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Fe updates from UCI #464

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70afe1f
add variable C to N
nicola-wiseman Sep 9, 2022
97bbb1b
Updates from J. K. Moore and J. Yu at UCI
mnlevy1981 May 23, 2024
9422a43
Fix code consistency issues in Fortran
mnlevy1981 May 23, 2024
961ca65
Clean up trailing white space in YAML
mnlevy1981 May 23, 2024
6681874
Re-enable Fe balance check, clean up code
mnlevy1981 May 23, 2024
caf8308
Merge branch 'development' into fe_updates_from_uci
mnlevy1981 May 24, 2024
b51320f
Update the 4p2z settings file and input files
mnlevy1981 May 24, 2024
d3a3cdb
Missing 'cocco' value in a couple of 4p2z defaults
mnlevy1981 May 24, 2024
46a90f6
Clean up variable P:C and N:C logic
mnlevy1981 May 25, 2024
123888a
Update older settings files
mnlevy1981 May 25, 2024
e04257d
Add most of the new settings to SPECRTA file
mnlevy1981 May 25, 2024
f771fd6
Add fixed_NtoC settings file for testing
mnlevy1981 May 25, 2024
df02542
Remove Qn_fixed from autotroph_settings_type
mnlevy1981 May 30, 2024
be7794d
Changes to pass call_compute_subroutines tests
mnlevy1981 Jun 4, 2024
9733088
initialize coccoN by scaling spC
mnlevy1981 Jun 4, 2024
1f36f5b
Merge tag 'marbl0.48.2' into fe_updates_from_uci
mnlevy1981 Dec 26, 2024
2d313de
Fix units and argument order
mnlevy1981 Jan 9, 2025
01f796f
Bugfix: update operator
mnlevy1981 Jan 9, 2025
66c1e42
Update diagnostics YAML file
mnlevy1981 Jan 10, 2025
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4 changes: 2 additions & 2 deletions MARBL_tools/run_test_suite.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -77,7 +77,7 @@ cd ${MARBL_ROOT}/MARBL_tools
(set -x ; ./MARBL_generate_settings_file.py)
STATUS=$(check_return $?)
print_status "MARBL_generate_settings_file.py" >> ${RESULTS_CACHE}
for shortname in cesm2.0 cesm2.1 cesm2.1+cocco latest latest+cocco; do
for shortname in cesm2.0 cesm2.1 cesm2.1+cocco latest latest+cocco latest+4p2z; do
(set -x ; ./MARBL_generate_settings_file.py -f ../defaults/json/settings_${shortname}.json -o marbl_${shortname}.settings)
STATUS=$(check_return $?)
print_status "MARBL_generate_settings_file.py (${shortname})" >> ${RESULTS_CACHE}
Expand Down Expand Up @@ -144,7 +144,7 @@ if [ "${STATUS}" == "PASS" ]; then
print_status "init.py ($(basename ${settingsfile}))" >> ${RESULTS_CACHE}
done
# Initialize MARBL with settings generated from every JSON file
for shortname in cesm2.0 cesm2.1 cesm2.1+cocco latest latest+cocco; do
for shortname in cesm2.0 cesm2.1 cesm2.1+cocco latest latest+cocco latest+4p2z; do
if [ -f ../../../MARBL_tools/marbl_${shortname}.settings ]; then
(set -x ; ./init.py -s ../../../MARBL_tools/marbl_${shortname}.settings)
STATUS=$(check_return $?)
Expand Down
59 changes: 59 additions & 0 deletions defaults/diagnostics_latest.yaml
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Expand Up @@ -1119,6 +1119,13 @@ DONr_remin :
frequency : low
operator : average
diag_mode : full
DON_loss_N_bal:
longname : DON loss, due to N budget balancing
units: mmol/m^3/s
vertical_grid : layer_avg
frequency: never
operator: average
diag_mode : full
DOP_prod :
dependencies :
base_bio_on : .true.
