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ekluzekekluzek
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Merge pull request #3625 from ekluzek/update_ctsm54_to_5385
 alpha-ctsm5.4.CMIP7.19.ctsm5.3.085: Update ctsm5.4 alpha branch to ctsm5.3.085
2 parents cd6a6c2 + ebef613 commit 3cfe210

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‎.github/workflows/docs-build-and-deploy.yml‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -33,6 +33,10 @@ concurrency:
3333
jobs:
3434

3535
build-and-deploy:
36+
37+
# Only run on upstream repository
38+
if: ${{ github.repository == 'ESCOMP/CTSM' }}
39+
3640
environment:
3741
name: github-pages
3842
url: ${{ steps.deployment.outputs.page_url }}

‎.gitmodules‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@
2828
[submodule "fates"]
2929
path = src/fates
3030
url = https://github.com/NGEET/fates
31-
fxtag = sci.1.87.2_api.41.0.0
31+
fxtag = sci.1.88.0_api.42.0.0
3232
fxrequired = AlwaysRequired
3333
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
3434
fxDONOTUSEurl = https://github.com/NGEET/fates
@@ -100,7 +100,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/CDEPS.git
100100
[submodule "share"]
101101
path = share
102102
url = https://github.com/ESCOMP/CESM_share
103-
fxtag = share1.1.9
103+
fxtag = share1.1.15
104104
fxrequired = ToplevelRequired
105105
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
106106
fxDONOTUSEurl = https://github.com/ESCOMP/CESM_share

‎bld/CLMBuildNamelist.pm‎

Lines changed: 62 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -3770,48 +3770,94 @@ sub setup_logic_c_isotope {
37703770
$log->warning("use_c14 is ONLY scientifically validated with the bgc=BGC configuration" );
37713771
}
37723772
}
3773+
my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
3774+
my $stream_fldfilename_atm_c14 = $nl->get_value('stream_fldfilename_atm_c14');
3775+
my $atm_c14_filename = $nl->get_value('atm_c14_filename');
37733776
if ( &value_is_true($use_c14) ) {
37743777
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14_bombspike', 'use_c14'=>$use_c14 );
3775-
my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
3778+
$use_c14_bombspike = $nl->get_value('use_c14_bombspike');
37763779
if ( &value_is_true($use_c14_bombspike) ) {
3777-
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
3778-
'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
3779-
'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
3780+
if ( defined($stream_fldfilename_atm_c14) ) {
3781+
setup_logic_c14_streams($opts, $nl_flags, $definition, $defaults, $nl);
3782+
} else {
3783+
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
3784+
'use_c14'=>$use_c14, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c14_bombspike'=>$nl->get_value('use_c14_bombspike'),
3785+
'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
3786+
}
3787+
$stream_fldfilename_atm_c14 = $nl->get_value('stream_fldfilename_atm_c14');
3788+
$atm_c14_filename = $nl->get_value('atm_c14_filename');
3789+
if ( defined($stream_fldfilename_atm_c14) && defined($atm_c14_filename) ) {
3790+
$log->fatal_error("Both stream_fldfilename_atm_c14 and atm_c14_filename set, only one should be set");
3791+
}
37803792
}
37813793
} else {
3782-
if ( defined($nl->get_value('use_c14_bombspike')) ||
3783-
defined($nl->get_value('atm_c14_filename')) ) {
3784-
$log->fatal_error("use_c14 is FALSE and use_c14_bombspike or atm_c14_filename set");
3794+
if ( defined($use_c14_bombspike) ||
3795+
defined($stream_fldfilename_atm_c14) ||
3796+
defined($atm_c14_filename) ) {
3797+
$log->fatal_error("use_c14 is FALSE and use_c14_bombspike, stream_fldfilename_atm_c14 or atm_c14_filename set");
37853798
}
37863799
}
3800+
my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
3801+
my $stream_fldfilename_atm_c13 = $nl->get_value('stream_fldfilename_atm_c13');
3802+
my $atm_c13_filename = $nl->get_value('atm_c13_filename');
37873803
if ( &value_is_true($use_c13) ) {
37883804
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13_timeseries', 'use_c13'=>$use_c13 );
3789-
my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
3805+
$use_c13_timeseries = $nl->get_value('use_c13_timeseries');
37903806
if ( &value_is_true($use_c13_timeseries) ) {
3791-
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
3792-
'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
3793-
'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
3807+
if ( defined($stream_fldfilename_atm_c13) ) {
3808+
setup_logic_c13_streams($opts, $nl_flags, $definition, $defaults, $nl);
3809+
} else {
3810+
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',
3811+
'use_c13'=>$use_c13, 'use_cn'=>$nl_flags->{'use_cn'}, 'use_c13_timeseries'=>$nl->get_value('use_c13_timeseries'),
3812+
'ssp_rcp'=>$nl_flags->{'ssp_rcp'} );
3813+
}
3814+
$stream_fldfilename_atm_c13 = $nl->get_value('stream_fldfilename_atm_c13');
3815+
$atm_c13_filename = $nl->get_value('atm_c13_filename');
3816+
if ( defined($stream_fldfilename_atm_c13) && defined($atm_c13_filename) ) {
3817+
$log->fatal_error("Both stream_fldfilename_atm_c13 and atm_c13_filename set, only one should be set");
3818+
}
37943819
}
37953820
} else {
37963821
if ( defined($nl->get_value('use_c13_timeseries')) ||
3822+
defined($nl->get_value('stream_fldfilename_atm_c13')) ||
37973823
defined($nl->get_value('atm_c13_filename')) ) {
3798-
$log->fatal_error("use_c13 is FALSE and use_c13_timeseries or atm_c13_filename set");
3824+
$log->fatal_error("use_c13 is FALSE and use_c13_timeseries, stream_fldfilename_atm_c13 or atm_c13_filename set");
37993825
}
38003826
}
38013827
} else {
38023828
if ( &value_is_true($use_c13) ||
38033829
&value_is_true($use_c14) ||
38043830
&value_is_true($nl->get_value('use_c14_bombspike')) ||
38053831
defined($nl->get_value('atm_c14_filename')) ||
3832+
defined($nl->get_value('stream_fldfilename_atm_c14')) ||
38063833
&value_is_true($nl->get_value('use_c13_timeseries')) ||
3807-
defined($nl->get_value('atm_c13_filename')) ) {
3834+
defined($nl->get_value('atm_c13_filename')) ||
3835+
defined($nl->get_value('stream_fldfilename_atm_c13')) ) {
38083836
$log->fatal_error("bgc=sp and C isotope namelist variables were set, both can't be used at the same time");
38093837
}
38103838
}
38113839
}
38123840

38133841
#-------------------------------------------------------------------------------
38143842

3843+
sub setup_logic_c13_streams {
3844+
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
3845+
#
3846+
# C13 stream file settings
3847+
#
3848+
}
3849+
3850+
#-------------------------------------------------------------------------------
3851+
3852+
sub setup_logic_c14_streams {
3853+
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
3854+
#
3855+
# C14 stream file settings
3856+
#
3857+
}
3858+
3859+
#-------------------------------------------------------------------------------
3860+
38153861
sub setup_logic_nitrogen_deposition {
38163862
my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
38173863

@@ -5334,6 +5380,9 @@ sub write_output_files {
53345380
push @groups, "clm_canopy_inparm";
53355381
push @groups, "prigentroughness";
53365382
push @groups, "zendersoilerod";
5383+
if ( &value_is_true($nl_flags->{'use_cn'}) ) {
5384+
push @groups, "carbon_isotope_streams";
5385+
}
53375386
if (remove_leading_and_trailing_quotes($nl->get_value('snow_cover_fraction_method')) eq 'SwensonLawrence2012') {
53385387
push @groups, "scf_swenson_lawrence_2012_inparm";
53395388
}

‎bld/namelist_files/namelist_definition_ctsm.xml‎

Lines changed: 45 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1806,6 +1806,51 @@ Mapping method from Nitrogen deposition input file to the model resolution
18061806
none = no interpolation
18071807
</entry>
18081808

