Skip to content

More MARBL updates for CESM3 #339

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
mnlevy1981 wants to merge 3 commits into
base: main
Choose a base branch
from
Draft

More MARBL updates for CESM3 #339

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
dad75e5
Add BGC support for tx2_3v3
mnlevy1981 Jun 26, 2026
a584bd1
Update to newer iron forcing scheme
mnlevy1981 Jun 26, 2026
b2c5c99
Fix logic in input_data_list.yaml
mnlevy1981 Jun 26, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
40 changes: 24 additions & 16 deletions param_templates/MOM_input.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -340,29 +340,35 @@ Global:
for the MARBL tracer package."
datatype: string
value:
$MARBL_CONFIG == "latest": ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc
$MARBL_CONFIG == "latest+4p2z": ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc
MARBL_FESEDFLUX_FILE:
$RUN_TYPE == "hybrid":
= f'./{$RUN_REFCASE}.mom6{$INST_SUFFIX}.r.{$RUN_REFDATE}-{$RUN_REFTOD}.nc'
else:
$MARBL_CONFIG == "latest": ${DIN_LOC_ROOT}/ocn/mom/grid_indpt/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc
$MARBL_CONFIG == "latest+4p2z": ${DIN_LOC_ROOT}/ocn/mom/grid_indpt/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc
MARBL_TRACERS_IC_FILE_IS_Z:
description: |
"Name of file containing iron sediment flux
forcing field for the MARBL tracer package."
datatype: string
"[Boolean] default = True
If true, MARBL_TRACERS_IC_FILE is in depth space, not layer space."
datatype: logical
units: Boolean
value:
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedflux_2024algo_tx2_3v2.c251229.nc
MARBL_FESEDFLUXRED_FILE:
$RUN_TYPE == "hybrid": False
MARBL_IC_MIN_VAL:
description: |
"Name of file containing iron reducing sediment flux
forcing field for the MARBL tracer package."
datatype: string
Minimum value of tracer initial conditions
datatype: real
units: conc units
value:
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedfluxRed_2024algo_tx2_3v2.c251229.nc
MARBL_FEVENTFLUX_FILE:
$TEST: 1e-50
$RUN_TYPE == "hybrid": -1e30
MARBL_FEFLUX_FILE:
description: |
"Name of file containing iron sediment flux
forcing field for the MARBL tracer package."
"Name of file containing iron sediment fluxes and vent
flux forcing fields for the MARBL tracer package."
datatype: string
value:
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': feventflux_5gmol_tx2_3v2.c231205.nc
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2"': fesedflux_2024algo_tx2_3v2.c251229.nc
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v3"': fefluxes_sed2024algo_vent2026algo_tx2_3v3.c260625.nc
READ_RIV_FLUXES:
description: |
"Use river fluxes provided by RIV_FLUX_FILE."
Expand All @@ -377,6 +383,8 @@ Global:
value:
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2" and $ROF_GRID == "JRA025"': riv_nut.gnews_gnm.rJRA025_to_tx2_3v2_nnsm_e333r100_230415.20240202.nc
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v2" and $ROF_GRID == "r05"': riv_nut.gnews_gnm.r05_to_tx2_3v2_nnsm_e250r250_230914.20240202.nc
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v3" and $ROF_GRID == "JRA025"': riv_nut.gnews_gnm.rJRA025_to_tx2_3v3_nnsm_e100r100_260306.20260424.nc
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS and $OCN_GRID == "tx2_3v3" and $ROF_GRID == "r05"': riv_nut.gnews_gnm.r05_to_tx2_3v3_nnsm_e100r100_260306.20260424.nc
MARBL_D14C_FILE_1:
description: |
"Name of file containing D14C forcing from 30 N to 90 N."
