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When I tried to run the "estuary" example after coupling uk-fvcom-FVCOM-FABM_v5_dev with ERSEM, the following Error appeared:
FABM yaml_settings: No value specified for setting fabm.yaml:/instances/O3/initialization/TA; cannot continue because this parameter does not have a default value either.
So I added the initial value of TA in O3 in fabm.yaml:
O3:
long_name: carbonate
model: ersem/carbonate
parameters:
iswCO2: 1 # carbonate system diagnostics (0: off, 1: on), default = 1
iswASFLUX: 1 # air-sea CO2 exchange (0: none, 1: Nightingale and Liss, 2: Wanninkhof 1992 without chemical enhancement, 3: Wanninkhof 1992 with chemical enhancement, 4: Wanninkhof 1999), default = 1
iswtalk: 5 # alkalinity formulation (1-4: from salinity and temperature, 5: dynamic alkalinity), default = 5
pHscale: 1 # pH scale (1: total, 0: SWS, -1: SWS backward compatible), default = 1
#iswbioalk: 1 # use bioalkalinity (0: off, 1: on), default = 1
initialization:
c: 2130.0 # total dissolved inorganic carbon (mmol C/m^3)
TA: 1.0 #new added
After adding the initial value, the error disappeared.
Similar errors were found in G2 and G4n, and I used similar ways and the errors disappeared:
FABM yaml_settings: No value specified for setting fabm.yaml:/instances/G2/initialization/o_deep; cannot continue because this parameter does not have a default value either.
G2:
long_name: benthic oxygen
model: ersem/benthic_column_dissolved_matter
parameters:
composition: o # composition (any combination of c,n,p,s,o,a)
last_layer: 1 # sediment layer where concentration drops to zero, default = 3
relax: 5.0 # rate of relaxation towards equilibrium concentration profile (1/d)
minD: 0.0001 # minimum depth of zero-concentration isocline (m)
initialization:
o: 0.0225 # oxygen (mmol/m^2)
o_deep: 0.0225 #new added
coupling:
o_pel: O2/o # pelagic oxygen (mmol/m^3)
FABM yaml_settings: No value specified for setting fabm.yaml:/instances/ben_nit/initialization/G4n; cannot continue because this parameter does not have a default value either.
ben_nit:
long_name: benthic nitrogen cycle
model: ersem/benthic_nitrogen_cycle
parameters:
q10nit: 2.0 # Q_10 temperature coefficient (-)
hM4M3: 10.0 # Michaelis-Menten constant for nitrate limitation (mmol/m^3)
ISWph: 1 # pH impact on nitrification (0: off, 1: on), default = 0
sM4M3: 4.0 # maximum nitrification rate at 10 degrees Celsius (1/d)
xno3: 2.0 # oxygen consumed per nitrate produced (mol O_2/mol N)
pammon: 0.5 # fraction of oxygen demand fulfilled by denitrification under anaerobic conditions (-)
pdenit: 0.05 # fraction of denitrification producing dinitrogen gas (remainder produces ammonium) (-)
xn2: 1.25 # oxygen demand fulfilled by reduction of nitrate to dinitrogen gas (mol O_2/mol N)
hM3G4: 1.0 # Michaelis-Menten constant for nitrate limitation of denitrification (mmol N/m^3)
coupling:
K3n: K3/per_layer/n1 # benthic nitrate in 1st layer (mmol N/m^2)
K4n: K4/per_layer/n1 # benthic ammonium in 1st layer (mmol N/m^2)
G2o: G2/per_layer/o1 # benthic oxygen in 1st layer (mmol O_2/m^2)
N4n: N4/n # pelagic ammonium (mmol N/m^3)
benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2)
benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2)
K3n2: K3/per_layer/n2 # benthic nitrate in 2nd layer (mmol N/m^2)
K4n2: K4/per_layer/n2 # benthic ammonium in 2nd layer (mmol N/m^2)
G2o2: G2/per_layer/o2 # oxygen in 2nd layer (mmol O_2/m^2)
layer2_thickness: ben_col/layer2_thickness # thickness of 2nd layer (m)
initialization:
G4n: 0 #new added
However, after this, the program made an error when coupling:
FABM model /Q6_remins/_1, process_coupling_tasks: Coupling target "" for "source" was not found.
And now I don't know what to do. May I ask what caused this error? Thank you.
