32)  :: subname = 'CNFUNParamsType'
   character(len=100) :: errCode = '-Error reading in parameters file:'
   logical            :: readv ! has variable been read in or not
   real(r8)           :: tempr ! temporary to read in parameter
@@ -107,6 +169,20 @@ subroutine readParams ( ncid )
     if ( .not. readv ) call endrun( msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
     params_inst%ndays_off=tempr
 
+    allocate(params_inst%nfix_tmin(0:mxpft))
+    tString='nfix_tmin'
+    call ncd_io(trim(tString), params_inst%nfix_tmin(:), 'read', ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
+
+    allocate(params_inst%nfix_topt(0:mxpft))
+    tString='nfix_topt'
+    call ncd_io(trim(tString), params_inst%nfix_topt(:), 'read', ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
+
+    allocate(params_inst%nfix_tmax(0:mxpft))
+    tString='nfix_tmax'
+    call ncd_io(trim(tString), params_inst%nfix_tmax(:), 'read', ncid, readvar=readv)
+    if ( .not. readv ) call endrun(msg=trim(errCode)//trim(tString)//errMsg(sourcefile, __LINE__))
 
  end subroutine readParams
 
@@ -135,7 +211,6 @@ subroutine CNFUNInit (bounds,cnveg_state_inst,cnveg_carbonstate_inst,cnveg_nitro
   integer           :: nstep                    ! time step number
   integer           :: nstep_fun                ! Number of
   !  atmospheric timesteps between calls to FUN
-  character(len=32) :: subname = 'CNFUNInit'
 !--------------------------------------------------------------------
   !---
 
@@ -290,7 +365,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
   real(r8)  :: litterfall_n(bounds%begp:bounds%endp)                 ! N loss based on the leafc to litter   (gN/m2)  
   real(r8)  :: litterfall_n_step(bounds%begp:bounds%endp,1:nstp)       ! N loss based on the leafc to litter   (gN/m2)
   real(r8)  :: litterfall_c_step(bounds%begp:bounds%endp,1:nstp)       ! N loss based on the leafc to litter   (gN/m2)
-  real(r8)  :: tc_soisno(bounds%begc:bounds%endc,1:nlevdecomp)       ! Soil temperature            (degrees Celsius)
+  real(r8)  :: tc_soisno(bounds%begc:bounds%endc,1:nlevdecomp)       ! Soil temperature                      (degrees Celsius)
   real(r8)  :: npp_remaining(bounds%begp:bounds%endp,1:nstp)         ! A temporary variable for npp_remaining(gC/m2) 
   real(r8)  :: n_passive_step(bounds%begp:bounds%endp,1:nstp)        ! N taken up by transpiration at substep(gN/m2)
   real(r8)  :: n_passive_acc(bounds%begp:bounds%endp)                ! N acquired by passive uptake          (gN/m2)
@@ -460,14 +535,13 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
   real(r8) :: total_N_resistance   ! C to of N for whole soil -leaf
   !  pathway
   real(r8) :: free_RT_frac=0.0_r8  !fraction of N retranslocation which is automatic/free.
-  !  SHould be made into a PFT parameter. 
+  !  Should be made into a PFT parameter.
   
   real(r8) :: paid_for_n_retrans
   real(r8) :: free_n_retrans
   real(r8) :: total_c_spent_retrans
   real(r8) :: total_c_accounted_retrans
 
-  
   !------end of not_use_nitrif_denitrif------!
   !--------------------------------------------------------------------
   !------------
@@ -495,9 +569,10 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
   !  fixers, 2 for non fixers. This will become redundant with the
   !   'fixer' parameter if it works. 
   
+  character(len=100) :: errCode
   !--------------------------------------------------------------------
   !---------------------------------
-  associate(ivt                    => patch%itype                                          , & ! Input:   [integer  (:) ]  p
+  associate(ivt                 => patch%itype                                          , & ! Input:   [integer  (:) ]  p
          leafcn                 => pftcon%leafcn                                        , & ! Input:   leaf C:N (gC/gN)
          season_decid           => pftcon%season_decid                                  , & ! Input:   binary flag for seasonal
          ! -deciduous leaf habit (0 or 1)
@@ -522,10 +597,10 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
          perecm                 => pftcon%perecm                                        , & ! Input:   The fraction of ECM
          ! -associated PFT 
          grperc                 => pftcon%grperc                                        , & ! Input:   growth percentage
-         fun_cn_flex_a           => pftcon%fun_cn_flex_a                                , & ! Parameter a of FUN-flexcn link code (def 5)
-         fun_cn_flex_b           => pftcon%fun_cn_flex_b                                , & ! Parameter b of FUN-flexcn link code (def 200)
-         fun_cn_flex_c           => pftcon%fun_cn_flex_c                                , & ! Parameter b of FUN-flexcn link code (def 80)         
-         FUN_fracfixers          => pftcon%FUN_fracfixers                               , & ! Fraction of C that can be used for fixation.    
+         fun_cn_flex_a          => pftcon%fun_cn_flex_a                                 , & ! Parameter a of FUN-flexcn link code (def 5)
+         fun_cn_flex_b          => pftcon%fun_cn_flex_b                                 , & ! Parameter b of FUN-flexcn link code (def 200)
+         fun_cn_flex_c          => pftcon%fun_cn_flex_c                                 , & ! Parameter b of FUN-flexcn link code (def 80)
+         FUN_fracfixers         => pftcon%FUN_fracfixers                                , & ! Fraction of C that can be used for fixation.
          leafcn_offset          => cnveg_state_inst%leafcn_offset_patch                 , & ! Output:
          !  [real(r8)  (:)]  Leaf C:N used by FUN
          plantCN                => cnveg_state_inst%plantCN_patch                       , & ! Output:  [real(r8)  (:)]  Plant
@@ -1041,9 +1116,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
          npp_to_nonmyc_nh4(:)        = 0.0_r8
          npp_to_fixation(:)          = 0.0_r8
          npp_to_retrans(:)           = 0.0_r8
-     
-  
-      
+
          unmetDemand              = .TRUE.
          plant_ndemand_pool_step(p,istp)   = plant_ndemand_pool(p)    * permyc(p,istp) 
          npp_remaining(p,istp)             = availc_pool(p)           * permyc(p,istp)
@@ -1051,32 +1124,42 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
   
          ! if (plant_ndemand_pool_step(p,istp) .gt. 0._r8) then   !
             !  plant_ndemand_pool_step > 0.0
-            
+         
             do j = 1, nlevdecomp
                tc_soisno(c,j)          = t_soisno(c,j)  -   tfrz
+
                if(pftcon%c3psn(patch%itype(p)).eq.1)then
                  fixer=1
                else
                  fixer=0
                endif
-               costNit(j,icostFix)     = fun_cost_fix(fixer,a_fix(ivt(p)),b_fix(ivt(p))&
-               ,c_fix(ivt(p)) ,big_cost,crootfr(p,j),s_fix(ivt(p)),tc_soisno(c,j))
+
+               select case (nfix_method)
+               case ('Houlton')
+                  costNit(j,icostFix) = fun_cost_fix(fixer, &
+                          a_fix(ivt(p)), b_fix(ivt(p)), c_fix(ivt(p)), &
+                          big_cost, crootfr(p,j), s_fix(ivt(p)), tc_soisno(c,j))
+               case ('Bytnerowicz')  ! no acclimation calculation
+                  costNit(j,icostFix) = fun_cost_fix_Bytnerowicz_noAcc(fixer, &
+                          params_inst%nfix_tmin(ivt(p)), params_inst%nfix_topt(ivt(p)), params_inst%nfix_tmax(ivt(p)), &
+                          big_cost,crootfr(p,j), s_fix(ivt(p)), tc_soisno(c,j))
+               case default
+                  errCode = ' ERROR: unknown nfix_method value: ' // nfix_method
+                  call endrun( msg=trim(errCode) // errMsg(sourcefile, __LINE__))
+               end select
+
             end do
             cost_fix(p,1:nlevdecomp)      = costNit(:,icostFix)
             
              
             !--------------------------------------------------------------------
-            !------------
             !         If passive uptake is insufficient, consider fixation,
             !          mycorrhizal 
             !         non-mycorrhizal, storage, and retranslocation.
             !--------------------------------------------------------------------
-            !------------
             !--------------------------------------------------------------------
-            !------------
             !          Costs of active uptake.
             !--------------------------------------------------------------------
-            !------------
             !------Mycorrhizal Uptake Cost-----------------!
             do j = 1,nlevdecomp
                rootc_dens_step            = rootc_dens(p,j) *  permyc(p,istp)
@@ -1608,6 +1691,44 @@ real(r8) function fun_cost_fix(fixer,a_fix,b_fix,c_fix,big_cost,crootfr,s_fix, t
   end if    ! ends up with the fixer or non-fixer decision
   
   end function fun_cost_fix
+
+
+!=========================================================================================
+  real(r8) function fun_cost_fix_Bytnerowicz_noAcc(fixer,nfix_tmin,nfix_topt,nfix_tmax,big_cost,crootfr,s_fix, tc_soisno)
+
+! Description:
+!   Calculate the cost of fixing N by nodules.
+! Code Description:
+!   This code is written to CTSM5.1 by Will Wieder 11/17/2022, modified for CLM6 11/01/2024
+
+  implicit none
+!--------------------------------------------------------------------------
+! Function result.
+!--------------------------------------------------------------------------
+! real(r8) , intent(out) :: cost_of_n   !!! cost of fixing N (kgC/kgN)
+!--------------------------------------------------------------------------
+  integer,  intent(in) :: fixer     ! flag indicating if plant is a fixer
+                                    ! 1=yes, otherwise no.
+  real(r8), intent(in) :: nfix_tmin ! As in Bytnerowicz et al. (2022)
+  real(r8), intent(in) :: nfix_topt ! As in Bytnerowicz et al. (2022)
+  real(r8), intent(in) :: nfix_tmax ! As in Bytnerowicz et al. (2022)
+  real(r8), intent(in) :: big_cost  ! an arbitrary large cost (gC/gN)
+  real(r8), intent(in) :: crootfr   ! fraction of roots for carbon that are in this layer
+  real(r8), intent(in) :: s_fix     ! Inverts the temperature function for a cost function
+  real(r8), intent(in) :: tc_soisno ! soil temperature (degrees Celsius)
+
+  if (fixer == 1 .and. crootfr > 1.e-6_r8 .and. tc_soisno > nfix_tmin .and. tc_soisno < nfix_tmax) then
+     fun_cost_fix_Bytnerowicz_noAcc  = (-s_fix) / ( ((nfix_tmax-tc_soisno)/(nfix_tmax-nfix_topt))*&
+                                                  ( ((tc_soisno-nfix_tmin)/(nfix_topt-nfix_tmin))**&
+                                                    ((nfix_topt- nfix_tmin)/(nfix_tmax-nfix_topt)) ) )
+     fun_cost_fix_Bytnerowicz_noAcc = min(fun_cost_fix_Bytnerowicz_noAcc,big_cost)
+  else
+     fun_cost_fix_Bytnerowicz_noAcc = big_cost
+  end if    ! ends up with the fixer or non-fixer decision
+
+  end function fun_cost_fix_Bytnerowicz_noAcc
+!=========================================================================================
+
 !=========================================================================================
   real(r8) function fun_cost_active(sminn_layer,big_cost,kc_active,kn_active,rootc_dens,crootfr,smallValue)         
 
diff --git a/src/biogeochem/CNPhenologyMod.F90 b/src/biogeochem/CNPhenologyMod.F90
index 73eadbb1a9..5ad4fb1157 100644
--- a/src/biogeochem/CNPhenologyMod.F90
+++ b/src/biogeochem/CNPhenologyMod.F90
@@ -392,19 +392,7 @@ subroutine CNPhenology (bounds, num_soilc, filter_soilc, num_soilp, &
             soilstate_inst, temperature_inst, atm2lnd_inst, wateratm2lndbulk_inst, cnveg_state_inst, &
             cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst)
 
-       ! BACKWARDS_COMPATIBILITY(wjs, 2022-02-03) Old restart files generated at the end
-       ! of the year can indicate that a crop was panted on Jan 1, because that used to be
-       ! the time given to the last time step of the year. This would cause problems if we
-       ! ran CropPhenology in time step 0, because now time step 0 is labeled as Dec 31,
-       ! so CropPhenology would see the crop as having been planted 364 days ago, and so
-       ! would want to harvest this newly-planted crop. To avoid this situation, we avoid
-       ! calling CropPhenology on time step 0.
-       !
-       ! This .not. is_first_step() condition can be removed either when we can rely on
-       ! all restart files having been generated with
-       ! https://github.com/ESCOMP/CTSM/issues/1623 resolved, or we stop having a time
-       ! step 0 (https://github.com/ESCOMP/CTSM/issues/925).
-       if (num_pcropp > 0 .and. .not. is_first_step()) then
+       if (num_pcropp > 0) then
           call CropPhenology(num_pcropp, filter_pcropp, &
                waterdiagnosticbulk_inst, temperature_inst, crop_inst, canopystate_inst, cnveg_state_inst, &
                cnveg_carbonstate_inst, cnveg_nitrogenstate_inst, cnveg_carbonflux_inst, cnveg_nitrogenflux_inst, &
diff --git a/src/biogeochem/CNVegetationFacade.F90 b/src/biogeochem/CNVegetationFacade.F90
index 706d52da27..dd20ce50a2 100644
--- a/src/biogeochem/CNVegetationFacade.F90
+++ b/src/biogeochem/CNVegetationFacade.F90
@@ -1285,7 +1285,7 @@ subroutine EndOfTimeStepVegDynamics(this, bounds, num_natvegp, filter_natvegp, &
        ! Call dv (dynamic vegetation) at last time step of year
 
        call t_startf('d2dgvm')
-       if (is_end_curr_year() .and. .not. is_first_step())  then
+       if (is_end_curr_year())  then
 
           ! Get date info.  kyr is used in lpj().  At end of first year, kyr = 2.
           call get_curr_date(yr, mon, day, sec)
@@ -1337,7 +1337,7 @@ subroutine WriteHistory(this, bounds)
 
     ! Write to CNDV history buffer if appropriate
     if (use_cndv) then
-       if (is_end_curr_year() .and. .not. is_first_step())  then
+       if (is_end_curr_year())  then
           call t_startf('clm_drv_io_hdgvm')
           call CNDVHist( bounds, this%dgvs_inst )
           if (masterproc) write(iulog,*) 'Annual CNDV calculations are complete'
diff --git a/src/biogeochem/CropType.F90 b/src/biogeochem/CropType.F90
index 0f650a4a9f..54395c4668 100644
--- a/src/biogeochem/CropType.F90
+++ b/src/biogeochem/CropType.F90
@@ -930,7 +930,7 @@ subroutine CropIncrementYear (this, num_pcropp, filter_pcropp)
     ! Update nyrs when it's the end of the year (unless it's the very start of the
     ! run). This assumes that, if this patch is active at the end of the year, then it was
     ! active for the whole year.
-    if ((kmo == 1 .and. kda == 1 .and. mcsec == 0) .and. .not. is_first_step()) then
+    if ((kmo == 1 .and. kda == 1 .and. mcsec == 0)) then
        do fp = 1, num_pcropp
           p = filter_pcropp(fp)
 
diff --git a/src/biogeochem/SatellitePhenologyMod.F90 b/src/biogeochem/SatellitePhenologyMod.F90
index 3e9341f430..9412d34586 100644
--- a/src/biogeochem/SatellitePhenologyMod.F90
+++ b/src/biogeochem/SatellitePhenologyMod.F90
@@ -13,7 +13,7 @@ module SatellitePhenologyMod
   use shr_log_mod  , only : errMsg => shr_log_errMsg
   use decompMod    , only : bounds_type
   use abortutils   , only : endrun
-  use clm_varctl   , only : iulog, use_lai_streams
+  use clm_varctl   , only : iulog, use_lai_streams, single_column
   use perf_mod     , only : t_startf, t_stopf
   use spmdMod      , only : masterproc, mpicom, iam
   use laiStreamMod , only : lai_init, lai_advance, lai_interp
@@ -311,7 +311,7 @@ subroutine readAnnualVegetation (bounds, canopystate_inst)
     call ncd_pio_openfile (ncid, trim(locfn), 0)
     call ncd_inqfdims (ncid, isgrid2d, ni, nj, ns)
 