Expand Down
21 changes: 10 additions & 11 deletions param_templates/input_data_list.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,21 +61,20 @@ mom.input_data_list:
DIAG_COORD_DEF_RHO2:
$OCN_GRID == "tx2_3v2": "${INPUTDIR}/ocean_rho2_190917.nc"
MARBL_TRACERS_IC_FILE:
$MARBL_CONFIG == "latest": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc"
$MARBL_CONFIG == "latest+4p2z": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc"
MARBL_FESEDFLUX_FILE:
$MARBL_CONFIG == "latest": "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc"
$MARBL_CONFIG == "latest+4p2z": "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc"
MARBL_FEFLUX_FILE:
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS':
$OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedflux_2024algo_tx2_3v2.c251229.nc"
MARBL_FESEDFLUXRED_FILE:
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS':
$OCN_GRID == "tx2_3v2": "${INPUTDIR}/fesedfluxRed_2024algo_tx2_3v2.c251229.nc"
MARBL_FEVENTFLUX_FILE:
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS':
$OCN_GRID == "tx2_3v2": "${INPUTDIR}/feventflux_5gmol_tx2_3v2.c231205.nc"
$OCN_GRID == "tx2_3v3": "${INPUTDIR}/fefluxes_sed2024algo_vent2026algo_tx2_3v3.c260625.nc"
RIV_FLUX_FILE:
'"BASE_BIO_ON=TRUE" in $MARBL_TRACER_OPTS':
'$ROF_GRID == "JRA025" and $OCN_GRID == "tx2_3v2"': "${INPUTDIR}/riv_nut.gnews_gnm.rJRA025_to_tx2_3v2_nnsm_e333r100_230415.20240202.nc"
'$ROF_GRID == "r05" and $OCN_GRID == "tx2_3v2"': "${INPUTDIR}/riv_nut.gnews_gnm.r05_to_tx2_3v2_nnsm_e250r250_230914.20240202.nc"
$OCN_GRID == "tx2_3v2":
$ROF_GRID == "JRA025": "${INPUTDIR}/riv_nut.gnews_gnm.rJRA025_to_tx2_3v2_nnsm_e333r100_230415.20240202.nc"
$ROF_GRID == "r05": "${INPUTDIR}/riv_nut.gnews_gnm.r05_to_tx2_3v2_nnsm_e250r250_230914.20240202.nc"
$OCN_GRID == "tx2_3v3":
$ROF_GRID == "JRA025": "${INPUTDIR}/riv_nut.gnews_gnm.rJRA025_to_tx2_3v3_nnsm_e100r100_260306.20260424.nc"
$ROF_GRID == "r05": "${INPUTDIR}/riv_nut.gnews_gnm.r05_to_tx2_3v3_nnsm_e100r100_260306.20260424.nc"
MARBL_D14C_FILE_1:
'"ABIO_DIC_ON=TRUE" in $MARBL_TRACER_OPTS': "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/atm_delta_C14_CMIP6_sector1_global_1850-2015_yearly_v2.0_c240202.nc"
MARBL_D14C_FILE_2:
Expand Down
37 changes: 23 additions & 14 deletions param_templates/json/MOM_input.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -243,29 +243,36 @@
"description": "\"Name of file containing initial conditions\nfor the MARBL tracer package.\"\n",
"datatype": "string",
"value": {
"$MARBL_CONFIG == \"latest\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc",
"$MARBL_CONFIG == \"latest+4p2z\"": "ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc"
"$RUN_TYPE == \"hybrid\"": "= f'./{$RUN_REFCASE}.mom6{$INST_SUFFIX}.r.{$RUN_REFDATE}-{$RUN_REFTOD}.nc'",
"else": {
"$MARBL_CONFIG == \"latest\"": "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc",
"$MARBL_CONFIG == \"latest+4p2z\"": "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc"
}
}
},
"MARBL_FESEDFLUX_FILE": {
"description": "\"Name of file containing iron sediment flux\n forcing field for the MARBL tracer package.\"\n",
"datatype": "string",
"MARBL_TRACERS_IC_FILE_IS_Z": {
"description": "\"[Boolean] default = True\nIf true, MARBL_TRACERS_IC_FILE is in depth space, not layer space.\"\n",
"datatype": "logical",
"units": "Boolean",
"value": {
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedflux_2024algo_tx2_3v2.c251229.nc"
"$RUN_TYPE == \"hybrid\"": false
}
},
"MARBL_FESEDFLUXRED_FILE": {
"description": "\"Name of file containing iron reducing sediment flux\n forcing field for the MARBL tracer package.\"\n",
"datatype": "string",
"MARBL_IC_MIN_VAL": {
"description": "Minimum value of tracer initial conditions\n",
"datatype": "real",
"units": "conc units",
"value": {
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedfluxRed_2024algo_tx2_3v2.c251229.nc"
"$TEST": "1e-50",
"$RUN_TYPE == \"hybrid\"": "-1e30"
