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gotm.yaml
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title: GOTM Simulation # simulation title used in output [default=GOTM simulation]
location:
name: Mendota # station name used in output [default=GOTM site]
latitude: 43 # latitude [degrees North; min=-90.0; max=90.0; default=0.0]
longitude: -89.41 # longitude [degrees East; min=-360.0; max=360.0; default=0.0]
depth: 25 # water depth [m; min=0.0; default=100.0]
hypsograph: hypsograph.dat # hypsograph [default=]
time:
start: 2009-01-01 00:00:00 # start date and time [yyyy-mm-dd HH:MM:SS; default=2017-01-01 00:00:00]
stop: 2015-12-30 00:00:00 # stop date and time [yyyy-mm-dd HH:MM:SS; default=2018-01-01 00:00:00]
dt: 3600 # time step for integration [s; min=0.0; default=3600.0]
grid:
nlev: 50 # number of layers [min=1; default=100]
method: 0 # layer thicknesses [0=equal by default with optional zooming, 1=prescribed relative fractions, 2=prescribed thicknesses; default=0]
ddu: 0.0 # surface zooming [dimensionless; min=0.0; default=0.0]
ddl: 0.0 # bottom zooming [dimensionless; min=0.0; default=0.0]
file: # file with custom grid [default=]
temperature: # temperature profile used for initialization and optionally relaxation
method: 2 # method [0=off, 1=analytical, 2=from file; default=0]
file: init_cond.dat # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
analytical:
method: 1 # type of analytical initial temperature profile [1=constant, 2=two layers, 3=from salinity and buoyancy frequency; default=1]
z_t1: 30.0 # upper layer thickness [m; min=0.0; default=0.0]
t_1: 20.0 # upper layer temperature [Celsius; min=0.0; max=40.0; default=0.0]
z_t2: 40.0 # lower layer thickness [m; min=0.0; default=0.0]
t_2: 15.0 # lower layer temperature [Celsius; min=0.0; max=40.0; default=0.0]
obs_NN: 0.0 # constant buoyancy frequency [s^-2; min=0.0; default=0.0]
relax: # relax model temperature to observed/prescribed value
tau: 1.00000000E+15 # time scale for interior layer [s; min=0.0; default=1.00000000E+15]
h_s: 0.0 # height of surface relaxation layer [m; min=0.0; default=0.0]
tau_s: 1.00000000E+15 # time scale for surface layer [s; min=0.0; default=1.00000000E+15]
h_b: 0.0 # height of bottom relaxation layer [m; min=0.0; default=0.0]
tau_b: 1.00000000E+15 # time scale for bottom layer [s; min=0.0; default=1.00000000E+15]
salinity: # salinity profile used for initialization and optionally relaxation
method: 0 # method [0=off, 1=analytical, 2=from file; default=0]
file: # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
analytical:
method: 1 # type of analytical initial salinity profile [1=constant, 2=two layers, 3=from temperature and buoyancy frequency; default=1]
z_s1: 30.0 # upper layer thickness [m; min=0.0; default=0.0]
s_1: 20.0 # upper layer salinity [psu; min=0.0; max=40.0; default=0.0]
z_s2: 40.0 # lower layer thickness [m; min=0.0; default=0.0]
s_2: 15.0 # lower layer salinity [psu; min=0.0; max=40.0; default=0.0]
obs_NN: 0.0 # constant buoyancy frequency [s^-2; min=0.0; default=0.0]
relax: # relax model salinity to observed/prescribed value
tau: 1.00000000E+15 # time scale for interior layer [s; min=0.0; default=1.00000000E+15]
surface:
fluxes: # heat and momentum fluxes
method: 2 # method to calculate fluxes from meteorology [0=use prescribed fluxes, 1=Kondo (1975), 2=Fairall et al. (1996); default=0]
heat: # prescribed total heat flux (sensible, latent and net back-radiation)
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [W/m^2; default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
tx: # prescribed momentum flux in West-East direction
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [Pa; default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
ty: # prescribed momentum flux in South-North direction
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [Pa; default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
meteo:
u10: # wind speed in West-East direction @ 10 m
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [m/s; default=0.0]
file: meteo_file.dat # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
v10: # wind speed in South-North direction @ 10 m
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [m/s; default=0.0]
file: meteo_file.dat # path to file with time series [default=]
column: 2 # index of column to read from [default=1]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
airp: # air pressure
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [Pa; default=0.0]
file: meteo_file.dat # path to file with time series [default=]
column: 3 # index of column to read from [default=1]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
airt: # air temperature @ 2 m
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [Celsius or K; default=0.0]
file: meteo_file.dat # path to file with time series [default=]
column: 4 # index of column to read from [default=1]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
hum: # humidity @ 2 m
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [default=0.0]
file: meteo_file.dat # path to file with time series [default=]
column: 5 # index of column to read from [default=1]
