Request for Help with GOTM and FABM Configuration

[fdaryabor]

Dear All,

I hope this email finds everyone in great spirits! I understand how busy things can get, but I’d be incredibly grateful if someone could help me with an issue I’m facing while configuring gotm.yaml and fabm.yaml.

I’ve attached both files for your reference. My goal is to set up the configuration to calculate DIC and pCO2. Unfortunately, I keep encountering the following error message:

"FATAL ERROR: coupling target is invalid."

I’ve been trying to resolve this on my own, but I haven’t had much luck. If anyone has insights or suggestions, your expertise would be greatly appreciated!

Thank you so much for taking the time to consider my request—it means a lot to me. Please don’t hesitate to reach out if you need any additional details from my side.

Looking forward to your guidance!

Warm regards,
Farshid

Noted:
gotm.zip
https://github.com/gotm-model/code

fabm.yaml; Section as defined for DIC, pCO2 configuration
coupling:
dic: O3/c
O3:
long_name: carbonate
model: pml/carbonate
parameters:
iswCO2: 1 # carbonate system diagnostics (0: off, 1: on), default = 1
iswASFLUX: 1 # air-sea CO2 exchange (0: none, 1: Nightingale et al. 2000, 2: Wanninkhof 1992 without chemical enhancement, 3: Wanninkhof 1992 with chemical enhancement, 4: Wanninkhof and McGillis 1999, 5: Wanninkhof 1992 switching to Wanninkhof and McGillis 1999, 6: Wan, default = 6
iswtalk: 2 # 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)
pCO2_atm:
model: surface_constant
parameters:
standard_name: mole_fraction_of_carbon_dioxide_in_air
value: 400

gotm.yaml; fabm setting

fabm:
use: true
freshwater_impact: true
feedbacks:
shade: false
albedo: true
surface_drag: true
repair_state: true
configuration_method: yaml
input:
msi_ergom1/po:
method: file
constant_value: 0.4
file: phosphate.dat
relax_tau: 3.15000000E+07
column: 1
msi_ergom1/nn:
method: file
constant_value: 8.
file: nitrate.dat
relax_tau: 3.15000000E+07
column: 1
msi_ergom1/aa:
method: constant
constant_value: 0.001
file:
column: 4
msi_ergom1/o2:
method: file
constant_value: 300.
file: oxygen.dat
relax_tau: 3.15000000E+07
column: 1
O3/c:
method: constant
constant_value: 2130.0
file:
column: 1
mole_fraction_of_carbon_dioxide_in_air:
method: constant
constant_value: 385.0
file:
column: 1

[jornbr]

Hi Farshid,

Is there any earlier eror message printed before the "FATAL ERROR"? I do not see anything strange in the yaml snippets you have included above, so can you attach your complete fabm.yaml file? And what version of FABM are you using?

Best,

Jorn

[fdaryabor]

Hi Jorn, Good to hear from you. The error has popped up again, and it is as follows: $~/source/repos/GOTM/setup$ cat gotm.log STOP 1 ------------------------------------------------------------------------ GOTM started on 2024/12/19 at 11:19:27 ------------------------------------------------------------------------ initialize_gotm ------------------------------------------------------------------------ Reading configuration from: gotm.yaml configuring modules .... init_airsea_yaml done init_observations_yaml init_stokes_drift_yaml done init_turbulence_yaml done. init_gotm_fabm_yaml Reading configuration from: fabm.yaml done. init_meanflow_yaml done init_eqstate_yaml init_density() Linearized - TEOS10 - using S0, T0, p0 S0= 35.000000000000000 T0= 10.000000000000000 p0= 0.0000000000000000 rho0= 1027.0000000000000 alpha= 1.6625612540220982E-004 beta= 7.5366784499087118E-004 cp= 3991.8679571196299 done. FATAL ERROR: model /msi_ergom1, process_coupling_tasks: Coupling target "O3/c" for "dic" was not found. Initializing msi_ergom1... model type: msi_ergom1 initialization succeeded. Initializing O3... model type: pml/carbonate initialization succeeded. Initializing pCO2_atm... model type: surface_constant initialization succeeded. The code I use was downloaded and compiled from the below repository; https://github.com/gotm-model/code, Please find attached 'fabm.yaml' and 'gotm.yaml' Thanks Jorn for your support, Cheers, Farshid

