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Updates from J. K. Moore and J. Yu at UCI
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@mnlevy1981
mnlevy1981 committed May 23, 2024
1 parent 70afe1f commit 97bbb1b
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Showing 7 changed files with 564 additions and 143 deletions.
133 changes: 132 additions & 1 deletion defaults/json/settings_latest+cocco.json
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,32 @@
"subcategory": "10. autotrophs",
"units": "eV"
},
"FeOpt": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": 0.0018,
"((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)) == \"cocco\"": 0.4,
"((autotroph_sname)) == \"diat\"": 0.4,
"((autotroph_sname)) == \"diaz\"": 0.4,
"((autotroph_sname)) == \"sp\"": 0.4,
"default": "1e34"
},
"longname": "N threshold in uptake ratio computations",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"Nfixer": {
"datatype": "logical",
"default_value": {
Expand All @@ -74,6 +100,32 @@
"subcategory": "10. autotrophs",
"units": "1/day"
},
"POpt": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": 0.8,
"((autotroph_sname)) == \"diat\"": 0.8,
"((autotroph_sname)) == \"diaz\"": 0.8,
"((autotroph_sname)) == \"sp\"": 0.8,
"default": "1e34"
},
"longname": "PO4 threshold in uptake ratio computations",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"Qn_fixed": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": "16.0/117",
"((autotroph_sname)) == \"diat\"": "16.0/117",
"((autotroph_sname)) == \"diaz\"": "0.32*(16.0/117)",
"((autotroph_sname)) == \"sp\"": "16.0/117",
"default": "1e34"
},
"longname": "N/C ratio when using fixed N/C ratios",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"Qp_fixed": {
"datatype": "real",
"default_value": {
Expand All @@ -87,6 +139,19 @@
"subcategory": "10. autotrophs",
"units": "unitless"
},
"SiOpt": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": 0.0,
"((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 @@ -137,7 +202,7 @@
"subcategory": "10. autotrophs",
"units": "non-numeric"
},
"gQfe_0": {
"gQfe_max": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": "30e-6",
Expand All @@ -163,6 +228,58 @@
"subcategory": "10. autotrophs",
"units": "unitless"
},
"gQn_max": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": 0.17,
"((autotroph_sname)) == \"diat\"": 0.17,
"((autotroph_sname)) == \"diaz\"": 0.17,
"((autotroph_sname)) == \"sp\"": 0.17,
"default": "1e34"
},
"longname": "Initial N/C ratio for growth",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"gQn_min": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": 0.11,
"((autotroph_sname)) == \"diat\"": 0.11,
"((autotroph_sname)) == \"diaz\"": 0.14,
"((autotroph_sname)) == \"sp\"": 0.11,
"default": "1e34"
},
"longname": "Minimum N/C ratio for growth",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"gQp_max": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": 0.011,
"((autotroph_sname)) == \"diat\"": 0.011,
"((autotroph_sname)) == \"diaz\"": 0.0083,
"((autotroph_sname)) == \"sp\"": 0.011,
"default": "1e34"
},
"longname": "Initial P/C ratio for growth",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"gQp_min": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": 0.0083,
"((autotroph_sname)) == \"diat\"": 0.0083,
"((autotroph_sname)) == \"diaz\"": 0.0037,
"((autotroph_sname)) == \"sp\"": 0.0075,
"default": "1e34"
},
"longname": "Minimum P/C ratio for growth",
"subcategory": "10. autotrophs",
"units": "unitless"
},
"imp_calcifier": {
"datatype": "logical",
"default_value": {
Expand Down Expand Up @@ -729,6 +846,13 @@
"long_name": "((autotroph_lname)) Iron",
"units": "mmol/m^3"
},
"((autotroph_sname))N": {
"dependencies": {
"lvariable_NtoC": ".true."
},
"long_name": "((autotroph_lname)) Nitrogen",
"units": "mmol/m^3"
},
"((autotroph_sname))P": {
"dependencies": {
"lvariable_PtoC": ".true."
