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Configure WOMBATlite in 1deg_jra55do_ryf_wombatlite #47

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Aug 22, 2024
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Configure WOMBATlite in 1deg_jra55do_ryf_wombatlite #47

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3 changes: 3 additions & 0 deletions MOM_input
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Expand Up @@ -150,6 +150,9 @@ EPS_OMESH = 1e-13
! === module MOM_tracer_flow_control ===
USE_IDEAL_AGE_TRACER = True ! [Boolean] default = False
! If true, use the ideal_age_example tracer package.
USE_generic_tracer = True ! [Boolean] default = False
! If true and _USE_GENERIC_TRACER is defined as a preprocessor macro, use the
! MOM_generic_tracer packages.

! === module ideal_age_example ===

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12 changes: 11 additions & 1 deletion config.yaml
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Expand Up @@ -14,7 +14,7 @@ jobfs: 10GB
mem: 192GB

walltime: 01:00:00
jobname: 1deg_jra55do_ryf
jobname: 1deg_jra55do_ryf_wombatlite

model: access-om3

Expand All @@ -25,12 +25,22 @@ input:
- /g/data/vk83/experiments/inputs/access-om3/share/meshes/share/2024.01.25/JRA55do-ESMFmesh.nc
- /g/data/vk83/experiments/inputs/access-om3/share/grids/global.1deg/2020.10.22/topog.nc
- /g/data/vk83/experiments/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/ocean_hgrid.nc
- /g/data/vk83/experiments/inputs/access-om3/mom/grids/mosaic/global.1deg/2020.05.30/ocean_mosaic.nc
- /g/data/vk83/experiments/inputs/access-om3/mom/grids/mosaic/global.1deg/2024.05.08/grid_spec.nc
- /g/data/vk83/experiments/inputs/access-om3/mom/grids/vertical/global.1deg/2023.07.28/ocean_vgrid.nc
- /g/data/vk83/experiments/inputs/access-om3/mom/initial_conditions/global.1deg/2020.10.22/ocean_temp_salt.res.nc
- /g/data/vk83/experiments/inputs/access-om3/mom/surface_salt_restoring/global.1deg/2020.05.30/salt_sfc_restore.nc
- /g/data/vk83/experiments/inputs/access-om3/cice/grids/global.1deg/2024.05.14/grid.nc
- /g/data/vk83/experiments/inputs/access-om3/cice/grids/global.1deg/2024.05.14/kmt.nc
- /g/data/vk83/experiments/inputs/access-om3/cice/initial_conditions/global.1deg/2023.07.28/iced.1900-01-01-10800.nc
- /g/data/vk83/experiments/inputs/access-om3/wombat/forcing/global.1deg/2022.02.24/dust.nc
- /g/data/vk83/experiments/inputs/access-om3/wombat/initial_conditions/global.1deg/2021.06.07/FEMIP_model_median_iron_2016_fillmiss.nc
- /g/data/vk83/experiments/inputs/access-om3/wombat/initial_conditions/global.1deg/2024.04.02/GLODAPv2.2016b.NO3_fillmiss.nc
- /g/data/vk83/experiments/inputs/access-om3/wombat/initial_conditions/global.1deg/2024.04.02/GLODAPv2.2016b.oxygen_fillmiss.nc
- /g/data/vk83/experiments/inputs/access-om3/wombat/initial_conditions/global.1deg/2024.04.02/GLODAPv2.2016b.PI_TCO2_fillmiss.nc
- /g/data/vk83/experiments/inputs/access-om3/wombat/initial_conditions/global.1deg/2024.04.02/GLODAPv2.2016b.TAlk_fillmiss.nc
- /g/data/vk83/experiments/inputs/access-om3/wombat/initial_conditions/global.1deg/2024.04.02/GLODAPv2.2016b.TCO2_fillmiss.nc
- /g/data/vk83/experiments/inputs/access-om3/wombat/initial_conditions/global.1deg/2024.04.02/init_ocean_wombatlite.res.nc
- /g/data/vk83/experiments/inputs/JRA-55/RYF/v1-4/data