Expand Down Expand Up @@ -1236,6 +1243,24 @@ FESEDFLUX :
frequency : never
operator : average
diag_mode : full
FEREDSEDFLUX :
dependencies :
base_bio_on : .true.
longname : Iron Red Sediment Flux
units : nmol/cm^2/s
vertical_grid : layer_avg
frequency : never
operator : average
diag_mode : full
FEVENTFLUX :
dependencies :
base_bio_on : .true.
longname : Iron Vent Flux
units : nmol/cm^2/s
vertical_grid : layer_avg
frequency : never
operator : average
diag_mode : full

# Particulate 2D diags
POC_FLUX_((particulate_flux_ref_depth_str)) :
Expand All @@ -1256,6 +1281,13 @@ POP_FLUX_((particulate_flux_ref_depth_str)) :
frequency : medium
operator : average
diag_mode : full
PON_FLUX_((particulate_flux_ref_depth_str)) :
longname : PON Flux at ((particulate_flux_ref_depth_str))
units : mmol/m^3 cm/s
vertical_grid : none
frequency : medium
operator : average
diag_mode : full
CaCO3_FLUX_((particulate_flux_ref_depth_str)) :
dependencies :
base_bio_on : .true.
Expand Down Expand Up @@ -1475,6 +1507,20 @@ POP_REMIN_PO4 :
frequency : low
operator : average
diag_mode : full
PON_FLUX_IN :
longname : PON Flux into Cell
units : mmol/m^3 cm/s
vertical_grid : layer_avg
frequency : medium
operator : average
diag_mode : full
PON_PROD :
longname : PON Production
units : mmol/m^3/s
vertical_grid : layer_avg
frequency : medium
operator : average
diag_mode : full
PON_REMIN_DONr :
dependencies :
base_bio_on : .true.
Expand Down Expand Up @@ -2259,6 +2305,19 @@ graze_((autotroph_sname))_((zooplankton_sname))_zint_100m :
frequency : medium
operator : average
diag_mode : full
((autotroph_sname))_Qn :
dependencies: # NOTE: POP treats this as a dependency, though MARBL defines
# these diagnostics independent of lvariable_NtoC; my
# thought is that we don't need these diagnostics with
# fixed N:C so I'd like to update the fortran as well
lvariable_NtoC : .true.
longname : ((autotroph_lname)) N:C ratio
units : 1
vertical_grid : layer_avg
truncate : true
frequency : medium
operator : average
diag_mode : full
photoC_((autotroph_sname)) :
longname : ((autotroph_lname)) C Fixation
units : mmol/m^3/s
Expand Down
66 changes: 66 additions & 0 deletions defaults/json/diagnostics_latest.json
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,18 @@
"units": 1,
"vertical_grid": "none"
},
"((autotroph_sname))_Qn": {
"dependencies": {
"lvariable_NtoC": ".true."
},
"diag_mode": "full",
"frequency": "medium",
"longname": "((autotroph_lname)) N:C ratio",
"operator": "average",
"truncate": true,
"units": 1,
"vertical_grid": "layer_avg"
},
"((autotroph_sname))_Qp": {
"dependencies": {
"lvariable_PtoC": ".true."
Expand Down Expand Up @@ -1575,6 +1587,14 @@
"units": "mmol/m^3 cm/s",
"vertical_grid": "none"
},
"DON_loss_N_bal": {
"diag_mode": "full",
"frequency": "never",
"longname": "DON loss, due to N budget balancing",
"operator": "average",
"units": "mmol/m^3/s",
"vertical_grid": "layer_avg"
},
"DON_prod": {
"dependencies": {
"base_bio_on": ".true."
Expand Down Expand Up @@ -1760,6 +1780,17 @@
"units": "cm/s",
"vertical_grid": "none"
},
"FEREDSEDFLUX": {
"dependencies": {
"base_bio_on": ".true."
},
"diag_mode": "full",
"frequency": "never",
"longname": "Iron Red Sediment Flux",
"operator": "average",
"units": "nmol/cm^2/s",
"vertical_grid": "layer_avg"
},
"FESEDFLUX": {
"dependencies": {
"base_bio_on": ".true."
Expand All @@ -1771,6 +1802,17 @@
"units": "nmol/cm^2/s",
"vertical_grid": "layer_avg"
},
"FEVENTFLUX": {
"dependencies": {
"base_bio_on": ".true."
},
"diag_mode": "full",
"frequency": "never",
"longname": "Iron Vent Flux",
"operator": "average",
"units": "nmol/cm^2/s",
"vertical_grid": "layer_avg"
},
"FG_ALT_CO2": {
"dependencies": {
"base_bio_on": ".true."
