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aed2.nml
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&aed_models
models = 'aed_sedflux','aed_tracer','aed_noncohesive','aed_oxygen','aed_carbon','aed_silica','aed_nitrogen','aed_phosphorus','aed_organic_matter','aed_phytoplankton','aed_totals','aed_zooplankton'
/
&aed_sedflux
sedflux_model = 'Constant2D'
/
&aed_sed_const2d
n_zones = 2
active_zones = 1, 2
Fsed_oxy = -197.820211583834, -66.4862960505021
Fsed_ch4 = 40.0320880871239, 39.3101535068239
Fsed_amm = 15, 15!28.3862395067636, 0.973323731521144
Fsed_nit = -14.1936566550285, -0.892286739833653
Fsed_frp = 0.249767287140187, 0.0580145229119808
Fsed_dic = 379.2962
/
&aed_tracer
retention_time = .true.
num_tracers = 1
/
&aed_noncohesive
num_ss = 1
ss_initial = 1, 1
Ke_ss = 0.006, 0.063
settling = 1
w_ss = -0.001, -0.001
d_ss = 2e-06, 1e-05
rho_ss = 1500, 1800
resuspension = 0
simSedimentMass = .true.
fs = 0.4, 0.4
sed_porosity = 0.6
/
&aed_oxygen
oxy_initial = 100
Fsed_oxy = -10
Ksed_oxy = 27.38276
theta_sed_oxy = 0.8
oxy_min = 0
oxy_max = 500
/
&aed_carbon
dic_initial = 100
Fsed_dic = 50
Ksed_dic = 35.08749
theta_sed_dic = 1.1
pH_initial = 7
atm_co2 = 0.00041
co2_model = 1
alk_mode = 2
ionic = 0.01
co2_piston_model = 1
ch4_initial = 5
Rch4ox = 0.9469993
Kch4ox = 0.7298476
vTch4ox = 0.91
Ksed_ch4 = 1.547945
theta_sed_ch4 = 1.15
methane_reactant_variable = 'OXY_oxy'
atm_ch4 = 1.76e-06
ch4_piston_model = 1
Fsed_ch4_variable = 'SDF_Fsed_ch4'
/
&aed_silica
rsi_initial = 85
Fsed_rsi = 17.92716
Ksed_rsi = 1.02
theta_sed_rsi = 1.11
silica_reactant_variable = 'OXY_oxy'
/
&aed_nitrogen
amm_initial = 2.6
nit_initial = 0.1!0.05
n2o_initial = 0.1
Rnitrif = 0.03!0.6392162
Knitrif = 20!118.6436
theta_nitrif = 1.09!1.15
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 = 0.001
kanammox = 2
Kanmx_nit = 0.2
Kanmx_amm = 5
Rdenit = 2
Kdenit = 1.000765
theta_denit = 1.15
Rdnra = 0.03
Kdnra_oxy = 5
Ksed_amm = 11
Ksed_nit = 6.227502
Fsed_n2o = 0
Ksed_n2o = 173!100
theta_sed_amm = 1.15
theta_sed_nit = 1.15
Fsed_nit = -9!-0.05
Fsed_amm_variable = 'SDF_Fsed_amm'
Fsed_nit_variable = 'SDF_Fsed_nit'
Fsed_nit_model = 0
/
&aed_phosphorus
frp_initial = 0.05
Ksed_frp = 60.86251
theta_sed_frp = 1.06
phosphorus_reactant_variable = 'OXY_oxy'
Fsed_frp_variable = 'SDF_Fsed_frp'
simPO4Adsorption = .false.
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
/
&aed_organic_matter
poc_initial = 5
doc_initial = 5
pon_initial = 2
don_initial = 1.1
pop_initial = 0.1
dop_initial = 0.01
docr_initial = 1
donr_initial = 9
dopr_initial = 0.15
cpom_initial = 0
Rdom_minerl = 0.01820946
Rpom_hydrol = 1e-04
Rpoc_hydrol = 0.001
Rpon_hydrol = 0.001
Rpop_hydrol = 1e-04
theta_hydrol = 1.07
theta_minerl = 1
Kpom_hydrol = 32.67907
Kdom_minerl = 78.27869
simDenitrification = 1
dom_miner_oxy_reactant_var = 'OXY_oxy'
doc_miner_product_variable = 'CAR_dic'
don_miner_product_variable = 'NIT_amm'
dop_miner_product_variable = 'PHS_frp'
dom_miner_nit_reactant_var = 'NIT_nit'
f_an = 0.2063885
K_nit = 10
simRPools = .true.
Rdomr_minerl = 0.01
Rcpom_bdown = 0.001
X_cpom_n = 0.005
X_cpom_p = 0.001
KeDOM = 0.005
KePOM = 0.00096
KeDOMR = 0.1
KeCPOM = 0.00096
simphotolysis = .false.
photo_c = 0.75
settling = 1
w_pom = -0.01
d_pom = 1e-05
rho_pom = 1200
w_cpom = -0.01
d_cpom = 1e-05
rho_cpom = 1400
resuspension = 0
resus_link = ''
sedimentOMfrac = 2e-04
Xsc = 0.5
Xsn = 0.05
Xsp = 0.005
Fsed_doc = 50
Fsed_don = 0
Fsed_dop = 0
Ksed_dom = 93.12891
theta_sed_dom = 1.057064
diag_level = 10
/
&aed_phytoplankton
num_phytos = 3
the_phytos = 1, 2, 3
settling = 1, 1, 1
do_mpb = 0
p_excretion_target_variable = 'OGM_dop'
n_excretion_target_variable = 'OGM_don'
c_excretion_target_variable = 'OGM_doc'
si_excretion_target_variable = 'SIL_rsi'
p_mortality_target_variable = 'OGM_pop'
n_mortality_target_variable = 'OGM_pon'
c_mortality_target_variable = 'OGM_poc'
si_mortality_target_variable = 'SIL_rsi'
p1_uptake_target_variable = 'PHS_frp'
n1_uptake_target_variable = 'NIT_amm'
n2_uptake_target_variable = 'NIT_nit'
si_uptake_target_variable = 'SIL_rsi'
do_uptake_target_variable = 'OXY_oxy'
c_uptake_target_variable = 'CAR_dic'
dbase = 'aed/aed2_phyto_pars.csv'
diag_level = 10
min_rho = 900
max_rho = 1200
/
&aed_totals
outputLight = .true.
TN_vars = 'NIT_nit','NIT_amm','OGM_don','OGM_donr','OGM_pon','PHY_in'
TN_varscale = 1, 1, 1, 1, 1, 0.15
TP_vars = 'PHS_frp','OGM_dop','OGM_dopr','OGM_pop','PHY_ip'
TP_varscale = 1, 1, 1, 1, 0.01
TOC_vars = 'OGM_doc','OGM_docr','OGM_poc','OGM_cpom','PHY_tphy'
TOC_varscale = 1, 1, 1, 1, 1
/
&aed_sediment
sediment_model = 'DYNAMIC'
mpb_link_variable = ''
mag_link_variable = ''
root_link_variable = ''
/
&aed_zooplankton
num_zoops = 3
the_zoops = 1, 2, 3
dn_target_variable = 'OGM_don'
pn_target_variable = 'OGM_pon'
dp_target_variable = 'OGM_dop'
pp_target_variable = 'OGM_pop'
dc_target_variable = 'OGM_doc'
pc_target_variable = 'OGM_poc'
dbase = 'aed/aed_zoop_pars.nml'
simZoopFeedback = .true.
/