Skip to content

Commit

Permalink
Update the 4p2z settings file and input files
Browse files Browse the repository at this point in the history 
Also removed trailing whitespace I inadvertantly added to marbl_diagnostics_mod
in the last commit
  • Loading branch information
@mnlevy1981
mnlevy1981 committed May 24, 2024
1 parent caf8308 commit b51320f
Show file tree
Hide file tree
Showing 9 changed files with 352 additions and 21 deletions.
133 changes: 132 additions & 1 deletion defaults/json/settings_latest+4p2z.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -54,6 +54,32 @@
"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 @@ -77,6 +103,31 @@
"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)) == \"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 @@ -90,6 +141,18 @@
"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 @@ -140,7 +203,7 @@
"subcategory": "10. autotrophs",
"units": "non-numeric"
},
"gQfe_0": {
"gQfe_max": {
"datatype": "real",
"default_value": {
"((autotroph_sname)) == \"cocco\"": "30e-6",
Expand All @@ -166,6 +229,58 @@
"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 @@ -801,6 +916,14 @@
"long_name": "((autotroph_lname)) Iron",
"units": "mmol/m^3"
},
"((autotroph_sname))N": {
"dependencies": {
"base_bio_on": ".true.",
"lvariable_NtoC": ".true."
},
"long_name": "((autotroph_lname)) Nitrogen",
"units": "mmol/m^3"
},
"((autotroph_sname))P": {
"dependencies": {
"base_bio_on": ".true.",
Expand Down Expand Up @@ -1272,6 +1395,14 @@
"subcategory": "3. config flags",
"units": "unitless"
},
"lvariable_NtoC": {
"datatype": "logical",
"default_value": ".true.",
"dependencies": "base_bio_on",
"longname": "Control if NtoC ratios in autotrophs vary",
"subcategory": "3. config flags",
"units": "unitless"
},
"lvariable_PtoC": {
"datatype": "logical",
"default_value": ".true.",
Expand Down
4 changes: 3 additions & 1 deletion defaults/json/settings_latest+cocco.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -872,6 +872,7 @@
},
"((autotroph_sname))N": {
"dependencies": {
"base_bio_on": ".true.",
"lvariable_NtoC": ".true."
},
"long_name": "((autotroph_lname)) Nitrogen",
Expand Down Expand Up @@ -1346,8 +1347,9 @@
"lvariable_NtoC": {
"datatype": "logical",
"default_value": ".true.",
"dependencies": "base_bio_on",
"longname": "Control if NtoC ratios in autotrophs vary",
"subcategory": "2. config flags",
"subcategory": "3. config flags",
"units": "unitless"
},
"lvariable_PtoC": {
Expand Down
4 changes: 3 additions & 1 deletion defaults/json/settings_latest.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -826,6 +826,7 @@
},
"((autotroph_sname))N": {
"dependencies": {
"base_bio_on": ".true.",
"lvariable_NtoC": ".true."
},
"long_name": "((autotroph_lname)) Nitrogen",
Expand Down Expand Up @@ -1301,8 +1302,9 @@
"lvariable_NtoC": {
"datatype": "logical",
"default_value": ".true.",
"dependencies": "base_bio_on",
"longname": "Control if NtoC ratios in autotrophs vary",
"subcategory": "2. config flags",
"subcategory": "3. config flags",
"units": "unitless"
},
"lvariable_PtoC": {
Expand Down
112 changes: 111 additions & 1 deletion defaults/settings_latest+4p2z.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -214,6 +214,12 @@ _tracer_list :
lvariable_PtoC : .true.
long_name : ((autotroph_lname)) Phosphorus
units : mmol/m^3
((autotroph_sname))N :
dependencies :
base_bio_on : .true.
lvariable_NtoC : .true.
long_name : ((autotroph_lname)) Nitrogen
units : mmol/m^3
# Per-autotroph (ciso only)
((autotroph_sname))13C :
dependencies :
Expand Down Expand Up @@ -373,6 +379,13 @@ general_parms :
units : unitless
datatype : logical
default_value : .true.
lvariable_NtoC :
dependencies : base_bio_on
longname : Control if NtoC ratios in autotrophs vary
subcategory : 3. config flags
units : unitless
datatype : logical
default_value : .true.
ladjust_bury_coeff :
dependencies : base_bio_on
longname : Control if bury coefficients are adjusted (rather than constant)
Expand Down Expand Up @@ -1010,7 +1023,27 @@ 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)
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
gQfe_max :
longname : Initial Fe/C ratio for growth
subcategory : 10. autotrophs
units : unitless
Expand All @@ -1032,6 +1065,83 @@ 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
4 changes: 3 additions & 1 deletion defaults/settings_latest+cocco.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -205,6 +205,7 @@ _tracer_list :
units : mmol/m^3
((autotroph_sname))N :
dependencies :
base_bio_on : .true.
lvariable_NtoC : .true.
long_name : ((autotroph_lname)) Nitrogen
units : mmol/m^3
Expand Down Expand Up @@ -363,8 +364,9 @@ general_parms :
datatype : logical
default_value : .true.
lvariable_NtoC :
dependencies : base_bio_on
longname : Control if NtoC ratios in autotrophs vary
subcategory : 2. config flags
subcategory : 3. config flags
units : unitless
datatype : logical
default_value : .true.
Expand Down
4 changes: 3 additions & 1 deletion defaults/settings_latest.yaml
View file
Original file line number Diff line number Diff line change
Expand Up @@ -205,6 +205,7 @@ _tracer_list :
units : mmol/m^3
((autotroph_sname))N :
dependencies :
base_bio_on : .true.
lvariable_NtoC : .true.
long_name : ((autotroph_lname)) Nitrogen
units : mmol/m^3
Expand Down Expand Up @@ -363,8 +364,9 @@ general_parms :
datatype : logical
default_value : .true.
lvariable_NtoC :
dependencies : base_bio_on
longname : Control if NtoC ratios in autotrophs vary
subcategory : 2. config flags
subcategory : 3. config flags
units : unitless
datatype : logical
default_value : .true.
Expand Down
Loading

0 comments on commit b51320f

Please sign in to comment.