-    if (ldomain%ns /= ns .or. ldomain%ni /= ni .or. ldomain%nj /= nj) then
+    if (.not. single_column .and. (ldomain%ns /= ns .or. ldomain%ni /= ni .or. ldomain%nj /= nj)) then
        write(iulog,*)trim(subname), 'ldomain and input file do not match dims '
        write(iulog,*)trim(subname), 'ldomain%ni,ni,= ',ldomain%ni,ni
        write(iulog,*)trim(subname), 'ldomain%nj,nj,= ',ldomain%nj,nj
diff --git a/src/biogeochem/dynCNDVMod.F90 b/src/biogeochem/dynCNDVMod.F90
index 76382d175b..d95313772a 100644
--- a/src/biogeochem/dynCNDVMod.F90
+++ b/src/biogeochem/dynCNDVMod.F90
@@ -99,7 +99,7 @@ subroutine dynCNDV_interp( bounds, dgvs_inst)
           patch%wtcol(p)   = dgvs_inst%fpcgrid_patch(p) + &
                     wt1 * (dgvs_inst%fpcgridold_patch(p) - dgvs_inst%fpcgrid_patch(p))
 
-          if (mon==1 .and. day==1 .and. sec==dtime .and. nstep>0) then
+          if (mon==1 .and. day==1 .and. sec==dtime) then
              dgvs_inst%fpcgridold_patch(p) = dgvs_inst%fpcgrid_patch(p)
           end if
        end if
diff --git a/src/biogeophys/UrbanParamsType.F90 b/src/biogeophys/UrbanParamsType.F90
index 4b7b80e4fe..c6443897fe 100644
--- a/src/biogeophys/UrbanParamsType.F90
+++ b/src/biogeophys/UrbanParamsType.F90
@@ -9,9 +9,9 @@ module UrbanParamsType
   use shr_log_mod  , only : errMsg => shr_log_errMsg
   use abortutils   , only : endrun
   use decompMod    , only : bounds_type, subgrid_level_gridcell, subgrid_level_landunit
-  use clm_varctl   , only : iulog, fsurdat
+  use clm_varctl   , only : iulog, fsurdat, single_column
   use clm_varcon   , only : grlnd, spval
-  use LandunitType , only : lun                
+  use LandunitType , only : lun
   !
   implicit none
   save
@@ -26,21 +26,21 @@ module UrbanParamsType
   !
   ! !PRIVATE TYPE
   type urbinp_type
-     real(r8), pointer :: canyon_hwr      (:,:)  
-     real(r8), pointer :: wtlunit_roof    (:,:)  
-     real(r8), pointer :: wtroad_perv     (:,:)  
-     real(r8), pointer :: em_roof         (:,:)   
-     real(r8), pointer :: em_improad      (:,:)  
-     real(r8), pointer :: em_perroad      (:,:)  
-     real(r8), pointer :: em_wall         (:,:)  
-     real(r8), pointer :: alb_roof_dir    (:,:,:)  
-     real(r8), pointer :: alb_roof_dif    (:,:,:)  
-     real(r8), pointer :: alb_improad_dir (:,:,:)  
-     real(r8), pointer :: alb_improad_dif (:,:,:)  
-     real(r8), pointer :: alb_perroad_dir (:,:,:)  
-     real(r8), pointer :: alb_perroad_dif (:,:,:)  
-     real(r8), pointer :: alb_wall_dir    (:,:,:)  
-     real(r8), pointer :: alb_wall_dif    (:,:,:)  
+     real(r8), pointer :: canyon_hwr      (:,:)
+     real(r8), pointer :: wtlunit_roof    (:,:)
+     real(r8), pointer :: wtroad_perv     (:,:)
+     real(r8), pointer :: em_roof         (:,:)
+     real(r8), pointer :: em_improad      (:,:)
+     real(r8), pointer :: em_perroad      (:,:)
+     real(r8), pointer :: em_wall         (:,:)
+     real(r8), pointer :: alb_roof_dir    (:,:,:)
+     real(r8), pointer :: alb_roof_dif    (:,:,:)
+     real(r8), pointer :: alb_improad_dir (:,:,:)
+     real(r8), pointer :: alb_improad_dif (:,:,:)
+     real(r8), pointer :: alb_perroad_dir (:,:,:)
+     real(r8), pointer :: alb_perroad_dif (:,:,:)
+     real(r8), pointer :: alb_wall_dir    (:,:,:)
+     real(r8), pointer :: alb_wall_dif    (:,:,:)
      real(r8), pointer :: ht_roof         (:,:)
      real(r8), pointer :: wind_hgt_canyon (:,:)
      real(r8), pointer :: tk_wall         (:,:,:)
@@ -92,14 +92,14 @@ module UrbanParamsType
      real(r8), pointer     :: eflx_traffic_factor (:)   ! lun multiplicative traffic factor for sensible heat flux from urban traffic (-)
    contains
 
-     procedure, public :: Init 
-     
+     procedure, public :: Init
+
   end type urbanparams_type
   !
   ! !Urban control variables
-  character(len= *), parameter, public :: urban_hac_off = 'OFF'                
-  character(len= *), parameter, public :: urban_hac_on =  'ON'                 
-  character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT'  
+  character(len= *), parameter, public :: urban_hac_off = 'OFF'
+  character(len= *), parameter, public :: urban_hac_on =  'ON'
+  character(len= *), parameter, public :: urban_wasteheat_on = 'ON_WASTEHEAT'
   character(len= 16), public           :: urban_hac = urban_hac_off
   logical, public                      :: urban_explicit_ac = .true.  ! whether to use explicit, time-varying AC adoption rate
   logical, public                      :: urban_traffic = .false.     ! urban traffic fluxes
@@ -112,7 +112,7 @@ module UrbanParamsType
 
   character(len=*), parameter, private :: sourcefile = &
        __FILE__
-  !----------------------------------------------------------------------- 
+  !-----------------------------------------------------------------------
 
 contains
 
@@ -132,11 +132,11 @@ subroutine Init(this, bounds)
     !
     ! !ARGUMENTS:
     class(urbanparams_type) :: this
-    type(bounds_type)      , intent(in)    :: bounds  
+    type(bounds_type)      , intent(in)    :: bounds
     !
     ! !LOCAL VARIABLES:
     integer             :: j,l,c,p,g       ! indices
-    integer             :: nc,fl,ib        ! indices 
+    integer             :: nc,fl,ib        ! indices
     integer             :: dindx           ! urban density type index
     integer             :: ier             ! error status
     real(r8)            :: sumvf           ! sum of view factors for wall or road
@@ -182,12 +182,12 @@ subroutine Init(this, bounds)
     allocate(this%em_perroad          (begl:endl))          ; this%em_perroad          (:)   = nan
     allocate(this%em_wall             (begl:endl))          ; this%em_wall             (:)   = nan
     allocate(this%alb_roof_dir        (begl:endl,numrad))   ; this%alb_roof_dir        (:,:) = nan
-    allocate(this%alb_roof_dif        (begl:endl,numrad))   ; this%alb_roof_dif        (:,:) = nan    
-    allocate(this%alb_improad_dir     (begl:endl,numrad))   ; this%alb_improad_dir     (:,:) = nan       
-    allocate(this%alb_perroad_dir     (begl:endl,numrad))   ; this%alb_perroad_dir     (:,:) = nan       
-    allocate(this%alb_improad_dif     (begl:endl,numrad))   ; this%alb_improad_dif     (:,:) = nan       
-    allocate(this%alb_perroad_dif     (begl:endl,numrad))   ; this%alb_perroad_dif     (:,:) = nan       
-    allocate(this%alb_wall_dir        (begl:endl,numrad))   ; this%alb_wall_dir        (:,:) = nan    
+    allocate(this%alb_roof_dif        (begl:endl,numrad))   ; this%alb_roof_dif        (:,:) = nan
+    allocate(this%alb_improad_dir     (begl:endl,numrad))   ; this%alb_improad_dir     (:,:) = nan
+    allocate(this%alb_perroad_dir     (begl:endl,numrad))   ; this%alb_perroad_dir     (:,:) = nan
+    allocate(this%alb_improad_dif     (begl:endl,numrad))   ; this%alb_improad_dif     (:,:) = nan
+    allocate(this%alb_perroad_dif     (begl:endl,numrad))   ; this%alb_perroad_dif     (:,:) = nan
+    allocate(this%alb_wall_dir        (begl:endl,numrad))   ; this%alb_wall_dir        (:,:) = nan
     allocate(this%alb_wall_dif        (begl:endl,numrad))   ; this%alb_wall_dif        (:,:) = nan
     allocate(this%eflx_traffic_factor (begl:endl))          ; this%eflx_traffic_factor (:)   = nan
 
@@ -261,7 +261,7 @@ subroutine Init(this, bounds)
           !              | \  vsr   / |       |         r   |  | \  vww   /   s
           !              |  \      /  |       h         o   w  |  \      /    k
           !        wall  |   \    /   | wall  |         a   |  |   \    /     y
-          !              |vwr \  / vwr|       |         d   |  |vrw \  / vsw 
+          !              |vwr \  / vwr|       |         d   |  |vrw \  / vsw
           !              ------\/------       -             -  |-----\/-----
           !                   road                                  wall   |
           !              <----- w ---->                                    |
@@ -272,20 +272,20 @@ subroutine Init(this, bounds)
           !                                               vsw = view factor of sky for wall
           !    vsr + vwr + vwr = 1                        vrw + vww + vsw = 1
           !
-          ! Source: Masson, V. (2000) A physically-based scheme for the urban energy budget in 
+          ! Source: Masson, V. (2000) A physically-based scheme for the urban energy budget in
           ! atmospheric models. Boundary-Layer Meteorology 94:357-397
           !
           ! - Calculate urban land unit aerodynamic constants using Macdonald (1998) as used in
           ! Grimmond and Oke (1999)
           ! ---------------------------------------------------------------------------------------
-          
-          ! road -- sky view factor -> 1 as building height -> 0 
+
+          ! road -- sky view factor -> 1 as building height -> 0
           ! and -> 0 as building height -> infinity
 
           this%vf_sr(l) = sqrt(lun%canyon_hwr(l)**2 + 1._r8) - lun%canyon_hwr(l)
           this%vf_wr(l) = 0.5_r8 * (1._r8 - this%vf_sr(l))
 
-          ! one wall -- sky view factor -> 0.5 as building height -> 0 
+          ! one wall -- sky view factor -> 0.5 as building height -> 0
           ! and -> 0 as building height -> infinity
 
           this%vf_sw(l) = 0.5_r8 * (lun%canyon_hwr(l) + 1._r8 - sqrt(lun%canyon_hwr(l)**2+1._r8)) / lun%canyon_hwr(l)
@@ -311,7 +311,7 @@ subroutine Init(this, bounds)
           ! Grimmond and Oke (1999)
           !----------------------------------------------------------------------------------
 
-          ! Calculate plan area index 
+          ! Calculate plan area index
           plan_ai = lun%canyon_hwr(l)/(lun%canyon_hwr(l) + 1._r8)
 
           ! Building shape shortside/longside ratio (e.g. 1 = square )
@@ -344,7 +344,7 @@ subroutine Init(this, bounds)
                   (1 - lun%z_d_town(l) / lun%ht_roof(l)) * frontal_ai)**(-0.5_r8))
           end if
 
-       else ! Not urban point 
+       else ! Not urban point
 
           this%eflx_traffic_factor(l) = spval
           this%t_building_min(l) = spval
@@ -366,7 +366,7 @@ end subroutine Init
   !-----------------------------------------------------------------------
   subroutine UrbanInput(begg, endg, mode)
     !
-    ! !DESCRIPTION: 
+    ! !DESCRIPTION:
     ! Allocate memory and read in urban input data
     !
     ! !USES:
@@ -375,7 +375,7 @@ subroutine UrbanInput(begg, endg, mode)
     use fileutils       , only : getavu, relavu, getfil, opnfil
     use spmdMod         , only : masterproc
     use domainMod       , only : ldomain
-    use ncdio_pio       , only : file_desc_t, ncd_io, ncd_inqvdlen, ncd_inqfdims 
+    use ncdio_pio       , only : file_desc_t, ncd_io, ncd_inqvdlen, ncd_inqfdims
     use ncdio_pio       , only : ncd_pio_openfile, ncd_pio_closefile, ncd_inqdid, ncd_inqdlen
     !
     ! !ARGUMENTS:
@@ -392,7 +392,7 @@ subroutine UrbanInput(begg, endg, mode)
     integer :: numrad_i              ! input grid: number of solar bands (VIS/NIR)
     integer :: numurbl_i             ! input grid: number of urban landunits
     integer :: ier,ret               ! error status
-    logical :: isgrid2d              ! true => file is 2d 
+    logical :: isgrid2d              ! true => file is 2d
     logical :: readvar               ! true => variable is on dataset
     logical :: has_numurbl           ! true => numurbl dimension is on dataset
     character(len=32) :: subname = 'UrbanInput' ! subroutine name
@@ -403,11 +403,11 @@ subroutine UrbanInput(begg, endg, mode)
     if (mode == 'initialize') then
 
        ! Read urban data
-       
+
        if (masterproc) then
           write(iulog,*)' Reading in urban input data from fsurdat file ...'
        end if
-       
+
        call getfil (fsurdat, locfn, 0)
        call ncd_pio_openfile (ncid, locfn, 0)
 
@@ -428,20 +428,20 @@ subroutine UrbanInput(begg, endg, mode)
        if ( nlevurb == 0 ) return
 
