diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs index fca4a8315b..089e9fbb12 100644 --- a/.git-blame-ignore-revs +++ b/.git-blame-ignore-revs @@ -52,3 +52,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0 753fda3ff0147837231a73c9c728dd9ce47b5997 f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c +bd535c710db78420b8e8b9d71d88d8339e899c59 diff --git a/.gitmodules b/.gitmodules index 2f99e10305..9c4aedab91 100644 --- a/.gitmodules +++ b/.gitmodules @@ -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 = cime6.1.49 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 = cmeps1.0.32 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 = cdeps1.0.57 +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 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/bld/unit_testers/build-namelist_test.pl b/bld/unit_testers/build-namelist_test.pl index 9959632470..d42487cfdb 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", diff --git a/cime b/cime index a8a04e2d9d..b2f271b174 160000 --- a/cime +++ b/cime @@ -1 +1 @@ -Subproject commit a8a04e2d9deac572e6f2222b4f893a575308db99 +Subproject commit b2f271b1742533715a05701b1bdd80a24bb2ad77 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 @@ - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck - $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/fates_sp + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_nociso_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_nociso_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_deck + $COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck run_component_ctsm env_case.xml diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml index d0130537bb..ea25c74f64 100644 --- a/cime_config/testdefs/ExpectedTestFails.xml +++ b/cime_config/testdefs/ExpectedTestFails.xml @@ -84,21 +84,21 @@ - + FAIL #2619 This failure relates to the following REP failure. - + FAIL #2619 This failure relates to the preceding ERP failure. - + FAIL #2619 @@ -114,7 +114,7 @@ - + FAIL #1733 @@ -127,6 +127,27 @@ + + + FAIL + #2914 + + + + + + FAIL + #2914 + + + + + + FAIL + #2905 + + + FAIL @@ -144,7 +165,28 @@ #2913 - + + + + FAIL + #2913 + + + + + + FAIL + #2913 + + + + + + FAIL + #2913 + + + FAIL @@ -163,6 +205,194 @@ + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + + + FAIL + #2916 + + + + + FAIL diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml index 2e900bd3bc..ed6aaba0b1 100644 --- a/cime_config/testdefs/testlist_clm.xml +++ b/cime_config/testdefs/testlist_clm.xml @@ -1524,7 +1524,7 @@ - + @@ -2412,7 +2412,7 @@ - + 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/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/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 similarity index 100% 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% rename from cime_config/usermods_dirs/newton_krylov_spinup/user_nl_clm 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 4165d0657d..0750c91753 160000 --- a/components/cdeps +++ b/components/cdeps @@ -1 +1 @@ -Subproject commit 4165d0657d6f60e8dba650e9a1771a1344972b76 +Subproject commit 0750c9175395d3ba3bf8eba65703dee230d08572 diff --git a/components/cmeps b/components/cmeps index 5b7d76978e..a91cedfe58 160000 --- a/components/cmeps +++ b/components/cmeps @@ -1 +1 @@ -Subproject commit 5b7d76978e2fdc661ec2de4ba9834b985decadc6 +Subproject commit a91cedfe58658a9fc391195481137a2d83372c25 diff --git a/doc/ChangeLog b/doc/ChangeLog index 58d1794ea5..cc415555ba 100644 --- a/doc/ChangeLog +++ b/doc/ChangeLog @@ -1,4 +1,130 @@ =============================================================== +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 diff --git a/doc/ChangeSum b/doc/ChangeSum index 3d265c41a0..2c0cec5d21 100644 --- a/doc/ChangeSum +++ b/doc/ChangeSum @@ -1,5 +1,6 @@ Tag Who Date Summary ============================================================================================================================ + 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 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/src/cpl/nuopc/lnd_comp_nuopc.F90 b/src/cpl/nuopc/lnd_comp_nuopc.F90 index 9631e807cd..c76414bf5d 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 @@ -1038,53 +1041,54 @@ subroutine ModelSetRunClock(gcomp, rc) call ESMF_LogWrite(subname//'setting alarms for ' // trim(name), ESMF_LOGMSG_INFO) !