…

On Thu, Dec 19, 2024 at 5:18 AM Jorn Bruggeman ***@***.***> wrote: Hi Farshid, Is there any earlier eror message printed before the "FATAL ERROR"? I do not see anything strange in the yaml snippets you have included above, so can you attach your complete fabm.yaml file? And what version of FABM are you using? Best, Jorn — Reply to this email directly, view it on GitHub <#106 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALMHF4IQNHEBU5NQNDEFEML2GKB5VAVCNFSM6AAAAABT3RTBF6VHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTCNRRGQ3DENQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[fdaryabor]

Dear Jorn, if you can find the attached files I can past below;

'fabm.yaml'

$~/source/repos/GOTM/setup$ cat fabm.yaml
instances:
msi_ergom1:
parameters:
env_type: marine # (Define environment type, either fresh or marine), default = marine
calc_dic: true # (Decide whether to calculate DIC), default = false
dic_variable: dic # (Define DIC variable)
nitrogen_fixation: true # (Nitrogen fixation of cyanos), default = true
wdz: -4.5 # Detritus sinking velocity (m/d), default = -4.5
wpz: -0.5 # Diatoms sinking velocity (m/d), default = -0.5
wfz: 0.0 # Zooplankton sinking velocity (m/d), default = 0.0
wbz: 0.1 # Cyanobacteria sinking velocity (positive) (m/d), default = 0.1
wpo4: -1.0 # P-Fe in water sinking velocity (m/d), default = -1.0
sfl_po: 0.0015 # Constant surface phosphate flux (mmol p/m2/d), default = 0.0015
sfl_nn: 0.083 # Constant surface nitrate flux (mmol n/m2/d), default = 0.083
sfl_aa: 0.06 # Constant surface ammonium flux (mmol n/m2/d), default = 0.06
nb: 0.01 # Phytoplankton excretion rate (pl -> aa) (1/d), default = 0.01
deltao: 0.02 # Phytoplankton mortality rate (pl -> dd) (1/d), default = 0.02
nue: 0.01 # Zooplankton respiration rate (zz -> aa) (m3/d/mmol n), default = 0.01
sigma_b: 0.03 # Zooplankton mortality rate (zz -> dd) (m3/d/mmol n), default = 0.03
dn: 0.003 # Detritus mineralization rate (dd -> aa) (1/d), default = 0.003
dn_sed: 0.002 # Sediment mineralization rate (fl -> aa) (1/d), default = 0.002
rp0: 1.3 # Diatoms uptake rate (1/d), default = 1.3
rf0: 0.4 # Flagellates uptake rate (1/d), default = 0.4
rb0: 0.75 # Cyanobacteria uptake rate (1/d), default = 0.75
cyanotll: 13.5 # Cyanobacteria lower temperature limit (deg C), default = 13.5
cyanosll: 1.0 # Cyanobacteria lower salinity limit (PSU), default = 1.0
cyanosul: 10.0 # Cyanobacteria upper salinity limit (PSU), default = 10.0
flagtll: 100.0 # Flagellates half-saturation temp, squared ((deg C)²), default = 100.0
alphap: 0.25 # Half-saturation const, diatoms (mmol n/m3), default = 0.25
alphaf: 0.1 # Half-saturation const, flagellates (mmol n/m3), default = 0.1
alphab: 0.4 # Half-saturation const, cyanobacteria (mmol n/m3), default = 0.4
Yc_diat: 6.25 # Carbon to Chla ratio (umol C/mg Chla), diatoms, default = 6.25
Yc_flag: 6.25 # Carbon to Chla ratio (umol C/mg Chla), flagellates, default = 6.25
Yc_cyan: 6.25 # Carbon to Chla ratio (umol C/mg Chla), cyanobacteria, default = 6.25