        ! Allocate dynamic memory
-       allocate(urbinp%canyon_hwr(begg:endg, numurbl), &  
-                urbinp%wtlunit_roof(begg:endg, numurbl), &  
+       allocate(urbinp%canyon_hwr(begg:endg, numurbl), &
+                urbinp%wtlunit_roof(begg:endg, numurbl), &
                 urbinp%wtroad_perv(begg:endg, numurbl), &
-                urbinp%em_roof(begg:endg, numurbl), &     
-                urbinp%em_improad(begg:endg, numurbl), &    
-                urbinp%em_perroad(begg:endg, numurbl), &    
-                urbinp%em_wall(begg:endg, numurbl), &    
-                urbinp%alb_roof_dir(begg:endg, numurbl, numrad), &    
-                urbinp%alb_roof_dif(begg:endg, numurbl, numrad), &    
-                urbinp%alb_improad_dir(begg:endg, numurbl, numrad), &    
-                urbinp%alb_perroad_dir(begg:endg, numurbl, numrad), &    
-                urbinp%alb_improad_dif(begg:endg, numurbl, numrad), &    
-                urbinp%alb_perroad_dif(begg:endg, numurbl, numrad), &    
-                urbinp%alb_wall_dir(begg:endg, numurbl, numrad), &    
+                urbinp%em_roof(begg:endg, numurbl), &
+                urbinp%em_improad(begg:endg, numurbl), &
+                urbinp%em_perroad(begg:endg, numurbl), &
+                urbinp%em_wall(begg:endg, numurbl), &
+                urbinp%alb_roof_dir(begg:endg, numurbl, numrad), &
+                urbinp%alb_roof_dif(begg:endg, numurbl, numrad), &
+                urbinp%alb_improad_dir(begg:endg, numurbl, numrad), &
+                urbinp%alb_perroad_dir(begg:endg, numurbl, numrad), &
+                urbinp%alb_improad_dif(begg:endg, numurbl, numrad), &
+                urbinp%alb_perroad_dif(begg:endg, numurbl, numrad), &
+                urbinp%alb_wall_dir(begg:endg, numurbl, numrad), &
                 urbinp%alb_wall_dif(begg:endg, numurbl, numrad), &
                 urbinp%ht_roof(begg:endg, numurbl), &
                 urbinp%wind_hgt_canyon(begg:endg, numurbl), &
@@ -461,7 +461,7 @@ subroutine UrbanInput(begg, endg, mode)
        endif
 
        call ncd_inqfdims (ncid, isgrid2d, ni, nj, ns)
-       if (ldomain%ns /= ns .or. ldomain%ni /= ni .or. ldomain%nj /= nj) then
+       if (.not. single_column .and. (ldomain%ns /= ns .or. ldomain%ni /= ni .or. ldomain%nj /= nj)) then
           write(iulog,*)trim(subname), 'ldomain and input file do not match dims '
           write(iulog,*)trim(subname), 'ldomain%ni,ni,= ',ldomain%ni,ni
           write(iulog,*)trim(subname), 'ldomain%nj,nj,= ',ldomain%nj,nj
@@ -655,7 +655,7 @@ subroutine UrbanInput(begg, endg, mode)
 
        call ncd_pio_closefile(ncid)
        if (masterproc) then
-          write(iulog,*)' Sucessfully read urban input data' 
+          write(iulog,*)' Sucessfully read urban input data'
           write(iulog,*)
        end if
 
@@ -955,7 +955,3 @@ end function IsProgBuildTemp
   !-----------------------------------------------------------------------
 
 end module UrbanParamsType
-
-
-
-
diff --git a/src/cpl/lilac/lnd_comp_esmf.F90 b/src/cpl/lilac/lnd_comp_esmf.F90
index 6c8bb2a491..0aa0fc9f81 100644
--- a/src/cpl/lilac/lnd_comp_esmf.F90
+++ b/src/cpl/lilac/lnd_comp_esmf.F90
@@ -374,7 +374,7 @@ subroutine lnd_init(comp, import_state, export_state, clock, rc)
     !--------------------------------
     ! Finish initializing ctsm
     !--------------------------------
-    call initialize2(ni,nj)
+    call initialize2(ni,nj, currTime)
     call ESMF_LogWrite(subname//"ctsm initialize2 done...", ESMF_LOGMSG_INFO)
 
     !--------------------------------
@@ -559,7 +559,6 @@ subroutine lnd_run(gcomp, import_state, export_state, clock, rc)
     integer                :: nstep          ! time step index
     logical                :: rstwr          ! .true. ==> write restart file before returning
     logical                :: nlend          ! .true. ==> last time-step
-    logical                :: dosend         ! true => send data back to driver
     logical                :: doalb          ! .true. ==> do albedo calculation on this time step
     real(r8)               :: nextsw_cday    ! calday from clock of next radiation computation
     real(r8)               :: caldayp1       ! ctsm calday plus dtime offset
@@ -626,161 +625,146 @@ subroutine lnd_run(gcomp, import_state, export_state, clock, rc)
     !--------------------------------
 
     dtime = get_step_size()
-    dosend = .false.
-    do while(.not. dosend)
-
-       ! We assume that the land model time step matches the coupling interval. However,
-       ! we still need this while loop to handle the initial time step (time 0). We may
-       ! want to get rid of this time step 0 in the lilac coupling, at which point we
-       ! should be able to remove this while loop and dosend variable.
-       !
-       ! See also https://github.com/ESCOMP/CTSM/issues/925
-       nstep = get_nstep()
-       if (nstep > 0) then
-          dosend = .true.
-       end if
 
-       !--------------------------------
-       ! Determine calendar day info
-       !--------------------------------
+    ! We assume that the land model time step matches the coupling interval.
+    nstep = get_nstep()
 
-       calday = get_curr_calday(reuse_day_365_for_day_366=.true.)
-       caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.)
+    !--------------------------------
+    ! Determine calendar day info
+    !--------------------------------
 
-       !--------------------------------
-       ! Get time of next atmospheric shortwave calculation
-       !--------------------------------
+    calday = get_curr_calday(reuse_day_365_for_day_366=.true.)
+    caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.)
 
-       ! TODO(NS): nextsw_cday should come directly from atmosphere!
-       ! For now I am setting nextsw_cday to be the same caldayp1
-       !
-       ! See also https://github.com/ESCOMP/CTSM/issues/860
+    !--------------------------------
+    ! Get time of next atmospheric shortwave calculation
+    !--------------------------------
 
-       nextsw_cday = calday
-       if (masterproc) then
-          write(iulog,*) trim(subname) // '... nextsw_cday is : ', nextsw_cday
-       end if
+    ! TODO(NS): nextsw_cday should come directly from atmosphere!
+    ! For now I am setting nextsw_cday to be the same caldayp1
+    !
+    ! See also https://github.com/ESCOMP/CTSM/issues/860
 
-       !--------------------------------
-       ! Obtain orbital values
-       !--------------------------------
-
-       call shr_orb_decl( calday     , eccen, mvelpp, lambm0, obliqr, declin  , eccf )
-       call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf )
-
-       if (masterproc) then
-          write(iulog,*) '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
-          write(iulog,F02) 'nextsw_cday is :  ', nextsw_cday
-          write(iulog,F02) 'calday is      :  ', calday
-          write(iulog,F02) 'eccen is       :  ', eccen
-          write(iulog,F02) 'mvelpp is      :  ', mvelpp
-          write(iulog,F02) 'lambm0 is      :  ', lambm0
-          write(iulog,F02) 'obliqr is      :  ', obliqr
-          write(iulog,F02) 'declin is      :  ', declin
-          write(iulog,F02) 'declinp1 is    :  ', declinp1
-          write(iulog,*  ) '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
-       end if
+    nextsw_cday = calday
+    if (masterproc) then
+       write(iulog,*) trim(subname) // '... nextsw_cday is : ', nextsw_cday
+    end if
 
-       !--------------------------------
-       ! Determine doalb based on nextsw_cday sent from atm model
-       !--------------------------------
-
-       if (nstep == 0) then
-          doalb = .false.
-          nextsw_cday = caldayp1
-       else if (nstep == 1) then
-          !doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8)
-          doalb = .false.
-       else
-          doalb = (nextsw_cday >= -0.5_r8)
-       end if
+    !--------------------------------
+    ! Obtain orbital values
+    !--------------------------------
 
-       if (masterproc) then
-          write(iulog,*) '------------  LILAC  ----------------'
-          write(iulog,*) 'nstep       : ', nstep
-          write(iulog,*) 'calday      : ', calday
-          write(iulog,*) 'caldayp1    : ', caldayp1
-          write(iulog,*) 'nextsw_cday : ', nextsw_cday
-          write(iulog,*) 'doalb       : ', doalb
-          write(iulog,*) '-------------------------------------'
-       end if
+    call shr_orb_decl( calday     , eccen, mvelpp, lambm0, obliqr, declin  , eccf )
+    call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf )
 
-       call update_rad_dtime(doalb)
+    if (masterproc) then
+       write(iulog,*) '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
+       write(iulog,F02) 'nextsw_cday is :  ', nextsw_cday
+       write(iulog,F02) 'calday is      :  ', calday
+       write(iulog,F02) 'eccen is       :  ', eccen
+       write(iulog,F02) 'mvelpp is      :  ', mvelpp
+       write(iulog,F02) 'lambm0 is      :  ', lambm0
+       write(iulog,F02) 'obliqr is      :  ', obliqr
+       write(iulog,F02) 'declin is      :  ', declin
+       write(iulog,F02) 'declinp1 is    :  ', declinp1
+       write(iulog,*  ) '~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~'
+    end if
 
-       !--------------------------------
-       ! Determine if time to write restart
-       !--------------------------------
+    !--------------------------------
+    ! Determine doalb based on nextsw_cday sent from atm model
+    !--------------------------------
 
-       call ESMF_ClockGetAlarm(clock, alarmname='lilac_restart_alarm', alarm=alarm, rc=rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    if (nstep == 1) then
+       !doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8)
+       doalb = .false.
+    else
+       doalb = (nextsw_cday >= -0.5_r8)
+    end if
 
-       if (ESMF_AlarmIsRinging(alarm, rc=rc)) then
-          if (ChkErr(rc,__LINE__,u_FILE_u)) return
-          rstwr = .true.
-          call ESMF_AlarmRingerOff( alarm, rc=rc )
-          if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       else
-          rstwr = .false.
-       endif
-       if (masterproc) then
-          write(iulog,*)' restart alarm is ',rstwr
-       end if
+    if (masterproc) then
+       write(iulog,*) '------------  LILAC  ----------------'
+       write(iulog,*) 'nstep       : ', nstep
+       write(iulog,*) 'calday      : ', calday
+       write(iulog,*) 'caldayp1    : ', caldayp1
+       write(iulog,*) 'nextsw_cday : ', nextsw_cday
+       write(iulog,*) 'doalb       : ', doalb
+       write(iulog,*) '-------------------------------------'
+    end if
 
-       !--------------------------------
-       ! Determine if time to stop
-       !--------------------------------
+    call update_rad_dtime(doalb)
 
-       call ESMF_ClockGetAlarm(clock, alarmname='lilac_stop_alarm', alarm=alarm, rc=rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    !--------------------------------
+    ! Determine if time to stop
+    !--------------------------------
 
-       if (ESMF_AlarmIsRinging(alarm, rc=rc)) then
-          if (ChkErr(rc,__LINE__,u_FILE_u)) return
-          nlend = .true.
-          call ESMF_AlarmRingerOff( alarm, rc=rc )
-          if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       else
-          nlend = .false.
-       endif
-       if (masterproc) then
-          write(iulog,*)' stop alarm is ',nlend
-       end if
+    call ESMF_ClockGetAlarm(clock, alarmname='lilac_stop_alarm', alarm=alarm, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       !--------------------------------
-       ! Run CTSM
-       !--------------------------------
+    if (ESMF_AlarmIsRinging(alarm, rc=rc)) then
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+       nlend = .true.
+       call ESMF_AlarmRingerOff( alarm, rc=rc )
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    else
+       nlend = .false.
+    endif
+    if (masterproc) then
+       write(iulog,*)' stop alarm is ',nlend
+    end if
 
-       call t_barrierf('sync_ctsm_run1', mpicom)
+    !--------------------------------
+    ! Determine if time to write restart
+    !--------------------------------
 
-       ! Restart File - use nexttimestr rather than currtimestr here since that is the time at the end of
-       ! the timestep and is preferred for restart file names
-       ! TODO: is this correct for lilac?
+    call ESMF_ClockGetAlarm(clock, alarmname='lilac_restart_alarm', alarm=alarm, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       call ESMF_ClockGetNextTime(clock, nextTime=nextTime, rc=rc)
+    if (ESMF_AlarmIsRinging(alarm, rc=rc)) then
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       call ESMF_TimeGet(nexttime, yy=yr_lilac, mm=mon_lilac, dd=day_lilac, s=tod_lilac, rc=rc)
+       rstwr = .true.
+       call ESMF_AlarmRingerOff( alarm, rc=rc )
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_lilac, mon_lilac, day_lilac, tod_lilac
+    else
+       rstwr = .false.
+    endif
+    if (masterproc) then
+       write(iulog,*)' restart alarm is ',rstwr
+    end if
 
-       call t_startf ('ctsm_run')
-       call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic=.false.)
-       call t_stopf ('ctsm_run')
+    !--------------------------------
+    ! Run CTSM
+    !--------------------------------
 
-       !--------------------------------
-       ! Pack export state
-       !--------------------------------
+    call t_barrierf('sync_ctsm_run1', mpicom)
 
-       call t_startf ('lc_lnd_export')
-       call export_fields(export_state, bounds,  rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       call t_stopf ('lc_lnd_export')
+    ! Restart File - use nexttimestr rather than currtimestr here since that is the time at the end of
+    ! the timestep and is preferred for restart file names
+    ! TODO: is this correct for lilac?
 
-       !--------------------------------
-       ! Advance ctsm time step
-       !--------------------------------
+    call ESMF_ClockGetNextTime(clock, nextTime=nextTime, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    call ESMF_TimeGet(nexttime, yy=yr_lilac, mm=mon_lilac, dd=day_lilac, s=tod_lilac, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_lilac, mon_lilac, day_lilac, tod_lilac
 
-       call advance_timestep()
+    call t_startf ('ctsm_run')
+    call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic=.false.)
+    call t_stopf ('ctsm_run')
 
-    end do
+    !--------------------------------
+    ! Pack export state
+    !--------------------------------
+
+    call t_startf ('lc_lnd_export')
+    call export_fields(export_state, bounds,  rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    call t_stopf ('lc_lnd_export')
+
+    !--------------------------------
+    ! Advance ctsm time step
+    !--------------------------------
+
+    call advance_timestep()
 
     !--------------------------------
     ! Check that internal clock is in sync with lilac driver clock
diff --git a/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90
index 9631e807cd..8ee6c2014e 100644
--- a/src/cpl/nuopc/lnd_comp_nuopc.F90
+++ b/src/cpl/nuopc/lnd_comp_nuopc.F90
@@ -655,7 +655,10 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     ! ---------------------
     ! Finish initializing ctsm
     ! ---------------------
-    call initialize2(ni, nj)
+    call ESMF_ClockGet(clock, currTime=currtime, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+
+    call initialize2(ni, nj, currtime)
 
     !--------------------------------
     ! Create land export state
@@ -740,7 +743,6 @@ subroutine ModelAdvance(gcomp, rc)
     integer                :: localPeCount   ! Number of local Processors
     logical                :: rstwr          ! .true. ==> write restart file before returning
     logical                :: nlend          ! .true. ==> last time-step
-    logical                :: dosend         ! true => send data back to driver
     logical                :: doalb          ! .true. ==> do albedo calculation on this time step
     real(r8)               :: nextsw_cday    ! calday from clock of next radiation computation
     real(r8)               :: caldayp1       ! ctsm calday plus dtime offset
@@ -816,112 +818,104 @@ subroutine ModelAdvance(gcomp, rc)
     !--------------------------------
 
     dtime = get_step_size()
-    dosend = .false.
-    do while(.not. dosend)
-
-       ! TODO: This is currently hard-wired - is there a better way for nuopc?
-       ! Note that the model clock is updated at the end of the time step not at the beginning
-       nstep = get_nstep()
-       if (nstep > 0) then
-          dosend = .true.
-       end if
 
-       !--------------------------------
-       ! Determine doalb based on nextsw_cday sent from atm model
-       !--------------------------------
-
-       caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.)
-
-       if (nstep == 0) then
-          doalb = .false.
-       else if (nstep == 1) then
-          doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8)
-       else
-          doalb = (nextsw_cday >= -0.5_r8)
-       end if
-       call update_rad_dtime(doalb)
+    ! TODO: This is currently hard-wired - is there a better way for nuopc?
+    ! Note that the model clock is updated at the end of the time step not at the beginning
+    nstep = get_nstep()
 
-       !--------------------------------
-       ! Determine if time to stop
-       !--------------------------------
+    !--------------------------------
+    ! Determine doalb based on nextsw_cday sent from atm model
+    !--------------------------------
 
-       call ESMF_ClockGetAlarm(clock, alarmname='alarm_stop', alarm=alarm, rc=rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    caldayp1 = get_curr_calday(offset=dtime, reuse_day_365_for_day_366=.true.)
 