Expand Down Expand Up @@ -2318,6 +2360,30 @@
"units": "mmol/m^3 cm/s",
"vertical_grid": "layer_avg"
},
"PON_FLUX_((particulate_flux_ref_depth_str))": {
"diag_mode": "full",
"frequency": "medium",
"longname": "PON Flux at ((particulate_flux_ref_depth_str))",
"operator": "average",
"units": "mmol/m^3 cm/s",
"vertical_grid": "none"
},
"PON_FLUX_IN": {
"diag_mode": "full",
"frequency": "medium",
"longname": "PON Flux into Cell",
"operator": "average",
"units": "mmol/m^3 cm/s",
"vertical_grid": "layer_avg"
},
"PON_PROD": {
"diag_mode": "full",
"frequency": "medium",
"longname": "PON Production",
"operator": "average",
"units": "mmol/m^3/s",
"vertical_grid": "layer_avg"
},
"PON_REMIN_DONr": {
"dependencies": {
"base_bio_on": ".true."
Expand Down
88 changes: 87 additions & 1 deletion defaults/json/settings_cesm2.0.json
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,31 @@
"subcategory": "10. autotrophs",
"units": "eV"
},
"FeOpt": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"diat\"": 0.0018,
"((autotroph_sname)) == \"diaz\"": 0.002,
"((autotroph_sname)) == \"sp\"": 0.0018,
"default": "1e34"
},
"longname": "Fe threshold in uptake ratio computations",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"NOpt": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"diat\"": 0.4,
"((autotroph_sname)) == \"diaz\"": 0.4,
"((autotroph_sname)) == \"sp\"": 0.4,
"default": "1e34"
},
"dependencies": "lvariable_NtoC",
"longname": "N threshold in uptake ratio computations",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"Nfixer": {
"datatype": "logical",
"default_value": {
Expand All @@ -75,6 +100,19 @@
"subcategory": "10. autotrophs",
"units": "1/day"
},
"POpt": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"diat\"": 0.8,
"((autotroph_sname)) == \"diaz\"": 0.8,
"((autotroph_sname)) == \"sp\"": 0.8,
"default": "1e34"
},
"dependencies": "lvariable_PtoC",
"longname": "PO4 threshold in uptake ratio computations",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"Qp_fixed": {
"datatype": "real",
"default_value": {
Expand All @@ -87,6 +125,18 @@
"subcategory": "10. autotrophs",
"units": "unitless"
},
"SiOpt": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"diat\"": 10.0,
"((autotroph_sname)) == \"diaz\"": 0.0,
"((autotroph_sname)) == \"sp\"": 0.0,
"default": "1e34"
},
"longname": "Si threshold in uptake ratio computations",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"_type_name": "autotroph_settings_type",
"agg_rate_max": {
"datatype": "real",
Expand Down Expand Up @@ -133,7 +183,7 @@
"subcategory": "10. autotrophs",
"units": "non-numeric"
},
"gQfe_0": {
"gQfe_max": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"diat\"": "35e-6",
Expand All @@ -157,6 +207,32 @@
"subcategory": "10. autotrophs",
"units": "unitless"
},
"gQp_max": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"diat\"": 0.011,
"((autotroph_sname)) == \"diaz\"": 0.0083,
"((autotroph_sname)) == \"sp\"": 0.011,
"default": "1e34"
},
"dependencies": "lvariable_PtoC",
"longname": "Initial P/C ratio for growth",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"gQp_min": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"diat\"": 0.0083,
"((autotroph_sname)) == \"diaz\"": 0.0037,
"((autotroph_sname)) == \"sp\"": 0.0075,
"default": "1e34"
},
"dependencies": "lvariable_PtoC",
"longname": "Minimum P/C ratio for growth",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"imp_calcifier": {
"datatype": "logical",
"default_value": {
Expand Down Expand Up @@ -1174,7 +1250,17 @@
"subcategory": "3. config flags",
"units": "unitless"
},
"lvariable_NtoC": {
"_append_to_config_keywords": true,
"datatype": "logical",
"default_value": ".false.",
"dependencies": "base_bio_on",
"longname": "Control if NtoC ratios in autotrophs vary",
"subcategory": "3. config flags",
"units": "unitless"
},
"lvariable_PtoC": {
"_append_to_config_keywords": true,
"datatype": "logical",
"default_value": ".true.",
"dependencies": "base_bio_on",
Expand Down
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