problem running AED2

CG

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Apr 27, 2026, 8:46:21 AM (4 days ago) Apr 27

to Aquatic Ecosystem MOdelling Network (AEMON) discussion forum

Hello all,

I am trying to run simulations using GLM–AED2, but I am not succeeding. I have been able to run simulations with GLM alone, and everything worked fine. However, when I add the biogeochemical module, the simulation stops after approximately two years (while temperature is still being modelled).

I am almost sure that the issue comes from the sediment module in the glm3.nml file, but I do not know how to correct it. I am running the model with GLM v3.0.5, but I also tried GLM v3.3, and it still does not work.

Another strange thing is that, in the overflow file, I have values for temperature, NIT_amm, NIT_nit, and PHS_frp, but not for OXY_oxy or SIL_rsi.

You can find my glm3.nml and aed2.nml files below. Do you have an idea of where it could come from ?

GLM :

&glm_setup
sim_name = 'EguzonGLMSimulation'
max_layers = 500
min_layer_vol = 0.05
min_layer_thick = 0.05
max_layer_thick = 1.044548
density_model = 1
/
&mixing
surface_mixing = 1
coef_mix_conv = 0.1235774
coef_wind_stir = 0.1807641
coef_mix_shear = 0.221332
coef_mix_turb = 0.5568999
coef_mix_KH = 0.1028209
deep_mixing = 2
coef_mix_hyp = 0.2576925
diff = 0
/
&wq_setup
wq_lib = 'aed2'
wq_nml_file = 'aed2/aed2.nml'
ode_method = 1
split_factor = 1
bioshade_feedback = .true.
repair_state = .true.
mobility_off = .false.
/
&morphometry
lake_name = 'Eguzon'
latitude = 46.45315
longitude = 1.61388
base_elev = 150
crest_elev = 201.7
bsn_len = 7392
bsn_wid = 403
bsn_vals = 72
H = 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 195.5, 195.7, 196, 196.3, 196.5, 196.7, 197, 197.3, 197.5, 197.7, 198, 198.3, 198.5, 198.7, 199, 199.3, 199.5, 199.7, 200, 200.3, 200.5, 200.7, 201, 201.3, 201.5, 201.7
A = 900, 8900, 18200, 28600, 36500, 44300, 51500, 59700, 68300, 77600, 85000, 95900, 107100, 120900, 135200, 156300, 180900, 197700, 210400, 254500, 330300, 405600, 472400, 544600, 608700, 664700, 742900, 809900, 872200, 937900, 1004400, 1079200, 1144900, 1209400, 1275000, 1341900, 1411600, 1488700, 1559500, 1630000, 1704300, 1773900, 1849600, 1924000, 2001100, 2113500, 2177400, 2208900, 2256400, 2295500, 2320500, 2346000, 2387800, 2424100, 2447300, 2473100, 2511900, 2550800, 2576600, 2602500, 2641300, 2680100, 2706000, 2731900, 2770700, 2809500, 2835400, 2861300, 2900100, 2938900, 2964800, 2990600
/
&time
timefmt = 2
start = '2020-01-01 00:00:00'
stop = '2024-12-31 00:00:00'
dt = 3600
timezone = 0
/
&output
out_dir = 'output'
out_fn = 'output'
nsave = 24
csv_lake_fname = 'eguzon'
csv_point_nlevs = 1
csv_point_fname = 'WQ_'
csv_point_at = 0.5
csv_point_nvars = 6
csv_point_vars = 'TEMP','OXY_oxy','SIL_rsi','NIT_amm','NIT_nit','PHS_frp'
csv_outlet_allinone = .false.
csv_outlet_fname = 'outlet_'
csv_outlet_nvars = 6
csv_outlet_vars = 'TEMP','OXY_oxy','SIL_rsi','NIT_amm','NIT_nit','PHS_frp'
csv_ovrflw_fname = 'overflow'
/
&init_profiles
lake_depth = 50.41
num_depths = 3
the_depths = 0.5, 10.5, 31.5
the_temps = 8.295, 8.195, 7.167
the_sals = 0, 0, 0
num_wq_vars = 10
wq_names = 'SIL_rsi','NIT_amm','NIT_nit','PHS_frp',
'OGM_pon','OGM_don','OGM_pop','OGM_dop','OGM_poc','OGM_doc'
wq_init_vals = 231, 231, 231,
1.8, 1.8, 1.8,
191, 191, 191,
0.6, 0.6, 0.6,
17, 17, 17,
142, 142, 142,
1.18, 1.18, 1.18,
8.6, 8.6, 8.6,
80, 80, 80,
675, 675, 675
/
&meteorology
met_sw = .true.
lw_type = 'LW_IN'
rain_sw = .false.
atm_stab = 0
rad_mode = 1
albedo_mode = 1
cloud_mode = 2
fetch_mode = 0
subdaily = .true.
meteo_fl = 'input_files/weather_v3_longwave.csv'
wind_factor = 0.8625975
sw_factor = 0.9177645
lw_factor = 1
at_factor = 1
rh_factor = 1
rain_factor = 1
ce = 0.002014294
ch = 0.002610605
cd = 0.001102113
catchrain = .false.
rain_threshold = 0.01
runoff_coef = 0.3
/
&light
light_mode = 0
n_bands = 4
light_extc = 1, 0.5, 2, 4
energy_frac = 0.51, 0.45, 0.035, 0.005
Benthic_Imin = 10
Kw = 1.393423
/
&bird_model
AP = 973
Oz = 0.279
WatVap = 1.1
AOD500 = 0.033
AOD380 = 0.038
Albedo = 0.2
/
&inflow
num_inflows = 3
names_of_strms = 'creuse','petite_creuse','sedelle'
strm_hf_angle = 75, 70, 30
strmbd_slope = 0.4, 0.4, 0.4
strmbd_drag = 0.016, 0.016, 0.016
inflow_factor = 1, 1, 1
inflow_fl = 'input_files/inflow_creuse_glm_aed2.csv','input_files/inflow_petite_creuse_glm_aed2.csv','input_files/inflow_sedelle_glm_aed2.csv'
inflow_varnum = 3
inflow_vars = 'flow','temp','salt'
coef_inf_entrain = 0
time_fmt = 'YYYY-MM-DD'
/
&outflow
num_outlet = 1
outlet_type = 1
outl_elvs = 185.1807
bsn_len_outl = 5100
bsn_wid_outl = 200
outflow_fl = 'input_files/outflow_glm_turb_res.csv'
outflow_factor = 1
time_fmt = 'YYYY-MM-DD'
/
&sediment
sed_heat_Ksoil = 0.01, 0.01, 0.01
sed_temp_depth = 0.15, 0.15, 0.15
sed_temp_mean = 6, 7, 18
sed_temp_amplitude = 3.5, 8, 20
sed_temp_peak_doy = 190, 190, 190
benthic_mode = 2
n_zones = 3
zone_heights = 10, 20, 51.7
sed_reflectivity = 0.1, 0.01, 0.01
sed_roughness = 0.1, 0.01, 0.01
/
&debugging
disable_evap = .false.
/

AED2 :