Expand Down Expand Up @@ -1092,6 +1216,13 @@
"subcategory": "2. config flags",
"units": "unitless"
},
"lvariable_NtoC": {
"datatype": "logical",
"default_value": ".true.",
"longname": "Control if NtoC ratios in autotrophs vary",
"subcategory": "2. config flags",
"units": "unitless"
},
"lvariable_PtoC": {
"datatype": "logical",
"default_value": ".true.",
Expand Down
112 changes: 111 additions & 1 deletion defaults/settings_latest+cocco.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -148,6 +148,11 @@ _tracer_list :
lvariable_PtoC : .true.
long_name : ((autotroph_lname)) Phosphorus
units : mmol/m^3
((autotroph_sname))N :
dependencies :
lvariable_NtoC : .true.
long_name : ((autotroph_lname)) Nitrogen
units : mmol/m^3
# Per-autotroph (ciso only)
((autotroph_sname))13C :
dependencies :
Expand Down Expand Up @@ -264,6 +269,12 @@ general_parms :
units : unitless
datatype : logical
default_value : .true.
lvariable_NtoC :
longname : Control if NtoC ratios in autotrophs vary
subcategory : 2. config flags
units : unitless
datatype : logical
default_value : .true.
ladjust_bury_coeff :
longname : Control if bury coefficients are adjusted (rather than constant)
subcategory : 2. config flags
Expand Down Expand Up @@ -838,7 +849,29 @@ PFT_derived_types :
((autotroph_sname)) == "diat" : 1.0/117
((autotroph_sname)) == "diaz" : 0.32*(1.0/117)
((autotroph_sname)) == "cocco" : 1.0/117
gQfe_0 :
Qn_fixed :
longname : N/C ratio when using fixed N/C ratios
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 16.0/117
((autotroph_sname)) == "diat" : 16.0/117
((autotroph_sname)) == "diaz" : 0.32*(16.0/117)
((autotroph_sname)) == "cocco" : 16.0/117
SiOpt :
longname : Si threshold in uptake ratio computations
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 0.0
((autotroph_sname)) == "diat" : 10.0
((autotroph_sname)) == "diaz" : 0.0
((autotroph_sname)) == "cocco" : 0.0
gQfe_max :
longname : Initial Fe/C ratio for growth
subcategory : 10. autotrophs
units : unitless
Expand All @@ -860,6 +893,83 @@ PFT_derived_types :
((autotroph_sname)) == "diat" : 2.5e-6
((autotroph_sname)) == "diaz" : 2.5e-6
((autotroph_sname)) == "cocco" : 2.5e-6
FeOpt :
longname : Fe threshold in uptake ratio computations
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 1.8e-3
((autotroph_sname)) == "diat" : 1.8e-3
((autotroph_sname)) == "diaz" : 2.0e-3
((autotroph_sname)) == "cocco" : 1.8e-3
gQp_max :
longname : Initial P/C ratio for growth
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 1.1e-2
((autotroph_sname)) == "diat" : 1.1e-2
((autotroph_sname)) == "diaz" : 8.3e-3
((autotroph_sname)) == "cocco" : 1.1e-2
gQp_min :
longname : Minimum P/C ratio for growth
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 7.5e-3
((autotroph_sname)) == "diat" : 8.3e-3
((autotroph_sname)) == "diaz" : 3.7e-3
((autotroph_sname)) == "cocco" : 8.3e-3
POpt :
longname : PO4 threshold in uptake ratio computations
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 0.8
((autotroph_sname)) == "diat" : 0.8
((autotroph_sname)) == "diaz" : 0.8
((autotroph_sname)) == "cocco" : 0.8
gQn_max :
longname : Initial N/C ratio for growth
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 1.7e-1
((autotroph_sname)) == "diat" : 1.7e-1
((autotroph_sname)) == "diaz" : 1.7e-1
((autotroph_sname)) == "cocco" : 1.7e-1
gQn_min :
longname : Minimum N/C ratio for growth
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 1.1e-1
((autotroph_sname)) == "diat" : 1.1e-1
((autotroph_sname)) == "diaz" : 1.4e-1
((autotroph_sname)) == "cocco" : 1.1e-1
NOpt :
longname : N threshold in uptake ratio computations
subcategory : 10. autotrophs
units : unitless
datatype : real
default_value :
default : 1e34
((autotroph_sname)) == "sp" : 0.4
((autotroph_sname)) == "diat" : 0.4
((autotroph_sname)) == "diaz" : 0.4
((autotroph_sname)) == "cocco" : 0.4
alphaPI_per_day :
longname : Initial slope of P_I curve (GD98)
subcategory : 10. autotrophs
Expand Down
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