collate: false
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8 changes: 8 additions & 0 deletions data_table
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@@ -0,0 +1,8 @@
# MOM/FMS data table
#
# gridname | fieldname_code | fieldname_file | file_name | ongrid | factor
# ---------------------------------------------------------------------------------------------------------------------------------
"OCN" , "co2_flux_pcair_atm" , "" , "" , "none" , 315.165e-06
"OCN" , "co2_nat_flux_pcair_atm" , "" , "" , "none" , 284.262e-06
"OCN" , "o2_flux_pcair_atm" , "" , "" , "none" , 0.21
"OCN" , "dry_dep_fe_flux_ice_ocn" , "dust" , "./INPUT/dust.nc" , "none" , -1.0e-06
81 changes: 81 additions & 0 deletions diag_table
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Expand Up @@ -7,6 +7,7 @@
"access-om3.mom6.h.z%4yr-%2mo", 1, "months", 1, "days", "time", 1, "months"
"access-om3.mom6.h.sfc%4yr-%2mo", 1, "days", 1, "days", "time", 1, "months"
"access-om3.mom6.h.static", -1, "days", 1, "days", "time"
"access-om3.mom6.h.wombatlite%4yr-%2mo", 1, "months", 1, "days", "time", 1, "years"

### Section-2: Fields List
#=========================
Expand Down Expand Up @@ -149,3 +150,83 @@
"ocean_model", "sin_rot", "sin_rot", "access-om3.mom6.h.static", "all", ".false.", "none", 2
"ocean_model", "cos_rot", "cos_rot", "access-om3.mom6.h.static", "all", ".false.", "none", 2