&aed2_models
models = 'aed2_noncohesive','aed2_oxygen','aed2_carbon','aed2_silica','aed2_nitrogen','aed2_phosphorus','aed2_organic_matter','aed2_phytoplankton','aed2_totals'
/
&aed2_noncohesive
num_ss = 1
ss_initial = 1
Ke_ss = 0.06
settling = 1
w_ss = -0.03
d_ss = 2e-06
rho_ss = 1500
resuspension = 0
epsilon = 0.007
tau_0 = 0.03
tau_r = 1
Ktau_0 = 0.001
macrophyte_link_var = ''
simSedimentMass = .true.
fs = 0.4
sed_porosity = 0.256
/
&aed2_oxygen
oxy_initial = 360
Fsed_oxy = -30
Ksed_oxy = 51.6
theta_sed_oxy = 1.02
/
&aed2_carbon
dic_initial = 1600.5
Fsed_dic = 3
Ksed_dic = 20
theta_sed_dic = 1.08
pH_initial = 7.5
atm_co2 = 0.00037
co2_model = 1
alk_mode = 1
ionic = 0.1
co2_piston_model = 1
ch4_initial = 27.6
Rch4ox = 0.01
Kch4ox = 0.5
vTch4ox = 1.08
Fsed_ch4 = 0.5
Ksed_ch4 = 100
theta_sed_ch4 = 1.08
methane_reactant_variable = 'OXY_oxy'
atm_ch4 = 1.76e-06
ch4_piston_model = 1
/
&aed2_silica
rsi_initial = 231
Fsed_rsi = 0.6
Ksed_rsi = 50
theta_sed_rsi = 1.08
silica_reactant_variable = 'OXY_oxy'
/
&aed2_nitrogen
amm_initial = 1.8
nit_initial = 191
n2o_initial = 0.03
Rnitrif = 0.03
Knitrif = 78.1
theta_nitrif = 1.08
nitrif_reactant_variable = 'OXY_oxy'
nitrif_ph_variable = ''
simNitrfpH = .false.
Rnh4o2 = 1
Rno2o2 = 1
simN2O = 0
Rn2o = 0.05
Kpart_ammox = 1
Kin_deamm = 1
atm_n2o = 3.2e-07
n2o_piston_model = 4
Rnh4no2 = 1
Ranammox = 0.001
Kanmx_nit = 2
Kanmx_amm = 2
Rdenit = 0.5
Kdenit = 2
theta_denit = 1.08
Rdnra = 0.01
Kdnra_oxy = 2
simDryDeposition = .true.
atm_din_dd = 0.5
simWetDeposition = .true.
atm_din_conc = 0.5
Fsed_amm = 1.35
Ksed_amm = 20
Fsed_nit = -0.5
Ksed_nit = 100
Fsed_n2o = 0
Ksed_n2o = 100
theta_sed_amm = 1.08
theta_sed_nit = 1.08
/
&aed2_phosphorus
frp_initial = 0.6
Fsed_frp = 0.08
Ksed_frp = 50
theta_sed_frp = 1.08
phosphorus_reactant_variable = 'OXY_oxy'
simPO4Adsorption = .true.
ads_use_external_tss = .false.
po4sorption_target_variable = 'NCS_ss1'
PO4AdsorptionModel = 1
Kpo4p = 0.1
ads_use_pH = .false.
Kadsratio = 1
Qmax = 1
w_po4ads = -9999
simDryDeposition = .true.
atm_pip_dd = 0
simWetDeposition = .false.
atm_frp_conc = 0
/
&aed2_organic_matter
poc_initial = 80
doc_initial = 675
pon_initial = 17
don_initial = 142
pop_initial = 1.18
dop_initial = 8.6