-       if (ESMF_AlarmIsRinging(alarm, rc=rc)) then
-          if (ChkErr(rc,__LINE__,u_FILE_u)) return
-          nlend = .true.
-          call ESMF_AlarmRingerOff( alarm, rc=rc )
-          if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       else
-          nlend = .false.
-       endif
+    if (nstep == 1) then
+       doalb = (abs(nextsw_cday- caldayp1) < 1.e-10_r8)
+    else
+       doalb = (nextsw_cday >= -0.5_r8)
+    end if
 
-       !--------------------------------
-       ! Determine if time to write restart
-       !--------------------------------
-       rstwr = .false.
-       if (nlend .and. write_restart_at_endofrun) then
-          rstwr = .true.
-       else
-          call ESMF_ClockGetAlarm(clock, alarmname='alarm_restart', alarm=alarm, rc=rc)
-          if (ChkErr(rc,__LINE__,u_FILE_u)) return
-          if (ESMF_AlarmIsCreated(alarm, rc=rc)) then
-             if (ESMF_AlarmIsRinging(alarm, rc=rc)) then
-                if (ChkErr(rc,__LINE__,u_FILE_u)) return
-                rstwr = .true.
-                call ESMF_AlarmRingerOff( alarm, rc=rc )
-                if (ChkErr(rc,__LINE__,u_FILE_u)) return
-             endif
-          endif
-       end if
+    call update_rad_dtime(doalb)
 
-       !--------------------------------
-       ! Run CTSM
-       !--------------------------------
+    !--------------------------------
+    ! Determine if time to stop
+    !--------------------------------
 
-       ! call ESMF_VMBarrier(vm, rc=rc)
-       ! if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    call ESMF_ClockGetAlarm(clock, alarmname='alarm_stop', alarm=alarm, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       call t_startf ('shr_orb_decl')
-       ! Note - the orbital inquiries set the values in clm_varorb via the module use statements
-       call  clm_orbital_update(clock, iulog, masterproc, eccen, obliqr, lambm0, mvelpp, rc)
+    if (ESMF_AlarmIsRinging(alarm, rc=rc)) then
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       calday = get_curr_calday(reuse_day_365_for_day_366=.true.)
-       call shr_orb_decl( calday     , eccen, mvelpp, lambm0, obliqr, declin  , eccf )
-       call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf )
-       call t_stopf ('shr_orb_decl')
-
-       call t_startf ('ctsm_run')
-       ! Restart File - use nexttimestr rather than currtimestr here since that is the time at the end of
-       ! the timestep and is preferred for restart file names
-       call ESMF_ClockGetNextTime(clock, nextTime=nextTime, rc=rc)
+       nlend = .true.
+       call ESMF_AlarmRingerOff( alarm, rc=rc )
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       call ESMF_TimeGet(nexttime, yy=yr_sync, mm=mon_sync, dd=day_sync, s=tod_sync, rc=rc)
+    else
+       nlend = .false.
+    endif
+
+    !--------------------------------
+    ! Determine if time to write restart
+    !--------------------------------
+    rstwr = .false.
+    if (nlend .and. write_restart_at_endofrun) then
+       rstwr = .true.
+    else 
+       call ESMF_ClockGetAlarm(clock, alarmname='alarm_restart', alarm=alarm, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_sync, mon_sync, day_sync, tod_sync
-       call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic)
-       call t_stopf ('ctsm_run')
+       if (ESMF_AlarmIsCreated(alarm, rc=rc)) then
+          if (ESMF_AlarmIsRinging(alarm, rc=rc)) then
+             if (ChkErr(rc,__LINE__,u_FILE_u)) return
+             rstwr = .true.
+             call ESMF_AlarmRingerOff( alarm, rc=rc )
+             if (ChkErr(rc,__LINE__,u_FILE_u)) return
+          endif
+       endif
+    end if
 
-       !--------------------------------
-       ! Pack export state
-       !--------------------------------
+    !--------------------------------
+    ! Run CTSM
+    !--------------------------------
 
-       call t_startf ('lc_lnd_export')
-       call export_fields(gcomp, bounds, glc_present, rof_prognostic, &
-            water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       call t_stopf ('lc_lnd_export')
+    ! call ESMF_VMBarrier(vm, rc=rc)
+    ! if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       !--------------------------------
-       ! Advance ctsm time step
-       !--------------------------------
+    call t_startf ('shr_orb_decl')
+    ! Note - the orbital inquiries set the values in clm_varorb via the module use statements
+    call  clm_orbital_update(clock, iulog, masterproc, eccen, obliqr, lambm0, mvelpp, rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    calday = get_curr_calday(reuse_day_365_for_day_366=.true.)
+    call shr_orb_decl( calday     , eccen, mvelpp, lambm0, obliqr, declin  , eccf )
+    call shr_orb_decl( nextsw_cday, eccen, mvelpp, lambm0, obliqr, declinp1, eccf )
+    call t_stopf ('shr_orb_decl')
+
+    call t_startf ('ctsm_run')
+    ! Restart File - use nexttimestr rather than currtimestr here since that is the time at the end of
+    ! the timestep and is preferred for restart file names
+    call ESMF_ClockGetNextTime(clock, nextTime=nextTime, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    call ESMF_TimeGet(nexttime, yy=yr_sync, mm=mon_sync, dd=day_sync, s=tod_sync, rc=rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    write(rdate,'(i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr_sync, mon_sync, day_sync, tod_sync
+    call clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, rof_prognostic)
+    call t_stopf ('ctsm_run')
 
-       call t_startf ('lc_ctsm2_adv_timestep')
-       call advance_timestep()
-       call t_stopf ('lc_ctsm2_adv_timestep')
+    !--------------------------------
+    ! Pack export state
+    !--------------------------------
 
-    end do
+    call t_startf ('lc_lnd_export')
+    call export_fields(gcomp, bounds, glc_present, rof_prognostic, &
+         water_inst%waterlnd2atmbulk_inst, lnd2atm_inst, lnd2glc_inst, rc)
+    if (ChkErr(rc,__LINE__,u_FILE_u)) return
+    call t_stopf ('lc_lnd_export')
+
+    !--------------------------------
+    ! Advance ctsm time step
+    !--------------------------------
+
+    call t_startf ('lc_ctsm2_adv_timestep')
+    call advance_timestep()
+    call t_stopf ('lc_ctsm2_adv_timestep')
 
     ! Check that internal clock is in sync with master clock
     ! Note that the driver clock has not been updated yet - so at this point
@@ -1037,9 +1031,35 @@ subroutine ModelSetRunClock(gcomp, rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
        call ESMF_LogWrite(subname//'setting alarms for ' // trim(name), ESMF_LOGMSG_INFO)
 
-       !----------------
+       !----------------------------------------------------------------------------------
+       ! Stop alarm
+       ! MUST be set before the restart alarm in case restarts happen at the stop alarm
+       !----------------------------------------------------------------------------------
+       call NUOPC_CompAttributeGet(gcomp, name="stop_option", value=stop_option, rc=rc)
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+
+       call NUOPC_CompAttributeGet(gcomp, name="stop_n", value=cvalue, rc=rc)
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+       read(cvalue,*) stop_n
+
+       call NUOPC_CompAttributeGet(gcomp, name="stop_ymd", value=cvalue, rc=rc)
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+       read(cvalue,*) stop_ymd
+
+       call alarmInit(mclock, stop_alarm, stop_option, &
+            opt_n   = stop_n,           &
+            opt_ymd = stop_ymd,         &
+            RefTime = mcurrTime,           &
+            alarmname = 'alarm_stop', rc=rc)
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+
+       call ESMF_AlarmSet(stop_alarm, clock=mclock, rc=rc)
+       if (ChkErr(rc,__LINE__,u_FILE_u)) return
+
+       !----------------------------------------------------------------------------------
        ! Restart alarm
-       !----------------
+       ! MUST be set after the stop alarm in case restarts happen at the stop alarm
+       !----------------------------------------------------------------------------------
        call NUOPC_CompAttributeGet(gcomp, name="restart_option", value=restart_option, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
@@ -1061,29 +1081,6 @@ subroutine ModelSetRunClock(gcomp, rc)
        call ESMF_AlarmSet(restart_alarm, clock=mclock, rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
-       !----------------
-       ! Stop alarm
-       !----------------
-       call NUOPC_CompAttributeGet(gcomp, name="stop_option", value=stop_option, rc=rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
-
-       call NUOPC_CompAttributeGet(gcomp, name="stop_n", value=cvalue, rc=rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       read(cvalue,*) stop_n
-
-       call NUOPC_CompAttributeGet(gcomp, name="stop_ymd", value=cvalue, rc=rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       read(cvalue,*) stop_ymd
-
-       call alarmInit(mclock, stop_alarm, stop_option, &
-            opt_n   = stop_n,           &
-            opt_ymd = stop_ymd,         &
-            RefTime = mcurrTime,           &
-            alarmname = 'alarm_stop', rc=rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
-
-       call ESMF_AlarmSet(stop_alarm, clock=mclock, rc=rc)
-       if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
     end if
 
diff --git a/src/fates b/src/fates
index e3e7d2cd86..296e1d6a45 160000
--- a/src/fates
+++ b/src/fates
@@ -1 +1 @@
-Subproject commit e3e7d2cd86a66f8ca0e8f6dc4a823246a2bdb95b
+Subproject commit 296e1d6a45f05a800073d376286d0537d2290e96
diff --git a/src/init_interp/initInterp.F90 b/src/init_interp/initInterp.F90
index f6027fe632..468c3207cd 100644
--- a/src/init_interp/initInterp.F90
+++ b/src/init_interp/initInterp.F90
@@ -820,13 +820,13 @@ subroutine findMinDist( dimname, begi, endi, bego, endo, ncidi, ncido, &
        write(iulog,*)'calling set_subgrid_info for ',trim(dimname), ' for input'
     end if
     call set_subgrid_info(beg=begi, end=endi, dimname=dimname, use_glob=.true., &
-         ncid=ncidi, active=activei, subgrid=subgridi)
+         ncid=ncidi, active=activei, subgrid=subgridi, allow_scm=.false.)
 
     if (masterproc) then
        write(iulog,*)'calling set_subgrid_info for ',trim(dimname), ' for output'
     end if
     call set_subgrid_info(beg=bego, end=endo, dimname=dimname, use_glob=.false., &
-         ncid=ncido, active=activeo, subgrid=subgrido)
+         ncid=ncido, active=activeo, subgrid=subgrido, allow_scm=.true.)
 
     select case (interp_method)
     case (interp_method_general)
@@ -859,7 +859,7 @@ end subroutine findMinDist
 
  !=======================================================================
 
-  subroutine set_subgrid_info(beg, end, dimname, use_glob, ncid, active, subgrid)
+  subroutine set_subgrid_info(beg, end, dimname, use_glob, ncid, active, subgrid, allow_scm)
 
     ! --------------------------------------------------------------------
     ! arguments
@@ -869,6 +869,7 @@ subroutine set_subgrid_info(beg, end, dimname, use_glob, ncid, active, subgrid)
     logical            , intent(in)    :: use_glob  ! if .true., use the 'glob' form of ncd_io
     logical            , intent(out)   :: active(beg:end)
     type(subgrid_type) , intent(inout) :: subgrid
+    logical            , intent(in)    :: allow_scm  ! if .true., allow single column model subset of data
     !
     ! local variables
     integer              :: n
@@ -896,32 +897,32 @@ subroutine set_subgrid_info(beg, end, dimname, use_glob, ncid, active, subgrid)
     end if
 
     if (dimname == 'pft') then
-       call read_var_double(ncid=ncid, varname='pfts1d_lon'    , data=subgrid%lon  , dim1name='pft', use_glob=use_glob)
-       call read_var_double(ncid=ncid, varname='pfts1d_lat'    , data=subgrid%lat  , dim1name='pft', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='pfts1d_itypveg', data=subgrid%ptype, dim1name='pft', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='pfts1d_itypcol', data=subgrid%ctype, dim1name='pft', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='pfts1d_ityplun', data=subgrid%ltype, dim1name='pft', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='pfts1d_active' , data=itemp        , dim1name='pft', use_glob=use_glob)
+       call read_var_double(ncid=ncid, varname='pfts1d_lon'    , data=subgrid%lon  , dim1name='pft', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_double(ncid=ncid, varname='pfts1d_lat'    , data=subgrid%lat  , dim1name='pft', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='pfts1d_itypveg', data=subgrid%ptype, dim1name='pft', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='pfts1d_itypcol', data=subgrid%ctype, dim1name='pft', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='pfts1d_ityplun', data=subgrid%ltype, dim1name='pft', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='pfts1d_active' , data=itemp        , dim1name='pft', use_glob=use_glob, allow_scm=allow_scm)
        if (associated(subgrid%topoglc)) then
-          call read_var_double(ncid=ncid, varname='pfts1d_topoglc', data=subgrid%topoglc, dim1name='pft', use_glob=use_glob)
+          call read_var_double(ncid=ncid, varname='pfts1d_topoglc', data=subgrid%topoglc, dim1name='pft', use_glob=use_glob, allow_scm=allow_scm)
        end if
     else if (dimname == 'column') then
-       call read_var_double(ncid=ncid, varname='cols1d_lon'    , data=subgrid%lon  , dim1name='column', use_glob=use_glob)
-       call read_var_double(ncid=ncid, varname='cols1d_lat'    , data=subgrid%lat  , dim1name='column', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='cols1d_ityp'   , data=subgrid%ctype, dim1name='column', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='cols1d_ityplun', data=subgrid%ltype, dim1name='column', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='cols1d_active' , data=itemp        , dim1name='column', use_glob=use_glob)
+       call read_var_double(ncid=ncid, varname='cols1d_lon'    , data=subgrid%lon  , dim1name='column', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_double(ncid=ncid, varname='cols1d_lat'    , data=subgrid%lat  , dim1name='column', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='cols1d_ityp'   , data=subgrid%ctype, dim1name='column', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='cols1d_ityplun', data=subgrid%ltype, dim1name='column', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='cols1d_active' , data=itemp        , dim1name='column', use_glob=use_glob, allow_scm=allow_scm)
        if (associated(subgrid%topoglc)) then
-          call read_var_double(ncid=ncid, varname='cols1d_topoglc', data=subgrid%topoglc, dim1name='column', use_glob=use_glob)
+          call read_var_double(ncid=ncid, varname='cols1d_topoglc', data=subgrid%topoglc, dim1name='column', use_glob=use_glob, allow_scm=allow_scm)
        end if
     else if (dimname == 'landunit') then
-       call read_var_double(ncid=ncid, varname='land1d_lon'    , data=subgrid%lon  , dim1name='landunit', use_glob=use_glob)
-       call read_var_double(ncid=ncid, varname='land1d_lat'    , data=subgrid%lat  , dim1name='landunit', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='land1d_ityplun', data=subgrid%ltype, dim1name='landunit', use_glob=use_glob)
-       call read_var_int(ncid=ncid, varname='land1d_active' , data=itemp        , dim1name='landunit', use_glob=use_glob)
+       call read_var_double(ncid=ncid, varname='land1d_lon'    , data=subgrid%lon  , dim1name='landunit', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_double(ncid=ncid, varname='land1d_lat'    , data=subgrid%lat  , dim1name='landunit', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='land1d_ityplun', data=subgrid%ltype, dim1name='landunit', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_int(ncid=ncid, varname='land1d_active' , data=itemp        , dim1name='landunit', use_glob=use_glob, allow_scm=allow_scm)
     else if (dimname == 'gridcell') then
-       call read_var_double(ncid=ncid, varname='grid1d_lon'    , data=subgrid%lon  , dim1name='gridcell', use_glob=use_glob)
-       call read_var_double(ncid=ncid, varname='grid1d_lat'    , data=subgrid%lat  , dim1name='gridcell', use_glob=use_glob)
+       call read_var_double(ncid=ncid, varname='grid1d_lon'    , data=subgrid%lon  , dim1name='gridcell', use_glob=use_glob, allow_scm=allow_scm)
+       call read_var_double(ncid=ncid, varname='grid1d_lat'    , data=subgrid%lat  , dim1name='gridcell', use_glob=use_glob, allow_scm=allow_scm)
 