# "access-om3.mom6.h.wombatlite%4yr-%2mo"
"ocean_model", "volcello", "volcello", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "pco2", "pco2", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "paco2", "paco2", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "light_limit", "light_limit", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "radbio3d", "radbio3d", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "radbio1", "radbio1", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "det_sed_remin", "det_sed_remin", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "det_sed_depst", "det_sed_depst", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "caco3_sed_remin", "caco3_sed_remin", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "caco3_sed_depst", "caco3_sed_depst", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "wdet100", "wdet100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "npp3d", "npp3d", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "npp2d", "npp2d", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "npp1", "npp1", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "pprod_gross", "pprod_gross", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "pprod_gross_2d", "pprod_gross_2d", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "zprod_gross", "zprod_gross", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_intmld", "dic_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_intmld", "adic_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2_intmld", "o2_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "no3_intmld", "no3_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "fe_intmld", "fe_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "phy_intmld", "phy_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "det_intmld", "det_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "pprod_gross_intmld", "pprod_gross_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "npp_intmld", "npp_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "radbio_intmld", "radbio_intmld", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_int100", "dic_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_int100", "adic_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2_int100", "o2_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "no3_int100", "no3_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "fe_int100", "fe_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "phy_int100", "phy_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "det_int100", "det_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "pprod_gross_int100", "pprod_gross_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "npp_int100", "npp_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "radbio_int100", "radbio_int100", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "no3", "no3", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "no3_stf", "no3_stf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "no3_vstf", "no3_vstf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "no3_btf", "no3_btf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "phy", "phy", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "phy_stf", "phy_stf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "phy_trunoff", "phy_trunoff", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2", "o2", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2_stf", "o2_stf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2_stf_gas", "o2_stf_gas", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2_btf", "o2_btf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2_alpha", "o2_alpha", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2_csurf", "o2_csurf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "o2_sc_no", "o2_sc_no", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "zoo", "zoo", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "det", "det", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "caco3", "caco3", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic", "adic", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_stf", "adic_stf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_stf_gas", "adic_stf_gas", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_vstf", "adic_vstf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_btf", "adic_btf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_alpha", "adic_alpha", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_csurf", "adic_csurf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "adic_sc_no", "adic_sc_no", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic", "dic", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_stf", "dic_stf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_stf_gas", "dic_stf_gas", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_vstf", "dic_vstf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_btf", "dic_btf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_alpha", "dic_alpha", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_csurf", "dic_csurf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "dic_sc_no", "dic_sc_no", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "alk", "alk", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "alk_stf", "alk_stf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "alk_vstf", "alk_vstf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "alk_btf", "alk_btf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "fe", "fe", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "fe_stf", "fe_stf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "fe_btf", "fe_btf", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "det_sediment", "det_sediment", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
"generic_wombatlite", "caco3_sediment", "caco3_sediment", "access-om3.mom6.h.wombatlite%4yr-%2mo", "all", "mean", "none", 2
115 changes: 115 additions & 0 deletions field_table
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# WOMBATlite field table
# ===============================================
"namelists","ocean_mod","generic_wombatlite/*global*"
/
"namelists","ocean_mod","generic_wombatlite"
init = f
#
no3_src_file = INPUT/GLODAPv2.2016b.NO3_fillmiss.nc
no3_src_var_name = NO3
no3_src_var_unit = micromoles_per_kg
no3_dest_var_name = no3
no3_dest_var_unit = mol kg-1
no3_src_var_record = 1
no3_src_var_gridspec = NONE
no3_valid_min = 0.0
#
phy_src_file = INPUT/init_ocean_wombatlite.res.nc
phy_src_var_name = phy
phy_src_var_unit = none
phy_dest_var_name = phy
phy_dest_var_unit = mol kg-1
phy_src_var_record = 1
phy_src_var_gridspec = NONE
phy_valid_min = 0.0
#
o2_src_file = INPUT/GLODAPv2.2016b.oxygen_fillmiss.nc
o2_src_var_name = oxygen
o2_src_var_unit = micromoles_per_kg
o2_dest_var_name = o2
o2_dest_var_unit = mol kg-1
o2_src_var_record = 1
o2_src_var_gridspec = NONE
o2_valid_min = 0.0
#
zoo_src_file = INPUT/init_ocean_wombatlite.res.nc
zoo_src_var_name = zoo
zoo_src_var_unit = none
zoo_dest_var_name = zoo
zoo_dest_var_unit = mol kg-1
zoo_src_var_record = 1
zoo_src_var_gridspec = NONE
zoo_valid_min = 0.0
#
det_src_file = INPUT/init_ocean_wombatlite.res.nc
det_src_var_name = det
det_src_var_unit = none
det_dest_var_name = det
det_dest_var_unit = mol kg-1
det_src_var_record = 1
det_src_var_gridspec = NONE
det_valid_min = 0.0
#
caco3_src_file = INPUT/init_ocean_wombatlite.res.nc
caco3_src_var_name = caco3
caco3_src_var_unit = none
caco3_dest_var_name = caco3
caco3_dest_var_unit = mol kg-1
caco3_src_var_record = 1
caco3_src_var_gridspec = NONE
caco3_valid_min = 0.0
#
adic_src_file = INPUT/GLODAPv2.2016b.TCO2_fillmiss.nc
adic_src_var_name = TCO2
adic_src_var_unit = micromoles_per_kg
adic_dest_var_name = adic
adic_dest_var_unit = mol kg-1
adic_src_var_record = 1
adic_src_var_gridspec = NONE
adic_valid_min = 0.0
#
dic_src_file = INPUT/GLODAPv2.2016b.PI_TCO2_fillmiss.nc
dic_src_var_name = PI_TCO2
dic_src_var_unit = micromoles_per_kg
dic_dest_var_name = dic
dic_dest_var_unit = mol kg-1
dic_src_var_record = 1
dic_src_var_gridspec = NONE
dic_valid_min = 0.0
#
alk_src_file = INPUT/GLODAPv2.2016b.TAlk_fillmiss.nc
alk_src_var_name = TAlk
alk_src_var_unit = micromoles_per_kg
alk_dest_var_name = alk
alk_dest_var_unit = mol kg-1
alk_src_var_record = 1
alk_src_var_gridspec = NONE
alk_valid_min = 0.0
#
fe_src_file = INPUT/FEMIP_model_median_iron_2016_fillmiss.nc
fe_src_var_name = IRON
fe_src_var_unit = moles_per_liter
fe_dest_var_name = fe
fe_dest_var_unit = mol kg-1
fe_src_var_record = 1
fe_src_var_gridspec = NONE
fe_valid_min = 0.0
#
caco3_sediment_src_file = INPUT/init_ocean_wombatlite.res.nc
caco3_sediment_src_var_name = caco3_sediment
caco3_sediment_src_var_unit = none
caco3_sediment_dest_var_name = caco3_sediment
caco3_sediment_dest_var_unit = mol m-2
caco3_sediment_src_var_record = 1
caco3_sediment_src_var_gridspec = NONE
caco3_sediment_valid_min = 0.0
#
det_sediment_src_file = INPUT/init_ocean_wombatlite.res.nc
det_sediment_src_var_name = det_sediment
det_sediment_src_var_unit = none
det_sediment_dest_var_name = det_sediment
det_sediment_dest_var_unit = mol m-2
det_sediment_src_var_record = 1
det_sediment_src_var_gridspec = NONE
det_sediment_valid_min = 0.0
/
10 changes: 10 additions & 0 deletions input.nml
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parameter_filename = 'MOM_input', 'MOM_override'
/

&generic_tracer_nml
do_generic_tracer=.true.
do_generic_WOMBATlite=.true.
force_update_fluxes=.false. !This has to be set for THERMO_SPANS_COUPLING to work
/

&generic_wombatlite_nml
co2_calc='ocmip2'
/

&fms_nml
clock_grain = 'ROUTINE'
clock_flags = 'NONE'
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