The text was updated successfully, but these errors were encountered:
When I tried to run the "estuary" example after coupling uk-fvcom-FVCOM-FABM_v5_dev with ERSEM, the following Error appeared:
FABM yaml_settings: No value specified for setting fabm.yaml:/instances/O3/initialization/TA; cannot continue because this parameter does not have a default value either.
So I added the initial value of TA in O3 in fabm.yaml:
O3:
long_name: carbonate
model: ersem/carbonate
parameters:
iswCO2: 1 # carbonate system diagnostics (0: off, 1: on), default = 1
iswASFLUX: 1 # air-sea CO2 exchange (0: none, 1: Nightingale and Liss, 2: Wanninkhof 1992 without chemical enhancement, 3: Wanninkhof 1992 with chemical enhancement, 4: Wanninkhof 1999), default = 1
iswtalk: 5 # alkalinity formulation (1-4: from salinity and temperature, 5: dynamic alkalinity), default = 5
pHscale: 1 # pH scale (1: total, 0: SWS, -1: SWS backward compatible), default = 1
#iswbioalk: 1 # use bioalkalinity (0: off, 1: on), default = 1
initialization:
c: 2130.0 # total dissolved inorganic carbon (mmol C/m^3)
TA: 1.0 #new added
After adding the initial value, the error disappeared.
Similar errors were found in G2 and G4n, and I used similar ways and the errors disappeared:
FABM yaml_settings: No value specified for setting fabm.yaml:/instances/G2/initialization/o_deep; cannot continue because this parameter does not have a default value either.
G2:
long_name: benthic oxygen
model: ersem/benthic_column_dissolved_matter
parameters:
composition: o # composition (any combination of c,n,p,s,o,a)
last_layer: 1 # sediment layer where concentration drops to zero, default = 3
relax: 5.0 # rate of relaxation towards equilibrium concentration profile (1/d)
minD: 0.0001 # minimum depth of zero-concentration isocline (m)
initialization:
o: 0.0225 # oxygen (mmol/m^2)
o_deep: 0.0225 #new added
coupling:
o_pel: O2/o # pelagic oxygen (mmol/m^3)
FABM yaml_settings: No value specified for setting fabm.yaml:/instances/ben_nit/initialization/G4n; cannot continue because this parameter does not have a default value either.
ben_nit:
long_name: benthic nitrogen cycle
model: ersem/benthic_nitrogen_cycle
parameters:
q10nit: 2.0 # Q_10 temperature coefficient (-)
hM4M3: 10.0 # Michaelis-Menten constant for nitrate limitation (mmol/m^3)
ISWph: 1 # pH impact on nitrification (0: off, 1: on), default = 0
sM4M3: 4.0 # maximum nitrification rate at 10 degrees Celsius (1/d)
xno3: 2.0 # oxygen consumed per nitrate produced (mol O_2/mol N)
pammon: 0.5 # fraction of oxygen demand fulfilled by denitrification under anaerobic conditions (-)
pdenit: 0.05 # fraction of denitrification producing dinitrogen gas (remainder produces ammonium) (-)
xn2: 1.25 # oxygen demand fulfilled by reduction of nitrate to dinitrogen gas (mol O_2/mol N)
hM3G4: 1.0 # Michaelis-Menten constant for nitrate limitation of denitrification (mmol N/m^3)
coupling:
K3n: K3/per_layer/n1 # benthic nitrate in 1st layer (mmol N/m^2)
K4n: K4/per_layer/n1 # benthic ammonium in 1st layer (mmol N/m^2)
G2o: G2/per_layer/o1 # benthic oxygen in 1st layer (mmol O_2/m^2)
N4n: N4/n # pelagic ammonium (mmol N/m^3)
benTA: zero_hz # benthic alkalinity in aerobic layer (mEq/m^2)
benTA2: zero_hz # benthic alkalinity in anaerobic layer (mEq/m^2)
K3n2: K3/per_layer/n2 # benthic nitrate in 2nd layer (mmol N/m^2)
K4n2: K4/per_layer/n2 # benthic ammonium in 2nd layer (mmol N/m^2)
G2o2: G2/per_layer/o2 # oxygen in 2nd layer (mmol O_2/m^2)
layer2_thickness: ben_col/layer2_thickness # thickness of 2nd layer (m)
initialization:
G4n: 0 #new added
However, after this, the program made an error when coupling:
FABM model /Q6_remins/_1, process_coupling_tasks: Coupling target "" for "source" was not found.
And now I don't know what to do. May I ask what caused this error? Thank you.
The text was updated successfully, but these errors were encountered: