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Bgc updates for cesm2 2 #35

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merged 10 commits into from
Jul 9, 2020
Merged

Bgc updates for cesm2 2 #35

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1639527
Add new valid values for OCN_BGC_CONFIG
mnlevy1981 Jun 18, 2020
244715d
Update fesedflux and init_ecosys files
mnlevy1981 Jun 18, 2020
51ed91e
Add support for C1850ECO_ECOCESM21 compset
mnlevy1981 Jun 19, 2020
89bd6d8
Update ecosys_add_cocco test
mnlevy1981 Jun 19, 2020
362f819
ecosys_add_cocco fails with CESM1850ECO_ECOCESM20
mnlevy1981 Jun 19, 2020
498e38f
Update a couple of init_ecosys_init file options
mnlevy1981 Jun 19, 2020
9a3f9b9
Add PHYS-DEV compset modifier
mnlevy1981 Jun 26, 2020
9484332
Merge branch 'master' into BGC_updates_for_cesm2_2
mnlevy1981 Jul 9, 2020
aea3a89
Updates from code review
mnlevy1981 Jul 9, 2020
e876a92
Use latest MARBL tag
mnlevy1981 Jul 9, 2020
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2 changes: 1 addition & 1 deletion Externals_POP.cfg
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ local_path = externals/CVMix
required = True

[MARBL]
tag = marbl0.35.0
tag = marbl0.39.0
protocol = git
repo_url = https://github.com/marbl-ecosys/MARBL
local_path = externals/MARBL
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3 changes: 2 additions & 1 deletion bld/build-namelist
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Expand Up @@ -344,6 +344,7 @@ my $OCN_TRACER_MODULES_OPT = "$xmlvars{'OCN_TRACER_MODULES_OPT'}";
my $OCN_TAVG_TRACER_BUDGET = "$xmlvars{'OCN_TAVG_TRACER_BUDGET'}";
my $OCN_TAVG_HIFREQ = "$xmlvars{'OCN_TAVG_HIFREQ'}";
my $OCN_ONEDIM = "$xmlvars{'OCN_ONEDIM'}";
my $OCN_PHYS_DEV = "$xmlvars{'OCN_PHYS_DEV'}";
my $POP_DECOMPTYPE = "$xmlvars{'POP_DECOMPTYPE'}";
my $INFO_DBUG = "$xmlvars{'INFO_DBUG'}";
my $RUN_TYPE = "$xmlvars{'RUN_TYPE'}";
Expand Down Expand Up @@ -920,7 +921,7 @@ add_default($nl, 'ah&hmix_del4t_nml');
add_default($nl, 'kappa_isop_choice');
add_default($nl, 'kappa_thic_choice');

add_default($nl, 'kappa_isop_deep');
add_default($nl, 'kappa_isop_deep','ocn_phys_dev'=>"$OCN_PHYS_DEV");
add_default($nl, 'kappa_thic_deep');

# All namelist values are stored in exactly the format
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20 changes: 14 additions & 6 deletions bld/namelist_files/namelist_defaults_pop.xml
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Expand Up @@ -596,10 +596,10 @@
<!-- enhanced diffusivity at depth, only default for 1 degree -->
<!-- until validated at other resolutions -->
<!-------------------------------------------------------------->
<kappa_thic_deep >0.1</kappa_thic_deep>
<kappa_isop_deep >0.1</kappa_isop_deep>
<kappa_isop_deep ocn_grid="gx1v6" >0.2</kappa_isop_deep>
<kappa_isop_deep ocn_grid="gx1v7" >0.2</kappa_isop_deep>
<kappa_thic_deep>0.1</kappa_thic_deep>
<kappa_isop_deep>0.1</kappa_isop_deep>
<kappa_isop_deep ocn_grid="gx1v6" ocn_phys_dev="FALSE">0.2</kappa_isop_deep>
<kappa_isop_deep ocn_grid="gx1v7" ocn_phys_dev="FALSE">0.2</kappa_isop_deep>

