Skip to content

Commit

Permalink
Merge tag 'ctsm5.3.019' into fates-switch-migration
Browse files Browse the repository at this point in the history
Stop running 0th time step

For consistency with CAM.
Fixes #925
Changes answers more than roundoff, same climate.
  • Loading branch information
glemieux committed Jan 15, 2025
2 parents f990b24 + 2f6b129 commit 13a16e5
Show file tree
Hide file tree
Showing 637 changed files with 1,664 additions and 453 deletions.
2 changes: 2 additions & 0 deletions .git-blame-ignore-revs
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ d866510188d26d51bcd6d37239283db690af7e82
e096358c832ab292ddfd22dd5878826c7c788968
475831f0fb0e31e97f630eac4e078c886558b61c
fd5f177131d63d39e79a13918390bdfb642d781e
a51816e0de380300b69db9fc3e2c7fa83b267b64
# Ran SystemTests and python/ctsm through black python formatter
5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
8056ae649c1b37f5e10aaaac79005d6e3a8b2380
Expand All @@ -52,3 +53,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
753fda3ff0147837231a73c9c728dd9ce47b5997
f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c
bd535c710db78420b8e8b9d71d88d8339e899c59
14 changes: 7 additions & 7 deletions .gitmodules
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@
[submodule "fates"]
path = src/fates
url = https://github.com/NGEET/fates
fxtag = sci.1.79.3_api.37.0.0
fxtag = sci.1.80.4_api.37.0.0
fxrequired = AlwaysRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/NCAR/fates-release
Expand All @@ -44,15 +44,15 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper
[submodule "rtm"]
path = components/rtm
url = https://github.com/ESCOMP/RTM
fxtag = rtm1_0_80
fxtag = rtm1_0_84
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/RTM

[submodule "mosart"]
path = components/mosart
url = https://github.com/ESCOMP/MOSART
fxtag = mosart1.1.02
fxtag = mosart1.1.06
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
Expand All @@ -76,31 +76,31 @@ 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

[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

[submodule "cdeps"]
path = components/cdeps
url = https://github.com/ESCOMP/CDEPS.git
fxtag = cdeps1.0.53
fxtag = cdeps1.0.61
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git

[submodule "share"]
path = share
url = https://github.com/ESCOMP/CESM_share
fxtag = share1.1.2
fxtag = share1.1.6
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share
Expand Down
4 changes: 2 additions & 2 deletions README
Original file line number Diff line number Diff line change
Expand Up @@ -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.
Expand Down
4 changes: 3 additions & 1 deletion bld/CLMBuildNamelist.pm
Original file line number Diff line number Diff line change
Expand Up @@ -3399,7 +3399,7 @@ sub setup_logic_mineral_nitrogen_dynamics {
#
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;

my @vars = ( "freelivfix_slope_wet", "freelivfix_intercept" );
my @vars = ( "freelivfix_slope_wet", "freelivfix_intercept", "nfix_method" );
if ( &value_is_true($nl_flags->{'use_cn'}) && &value_is_true($nl->get_value('use_fun')) ) {
foreach my $var ( @vars ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
Expand All @@ -3412,6 +3412,7 @@ sub setup_logic_mineral_nitrogen_dynamics {
}
}
}

}


Expand Down Expand Up @@ -5216,6 +5217,7 @@ sub write_output_files {
}
push @groups, "clm_humanindex_inparm";
push @groups, "cnmresp_inparm";
push @groups, "cnfun_inparm";
push @groups, "photosyns_inparm";
push @groups, "cnfire_inparm";
push @groups, "cn_general";
Expand Down
9 changes: 5 additions & 4 deletions bld/namelist_files/namelist_defaults_ctsm.xml
Original file line number Diff line number Diff line change
Expand Up @@ -524,10 +524,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<!-- The default filenames are given relative to the root directory
for the CLM2 data in the CESM distribution -->
<!-- Plant function types (relative to {csmdata}) -->
<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241017.nc</paramfile>
<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c241017.nc</paramfile>
<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241017.nc</paramfile>
<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241017.nc</paramfile>
<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241119.nc</paramfile>
<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241119.nc</paramfile>
<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241119.nc</paramfile>

<!-- ================================================================== -->
<!-- FATES default parameter file -->
Expand Down Expand Up @@ -1894,6 +1893,8 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
<freelivfix_intercept use_fun=".true." use_cn=".true.">0.0117d00</freelivfix_intercept>
<freelivfix_slope_wet use_fun=".true." use_cn=".true.">0.0006d00</freelivfix_slope_wet>

<nfix_method>Houlton</nfix_method>

<br_root>0.83d-06</br_root>

<!-- Scalar of leaf respiration to vcmax (used for SP mode and with luna) (could vary with physics version) -->
Expand Down
5 changes: 5 additions & 0 deletions bld/namelist_files/namelist_definition_ctsm.xml
Original file line number Diff line number Diff line change
Expand Up @@ -388,6 +388,11 @@ Slope of free living Nitrogen fixation with annual ET
Intercept of free living Nitrogen fixation with zero annual ET
</entry>

<entry id="nfix_method" type="char*25" category="cnfun_inparm"
group="cnfun_inparm" valid_values="Houlton,Bytnerowicz" value="Houlton" >
Choice of nfix parameterization
</entry>

<entry id="use_undercanopy_stability" type="logical" category="clm_physics"
group="canopyfluxes_inparm" valid_values="" >
If TRUE use the undercanopy stability term used with CLM4.5 (Sakaguchi&amp;Zeng, 2008)
Expand Down
4 changes: 2 additions & 2 deletions bld/unit_testers/build-namelist_test.pl
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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 $site (
"AR-SLu", "AU-Emr", "AU-TTE", "CA-NS1", "CA-SF3", "CN-HaM", "DE-Obe", "ES-ES1", "FR-Gri", "IE-Dri", "IT-LMa", "IT-SRo", "RU-Fyo", "US-Aud", "US-Ho1", "US-Ne2", "US-Syv", "ZM-Mon",
"AT-Neu", "AU-Gin", "AU-Tum", "CA-NS2", "CH-Cha", "CN-Qia", "DE-Seh", "ES-ES2", "FR-Hes", "IT-Amp", "IT-Mal", "JP-SMF", "RU-Zot", "US-Bar", "US-KS2", "US-Ne3", "US-Ton",
Expand Down
18 changes: 9 additions & 9 deletions cime_config/config_component.xml
Original file line number Diff line number Diff line change
Expand Up @@ -355,15 +355,15 @@
<valid_values></valid_values>
<default_value></default_value>
<values match="last">
<value compset="_CLM60%[^_]*FATES-SP[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/fates_sp</value>
<value compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
<value compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
<value compset="_CLM60%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_nociso_deck</value>
<value compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_deck</value>
<value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/cmip6_waccm_nociso_deck</value>
<value compset="_CLM60%[^_]*FATES-SP[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/fates_sp</value>
<value compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_nociso_deck</value>
<value compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_deck</value>
<value grid="l%1.9x2.5" compset="_CLM50%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck</value>
<value compset="_CLM60%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_deck</value>
<value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6DECK[%_]" >$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_nociso_deck</value>
<value compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_deck</value>
<value grid="l%1.9x2.5" compset="_CLM60%[^_]*CMIP6WACCMDECK[%_]">$COMP_ROOT_DIR_LND/cime_config/usermods_dirs/clm/cmip6_waccm_nociso_deck</value>
</values>
<group>run_component_ctsm</group>
<file>env_case.xml</file>
Expand Down
Loading

0 comments on commit 13a16e5

Please sign in to comment.