docr_initial = 350
donr_initial = 13
dopr_initial = 3
cpom_initial = 100
Rpoc_hydrol = 0.01
Rdoc_minerl = 0.104411
Rpon_hydrol = 0.05
Rdon_minerl = 0.05
Rpop_hydrol = 1e-04
Rdop_minerl = 0.05
theta_hydrol = 1.08
theta_minerl = 1.067978
Kpom_hydrol = 31.25
Kdom_minerl = 156.25
simDenitrification = 1
dom_miner_oxy_reactant_var = 'OXY_oxy'
doc_miner_product_variable = ''
don_miner_product_variable = 'NIT_amm'
dop_miner_product_variable = 'PHS_frp'
dom_miner_nit_reactant_var = 'NIT_nit'
f_an = 1
K_nit = 10
simRPools = .false.
Rdomr_minerl = 1e-04
Rcpom_bdown = 1e-04
X_cpom_n = 5e-04
X_cpom_p = 1e-04
KeDOM = 5e-06
KePOM = 0.00096
KeDOMR = 0.1
KeCPOM = 0.00096
simphotolysis = .false.
photo_c = 0.75
settling = 3
w_pom = -0.06
d_pom = 1e-05
rho_pom = 1200
w_cpom = -0.01
d_cpom = 1e-05
rho_cpom = 1400
resuspension = 0
resus_link = 'NCS_resus'
sedimentOMfrac = 2e-04
Xsc = 0.5
Xsn = 0.05
Xsp = 0.005
Fsed_doc = 0
Fsed_don = 0
Fsed_dop = 0
Ksed_dom = 4.5
theta_sed_dom = 1.08
extra_diag = .false.
/
&aed2_phytoplankton
num_phytos = 10
the_phytos = 1, 2, 3, 4, 6, 7, 8, 9, 10, 11
settling = 1, 1, 1, 4, 1, 1, 1, 1, 1, 1
do_mpb = 0
R_mpbg = 0.5
R_mpbr = 0.05
I_Kmpb = 100
mpb_max = 1000
resuspension = 0, 0, 0, 0, 0, 0, 0, 0, 0, 0
resus_link = ''
n_zones = 3
active_zones = 1
p_excretion_target_variable = 'OGM_dop'
n_excretion_target_variable = 'OGM_don'
c_excretion_target_variable = 'OGM_doc'
si_excretion_target_variable = ''
p_mortality_target_variable = 'OGM_pop'
n_mortality_target_variable = 'OGM_pon'
c_mortality_target_variable = 'OGM_poc'
si_mortality_target_variable = ''
p1_uptake_target_variable = 'PHS_frp'
n1_uptake_target_variable = 'NIT_nit'
n2_uptake_target_variable = 'NIT_amm'
si_uptake_target_variable = 'SIL_rsi'
do_uptake_target_variable = 'OXY_oxy'
c_uptake_target_variable = 'CAR_dic'
dbase = 'aed2/aed2_phyto_pars_v1.nml'
extra_diag = .false.
min_rho = 900
max_rho = 1200
/
&aed2_totals
TN_vars = 'NIT_nit','NIT_amm','OGM_don','OGM_pon','PHY_green_IN'
TN_varscale = 1, 1, 1, 1, 0.15
TP_vars = 'PHS_frp','PHS_frp_ads','OGM_dop','OGM_pop','PHY_green_IP'
TP_varscale = 1, 1, 1, 1, 0.01
TOC_vars = 'OGM_doc','OGM_poc','PHY_green','PHY_diatom','PHY_crypto'
TOC_varscale = 1, 1, 1, 1, 1
/