<!---------------------------->
<!-- hmix_gm_nml -->
Expand Down Expand Up @@ -1384,7 +1384,11 @@

<fesedflux_input%filename ocn_grid="gx3v7">ocn/pop/gx3v7/forcing/fesedflux_gx3v7_cesm1_97_2017.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v6">ocn/pop/gx1v6/forcing/fesedfluxTot_gx1v6_cesm2_2018_c180618.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v7">ocn/pop/gx1v6/forcing/fesedfluxTot_gx1v6_cesm2_2018_c180618.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v7">ocn/pop/gx1v6/forcing/fesedflux_total_reduce_oxic_POP_gx1v7.c200618.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v6" ocn_bgc_config="cesm2.1">ocn/pop/gx1v6/forcing/fesedfluxTot_gx1v6_cesm2_2018_c180618.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v7" ocn_bgc_config="cesm2.1">ocn/pop/gx1v6/forcing/fesedfluxTot_gx1v6_cesm2_2018_c180618.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v6" ocn_bgc_config="cesm2.1+cocco">ocn/pop/gx1v6/forcing/fesedfluxTot_gx1v6_cesm2_2018_c180618.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v7" ocn_bgc_config="cesm2.1+cocco">ocn/pop/gx1v6/forcing/fesedfluxTot_gx1v6_cesm2_2018_c180618.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v6" ocn_bgc_config="cesm2.0">ocn/pop/gx1v6/forcing/fesedflux_gx1v6_cesm2_2017.nc</fesedflux_input%filename>
<fesedflux_input%filename ocn_grid="gx1v7" ocn_bgc_config="cesm2.0">ocn/pop/gx1v6/forcing/fesedflux_gx1v6_cesm2_2017.nc</fesedflux_input%filename>

Expand Down Expand Up @@ -1636,16 +1640,20 @@
<!----------------------------->

<init_ecosys_init_file ocn_grid="gx3v7">ocn/pop/gx3v7/ic/ecosys_jan_IC_gx3v7_20180308.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx3v7" ocn_bgc_config="latest+cocco">ocn/pop/gx3v7/ic/ecosys_jan_IC_gx3v7_20200325.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx3v7" ocn_bgc_config="cesm2.1+cocco">ocn/pop/gx3v7/ic/ecosys_jan_IC_gx3v7_20200325.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx3v7" ocn_bgc_config="SPECTRA1.0">ocn/pop/gx3v7/ic/ecosys_jan_IC_gx3v7_9p6z_20200325_3impCalc.nc</init_ecosys_init_file>

<init_ecosys_init_file ocn_grid="gx1v6">ocn/pop/gx1v6/ic/ecosys_jan_IC_gx1v6_20180308.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v6" ocn_bgc_config="latest+cocco">ocn/pop/gx1v6/ic/ecosys_jan_IC_gx1v6_20200325.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v6" ocn_bgc_config="cesm2.1+cocco">ocn/pop/gx1v6/ic/ecosys_jan_IC_gx1v6_20200325.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v6" ocn_bgc_config="SPECTRA1.0">ocn/pop/gx1v6/ic/ecosys_jan_IC_gx1v6_9p6z_20200325_3impCalc.nc</init_ecosys_init_file>

<init_ecosys_init_file ocn_grid="gx1v7">ocn/pop/gx1v6/ic/ecosys_jan_IC_omip_POP_gx1v7_c200323.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v7" ocn_bgc_config="cesm2.0">ocn/pop/gx1v6/ic/ecosys_jan_IC_gx1v6_20180308.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v7" ocn_bgc_config="latest+cocco">ocn/pop/gx1v6/ic/ecosys_jan_IC_omip_POP_gx1v7_c200617.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v7" ocn_bgc_config="cesm2.1">ocn/pop/gx1v6/ic/ecosys_jan_IC_omip_POP_gx1v7_c200323.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v7" ocn_bgc_config="cesm2.1+cocco">ocn/pop/gx1v6/ic/ecosys_jan_IC_gx1v6_20200325.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v7" ocn_bgc_config="cesm2.0">ocn/pop/gx1v6/ic/ecosys_jan_IC_gx1v6_20180308.nc</init_ecosys_init_file>
<init_ecosys_init_file ocn_grid="gx1v7" ocn_bgc_config="SPECTRA1.0">ocn/pop/gx1v6/ic/ecosys_jan_IC_gx1v6_9p6z_20200325_3impCalc.nc</init_ecosys_init_file>