        ! All gridcells in the restart file are active
        itemp(beg:end) = 1
@@ -942,7 +943,7 @@ subroutine set_subgrid_info(beg, end, dimname, use_glob, ncid, active, subgrid)
 
   contains
 
-    subroutine read_var_double(ncid, varname, data, dim1name, use_glob)
+    subroutine read_var_double(ncid, varname, data, dim1name, use_glob, allow_scm)
       ! Wraps the ncd_io call, providing logic related to whether we're using the 'glob'
       ! form of ncd_io
       type(file_desc_t)  , intent(inout) :: ncid
@@ -950,15 +951,29 @@ subroutine read_var_double(ncid, varname, data, dim1name, use_glob)
       real(r8), pointer  , intent(inout) :: data(:)
       character(len=*)   , intent(in)    :: dim1name
       logical            , intent(in)    :: use_glob  ! if .true., use the 'glob' form of ncd_io
+      logical            , intent(in)    :: allow_scm  ! if .true., allow single column model subset of data
+
+      ! local
+      character(16)                      :: readflag
+
+      if (allow_scm) then
+         readflag='read'
+      else
+         ! Flag to distinguish the times during IC interpolation when running in single column mode but
+         ! need to read the full data grid. Normally single_column means
+         ! "read the data grid and extract the closest column" but
+         ! during IC interpolation you need to read in the full grid to be interpolated regardless of the single_column flag.
+         readflag='read_noscm'
+      endif
 
       if (use_glob) then
-         call ncd_io(ncid=ncid, varname=varname, flag='read', data=data)
+         call ncd_io(ncid=ncid, varname=varname, flag=trim(readflag), data=data)
       else
-         call ncd_io(ncid=ncid, varname=varname, flag='read', data=data, dim1name=dim1name)
+         call ncd_io(ncid=ncid, varname=varname, flag=trim(readflag), data=data, dim1name=dim1name)
       end if
     end subroutine read_var_double
 
-    subroutine read_var_int(ncid, varname, data, dim1name, use_glob)
+    subroutine read_var_int(ncid, varname, data, dim1name, use_glob, allow_scm)
       ! Wraps the ncd_io call, providing logic related to whether we're using the 'glob'
       ! form of ncd_io
       type(file_desc_t)  , intent(inout) :: ncid
@@ -966,11 +981,25 @@ subroutine read_var_int(ncid, varname, data, dim1name, use_glob)
       integer, pointer   , intent(inout) :: data(:)
       character(len=*)   , intent(in)    :: dim1name
       logical            , intent(in)    :: use_glob  ! if .true., use the 'glob' form of ncd_io
+      logical            , intent(in)    :: allow_scm  ! if .true., allow single column model subset of data
+
+      ! local
+      character(16)                      :: readflag
+
+      if (allow_scm) then
+         readflag='read'
+      else
+         ! Flag to distinguish the times during IC interpolation when running in single column mode but
+         ! need to read the full data grid. Normally single_column means
+         ! "read the data grid and extract the closest column" but
+         ! during IC interpolation you need to read in the full grid to be interpolated regardless of the single_column flag.
+         readflag='read_noscm'
+      endif
 
       if (use_glob) then
-         call ncd_io(ncid=ncid, varname=varname, flag='read', data=data)
+         call ncd_io(ncid=ncid, varname=varname, flag=trim(readflag), data=data)
       else
-         call ncd_io(ncid=ncid, varname=varname, flag='read', data=data, dim1name=dim1name)
+         call ncd_io(ncid=ncid, varname=varname, flag=trim(readflag), data=data, dim1name=dim1name)
       end if
     end subroutine read_var_int
 
@@ -1038,7 +1067,7 @@ subroutine interp_1d_double (varname, varname_i, dimname, begi, endi, bego, endo
     end if
 
     allocate (rbufsli(begi:endi), rbufslo(bego:endo))
-    call ncd_io(ncid=ncidi, varname=trim(varname_i), flag='read', data=rbufsli)
+    call ncd_io(ncid=ncidi, varname=trim(varname_i), flag='read_noscm', data=rbufsli)
     call ncd_io(ncid=ncido, varname=trim(varname), flag='read', data=rbufslo, &
          dim1name=dimname)
 
@@ -1080,7 +1109,7 @@ subroutine interp_1d_int (varname, varname_i, dimname, begi, endi, bego, endo, n
 
     allocate (ibufsli(begi:endi), ibufslo(bego:endo))
 
-    call ncd_io(ncid=ncidi, varname=trim(varname_i), flag='read', &
+    call ncd_io(ncid=ncidi, varname=trim(varname_i), flag='read_noscm', &
          data=ibufsli)
     call ncd_io(ncid=ncido, varname=trim(varname), flag='read', &
          data=ibufslo, dim1name=dimname)
diff --git a/src/init_interp/initInterpMultilevelContainer.F90 b/src/init_interp/initInterpMultilevelContainer.F90
index 5a7b14832a..d26e51c71c 100644
--- a/src/init_interp/initInterpMultilevelContainer.F90
+++ b/src/init_interp/initInterpMultilevelContainer.F90
@@ -732,7 +732,7 @@ subroutine create_snow_interpolators(interp_multilevel_levsno, interp_multilevel
 
     ! Read snlsno_source_sgrid
     allocate(snlsno_source_sgrid(bounds_source%get_begc() : bounds_source%get_endc()))
-    call ncd_io(ncid=ncid_source, varname='SNLSNO', flag='read', &
+    call ncd_io(ncid=ncid_source, varname='SNLSNO', flag='read_noscm', &
          data=snlsno_source_sgrid)
     snlsno_source_sgrid(:) = abs(snlsno_source_sgrid(:))
 
diff --git a/src/main/clm_driver.F90 b/src/main/clm_driver.F90
index 454ff87463..f93143d9e3 100644
--- a/src/main/clm_driver.F90
+++ b/src/main/clm_driver.F90
@@ -1368,41 +1368,39 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
     ! FIX(SPM, 082814) - in the fates branch RF and I commented out the if(.not.
     ! use_fates) then statement ... double check if this is required and why
 
-    if (nstep > 0) then
-       call t_startf('accum')
+    call t_startf('accum')
 
-       call atm2lnd_inst%UpdateAccVars(bounds_proc)
+    call atm2lnd_inst%UpdateAccVars(bounds_proc)
 
-       call temperature_inst%UpdateAccVars(bounds_proc, crop_inst)
+    call temperature_inst%UpdateAccVars(bounds_proc, crop_inst)
 
-       call canopystate_inst%UpdateAccVars(bounds_proc)
+    call canopystate_inst%UpdateAccVars(bounds_proc)
 
-       call water_inst%UpdateAccVars(bounds_proc)
+    call water_inst%UpdateAccVars(bounds_proc)
 
-       call energyflux_inst%UpdateAccVars(bounds_proc)
+    call energyflux_inst%UpdateAccVars(bounds_proc)
 
-       ! COMPILER_BUG(wjs, 2014-11-30, pgi 14.7) For pgi 14.7 to be happy when
-       ! compiling this threaded, I needed to change the dummy arguments to be
-       ! pointers, and get rid of the explicit bounds in the subroutine call.
-       ! call bgc_vegetation_inst%UpdateAccVars(bounds_proc, &
-       !      t_a10_patch=temperature_inst%t_a10_patch(bounds_proc%begp:bounds_proc%endp), &
-       !      t_ref2m_patch=temperature_inst%t_ref2m_patch(bounds_proc%begp:bounds_proc%endp))
-       call bgc_vegetation_inst%UpdateAccVars(bounds_proc, &
-            t_a10_patch=temperature_inst%t_a10_patch, &
-            t_ref2m_patch=temperature_inst%t_ref2m_patch)
+    ! COMPILER_BUG(wjs, 2014-11-30, pgi 14.7) For pgi 14.7 to be happy when
+    ! compiling this threaded, I needed to change the dummy arguments to be
+    ! pointers, and get rid of the explicit bounds in the subroutine call.
+    ! call bgc_vegetation_inst%UpdateAccVars(bounds_proc, &
+    !      t_a10_patch=temperature_inst%t_a10_patch(bounds_proc%begp:bounds_proc%endp), &
+    !      t_ref2m_patch=temperature_inst%t_ref2m_patch(bounds_proc%begp:bounds_proc%endp))
+    call bgc_vegetation_inst%UpdateAccVars(bounds_proc, &
+         t_a10_patch=temperature_inst%t_a10_patch, &
+         t_ref2m_patch=temperature_inst%t_ref2m_patch)
 
-       if (use_crop) then
-          call crop_inst%CropUpdateAccVars(bounds_proc, &
-               temperature_inst%t_ref2m_patch, temperature_inst%t_soisno_col)
-       end if
-
-       if(use_fates) then
-          call clm_fates%UpdateAccVars(bounds_proc)
-       end if
+    if (use_crop) then
+       call crop_inst%CropUpdateAccVars(bounds_proc, &
+            temperature_inst%t_ref2m_patch, temperature_inst%t_soisno_col)
+    end if
 
-       call t_stopf('accum')
+    if(use_fates) then
+       call clm_fates%UpdateAccVars(bounds_proc)
     end if
 
+    call t_stopf('accum')
+
     ! ============================================================================
     ! Update history buffer
     ! ============================================================================
diff --git a/src/main/clm_initializeMod.F90 b/src/main/clm_initializeMod.F90
index e3d9eeda06..46353539ce 100644
--- a/src/main/clm_initializeMod.F90
+++ b/src/main/clm_initializeMod.F90
@@ -125,12 +125,13 @@ subroutine initialize1(dtime)
   end subroutine initialize1
 
   !-----------------------------------------------------------------------
-  subroutine initialize2(ni,nj)
+  subroutine initialize2(ni,nj, currtime)
     !
     ! !DESCRIPTION:
     ! CLM initialization second phase
     !
     ! !USES:
+    use ESMF                          , only : ESMF_Time
     use clm_varcon                    , only : spval
     use clm_varpar                    , only : natpft_lb, natpft_ub, cft_lb, cft_ub, maxpatch_glc
     use clm_varpar                    , only : surfpft_lb, surfpft_ub
@@ -186,6 +187,7 @@ subroutine initialize2(ni,nj)
     !
     ! !ARGUMENTS
     integer, intent(in) :: ni, nj         ! global grid sizes
+    type(ESMF_Time), intent(in) :: currtime
     !
     ! !LOCAL VARIABLES:
     integer            :: c,g,i,j,k,l,n,p ! indices
@@ -345,10 +347,12 @@ subroutine initialize2(ni,nj)
          source=create_nutrient_competition_method(bounds_proc))
     call readParameters(photosyns_inst)
 
+    
     ! Initialize time manager
     if (nsrest == nsrStartup) then
        call timemgr_init()
     else
+       call timemgr_init(curr_date_in=currtime)
        call restFile_getfile(file=fnamer, path=pnamer)
        call restFile_open( flag='read', file=fnamer, ncid=ncid )
        call timemgr_restart_io( ncid=ncid, flag='read' )
diff --git a/src/main/controlMod.F90 b/src/main/controlMod.F90
index 3f5c58ac0e..e8121519aa 100644
--- a/src/main/controlMod.F90
+++ b/src/main/controlMod.F90
@@ -119,6 +119,7 @@ subroutine control_init(dtime)
     !
     ! !USES:
     use CNMRespMod                       , only : CNMRespReadNML
+    use CNFUNMod                         , only : CNFUNReadNML
     use CNNDynamicsMod                   , only : CNNDynamicsReadNML
     use CNPhenologyMod                   , only : CNPhenologyReadNML
     use landunit_varcon                  , only : max_lunit
@@ -596,6 +597,7 @@ subroutine control_init(dtime)
 
     if ( use_fun ) then
        call CNMRespReadNML( NLFilename )
+       call CNFUNReadNML( NLFilename )
     end if
 
     call soilHydReadNML(   NLFilename )
diff --git a/src/main/histFileMod.F90 b/src/main/histFileMod.F90
index 381e1f1170..3c16a2b30f 100644
--- a/src/main/histFileMod.F90
+++ b/src/main/histFileMod.F90
@@ -147,7 +147,7 @@ module histFileMod
   public :: hist_addfld1d        ! Add a 1d single-level field to the list of all history fields
   public :: hist_addfld2d        ! Add a 2d multi-level field to the list of all history fields
   public :: hist_addfld_decomp   ! Add a 1d/2d field based on patch or column data
-  public :: hist_add_subscript   ! Add a 2d subscript dimension
+
 
   public :: hist_printflds       ! Print summary of list of all history fields
   public :: htapes_fieldlist     ! Finalize history file field lists, intersecting allhistfldlist with
@@ -196,10 +196,6 @@ module histFileMod
                                                   ! is 255. But this can't be increased until all hard
                                                   ! coded values throughout the i/o stack are updated.
   integer, parameter :: max_chars = 199        ! max chars for char variables
-  integer, parameter :: max_subs = 100         ! max number of subscripts
-  integer            :: num_subs = 0           ! actual number of subscripts
-  character(len=32)  :: subs_name(max_subs)    ! name of subscript
-  integer            :: subs_dim(max_subs)     ! dimension of subscript
 