---------------- - ! Restart alarm + ! Stop alarm !---------------- - call NUOPC_CompAttributeGet(gcomp, name="restart_option", value=restart_option, rc=rc) + 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="restart_n", value=cvalue, rc=rc) + call NUOPC_CompAttributeGet(gcomp, name="stop_n", value=cvalue, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return - read(cvalue,*) restart_n + read(cvalue,*) stop_n - call NUOPC_CompAttributeGet(gcomp, name="restart_ymd", value=cvalue, rc=rc) + call NUOPC_CompAttributeGet(gcomp, name="stop_ymd", value=cvalue, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return - read(cvalue,*) restart_ymd + read(cvalue,*) stop_ymd - call alarmInit(mclock, restart_alarm, restart_option, & - opt_n = restart_n, & - opt_ymd = restart_ymd, & + call alarmInit(mclock, stop_alarm, stop_option, & + opt_n = stop_n, & + opt_ymd = stop_ymd, & RefTime = mcurrTime, & - alarmname = 'alarm_restart', rc=rc) + alarmname = 'alarm_stop', rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return - call ESMF_AlarmSet(restart_alarm, clock=mclock, rc=rc) + call ESMF_AlarmSet(stop_alarm, clock=mclock, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return !---------------- - ! Stop alarm + ! Restart alarm !---------------- - call NUOPC_CompAttributeGet(gcomp, name="stop_option", value=stop_option, rc=rc) + call NUOPC_CompAttributeGet(gcomp, name="restart_option", value=restart_option, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return - call NUOPC_CompAttributeGet(gcomp, name="stop_n", value=cvalue, rc=rc) + call NUOPC_CompAttributeGet(gcomp, name="restart_n", value=cvalue, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return - read(cvalue,*) stop_n + read(cvalue,*) restart_n - call NUOPC_CompAttributeGet(gcomp, name="stop_ymd", value=cvalue, rc=rc) + call NUOPC_CompAttributeGet(gcomp, name="restart_ymd", value=cvalue, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return - read(cvalue,*) stop_ymd + read(cvalue,*) restart_ymd - call alarmInit(mclock, stop_alarm, stop_option, & - opt_n = stop_n, & - opt_ymd = stop_ymd, & + call alarmInit(mclock, restart_alarm, restart_option, & + opt_n = restart_n, & + opt_ymd = restart_ymd, & RefTime = mcurrTime, & - alarmname = 'alarm_stop', rc=rc) + alarmname = 'alarm_restart', rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return - call ESMF_AlarmSet(stop_alarm, clock=mclock, rc=rc) + call ESMF_AlarmSet(restart_alarm, clock=mclock, rc=rc) if (ChkErr(rc,__LINE__,u_FILE_u)) return + end if !-------------------------------- 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/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/utils/clm_time_manager.F90 b/src/utils/clm_time_manager.F90 index 955d98057a..b0bcef0691 100644 --- a/src/utils/clm_time_manager.F90 +++ b/src/utils/clm_time_manager.F90 @@ -177,7 +177,8 @@ end subroutine set_timemgr_init !========================================================================================= - subroutine timemgr_init( ) + subroutine timemgr_init(curr_date_in ) + type(ESMF_Time), intent(in), optional :: curr_date_in !--------------------------------------------------------------------------------- ! Initialize the ESMF time manager from the sync clock @@ -187,8 +188,8 @@ 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 +212,11 @@ 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') @@ -253,7 +257,7 @@ 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 +281,7 @@ 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 +304,10 @@ 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 +502,12 @@ end subroutine timemgr_restart_io !========================================================================================= - subroutine timemgr_restart( ) + subroutine timemgr_restart() !--------------------------------------------------------------------------------- ! Restart the ESMF time manager using the synclock for ending date. ! + character(len=*), parameter :: sub = 'clm::timemgr_restart' integer :: rc ! return code integer :: yr, mon, day, tod ! Year, month, day, and second as integers @@ -520,16 +527,15 @@ subroutine timemgr_restart( ) 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 +546,6 @@ 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. 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)