<init_ecosys_init_file_fmt>nc</init_ecosys_init_file_fmt>
Expand Down
20 changes: 18 additions & 2 deletions cime_config/config_component.xml
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Expand Up @@ -2,9 +2,11 @@

<entry_id version="3.0">
<description modifier_mode="*">
<desc ocn="POP2[%1D][%ECO][%ECOCESM20][%ABIO-DIC][%PHYS-CYCLE][%DAR][%NDEP]">POP2 </desc>
<desc ocn="POP2[%1D][%PHYS-DEV][%ECO][%ECOCESM21][%ECOCESM20][%ABIO-DIC][%PHYS-CYCLE][%DAR][%NDEP]">POP2 </desc>
<desc option="1D" >Single column </desc>
<desc option="PHYS-DEV">Use development namelist defaults</desc>
<desc option="ECO">Ecosystem</desc>
<desc option="ECOCESM21">Ecosystem, using CESM 2.1 settings</desc>
<desc option="ECOCESM20">Ecosystem, using CESM 2.0 settings</desc>
<desc option="ABIO-DIC">Abiotic DIC/DIC14</desc>
<desc option="PHYS-CYCLE">phys cycle option</desc>
Expand Down Expand Up @@ -81,6 +83,19 @@
<desc>TRUE turns off all horizontal motion in POP (single column)</desc>
</entry>

<entry id="OCN_PHYS_DEV">
<type>logical</type>
<valid_values>TRUE,FALSE</valid_values>
<default_value>FALSE</default_value>
<values>
<value compset = "_POP2%[^_]*PHYS-DEV">TRUE</value>
</values>
<group>run_component_pop</group>
<file>env_run.xml</file>
<desc>TRUE uses development parameter settings that haven't necessarily
been scientifically vetted for all compsets in the POP namelist</desc>
</entry>

<entry id="OCN_NDEP_DRIVER">
<type>logical</type>
<valid_values>TRUE,FALSE</valid_values>
Expand Down Expand Up @@ -203,9 +218,10 @@

<entry id="OCN_BGC_CONFIG">
<type>char</type>
<valid_values>latest,cesm2.0,SPECTRA1.0,cesm2.1+cocco</valid_values>
<valid_values>latest,latest+cocco,cesm2.1,cesm2.1+cocco,cesm2.0,SPECTRA1.0</valid_values>
<default_value>latest</default_value>
<values>
<value compset="POP2%[^_]*ECOCESM21">cesm2.1</value>
<value compset="POP2%[^_]*ECOCESM20">cesm2.0</value>
</values>
<group>run_component_pop</group>
Expand Down
11 changes: 8 additions & 3 deletions cime_config/config_compsets.xml
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Expand Up @@ -81,6 +81,11 @@
<lname>1850_DATM%NYF_SLND_DICE%SSMI_POP2%ECO_DROF%NYF_SGLC_WW3</lname>
</compset>

<compset>
<alias>C1850ECO_ECOCESM21</alias>
<lname>1850_DATM%NYF_SLND_DICE%SSMI_POP2%ECOCESM21_DROF%NYF_SGLC_WW3</lname>
</compset>

<compset>
<alias>C1850ECO_ECOCESM20</alias>
<lname>1850_DATM%NYF_SLND_DICE%SSMI_POP2%ECOCESM20_DROF%NYF_SGLC_WW3</lname>
Expand Down Expand Up @@ -143,9 +148,9 @@
</compset>