   ! type2d value for a field without a level dimension. This value is important for the
   ! following reasons (as of 2023-08-21):
@@ -256,8 +252,11 @@ end subroutine copy_entry_interface
   end interface
 
   ! Additional per-field metadata. See also history_entry. 
-  ! These values are specified in hist_addfld* calls but then can be
-  ! overridden by namelist params like hist_fincl1.
+  ! For the primary history tape, some fields are enabled here (inside hist_addfld* 
+  ! call)  but then can be overridden by namelist params (like hist_fincl1). The
+  ! fields for other history tapes are theoretically settable here but in
+  ! practice are all disabled.  Fields for those tapes have to be specified
+  ! explicitly and manually via hist_fincl2 et al.
   type, extends(entry_base) :: allhistfldlist_entry
      logical :: actflag(max_tapes)  ! which history tapes to write to. 
      character(len=avgflag_strlen) :: avgflag(max_tapes)  ! type of time averaging
@@ -307,8 +306,8 @@ end subroutine copy_entry_interface
   type (clmpoint_ra) :: clmptr_ra(max_mapflds) ! Real array data (2D)
   !
   ! History field metadata including which history tapes (if any) it should be output to, and
-  ! type of accumulation to perform. The field ordering is arbitrary, depending on the order of
-  ! hist_addfld* calls in the code.
+  ! type of accumulation to perform. This list contains all possible fields, and their field ordering 
+  ! is arbitrary, as it depends on the order of hist_addfld* calls in the code.
   ! For the field data itself, see 'tape'.
   !
   type (allhistfldlist_entry) :: allhistfldlist(max_flds)  ! list of all history fields
@@ -1172,6 +1171,7 @@ subroutine htape_addfld (t, f, avgflag)
     integer :: beg1d,end1d          ! beginning and ending indices for this field (assume already set)
     integer :: num1d_out            ! history output 1d size
     type(bounds_type) :: bounds
+    character(len=avgflag_strlen) :: avgflag_temp  ! local copy of hist_avgflag_pertape(t)
     character(len=*),parameter :: subname = 'htape_addfld'
     !-----------------------------------------------------------------------
 
@@ -1302,6 +1302,19 @@ subroutine htape_addfld (t, f, avgflag)
        tape(t)%hlist(n)%avgflag = avgflag
     end if
 
+    ! Override this tape's avgflag if nhtfrq == 1
+    if (tape(t)%nhtfrq == 1) then  ! output is instantaneous
+       hist_avgflag_pertape(t) = 'I'
+    end if
+    ! Override this field's avgflag if the namelist or the previous line
+    ! has set this tape to
+    ! - instantaneous (I) or
+    ! - local time (L)
+    avgflag_temp = hist_avgflag_pertape(t)
+    if (avgflag_temp == 'I' .or. avgflag_temp(1:1) == 'L') then
+       tape(t)%hlist(n)%avgflag = avgflag_temp
+    end if
+
   end subroutine htape_addfld
 
   !-----------------------------------------------------------------------
@@ -2490,9 +2503,6 @@ subroutine htape_create (t, histrest)
     ! (although on the history file it will go 1:(nec+1) rather than 0:nec)
     call ncd_defdim(lnfid, 'elevclas' , maxpatch_glc + 1, dimid)
 
-    do n = 1,num_subs
-       call ncd_defdim(lnfid, subs_name(n), subs_dim(n), dimid)
-    end do
     call ncd_defdim(lnfid, 'string_length', hist_dim_name_length, strlen_dimid)
     call ncd_defdim(lnfid, 'scale_type_string_length', scale_type_strlen, dimid)
     call ncd_defdim( lnfid, 'levdcmp', nlevdecomp_full, dimid)
@@ -2662,7 +2672,7 @@ subroutine htape_timeconst3D(t, &
     ! !DESCRIPTION:
     ! Write time constant 3D variables to history tapes.
     ! Only write out when this subroutine is called (normally only for
-    ! primary history files at very first time-step, nstep=0).
+    ! primary history files at very first time-step, nstep=1).
     ! Issue the required netcdf wrapper calls to define the history file
     ! contents.
     !
@@ -3098,6 +3108,7 @@ subroutine htape_timeconst(t, mode)
     integer :: mcdate                     ! current date
     integer :: yr,mon,day,nbsec           ! year,month,day,seconds components of a date
     integer :: hours,minutes,secs         ! hours,minutes,seconds of hh:mm:ss
+    character(len= 12) :: step_or_bounds  ! string used in long_name of several time variables
     character(len= 10) :: basedate        ! base date (yyyymmdd)
     character(len=  8) :: basesec         ! base seconds
     character(len=  8) :: cdate           ! system date
@@ -3357,8 +3368,18 @@ subroutine htape_timeconst(t, mode)
 
        dim1id(1) = time_dimid
        str = 'days since ' // basedate // " " // basesec
-       call ncd_defvar(nfid(t), 'time', tape(t)%ncprec, 1, dim1id, varid, &
-            long_name='time',units=str)
+       if (hist_avgflag_pertape(t) /= 'I') then  ! NOT instantaneous fields tape
+          step_or_bounds = 'time_bounds'
+          long_name = 'time at exact middle of ' // step_or_bounds
+          call ncd_defvar(nfid(t), 'time', tape(t)%ncprec, 1, dim1id, varid, &
+               long_name=long_name, units=str)
+          call ncd_putatt(nfid(t), varid, 'bounds', 'time_bounds')
+       else  ! instantaneous fields tape
+          step_or_bounds = 'time step'
+          long_name = 'time at end of ' // step_or_bounds
+          call ncd_defvar(nfid(t), 'time', tape(t)%ncprec, 1, dim1id, varid, &
+               long_name=long_name, units=str)
+       end if
        cal = get_calendar()
        if (      trim(cal) == NO_LEAP_C   )then
           caldesc = "noleap"
@@ -3366,11 +3387,11 @@ subroutine htape_timeconst(t, mode)
           caldesc = "gregorian"
        end if
        call ncd_putatt(nfid(t), varid, 'calendar', caldesc)
-       call ncd_putatt(nfid(t), varid, 'bounds', 'time_bounds')
 
        dim1id(1) = time_dimid
+       long_name = 'current date (YYYYMMDD) at end of ' // step_or_bounds
        call ncd_defvar(nfid(t) , 'mcdate', ncd_int, 1, dim1id , varid, &
-          long_name = 'current date (YYYYMMDD)')
+          long_name = long_name)
        !
        ! add global attribute time_period_freq
        !
@@ -3397,18 +3418,23 @@ subroutine htape_timeconst(t, mode)
        call ncd_putatt(nfid(t), ncd_global, 'time_period_freq',          &
                           trim(time_period_freq))
 
+       long_name = 'current seconds of current date at end of ' // step_or_bounds
        call ncd_defvar(nfid(t) , 'mcsec' , ncd_int, 1, dim1id , varid, &
-          long_name = 'current seconds of current date', units='s')
+          long_name = long_name, units='s')
+       long_name = 'current day (from base day) at end of ' // step_or_bounds
        call ncd_defvar(nfid(t) , 'mdcur' , ncd_int, 1, dim1id , varid, &
-          long_name = 'current day (from base day)')
+          long_name = long_name)
+       long_name = 'current seconds of current day at end of ' // step_or_bounds
        call ncd_defvar(nfid(t) , 'mscur' , ncd_int, 1, dim1id , varid, &
-          long_name = 'current seconds of current day')
+          long_name = long_name)
        call ncd_defvar(nfid(t) , 'nstep' , ncd_int, 1, dim1id , varid, &
           long_name = 'time step')
 
        dim2id(1) = hist_interval_dimid;  dim2id(2) = time_dimid
-       call ncd_defvar(nfid(t), 'time_bounds', ncd_double, 2, dim2id, varid, &
-          long_name = 'history time interval endpoints')
+       if (hist_avgflag_pertape(t) /= 'I') then  ! NOT instantaneous fields tape
+          call ncd_defvar(nfid(t), 'time_bounds', ncd_double, 2, dim2id, varid, &
+             long_name = 'history time interval endpoints')
+       end if
 
        dim2id(1) = strlen_dimid;  dim2id(2) = time_dimid
        call ncd_defvar(nfid(t), 'date_written', ncd_char, 2, dim2id, varid)
@@ -3436,13 +3462,16 @@ subroutine htape_timeconst(t, mode)
        call ncd_io('mscur' , mscur , 'write', nfid(t), nt=tape(t)%ntimes)
        call ncd_io('nstep' , nstep , 'write', nfid(t), nt=tape(t)%ntimes)
 
-       time = mdcur + mscur/secspday
+       timedata(1) = tape(t)%begtime  ! beginning time
+       timedata(2) = mdcur + mscur/secspday  ! end time
+       if (hist_avgflag_pertape(t) /= 'I') then  ! NOT instantaneous fields tape
+          time = (timedata(1) + timedata(2)) * 0.5_r8
+          call ncd_io('time_bounds', timedata, 'write', nfid(t), nt=tape(t)%ntimes)
+       else
+          time = timedata(2)
+       end if
        call ncd_io('time'  , time  , 'write', nfid(t), nt=tape(t)%ntimes)
 
-       timedata(1) = tape(t)%begtime
-       timedata(2) = time
-       call ncd_io('time_bounds', timedata, 'write', nfid(t), nt=tape(t)%ntimes)
-
        call getdatetime (cdate, ctime)
        call ncd_io('date_written', cdate, 'write', nfid(t), nt=tape(t)%ntimes)
 
@@ -4137,12 +4166,6 @@ subroutine hist_htapes_wrapup( rstwr, nlend, bounds, &
           cycle
        end if
 
-       ! Skip nstep=0 if monthly average
-
-       if (nstep==0 .and. tape(t)%nhtfrq==0) then
-          cycle
-       end if
-
        ! Determine if end of history interval
        tape(t)%is_endhist = .false.
        if (tape(t)%nhtfrq==0) then   !monthly average
@@ -5070,9 +5093,9 @@ subroutine hist_restart_ncd (bounds, ncid, flag, rdate)
                    end if
 
                    call ncd_io(ncid=ncid_hist(t), flag='read', varname=trim(name), &
-                        dim1name=type1d_out, data=hbuf1d)
+                        dim1name=type1d_out, data=hbuf1d, posNOTonfile=.true.)
                    call ncd_io(ncid=ncid_hist(t), flag='read', varname=trim(name_acc), &
-                        dim1name=type1d_out, data=nacs1d)
+                        dim1name=type1d_out, data=nacs1d, posNOTonfile=.true.)
 
                    hbuf(beg1d_out:end1d_out,1) = hbuf1d(beg1d_out:end1d_out)
                    nacs(beg1d_out:end1d_out,1) = nacs1d(beg1d_out:end1d_out)
@@ -5081,9 +5104,9 @@ subroutine hist_restart_ncd (bounds, ncid, flag, rdate)
                    deallocate(nacs1d)
                 else
                    call ncd_io(ncid=ncid_hist(t), flag='read', varname=trim(name), &
-                        dim1name=type1d_out, data=hbuf)
+                        dim1name=type1d_out, data=hbuf, posNOTonfile=.true.)
                    call ncd_io(ncid=ncid_hist(t), flag='read', varname=trim(name_acc), &
-                        dim1name=type1d_out, data=nacs)
+                        dim1name=type1d_out, data=nacs, posNOTonfile=.true.)
                 end if
              end do
 
@@ -5940,31 +5963,6 @@ integer function next_history_pointer_index ()
 
   end function next_history_pointer_index
 
-  !-----------------------------------------------------------------------
-  subroutine hist_add_subscript(name, dim)
-    !
-    ! !DESCRIPTION:
-    ! Add a history variable to the output history tape.
-    !
-    ! !ARGUMENTS:
-    character(len=*), intent(in) :: name ! name of subscript
-    integer         , intent(in) :: dim  ! dimension of subscript
-    !
-    ! !LOCAL VARIABLES:
-    character(len=*),parameter :: subname = 'hist_add_subscript'
-    !-----------------------------------------------------------------------
-
-    num_subs = num_subs + 1
-    if (num_subs > max_subs) then
-       write(iulog,*) trim(subname),' ERROR: ',&
-            ' num_subs = ',num_subs,' greater than max_subs= ',max_subs
-       call endrun(msg=errMsg(sourcefile, __LINE__))
-    endif
-    subs_name(num_subs) = name
-    subs_dim(num_subs) =  dim
-
-  end subroutine hist_add_subscript
-
   !-----------------------------------------------------------------------
 
   subroutine strip_null(str)
diff --git a/src/main/ncdio_pio.F90.in b/src/main/ncdio_pio.F90.in
index 6d58ded872..04ed90a6cd 100644
--- a/src/main/ncdio_pio.F90.in
+++ b/src/main/ncdio_pio.F90.in
@@ -541,14 +541,6 @@ contains
     character(len=32) :: subname = 'ncd_inqfdims' ! subroutine name
     !-----------------------------------------------------------------------
 
-    if (single_column) then
-       ni = 1
-       nj = 1
-       ns = 1
-       isgrid2d = .true.
-       RETURN
-    end if
-
     ni = 0
     nj = 0
 
@@ -1353,7 +1345,7 @@ contains
     start(:) = 0
     count(:) = 0
 
-    if (flag == 'read') then
+    if (flag == 'read' .or. flag == 'read_noscm') then
 
        call ncd_inqvid(ncid, varname, varid, vardesc, readvar=varpresent)
 
@@ -1382,7 +1374,7 @@ contains
 #else
        if (varpresent) then
           allocate(idata1d(size(data)))
-          if (single_column) then
+          if (single_column .and. flag == 'read') then
              call scam_field_offsets(ncid,'undefined', vardesc,&
                   start, count, found=found, posNOTonfile=posNOTonfile)
              if ( found )then
@@ -1478,7 +1470,7 @@ contains
     start(:) = 0
     count(:) = 0
 
-    if (flag == 'read') then
+    if (flag == 'read' .or. flag == 'read_noscm') then
 
        call ncd_inqvid(ncid, varname, varid, vardesc, readvar=varpresent)
 
@@ -1499,7 +1491,7 @@ contains
        end if
 #else
        if (varpresent) then
-          if (single_column) then
+          if (single_column .and. flag == 'read') then
              call scam_field_offsets(ncid,'undefined', vardesc,&
                   start, count, found=found, posNOTonfile=posNOTonfile)
              if ( found )then
@@ -1648,7 +1640,7 @@ contains
   !-----------------------------------------------------------------------
 