Thanks a lot for your help!

Best regards,
Clara

Tuba Bucak

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Apr 28, 2026, 3:23:21 AM (4 days ago) Apr 28

to aquaticm...@googlegroups.com

Hi Clara,

I just tried running my current lake model setup using your aed2 file (also including the sediment module in glm). Since I didn't have your phytoplankton .nml file, I had to ignore that module for now.

The model ran successfully without crashing - but of course we have different boundary conditions-. The overflow file output is quite interesting as you mentioned: OXY_oxy and SIL_rsi are missing though output.nc seems to be fine. How critical is the overflow WQ file for you? I guess the water quality in the overflow should be identical to the surface layer concentrations. If you just need the data, we can also extract those variables directly from the output.nc file instead. But of course that would be nice to know why we have interesting output in overflow.

If you could share your complete setup, including the phytoplankton file, I can try to have a look again.

Best

CG <clara...@gmail.com>, 27 Nis 2026 Pzt, 14:46 tarihinde şunu yazdı:

nit_initial = 191*0.014

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CG

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Apr 29, 2026, 3:03:57 AM (3 days ago) Apr 29

to Aquatic Ecosystem MOdelling Network (AEMON) discussion forum

Hi,

Thank you for your reply!

I don’t necessarily need the overflow file; I just found it odd that OXY_oxy and SIL_rsi were missing, and I was wondering whether there was something weird in my setup.

I think there is definitely something going on with the sediment module, because I changed the configuration to two zones and now it is running. However, when I look at the generated graphs, there is something really strange with the phosphate flux from the sediments.