iv: 1.2 # Ivlev constant, quadratic (1/(mmol n/m3)³), default = 1.2
graz: 0.5 # Zooplankton grazing rate (1/d), default = 0.5
toptz: 20.0 # Optimal temperature for grazing (deg C), default = 20.0
zcl1: 50.0 # Zooplankton closure parameter (-), default = 50.0
p0: 0.001 # Diatoms background value (mmol n/m3), default = 0.001
f0: 0.001 # Flagellates background value (mmol n/m3), default = 0.001
b0: 0.001 # Cyanobacteria background value (mmol n/m3), default = 0.001
z0: 0.001 # Zooplankton background value (mmol n/m3), default = 0.001
imin_di: 35.0 # Minimal optimal light radiation, diatoms (W/m²), default = 35.0
imin: 50.0 # Minimal optimal light radiation, others (W/m²), default = 50.0
kc: 0.03 # Attenuation constant for self-shading effect (m²/mmol n)
q10_rec: 0.15 # Sediment recycling Q10 rule factor (-), default = 0.15
ade_r0: 0.1 # Chemoautolithotrophic denitrification rate (1/d), default = 0.1
alphaade: 1.0 # Half-saturation constant for ade (mmol n/m³), default = 1.0
q10_recs: 0.175 # Sediment recycling Q10 rule factor (-), default = 0.175
rfr: 0.0625 # Redfield ratio P/N (-), default = 0.0625
rfc: 6.625 # Redfield ratio C/N (-), default = 6.625
sedrate: 2.25 # Detritus sedimentation rate (m/d), default = 2.25
erorate: 6.0 # Sediment erosion rate (m/d), default = 6.0
sedratepo4: 0.5 # P-Fe sedimentation rate (m/d), default = 0.5
eroratepo4: 6.0 # P-Fe erosion rate (m/d), default = 6.0
po4ret: 0.18 # Phosphate retention rate, oxic sediments (-), default = 0.18
pburialrate: 0.007 # Phosphate burial rate (-), default = 0.007
fl_burialrate: 0.001 # Sediment burial rate (-), default = 0.001
pliberationrate: 0.1 # Phosphate liberation rate, anoxic sediments (-), default = 0.1
ipo4th: 100.0 # Increased phosphate burial threshold (mmol p/m²), default = 100.0
maxsed: 1000.0 # Maximum active sediment concentration (-), default = 1000.0
br0: 0.03 # Bioresuspension rate (1/d), default = 0.03
fds: 0.7 # Sediment denitrification rate, oxic (-), default = 0.7
pvel: 5.0 # Piston velocity (m/d), default = 5.0
newflux: 2 # Oxygen flux type (-), default = 2
tau_crit: 0.07 # Critical shear stress (N/m²), default = 0.07
initialization:
pp: 0.001 # Diatoms (mmol n/m³)
ff: 0.001 # Flagellates (mmol n/m³)
bb: 0.001 # Cyanobacteria (mmol n/m³)
zz: 0.001 # Zooplankton (mmol n/m³)
dd: 0.01 # Detritus (mmol n/m³)
aa: 0.001 # Ammonium (mmol n/m³)
nn: 8.0 # Nitrate (mmol n/m³)
po: 1.0 # Phosphate (mmol p/m³)
o2: 300.0 # Oxygen (mmol o₂/m³)
fl: 100.0 # Fluff (mmol n/m²)
pb: 0.001 # PFe_s (mmol p/m²)
pw: 0.001 # PFe_w (mmol p/m³)
coupling:
dic: O3/c
O3:
long_name: carbonate
model: pml/carbonate
parameters:
iswCO2: 1 # carbonate system diagnostics (0: off, 1: on), default = 1
iswASFLUX: 1 # air-sea CO2 exchange(0: none, 1:, 2: without chemical enhancement, 3: with chemical enhancement)
iswtalk: 2 # 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)
pCO2_atm:
model: surface_constant
parameters:
standard_name: mole_fraction_of_carbon_dioxide_in_air
value: 400