<compset>
<!-- latest JRA forcing -->
<alias>G1850ECOIAF_JRA</alias>
<lname>1850_DATM%JRA-1p4-2018_SLND_CICE_POP2%ECO_DROF%JRA-1p4-2018_SGLC_WW3</lname>
<!-- latest JRA forcing with OCN_PHYS_DEV=TRUE -->
<alias>G1850ECOIAF_JRA_PHYS_DEV</alias>
<lname>1850_DATM%JRA-1p4-2018_SLND_CICE_POP2%ECO%PHYS-DEV_DROF%JRA-1p4-2018_SGLC_WW3</lname>
</compset>

<compset>
Expand Down
20 changes: 19 additions & 1 deletion cime_config/testdefs/testlist_pop.xml
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Expand Up @@ -458,6 +458,12 @@
<machine name="cheyenne" compiler="intel" category="aux_cime_baselines"/>
</machines>
</test>
<test name="SMS" grid="T62_g37" compset="C1850ECO_ECOCESM21" testmods="pop/ecosys_add_cocco">
<machines>
<machine name="cheyenne" compiler="intel" category="aux_pop_MARBL"/>
<machine name="hobart" compiler="nag" category="aux_pop_MARBL"/>
</machines>
</test>
<test name="SMS" grid="T62_g17" compset="C1850ECO" testmods="pop/ecosys_add_cocco">
<machines>
<machine name="cheyenne" compiler="intel" category="aux_pop_MARBL"/>
Expand All @@ -468,6 +474,18 @@
<machine name="hobart" compiler="nag" category="aux_pop_MARBL"/>
</machines>
</test>
<test name="SMS" grid="T62_g37" compset="C1850ECO_ECOCESM21" testmods="pop/ecosys">
<machines>
<machine name="cheyenne" compiler="intel" category="aux_pop_MARBL"/>
<machine name="hobart" compiler="nag" category="aux_pop_MARBL"/>
</machines>
</test>
<test name="SMS" grid="T62_g17" compset="C1850ECO_ECOCESM21" testmods="pop/ecosys">
<machines>
<machine name="cheyenne" compiler="intel" category="aux_pop"/>
<machine name="cheyenne" compiler="intel" category="aux_pop_MARBL"/>
</machines>
</test>
<test name="SMS" grid="T62_g37" compset="C1850ECO_ECOCESM20" testmods="pop/ecosys">
<machines>
<machine name="cheyenne" compiler="intel" category="aux_pop_MARBL"/>
Expand Down Expand Up @@ -536,7 +554,7 @@
<machine name="cheyenne" compiler="intel" category="aux_cime_baselines"/>
</machines>
</test>
<test name="SMS_D_Ld2" grid="TL319_g17" compset="G1850ECOIAF_JRA" testmods="pop/cice_ecosys">
<test name="SMS_D_Ld2" grid="TL319_g17" compset="G1850ECOIAF_JRA_PHYS_DEV" testmods="pop/cice_ecosys">
<machines>
<machine name="cheyenne" compiler="intel" category="aux_pop_MARBL"/>
<machine name="cheyenne" compiler="intel" category="aux_pop"/>
Expand Down
12 changes: 11 additions & 1 deletion cime_config/testdefs/testmods_dirs/pop/ecosys_add_cocco/shell_commands
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@@ -1 +1,11 @@
./xmlchange OCN_BGC_CONFIG=cesm2.1+cocco
# Check current value of OCN_BGC_CONFIG
ocn_bgc_config=(`./xmlquery OCN_BGC_CONFIG --value`)

if [[ "${ocn_bgc_config}" == "latest" ]]; then
./xmlchange OCN_BGC_CONFIG=latest+cocco
elif [[ "${ocn_bgc_config}" == "cesm2.1" ]]; then
./xmlchange OCN_BGC_CONFIG=cesm2.1+cocco
elif [[ "${ocn_bgc_config}" != *"cocco"* ]]; then
echo "ERROR: OCN_BGC_CONFIG=${ocn_bgc_config} does not have equivalent option with coccolithophores"
exit 1
fi