   !TYPE int,double,logical
-  subroutine ncd_io_1d_{TYPE}(varname, data, dim1name, flag, ncid, nt, readvar, cnvrtnan2fill)
+  subroutine ncd_io_1d_{TYPE}(varname, data, dim1name, flag, ncid, nt, readvar, cnvrtnan2fill, posNOTonfile)
     !
     ! !DESCRIPTION:
     ! netcdf I/O for 1d
@@ -1662,6 +1654,7 @@ contains
     integer          , optional, intent(in)  :: nt            ! time sample index
     logical          , optional, intent(out) :: readvar       ! true => variable is on initial dataset (read only)
     logical          , optional, intent(in)  :: cnvrtnan2fill ! true => convert any NaN's to _FillValue (spval)
+    logical          , optional, intent(in)  :: posNOTonfile  ! Position is NOT on this file
     !
     ! Local Variables
     character(len=8)                 :: subgrid_level_name   ! nameg, namel, etc.
@@ -1676,12 +1669,15 @@ contains
     integer                          :: start(3)   ! netcdf start index
     integer                          :: count(3)   ! netcdf count index
     integer                          :: status     ! error code
+    logical                          :: found      ! if true, found lat/lon dims on file
     logical                          :: varpresent ! if true, variable is on tape
     integer                          :: xtype      ! type of var in file
     integer                , pointer :: idata(:)   ! Temporary integer data to send to file
     type(iodesc_plus_type) , pointer :: iodesc_plus
     type(var_desc_t)                 :: vardesc
     integer                          :: oldhandle  ! previous value of pio_error_handle
+    integer                          :: ni,nj,ns   ! lat/lon indicies
+    logical                          :: isgrid2d   ! if true, latlon grid
     character(len=*),parameter       :: subname='ncd_io_1d_{TYPE}' ! subroutine name
     !-----------------------------------------------------------------------
 
@@ -1703,14 +1699,15 @@ contains
     end if
 #endif
 
-    if (flag == 'read') then
+    if (flag == 'read' .or. flag == 'read_noscm') then
 
        call ncd_inqvid(ncid, varname, varid, vardesc, readvar=varpresent)
        if (varpresent) then
           if (single_column) then
              start(:) = 1 ; count(:) = 1
-             call scam_field_offsets(ncid,subgrid_level_name,vardesc,start,count)
-             if (trim(subgrid_level_name) == grlnd) then
+             call scam_field_offsets(ncid,subgrid_level_name,vardesc,start,count,found=found,posNOTonfile=posNOTonfile)
+             call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
+             if (isgrid2d) then
                 n=2
                 if (present(nt)) then
                    start(3) = nt ; count(3) = 1
@@ -1823,7 +1820,7 @@ contains
 
   !TYPE int,double
   subroutine ncd_io_2d_{TYPE}(varname, data, dim1name, lowerb2, upperb2, &
-       flag, ncid, nt, readvar, switchdim, cnvrtnan2fill)
+       flag, ncid, nt, readvar, switchdim, cnvrtnan2fill, posNOTonfile )
     !
     ! !DESCRIPTION:
     ! Netcdf i/o of 2d
@@ -1839,7 +1836,7 @@ contains
     logical, optional, intent(out) :: readvar         ! true => variable is on initial dataset (read only)
     logical, optional, intent(in)  :: switchdim       ! true=> permute dim1 and dim2 for output
     logical, optional, intent(in)  :: cnvrtnan2fill   ! true => convert any NaN's to _FillValue (spval)
-    !
+    logical, optional, intent(in)  :: posNOTonfile    ! Position is NOT on this file    !
     ! !LOCAL VARIABLES:
 #if ({ITYPE}==TYPEINT)
     integer , pointer :: temp(:,:)
@@ -1862,7 +1859,10 @@ contains
     logical           :: varpresent ! if true, variable is on tape
     integer           :: lb1,lb2
     integer           :: ub1,ub2
+    integer           :: ni,nj,ns
+    logical           :: isgrid2d   ! if true, latlon grid
     integer           :: xtype      ! netcdf type of variable on file
+    logical           :: found      ! if true, found lat/lon dims on file
 
     type(iodesc_plus_type) , pointer  :: iodesc_plus
     type(var_desc_t)                  :: vardesc
@@ -1898,14 +1898,16 @@ contains
        allocate(temp(lb2:ub2,lb1:ub1))
     end if
 
-    if (flag == 'read') then
+    if (flag == 'read' .or. flag == 'read_noscm') then
 
        call ncd_inqvid(ncid, varname, varid, vardesc, readvar=varpresent)
        if (varpresent) then
-          if (single_column) then
+          if (single_column .and. flag == 'read') then
              start(:) = 1 ; count(:) = 1
-             call scam_field_offsets(ncid, subgrid_level_name, vardesc, start, count)
-             if (trim(subgrid_level_name) == grlnd) then
+             call scam_field_offsets(ncid, subgrid_level_name, vardesc, start, count,found=found,posNOTonfile=posNOTonfile)
+             call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
+             call ncd_inqvdims(ncid, ndims, vardesc)
+             if (isgrid2d) then
                 count(3) = size(data,dim=2)
                 n=3
                 if (present(nt)) then
@@ -1913,11 +1915,9 @@ contains
                    n=4
                 end if
              else
-                count(2) = size(data,dim=2)
-                n=2
+                n=ndims
                 if (present(nt)) then
-                   start(3) = nt ; count(3) = 1
-                   n=3
+                   start(n) = nt ; count(n) = 1
                 end if
              end if
              if (present(switchdim)) then
@@ -2067,7 +2067,7 @@ contains
   !-----------------------------------------------------------------------
 
   !TYPE int,double
-  subroutine ncd_io_3d_{TYPE}(varname, data, dim1name, flag, ncid, nt, readvar)
+  subroutine ncd_io_3d_{TYPE}(varname, data, dim1name, flag, ncid, nt, readvar, posNOTonfile)
     !
     ! !DESCRIPTION:
     ! Netcdf i/o of 3d
@@ -2080,7 +2080,7 @@ contains
     character(len=*) , intent(in)  :: dim1name        ! dimension 1 name
     integer, optional, intent(in)  :: nt              ! time sample index
     logical, optional, intent(out) :: readvar         ! true => variable is on initial dataset (read only)
-    !
+    logical, optional, intent(in)  :: posNOTonfile ! Position is NOT on this file    !
     ! !LOCAL VARIABLES:
     integer                          :: ndim1,ndim2
     character(len=8)                 :: subgrid_level_name   ! nameg, namel, etc.
@@ -2099,6 +2099,9 @@ contains
     logical                          :: varpresent ! if true, variable is on tape
     type(iodesc_plus_type) , pointer :: iodesc_plus
     type(var_desc_t)                 :: vardesc
+    integer                          :: ni,nj,ns
+    logical                          :: isgrid2d   ! if true, latlon grid
+    logical                          :: found      ! if true, found lat/lon dims on file
     character(len=*),parameter :: subname='ncd_io_3d_{TYPE}' ! subroutine name
     !-----------------------------------------------------------------------
 
@@ -2108,15 +2111,16 @@ contains
        write(iulog,*) trim(subname),' ',trim(flag),' ',trim(varname),' ',trim(subgrid_level_name)
     end if
 
-    if (flag == 'read') then
+    if (flag == 'read' .or. flag == 'read_noscm') then
 
        call ncd_inqvid(ncid, varname, varid, vardesc, readvar=varpresent)
        if (varpresent) then
-          if (single_column) then
+          if (single_column .and. flag == 'read') then
              start(:) = 1
              count(:) = 1
-             call scam_field_offsets(ncid, subgrid_level_name, vardesc, start, count)
-             if (trim(subgrid_level_name) == grlnd) then
+             call scam_field_offsets(ncid, subgrid_level_name, vardesc, start, count,found=found,posNOTonfile=posNOTonfile)
+             call ncd_inqfdims(ncid, isgrid2d, ni, nj, ns)
+             if (isgrid2d) then
                 count(3) = size(data,dim=2);
                 count(4) = size(data,dim=3)
                 n=4
@@ -2435,7 +2439,10 @@ contains
        if ( trim(dimname)=='nj'.or. trim(dimname)=='lat'.or. trim(dimname)=='lsmlat') then
           start(i)=latidx
           count(i)=1
-       else if ( trim(dimname)=='ni'.or. trim(dimname)=='lon'.or. trim(dimname)=='lsmlon') then
+       else if ( trim(dimname)=='ni'.or. trim(dimname)=='lon'.or. trim(dimname)=='lsmlon'.or. trim(dimname)=='gridcell') then
+          start(i)=lonidx
+          count(i)=1
+       else if ( trim(dimname)=='gridcell') then
           start(i)=lonidx
           count(i)=1
        else if ( trim(dimname)=='column') then
diff --git a/src/main/organicFileMod.F90 b/src/main/organicFileMod.F90
index 3adbd5b6f1..5b61a8c0db 100644
--- a/src/main/organicFileMod.F90
+++ b/src/main/organicFileMod.F90
@@ -6,8 +6,8 @@ module organicFileMod
 ! !MODULE: organicFileMod
 !
 ! !DESCRIPTION:
-! Contains methods for reading in organic matter data file which has 
-! organic matter density for each grid point and soil level 
+! Contains methods for reading in organic matter data file which has
+! organic matter density for each grid point and soil level
 !
 ! !USES
   use abortutils   , only : endrun
@@ -30,7 +30,7 @@ module organicFileMod
 !
 !EOP
 !
-!----------------------------------------------------------------------- 
+!-----------------------------------------------------------------------
 
 contains
 
@@ -42,7 +42,7 @@ module organicFileMod
 ! !INTERFACE:
   subroutine organicrd(organic)
 !
-! !DESCRIPTION: 
+! !DESCRIPTION:
 ! Read the organic matter dataset.
 !
 ! !USES:
@@ -68,7 +68,7 @@ subroutine organicrd(organic)
 !EOP
     character(len=256) :: locfn                 ! local file name
     type(file_desc_t)  :: ncid                  ! netcdf id
-    integer            :: ni,nj,ns              ! dimension sizes  
+    integer            :: ni,nj,ns              ! dimension sizes
     logical            :: isgrid2d              ! true => file is 2d
     logical            :: readvar               ! true => variable is on dataset
     character(len=32)  :: subname = 'organicrd' ! subroutine name
@@ -77,9 +77,9 @@ subroutine organicrd(organic)
     ! Initialize data to zero - no organic matter dataset
 
     organic(:,:)   = 0._r8
-       
+
     ! Read data if file was specified in namelist
-       
+
     if (fsurdat /= ' ') then
        if (masterproc) then
           write(iulog,*) 'Attempting to read organic matter data .....'
@@ -90,14 +90,14 @@ subroutine organicrd(organic)
        call ncd_pio_openfile (ncid, locfn, 0)
 
        call ncd_inqfdims (ncid, isgrid2d, ni, nj, ns)
-       if (ldomain%ns /= ns .or. ldomain%ni /= ni .or. ldomain%nj /= nj) then
+       if (.not. single_column .and. (ldomain%ns /= ns .or. ldomain%ni /= ni .or. ldomain%nj /= nj)) then
           write(iulog,*)trim(subname), 'ldomain and input file do not match dims '
           write(iulog,*)trim(subname), 'ldomain%ni,ni,= ',ldomain%ni,ni
           write(iulog,*)trim(subname), 'ldomain%nj,nj,= ',ldomain%nj,nj
           write(iulog,*)trim(subname), 'ldomain%ns,ns,= ',ldomain%ns,ns
           call endrun()
        end if
-       
+
        call ncd_io(ncid=ncid, varname='ORGANIC', flag='read', data=organic, &
             dim1name=grlnd, readvar=readvar)
        if (.not. readvar) call endrun('organicrd: errror reading ORGANIC')
diff --git a/src/main/restFileMod.F90 b/src/main/restFileMod.F90
index c7dbf0da72..d82505f4ff 100644
--- a/src/main/restFileMod.F90
+++ b/src/main/restFileMod.F90
@@ -6,13 +6,13 @@ module restFileMod
   !
   ! !USES:
 #include "shr_assert.h"
-  use shr_kind_mod     , only : r8 => shr_kind_r8
+  use shr_kind_mod     , only : r8 => shr_kind_r8, CL=>shr_kind_CL
   use decompMod        , only : bounds_type, get_proc_clumps, get_clump_bounds
   use decompMod        , only : bounds_level_proc
   use spmdMod          , only : masterproc, mpicom
   use abortutils       , only : endrun
   use shr_log_mod      , only : errMsg => shr_log_errMsg
-  use clm_time_manager , only : timemgr_restart_io, get_nstep
+  use clm_time_manager , only : timemgr_restart_io, get_nstep, get_curr_date
   use subgridRestMod   , only : subgridRestWrite, subgridRestRead, subgridRest_read_cleanup
   use accumulMod       , only : accumulRest
   use clm_instMod      , only : clm_instRest
@@ -340,6 +340,7 @@ subroutine restFile_read_pfile( pnamer )
     ! !USES:
     use fileutils , only : opnfil, getavu, relavu
     use clm_varctl, only : rpntfil, rpntdir, inst_suffix
+    use mpi, only : MPI_CHARACTER
     !
     ! !ARGUMENTS:
     character(len=*), intent(out) :: pnamer ! full path of restart file
@@ -347,8 +348,11 @@ subroutine restFile_read_pfile( pnamer )
     ! !LOCAL VARIABLES:
     !EOP
     integer :: i                  ! indices
+    integer :: yr, mon, day, tod
+    character(len=17) :: timestamp
     integer :: nio                ! restart unit
     integer :: status             ! substring check status
+    logical :: found
     character(len=256) :: locfn   ! Restart pointer file name
     !-----------------------------------------------------------------------
 
@@ -359,17 +363,24 @@ subroutine restFile_read_pfile( pnamer )
     ! New history files are always created for branch runs.
 
     if (masterproc) then
-       write(iulog,*) 'Reading restart pointer file....'
+       nio = getavu()
+       call get_curr_date(yr, mon, day, tod)
+       write(timestamp,'(".",i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr,mon,day,tod
+       locfn = trim(rpntdir) //'/'// trim(rpntfil)//trim(inst_suffix)//timestamp
+       inquire(file=trim(locfn), exist=found)
+       if(.not. found) then
+          locfn = trim(rpntdir) //'/'// trim(rpntfil)//trim(inst_suffix)
+       endif
+       write(iulog,*) 'Reading restart pointer file: ',trim(locfn)
+
+       call opnfil (locfn, nio, 'f')
+       read (nio,'(a256)') pnamer
+       call relavu (nio)
     endif
-
-    nio = getavu()
-    locfn = trim(rpntdir) //'/'// trim(rpntfil)//trim(inst_suffix)
-    call opnfil (locfn, nio, 'f')
-    read (nio,'(a256)') pnamer
-    call relavu (nio)
+    call mpi_bcast (pnamer, CL, MPI_CHARACTER, 0, mpicom, status)
 
     if (masterproc) then
-       write(iulog,*) 'Reading restart data.....'
+       write(iulog,*) 'Reading restart data: ',trim(pnamer)
        write(iulog,'(72a1)') ("-",i=1,60)
     end if
 