---

'gotm.yaml'

$~/source/repos/GOTM/setup$ cat gotm.yaml
version: 7
title: GOTM-ERGOM at Arkona
location:
name: Arikona station
latitude: 54.883
longitude: 13.867
depth: 45.0
time:
start: 2019-01-01 00:00:00
stop: 2019-04-01 00:00:00
dt: 900.0
grid:
nlev: 71
method: file_sigma
ddu: 1.0
ddl: 1.0
file: grid.dat
temperature:
method: file
constant_value: 15.0
file: tprof.dat
column: 1
two_layer:
z_s: 30.0
t_s: 15.0
z_b: 40.0
t_b: 10.0
NN: 0.000256
relax:
tau: 2592000.0
tau_s: 2592000.0
tau_b: 2592000.0
salinity:
method: file
constant_value: 35.0
file: sprof.dat
column: 1
two_layer:
z_s: 30.0
s_s: 35.0
z_b: 40.0
s_b: 36.0
NN: 0.000256
relax:
tau: 2592000.0
tau_s: 25292000.0
tau_b: 25292000.0
surface:
fluxes:
method: fairall
heat:
method: constant
constant_value: 0.0
file:
column: 1
tx:
method: constant
constant_value: 0.0
file:
column: 1
ty:
method: constant
constant_value: 0.0
file:
column: 1
u10:
method: file
constant_value: 0.0
file: meteo.dat
column: 1
v10:
method: file
constant_value: 0.0
file: meteo.dat
column: 2
ssuv_method: absolute
airp:
method: file
constant_value: 0.0
file: meteo.dat
column: 3
scale_factor: 100.0
airt:
method: file
constant_value: 0.0
file: meteo.dat
column: 4
hum:
method: file
constant_value: 0.0
file: meteo.dat
column: 5
type: dew_point
cloud:
method: file
constant_value: 0.0
file: meteo.dat
column: 6
precip:
method: file
constant_value: 0.0
file: precip.dat
column: 1
flux_impact: true
calc_evaporation: true
swr:
method: file
constant_value: 0.0
file: ssr.dat
column: 1
longwave_radiation:
method: clark
file:
column: 1
albedo:
method: constant
constant_value: 0.0
roughness:
charnock: false
charnock_val: 1400.0
z0s_min: 0.02
bottom:
h0b: 0.05
light_extinction:
method: jerlov-iii
A:
method: constant
constant_value: 0.7
file:
column: 1
g1:
method: constant
constant_value: 0.4
file:
column: 1
g2:
method: constant
constant_value: 8.0
file:
column: 1
turbulence:
turb_method: second_order
tke_method: tke
len_scale_method: dissipation
stab_method: schumann_gerz
turb_param:
cm0_fix: 0.5477
Prandtl0_fix: 0.74
cw: 100.0
compute_kappa: false
kappa: 0.4
compute_c3: true
Ri_st: 0.25
length_lim: true
galp: 0.53
const_num: 0.0005
const_nuh: 0.0005
k_min: 1.0e-06
eps_min: 1.0e-12
kb_min: 1.0e-10
epsb_min: 1.0e-14
generic:
gen_m: 1.0
gen_n: -0.67
cpsi1: 1.0
cpsi2: 1.22
cpsi3minus: 0.05
sig_kpsi: 0.8
sig_psi: 1.07
keps:
ce3minus: -0.4
my:
length: linear
scnd:
method: quasi_eq
iw:
alpha: 0.7
mimic_3d:
ext_pressure:
type: velocity
dpdx:
method: file
constant_value: 0.0
file: ext_press.dat
column: 2
tidal:
amp_1: 0.2429
phase_1: 32171.1
amp_2: 0.085
phase_2: 36650.0
dpdy:
method: file
constant_value: 0.0
file: ext_press.dat
column: 3
tidal:
amp_1: 0.0734
phase_1: 14490.5
amp_2: 0.0257
phase_2: 19567.8
h:
method: file
constant_value: 1.0
file: ext_press.dat
column: 1
period_1: 44714.0
period_2: 43200.0
zeta:
method: file
constant_value: 0.0
file: zeta.dat
column: 1
tidal:
period_1: 44714.0
amp_1: 1.4287
phase_1: 28645.5
period_2: 43200.0
amp_2: 0.5
phase_2: 33243.4
w:
max:
method: off
constant_value: 0.0
file:
column: 1
height:
method: constant
constant_value: 0.0
file:
column: 1
adv_discr: superbee
int_pressure:
t_adv: false
s_adv: false
gradients:
dtdx:
method: off
constant_value: 0.0
file:
column: 1
dtdy:
method: off
constant_value: 0.0
file:
column: 1
dsdx:
method: off
constant_value: 0.0
file:
column: 1
dsdy:
method: off
constant_value: 0.0
file:
column: 1
o2:
scale_factor: 31.25
fabm:
use: true
freshwater_impact: true
feedbacks:
shade: false
albedo: true
surface_drag: true
repair_state: true
configuration_method: yaml
input:
msi_ergom1/po:
method: file
constant_value: 0.4
file: phosphate.dat
relax_tau: 3.15000000E+07
column: 1
msi_ergom1/nn:
method: file
constant_value: 8.
file: nitrate.dat
relax_tau: 3.15000000E+07
column: 1
msi_ergom1/aa:
method: constant
constant_value: 0.001
file:
column: 4
msi_ergom1/o2:
method: file
constant_value: 300.
file: oxygen.dat
relax_tau: 3.15000000E+07
column: 1
O3/c:
method: constant
constant_value: 2130.0
file:
column: 1
mole_fraction_of_carbon_dioxide_in_air:
method: constant
constant_value: 385.0
file:
column: 1
equation_of_state:
method: linear_teos-10 # or linear_custom
rho0: 1027.0
linear:
T0: 10.0
S0: 35.0
p0: 0.0
alpha: -0.17 # thermal expansion coefficient (Replace dtr0 with alpha)
beta: 0.78 # saline expansion coefficient (Replace dsr0 with beta)
restart:
load: false
output:
result:
format: netcdf
time_unit: day
time_step: 1
time_method: mean
variables:
- source: /*