}
},
"MARBL_FEVENTFLUX_FILE": {
"description": "\"Name of file containing iron sediment flux\n forcing field for the MARBL tracer package.\"\n",
"MARBL_FEFLUX_FILE": {
"description": "\"Name of file containing iron sediment fluxes and vent\n flux forcing fields for the MARBL tracer package.\"\n",
"datatype": "string",
"value": {
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "feventflux_5gmol_tx2_3v2.c231205.nc"
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\"": "fesedflux_2024algo_tx2_3v2.c251229.nc",
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v3\"": "fefluxes_sed2024algo_vent2026algo_tx2_3v3.c260625.nc"
}
},
"READ_RIV_FLUXES": {
Expand All @@ -280,7 +287,9 @@
"datatype": "string",
"value": {
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\" and $ROF_GRID == \"JRA025\"": "riv_nut.gnews_gnm.rJRA025_to_tx2_3v2_nnsm_e333r100_230415.20240202.nc",
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\" and $ROF_GRID == \"r05\"": "riv_nut.gnews_gnm.r05_to_tx2_3v2_nnsm_e250r250_230914.20240202.nc"
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v2\" and $ROF_GRID == \"r05\"": "riv_nut.gnews_gnm.r05_to_tx2_3v2_nnsm_e250r250_230914.20240202.nc",
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v3\" and $ROF_GRID == \"JRA025\"": "riv_nut.gnews_gnm.rJRA025_to_tx2_3v3_nnsm_e100r100_260306.20260424.nc",
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS and $OCN_GRID == \"tx2_3v3\" and $ROF_GRID == \"r05\"": "riv_nut.gnews_gnm.r05_to_tx2_3v3_nnsm_e100r100_260306.20260424.nc"
}
},
"MARBL_D14C_FILE_1": {
Expand Down
29 changes: 13 additions & 16 deletions param_templates/json/input_data_list.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -78,28 +78,25 @@
"$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/ocean_rho2_190917.nc"
},
"MARBL_TRACERS_IC_FILE": {
"$MARBL_CONFIG == \"latest\"": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc",
"$MARBL_CONFIG == \"latest+4p2z\"": "${INPUTDIR}/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc"
"$MARBL_CONFIG == \"latest\"": "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc",
"$MARBL_CONFIG == \"latest+4p2z\"": "${DIN_LOC_ROOT}/ocn/mom/grid_indpt/ecosys_jan_IC_omip_latlon_1x1_180W_c250613.nc"
},
"MARBL_FESEDFLUX_FILE": {
"MARBL_FEFLUX_FILE": {
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS": {
"$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedflux_2024algo_tx2_3v2.c251229.nc"
}
},
"MARBL_FESEDFLUXRED_FILE": {
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS": {
"$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedfluxRed_2024algo_tx2_3v2.c251229.nc"
}
},
"MARBL_FEVENTFLUX_FILE": {
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS": {
"$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/feventflux_5gmol_tx2_3v2.c231205.nc"
"$OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/fesedflux_2024algo_tx2_3v2.c251229.nc",
"$OCN_GRID == \"tx2_3v3\"": "${INPUTDIR}/fefluxes_sed2024algo_vent2026algo_tx2_3v3.c260625.nc"
}
},
"RIV_FLUX_FILE": {
"\"BASE_BIO_ON=TRUE\" in $MARBL_TRACER_OPTS": {
"$ROF_GRID == \"JRA025\" and $OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/riv_nut.gnews_gnm.rJRA025_to_tx2_3v2_nnsm_e333r100_230415.20240202.nc",
"$ROF_GRID == \"r05\" and $OCN_GRID == \"tx2_3v2\"": "${INPUTDIR}/riv_nut.gnews_gnm.r05_to_tx2_3v2_nnsm_e250r250_230914.20240202.nc"
"$OCN_GRID == \"tx2_3v2\"": {
"$ROF_GRID == \"JRA025\"": "${INPUTDIR}/riv_nut.gnews_gnm.rJRA025_to_tx2_3v2_nnsm_e333r100_230415.20240202.nc",
"$ROF_GRID == \"r05\"": "${INPUTDIR}/riv_nut.gnews_gnm.r05_to_tx2_3v2_nnsm_e250r250_230914.20240202.nc"
},
"$OCN_GRID == \"tx2_3v3\"": {
"$ROF_GRID == \"JRA025\"": "${INPUTDIR}/riv_nut.gnews_gnm.rJRA025_to_tx2_3v3_nnsm_e100r100_260306.20260424.nc",
"$ROF_GRID == \"r05\"": "${INPUTDIR}/riv_nut.gnews_gnm.r05_to_tx2_3v3_nnsm_e100r100_260306.20260424.nc"
}
}
},
"MARBL_D14C_FILE_1": {
Expand Down
Loading