For the GLM, I am using the following configuration for the sediment module:

&sediment

sed_heat_Ksoil = 0.01, 0.01

sed_temp_depth = 0.15, 0.15

sed_temp_mean = 7, 18

sed_temp_amplitude = 8, 25

sed_temp_peak_doy = 227, 227

benthic_mode = 2

n_zones = 2

zone_heights = 30, 51.7

sed_reflectivity = 0.01, 0.01

sed_roughness = 0.01, 0.01

/

Here is my phytoplankton file:

&phyto_data

pd%p_name = 'cyano_microcys','cyano_2','green','diatom','crypto'

pd%p_initial = 0.1, 0.1, 0.1, 3, 0.1

pd%p0 = 0.03, 0.03, 0.03, 0.03, 0.03

pd%w_p = 0, 0, 0, -0.86, 0

pd%Xcc = 50, 50, 40, 50, 40

pd%R_growth = 1.9, 1.9, 1.9, 1.9, 1.9

pd%fT_Method = 1, 1, 1, 1, 1

pd%theta_growth = 1.08, 1.08, 1.08, 1.08, 1.08

pd%T_std = 20, 20, 20, 20, 20

pd%T_opt = 27.5, 20, 26.3, 16, 18

pd%T_max = 38.4, 31, 35, 22, 23

pd%lightModel = 0, 0, 0, 0, 0

pd%I_K = 25, 25, 58, 20, 25

pd%KePHY = 0.005, 0.005, 0.005, 0.005, 0.005

pd%f_pr = 0.005, 0.005, 0.005, 0.005, 0.005

pd%R_resp = 0.05, 0.05, 0.05, 0.05, 0.05

pd%theta_resp = 1.08, 1.08, 1.08, 1.08, 1.08

pd%k_fres = 0.25, 0.25, 0.25, 0.25, 0.25

pd%k_fdom = 0.20, 0.20, 0.20, 0.20, 0.20

pd%salTol = 0, 0, 0, 0, 0

pd%S_bep = 2, 2, 2, 2, 2

pd%S_maxsp = 35, 35, 35, 35, 35

pd%S_opt = 0.1, 0.1, 0.1, 0.1, 0.1

pd%simDINUptake = 1, 1, 1, 1, 1

pd%simDONUptake = 0, 0, 0, 0, 0

pd%simNFixation = 0, 0, 0, 0, 0

pd%simINDynamics = 2, 2, 2, 2, 2

pd%N_o = 0.25, 0.25, 0.25, 0.25, 0.25

pd%K_N = 1, 1, 1, 1, 1

pd%X_ncon = 0.035, 0.035, 0.035, 0.035, 0.035

pd%X_nmin = 0.00086, 0.00086, 0.04, 0.0073, 0.0086

pd%X_nmax = 0.032, 0.032, 0.08, 0.029, 0.032

pd%R_nuptake = 0.032, 0.032, 0.028, 0.028, 0.02

pd%k_nfix = 0, 0, 0, 0, 1

pd%R_nfix = 0, 0, 0, 0, 0

pd%simDIPUptake = 1, 1, 1, 1, 1

pd%simIPDynamics = 2, 2, 2, 2, 2

pd%P_0 = 0.03, 0.03, 0.03, 0.03, 0.03

pd%K_P = 0.05, 0.05, 0.05, 0.5, 0.05

pd%X_pcon = 0.0015, 0.0015, 0.0015, 0.0015, 0.0015

pd%X_pmin = 0.004, 0.004, 0.004, 0.004, 0.004

pd%X_pmax = 0.009, 0.009, 0.009, 0.009, 0.009

pd%R_puptake = 0.006, 0.006, 0.006, 0.007, 0.006

pd%simSiUptake = 0, 0, 0, 1, 0

pd%Si_0 = 0.3, 0.3, 0.3, 0.3, 0.3

pd%K_Si = 2.5, 2.5, 2.5, 2.5, 2.5

pd%X_sicon = 0.4, 0.4, 0.4, 0.4, 0.4

/

Thanks a lot for your help!

Clara

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