[jornbr]

Hi Farshid,

The issue is due to having a mixture of the old and new PML carbonate model in your fabm.yaml. If you replace model: pml/carbonate (the old model version) with model: ersem/carbonate (the new version), and you have compiled FABM with ERSEM included, it all works fine.

Alternatively, if you really do want to use the old carbonate model, you'd have to change the O3 section to something like:

  O3:
    long_name: carbonate
    model: pml/carbonate
    initialization:
      dic: 2130.0 # total dissolved inorganic carbon (mmol C/m^3)

And your coupling section of msi_ergom1 to:

    coupling:
      dic: O3/dic

However, I note the settings in your gotm.yaml file (e.g., the mention of O3/c) are also specific to the new carbonate model, so likely that's the one you want.

Best,

Jorn

[fdaryabor]

Hi Jorn,

Thank you very much for your helpful suggestion.

After recompiling GOTM-FABM with ERSEM included, the model ran exactly as expected, similar to my previous runs. Unfortunately, I had forgotten to compile ERSEM with GOTM earlier, so I had been using the carbonate system configuration, as shown below:

coupling:
dic: O3/c
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 et al. 2000, 2: Wanninkhof 1992 without chemical enhancement, 3: Wanninkhof 1992 with chemical enhancement, 4: Wanninkhof and McGillis 1999, 5: Wanninkhof 1992 switching to Wanninkhof and McGillis 1999, 6: Wan, default = 6)
iswtalk: 2 # 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)

Below, I leave the command used for recompiling:

cmake ../code/ -DFABM_INSTITUTES="msi;ersem;pml;au;bb;gotm;su" -DFABM_ERSEM_BASE=../../ersem/

make install -j4

To make sure ersem/carbonate has already compiled 'find -name "ersem" -or -name "carbonate"'

CHEERS,