@@ -422,12 +433,16 @@ subroutine restFile_write_pfile( fnamer )
     ! !LOCAL VARIABLES:
     integer :: m                    ! index
     integer :: nio                  ! restart pointer file
+    integer :: yr, mon, day, tod
+    character(len=17) :: timestamp
     character(len=256) :: filename  ! local file name
     !-----------------------------------------------------------------------
 
     if (masterproc) then
+       call get_curr_date(yr, mon, day, tod)
+       write(timestamp,'(".",i4.4,"-",i2.2,"-",i2.2,"-",i5.5)') yr, mon, day, tod
        nio = getavu()
-       filename= trim(rpntdir) //'/'// trim(rpntfil)//trim(inst_suffix)
+       filename= trim(rpntdir) //'/'// trim(rpntfil)//trim(inst_suffix)//timestamp
        call opnfil( filename, nio, 'f' )
 
        write(nio,'(a)') fnamer
@@ -466,7 +481,7 @@ subroutine restFile_open( flag, file, ncid )
        ! Open netcdf restart file
 
        if (masterproc) then
-          write(iulog,*) 'Reading restart dataset'
+          write(iulog,*) 'Reading restart dataset: ', trim(file)
        end if
        call ncd_pio_openfile (ncid, trim(file), 0)
 
diff --git a/src/main/surfrdMod.F90 b/src/main/surfrdMod.F90
index 4005ec7845..c70ec28fa0 100644
--- a/src/main/surfrdMod.F90
+++ b/src/main/surfrdMod.F90
@@ -363,8 +363,10 @@ subroutine surfrd_get_num_patches (lfsurdat, actual_maxsoil_patches, actual_nump
     type(file_desc_t) :: ncid                 ! netcdf file id
     integer :: dimid                          ! netCDF dimension id
     logical :: cft_dim_exists                 ! dimension exists on dataset
+    logical :: natpft_dim_exists              ! dimension exists on dataset
     integer :: check_numpft                   ! Surface dataset count of numpft, should
                                               ! match maxsoil_patches - actual_numcft
+    integer :: actual_numnatpft               ! natpft value from sfc dataset
     character(len=32) :: subname = 'surfrd_get_num_patches'  ! subroutine name
     !-----------------------------------------------------------------------
 
@@ -396,9 +398,17 @@ subroutine surfrd_get_num_patches (lfsurdat, actual_maxsoil_patches, actual_nump
     call ncd_inqdlen(ncid, dimid, actual_maxsoil_patches, 'lsmpft')
     actual_numpft = actual_maxsoil_patches - actual_numcft
 
-    call ncd_inqdlen(ncid, dimid, check_numpft, 'natpft')
+    ! Read numpft
+    call ncd_inqdid(ncid, 'natpft', dimid, natpft_dim_exists)
+    if ( natpft_dim_exists ) then
+       call ncd_inqdlen(ncid, dimid, actual_numnatpft, 'natpft')
+       call ncd_inqdlen(ncid, dimid, check_numpft, 'natpft')
+    else
+       actual_numnatpft = 0
+    end if
 
-    if(check_numpft.ne.actual_numpft)then
+!jt    if(check_numpft.ne.actual_numpft)then
+    if(actual_numcft+actual_numnatpft.ne.actual_maxsoil_patches)then
        write(iulog,*)'the sum of the cftdim and the natpft dim should match the lsmpft dim in the surface file'
        write(iulog,*)'natpft: ',check_numpft
        write(iulog,*)'lsmpft: ',actual_maxsoil_patches
diff --git a/src/unit_test_shr/unittestTimeManagerMod.F90 b/src/unit_test_shr/unittestTimeManagerMod.F90
index 44109d5b86..8e1cdb3f36 100644
--- a/src/unit_test_shr/unittestTimeManagerMod.F90
+++ b/src/unit_test_shr/unittestTimeManagerMod.F90
@@ -177,9 +177,6 @@ subroutine unittest_timemgr_set_nstep(nstep)
     ! !DESCRIPTION:
     ! Set the time step number
     !
-    ! Note that the starting time step number is 0, so calling this with nstep = 1
-    ! advances the time step beyond the starting time step.
-    !
     ! !USES:
     use clm_time_manager, only : advance_timestep
     !
@@ -192,7 +189,7 @@ subroutine unittest_timemgr_set_nstep(nstep)
     character(len=*), parameter :: subname = 'unittest_timemgr_set_nstep'
     !-----------------------------------------------------------------------
 
-    do n = 1, nstep
+    do n = 2, nstep
        call advance_timestep()
     end do
 
diff --git a/src/utils/AnnualFluxDribbler.F90 b/src/utils/AnnualFluxDribbler.F90
index c7a3b792fe..8ea854b904 100644
--- a/src/utils/AnnualFluxDribbler.F90
+++ b/src/utils/AnnualFluxDribbler.F90
@@ -258,7 +258,8 @@ subroutine set_curr_delta(this, bounds, delta)
        do i = beg_index, end_index
           this%amount_from_this_timestep(i) = delta(i)
        end do
-       if (.not. this%allows_non_annual_delta .and. .not. is_first_step()) then
+       ! is_first_step check no longer necessary since there is no nstep=0
+       if (.not. this%allows_non_annual_delta) then
           do i = beg_index, end_index
              if (this%amount_from_this_timestep(i) /= 0._r8) then
                 write(iulog,*) subname//' ERROR: found unexpected non-zero delta mid-year'
diff --git a/src/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90
index 955d98057a..f606c2832b 100644
--- a/src/utils/clm_time_manager.F90
+++ b/src/utils/clm_time_manager.F90
@@ -19,9 +19,9 @@ module clm_time_manager
 
    public ::&
         set_timemgr_init,         &! setup startup values
-        timemgr_init,             &! time manager initialization
+        timemgr_init,             &! time manager initialization, called always
         timemgr_restart_io,       &! read/write time manager restart info and restart time manager
-        timemgr_restart,          &! restart the time manager using info from timemgr_restart
+        timemgr_restart,          &! check that time manager is setup coorectly upcon restart
         timemgr_datediff,         &! calculate difference between two time instants
         advance_timestep,         &! increment timestep number
         get_curr_ESMF_Time,       &! get current time in terms of the ESMF_Time
@@ -157,7 +157,7 @@ subroutine set_timemgr_init( calendar_in,      start_ymd_in,     start_tod_in, r
     !
     character(len=*), parameter :: sub = 'clm::set_timemgr_init'
 
-    if ( timemgr_set ) call shr_sys_abort( sub//":: timemgr_init or timemgr_restart already called" )
+    if ( timemgr_set ) call shr_sys_abort( sub//":: timemgr_init already called" )
     if (present(calendar_in)      ) calendar         = trim(calendar_in)
     if (present(start_ymd_in)     ) start_ymd        = start_ymd_in
     if (present(start_tod_in)     ) start_tod        = start_tod_in
@@ -177,7 +177,11 @@ end subroutine set_timemgr_init
 
   !=========================================================================================
 
-  subroutine timemgr_init( )
+  subroutine timemgr_init(curr_date_in )
+
+    use clm_varctl, only : nsrest, nsrContinue, nsrBranch
+
+    type(ESMF_Time), intent(in), optional :: curr_date_in 
 
     !---------------------------------------------------------------------------------
     ! Initialize the ESMF time manager from the sync clock
@@ -187,8 +191,8 @@ subroutine timemgr_init( )
     character(len=*), parameter :: sub = 'clm::timemgr_init'
     integer :: rc                            ! return code
     type(ESMF_Time) :: start_date            ! start date for run
-    type(ESMF_Time) :: curr_date             ! temporary date used in logic
     type(ESMF_Time) :: ref_date              ! reference date for time coordinate
+    type(ESMF_Time) :: curr_date             ! temporary date used in logic
     type(ESMF_TimeInterval) :: day_step_size ! day step size
     type(ESMF_TimeInterval) :: step_size     ! timestep size
     !---------------------------------------------------------------------------------
@@ -211,8 +215,11 @@ subroutine timemgr_init( )
     start_date = TimeSetymd( start_ymd, start_tod, "start_date" )
 
     ! Initialize current date
-
-    curr_date = start_date
+    if(present(curr_date_in)) then
+       curr_date = curr_date_in
+    else
+       curr_date = start_date
+    endif
 
     call ESMF_TimeIntervalSet( step_size, s=dtime, rc=rc )
     call chkrc(rc, sub//': error return from ESMF_TimeIntervalSet: setting step_size')
@@ -238,6 +245,11 @@ subroutine timemgr_init( )
        tm_perp_date = TimeSetymd( perpetual_ymd, 0, "tm_perp_date" )
     end if
 
+    ! Advance time step to start at nstep=1
+    if (nsrest /= nsrContinue .and. nsrest /= nsrBranch) then
+       call advance_timestep()
+    end if
+
     ! Print configuration summary to log file (stdout).
 
     if (masterproc) call timemgr_print()
@@ -253,7 +265,7 @@ subroutine init_clock( start_date, ref_date, curr_date )
     !---------------------------------------------------------------------------------
     ! Purpose: Initialize the clock based on the start_date, ref_date and curr_date
     !
-    use ESMF       , only : ESMF_ClockCreate, ESMF_ClockAdvance
+    use ESMF       , only : ESMF_ClockCreate, ESMF_ClockAdvance, esmf_clockiscreated
 
     type(ESMF_Time), intent(in) :: start_date  ! start date for run
     type(ESMF_Time), intent(in) :: ref_date    ! reference date for time coordinate
@@ -277,6 +289,7 @@ subroutine init_clock( start_date, ref_date, curr_date )
     ! manager included in cime appears to require stopTime.
     call ESMF_TimeSet(stop_date, yy=really_big_year, mm=12, dd=31, s=0, &
          calendar=tm_cal, rc=rc)
+    call chkrc(rc, sub//': error return from ESMF_TimeIntervalSet: setting step_size')
 
     ! Error check 
 
@@ -299,9 +312,10 @@ subroutine init_clock( start_date, ref_date, curr_date )
 
     ! Initialize the clock
 
+    
     tm_clock = ESMF_ClockCreate(name="CLM Time-manager clock", timeStep=step_size, startTime=start_date, &
          stopTime=stop_date, refTime=ref_date, rc=rc)
-    call chkrc(rc, sub//': error return from ESMF_ClockSetup')
+    call chkrc(rc, sub//': error return from ESMF_ClockCreate')
 
     ! Advance clock to the current time (in case of a restart)
 
@@ -496,11 +510,15 @@ end subroutine timemgr_restart_io
 
   !=========================================================================================
 
-  subroutine timemgr_restart( )
+  subroutine timemgr_restart()
 
     !---------------------------------------------------------------------------------
-    ! Restart the ESMF time manager using the synclock for ending date.
+    ! On restart do some checkcing to make sure time is synchronized with the clock from CESM.
+    ! Set a couple of variables, and advance the clock, so time is aligned properly.
+   !
+    ! timemgr_init MIST be called before this
     !
+
     character(len=*), parameter :: sub = 'clm::timemgr_restart'
     integer :: rc                            ! return code
     integer :: yr, mon, day, tod             ! Year, month, day, and second as integers
@@ -510,26 +528,22 @@ subroutine timemgr_restart( )
     type(ESMF_TimeInterval) :: day_step_size ! day step size
     type(ESMF_TimeInterval) :: step_size     ! timestep size
     !---------------------------------------------------------------------------------
-    call timemgr_spmdbcast( )
-
-    ! Initialize calendar from restart info
-
-    call init_calendar()
+    ! Check that timemgr_init was already called
+    if ( .not. check_timemgr_initialized(sub) ) return
 
-    ! Initialize the timestep from restart info
+    ! Initialize the timestep
 
     dtime = rst_step_sec
 
-    ! Initialize start date from restart info
-
-    start_date = TimeSetymd( rst_start_ymd, rst_start_tod, "start_date" )
+    ! Check start date from restart info
 
-    ! Initialize current date from restart info
+    if (rst_start_ymd .ne. start_ymd .or. rst_start_tod .ne. start_tod) then
+       call shr_sys_abort(sub//'ERROR: mismatch in start date with restart file')
+    endif
 
-    curr_date = TimeSetymd( rst_curr_ymd, rst_curr_tod, "curr_date" )
-
-    call ESMF_TimeIntervalSet( step_size, s=dtime, rc=rc )
-    call chkrc(rc, sub//': error return from ESMF_TimeIntervalSet: setting step_size')
+    if (rst_ref_ymd .ne. ref_ymd .or. rst_ref_tod .ne. ref_tod) then
+       call shr_sys_abort(sub//'ERROR: mismatch in reference date with restart file')
+    endif
 
     call ESMF_TimeIntervalSet( day_step_size, d=1, rc=rc )
     call chkrc(rc, sub//': error return from ESMF_TimeIntervalSet: setting day_step_size')
@@ -540,12 +554,6 @@ subroutine timemgr_restart( )
 
     ! Initialize ref date from restart info
 
-    ref_date = TimeSetymd( rst_ref_ymd, rst_ref_tod, "ref_date" )
-
-    ! Initialize clock 
-
-    call init_clock( start_date, ref_date, curr_date)
-
     ! Advance the timestep.  
     ! Data from the restart file corresponds to the last timestep of the previous run.
 
@@ -555,12 +563,6 @@ subroutine timemgr_restart( )
 
     tm_first_restart_step = .true.
 
-    ! Print configuration summary to log file (stdout).
-
-    if (masterproc) call timemgr_print()
-
-    timemgr_set = .true.
-
   end subroutine timemgr_restart
 
   !=========================================================================================
@@ -1731,7 +1733,7 @@ end function is_end_curr_year
   logical function is_first_step()
 
     !---------------------------------------------------------------------------------
-    ! Return true on first step of initial run only.
+    ! Return true on first step of startup and hybrid runs.
 
     ! Local variables
     character(len=*), parameter :: sub = 'clm::is_first_step'
@@ -1745,7 +1747,7 @@ logical function is_first_step()
     call ESMF_ClockGet( tm_clock, advanceCount=step_no, rc=rc )
     call chkrc(rc, sub//': error return from ESMF_ClockGet')
     nstep = step_no
-    is_first_step = (nstep == 0)
+    is_first_step = (nstep == 1)
 
   end function is_first_step
   !=========================================================================================
diff --git a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf
index df8a59de4b..d2f984aa5b 100644
--- a/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf
+++ b/src/utils/test/clm_time_manager_test/test_clm_time_manager.pf
@@ -276,7 +276,7 @@ contains
   end subroutine getPrevYearfrac_leapYearAtYearBoundary_returnsCorrectValue
 
   @Test
-  subroutine getNstep_step0(this)
+  subroutine getNstep_step1(this)
     class(TestTimeManager), intent(inout) :: this
     integer :: nstep
 
@@ -284,8 +284,8 @@ contains
 
     nstep = get_nstep()
 
-    @assertEqual(0, nstep)
-  end subroutine getNstep_step0
+    @assertEqual(1, nstep)
+  end subroutine getNstep_step1
 
   @Test
   subroutine getNstep_step3(this)
@@ -377,7 +377,7 @@ contains
 
     call unittest_timemgr_setup(dtime=dtime_int)
 
-    call set_nstep(1)
+    call set_nstep(2)
 
     is_first = is_first_step()
 
diff --git a/tools/site_and_regional/neon_gcs_upload b/tools/site_and_regional/neon_gcs_upload
index 40afef8e74..1c931e3b8d 100755
--- a/tools/site_and_regional/neon_gcs_upload
+++ b/tools/site_and_regional/neon_gcs_upload
@@ -126,7 +126,7 @@ def main(description):
     #os.path.join(os.environ["HOME"],"gcwriter")
 
     # Get the list of supported neon sites from usermods
-    valid_neon_sites = glob.glob(os.path.join(cesmroot,"cime_config","usermods_dirs","NEON","[!d]*"))
+    valid_neon_sites = glob.glob(os.path.join(cesmroot,"cime_config","usermods_dirs","clm","NEON","[!d]*"))
     valid_neon_sites = [v.split('/')[-1] for v in valid_neon_sites]
     filedatestamp = datetime.datetime.now().date()
     site_list, output_root, file_date, upload_finidat, upload_history = get_parser(sys.argv, description, valid_neon_sites)