1809+
<!-- ========================================================================================
1810+
Carbon isotope streams Namelist (only used when use_c13/use_c14 is on and bgc=cn or bgc)
1811+
(Atmospheric C13 and C14 ratios in terms of a delta)
1812+
======================================================================================== -->
1813+
1814+
<entry id="stream_year_first_atm_c14" type="integer" category="datasets"
1815+
group="carbon_isotope_streams" valid_values="" >
1816+
First year to loop over for atmospheric C14 isotope delta data
1817+
</entry>
1818+
1819+
<entry id="stream_year_last_atm_c14" type="integer" category="datasets"
1820+
group="carbon_isotope_streams" valid_values="" >
1821+
Last year to loop over for data atmospheric C14 isotope delta data
1822+
</entry>
1823+
1824+
<entry id="stream_model_year_align_atm_c14" type="integer" category="datasets"
1825+
group="carbon_isotope_streams" valid_values="" >
1826+
Simulation year that aligns with stream_year_first_atm_c14 value
1827+
</entry>
1828+
1829+
<entry id="stream_fldfilename_atm_c14" type="char*512" category="datasets"
1830+
input_pathname="abs" group="carbon_isotope_streams" valid_values="" >
1831+
Filename of input stream data for atmospheric C14 isotope delta data
1832+
</entry>
1833+
1834+
<entry id="stream_year_first_atm_c13" type="integer" category="datasets"
1835+
group="carbon_isotope_streams" valid_values="" >
1836+
First year to loop over for atmospheric C13 isotope delta data
1837+
</entry>
1838+
1839+
<entry id="stream_year_last_atm_c13" type="integer" category="datasets"
1840+
group="carbon_isotope_streams" valid_values="" >
1841+
Last year to loop over for data atmospheric C13 isotope delta data
1842+
</entry>
1843+
1844+
<entry id="stream_model_year_align_atm_c13" type="integer" category="datasets"
1845+
group="carbon_isotope_streams" valid_values="" >
1846+
Simulation year that aligns with stream_year_first_atm_c13 value
1847+
</entry>
1848+
1849+
<entry id="stream_fldfilename_atm_c13" type="char*512" category="datasets"
1850+
input_pathname="abs" group="carbon_isotope_streams" valid_values="" >
1851+
Filename of input stream data for atmospheric C13 isotope delta data
1852+
</entry>
1853+
18091854
<!-- ======================================================================================== -->
18101855
<!-- Prigent roughness stream -->
18111856
<!-- ======================================================================================== -->

‎bld/unit_testers/build-namelist_test.pl‎

Lines changed: 25 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
163163
#
164164
# Figure out number of tests that will run
165165
#
166-
my $ntests = 3396;
166+
my $ntests = 3402;
167167

168168
if ( defined($opts{'compare'}) ) {
169169
$ntests += 2061;
@@ -821,6 +821,30 @@ sub cat_and_create_namelistinfile {
821821
namelst=>"use_c14_bombspike=.true.",
822822
phys=>"clm5_0",
823823
},
824+
"bombspike file and stream" =>{ options=>"-bgc bgc -envxml_dir .",
825+
namelst=>"use_c14=TRUE use_c14_bombspike=.true. stream_fldfilename_atm_c14='/dev/null', atm_c14_filename='/dev/null'",
826+
phys=>"clm6_0",
827+
},
828+
"c13 file and stream" =>{ options=>"-bgc bgc -envxml_dir .",
829+
namelst=>"use_c13_timeseries=.true. stream_fldfilename_atm_c13='/dev/null', atm_c13_filename='/dev/null'",
830+
phys=>"clm6_0",
831+
},
832+
"c13 off, but stream" =>{ options=>"-bgc bgc -envxml_dir .",
833+
namelst=>"use_c13=.false. stream_fldfilename_atm_c13='/dev/null'",
834+
phys=>"clm6_0",
835+
},
836+
"c14 off, but stream" =>{ options=>"-bgc bgc -envxml_dir .",
837+
namelst=>"use_c14=.false. stream_fldfilename_atm_c14='/dev/null'",
838+
phys=>"clm6_0",
839+
},
840+
"sp, but c13 stream" =>{ options=>"-bgc sp -envxml_dir .",
841+
namelst=>"stream_fldfilename_atm_c13='/dev/null'",
842+
phys=>"clm6_0",
843+
},
844+
"sp, but c14 stream" =>{ options=>"-bgc sp -envxml_dir .",
845+
namelst=>"stream_fldfilename_atm_c14='/dev/null'",
846+
phys=>"clm6_0",
847+
},
824848
"lightres no cn" =>{ options=>"-bgc sp -envxml_dir . -light_res 360x720",
825849
namelst=>"",
826850
phys=>"clm5_0",

‎cime_config/testdefs/ExpectedTestFails.xml‎

Lines changed: 9 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -247,6 +247,15 @@
247247

248248
<!-- fates test suite failures -->
249249

250+
<!-- This is commented out because cime currently does NOT allow longnames in the XML in the XSD for this file
251+
<test name="ERS_D_Ld30.f45_f45_mg37.HIST_DATM%CRUv7_CLM50%FATES_SICE_SOCN_SROF_SGLC_SWAV_SESP.izumi_nag.clm-FatesColdLandUse">
252+
<phase name="RUN">
253+
<status>FAIL</status>
254+
<issue>#3500</issue>
255+
</phase>
256+
</test>
257+
-->
258+
250259
<test name="ERS_D_Ld30.f45_f45_mg37.I2000Clm50FatesCruRsGs.izumi_nag.clm-FatesColdLUH2">
251260
<phase name="RUN">
252261
<status>FAIL</status>

‎cime_config/testdefs/testlist_clm.xml‎

Lines changed: 20 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -195,6 +195,25 @@
195195
<option name="comment">Testing that a initial condition file with an missing urban landunit will be filled with another urban landunit</option>
196196
</options>
197197
</test>
198+
199+
<test name="SMS_Ly3" grid="f10_f10_mt232" compset="IHistClm60BgcCropCrujra" testmods="clm-ciso_monthly_2013Start">
200+
<machines>
201+
<machine name="derecho" compiler="intel" category="aux_clm"/>
202+
</machines>
203+
<options>
204+
<option name="wallclock">01:40:00</option>
205+
<option name="comment">Testing a few years with CMIP6 carbon isotopes</option>
206+
</options>
207+
</test>
208+
<test name="SMS_Ly3" grid="f10_f10_mt232" compset="IHistClm60BgcCropCrujra" testmods="clm-ciso_cmip7_monthly_2013Start">
209+
<machines>
210+
<machine name="derecho" compiler="intel" category="aux_clm"/>
211+
</machines>
212+
<options>
213+
<option name="wallclock">01:40:00</option>
214+
<option name="comment">Testing a few years with CMIP7 carbon isotopes</option>
215+
</options>
216+
</test>
198217
<test name="ERS_D_Ld9" grid="ne30pg3_t232" compset="I1850Clm60BgcCropG" testmods="clm/clm60cam7LndTuningMode">
199218
<machines>
200219
<machine name="derecho" compiler="intel" category="aux_clm"/>
@@ -4445,6 +4464,7 @@
44454464
<test name="FUNITCTSM_P1x1" grid="f10_f10_mg37" compset="I2000Clm50Sp">
44464465
<machines>
44474466
<machine name="derecho" compiler="intel" category="aux_clm"/>
4467+
<machine name="derecho" compiler="intel" category="prealpha"/>
44484468
<machine name="izumi" compiler="intel" category="aux_clm"/>
44494469
</machines>
44504470
<options>

‎cime_config/testdefs/testmods_dirs/clm/ciso_cmip7_monthly_2013Start/include_user_mods‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
../ciso_monthly_2013Start

‎cime_config/testdefs/testmods_dirs/clm/ciso_cmip7_monthly_2013Start/user_nl_clm‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
stream_fldfilename_atm_c13 = '$DIN_LOC_ROOT/lnd/clm2/isotopes/ctsmforc.Graven.atm_delta_C13_CMIP7_global_1700-2023_yearly_v3.0_c251013.nc'
2+
stream_fldfilename_atm_c14 = '$DIN_LOC_ROOT/lnd/clm2/isotopes/ctsmforc.Graven.atm_delta_C14_CMIP7_4x1_global_1700-2023_yearly_v3.0_c251013.nc'
3+
stream_year_first_atm_c14 = 2013
4+
stream_model_year_align_atm_c14 = 2013
5+
stream_year_first_atm_c13 = 2013
6+
stream_model_year_align_atm_c13 = 2013

‎cime_config/testdefs/testmods_dirs/clm/ciso_monthly_2013Start/include_user_mods‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1 @@
1+
../ciso_monthly

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