type: 1 # humidity metric [1=relative humidity (%), 2=wet-bulb temperature, 3=dew point temperature, 4=specific humidity (kg/kg); default=1]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
cloud: # cloud cover
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.0]
file: meteo_file.dat # path to file with time series [default=]
column: 6 # index of column to read from [default=1]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
swr: # shortwave radiation
method: 2 # method [0=constant, 2=from file, 3=from time, location and cloud cover; default=0]
constant_value: 0.0 # value to use throughout the simulation [W/m^2; min=0.0; default=0.0]
file: meteo_file.dat # path to file with time series [default=]
column: 7 # index of column to read from [default=1]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
precip: # precipitation
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [m/s; default=0.0]
file: meteo_file.dat # path to file with time series [default=]
column: 8 # index of column to read from [default=1]
flux_impact: true # include effect on fluxes of sensible heat and momentum [default=false]
scale_factor: 1 # scale factor to be applied to values read from file [default=1.0]
calc_evaporation: true # calculate evaporation from meteorological conditions [default=false]
ssuv_method: 0 # wind treatment [0=use absolute wind speed, 1=use wind speed relative to current velocity; default=1]
longwave_radiation: # net longwave radiation
method: 1 # method [0=from file, 1=Clark, 2=Hastenrath, 3=Bignami, 4=Berliand; default=1]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
albedo:
method: 1 # method to compute albedo [0=constant, 1=Payne (1972), 2=Cogley (1979); default=1]
constant_value: 0.0 # constant value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.0]
ice:
model: 2 # model [0=none, 1=Lebedev (1938), 2=MyLake, 3=Winton; default=0]
H: 0.0 # initial ice thickness [m; default=0.0]
roughness:
charnock: false # use Charnock (1955) roughness adaptation [default=false]
charnock_val: 1400.0 # empirical constant for roughness adaptation [dimensionless; min=0.0; default=1400.0]
z0s_min: 0.02 # hydrodynamic roughness (minimum value if Charnock adaptation is used) [m; min=0.0; default=0.02]
bottom:
h0b: 0.05 # physical bottom roughness [m; min=0.0; default=0.05]
light_extinction:
method: 7 # water type [1=Jerlov type I, 2=Jerlov type 1 (upper 50 m), 3=Jerlov type IA, 4=Jerlov type IB, 5=Jerlov type II, 6=Jerlov type III, 7=custom; default=1]
A: # non-visible fraction of shortwave radiation
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: 0.550 # value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.7]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
g1: # e-folding depth of non-visible shortwave radiation
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: 0.5 # value to use throughout the simulation [m; min=0.0; default=0.4]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
g2: # e-folding depth of visible shortwave radiation
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: 2.5 # value to use throughout the simulation [m; min=0.0; default=8.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
turbulence:
turb_method: 3 # turbulence closure [0=convective adjustment, 2=first-order, 3=second-order; default=3]
tke_method: 2 # turbulent kinetic energy equation [1=algebraic length scale equation, 2=differential equation for tke (k-epsilon style), 3=differential equation for q^2/2 (Mellor-Yamada style); default=2]
len_scale_method: 8 # dissipative length scale [1=parabolic, 2=triangular, 3=Xing and Davies (1995), 4=Robert and Ouellet (1987), 5=Blackadar (two boundaries) (1962), 6=Bougeault and Andre (1986), 7=Eifler and Schrimpf (ISPRAMIX) (1992), 8=dynamic dissipation rate equation, 9=dynamic Mellor-Yamada q^2 l-equation, 10=generic length scale (GLS); default=8]
stab_method: 3 # stability functions [1=constant, 2=Munk and Anderson (1954), 3=Schumann and Gerz (1995), 4=Eifler and Schrimpf (1992); default=1]
turb_param:
cm0_fix: 5.47700000E-01 # value of cm0 [dimensionless; min=0.0; default=5.47700000E-01]
Prandtl0_fix: 0.74 # turbulent Prandtl-number [dimensionless; min=0.0; default=0.74]
cw: 100.0 # constant of the wave-breaking model [dimensionless; min=0.0; default=100.0]
compute_kappa: false # compute von Karman constant from model parameters [default=false]
kappa: 0.4 # von Karman constant [dimensionless; min=0.0; default=0.4]
compute_c3: true # compute c3 (E3 for Mellor-Yamada) from steady-state Richardson number [default=true]
Ri_st: 0.25 # desired steady-state Richardson number [dimensionless; min=0.0; default=0.25]
length_lim: true # apply Galperin et al. (1988) length scale limitation [default=true]
galp: 0.27 # coefficient for length scale limitation [dimensionless; min=0.0; default=0.27]
const_num: 5.00000000E-04 # constant eddy diffusivity [m^2/s; min=0.0; default=5.00000000E-04]
const_nuh: 5.00000000E-04 # constant heat diffusivity [m^2/s; min=0.0; default=5.00000000E-04]
k_min: 3.6e-06 # minimum turbulent kinetic energy [m^2/s^2; min=0.0; default=1.00000000E-10]
eps_min: 1.00000000E-12 # minimum dissipation rate [m^2/s^3; min=0.0; default=1.00000000E-12]
kb_min: 1.00000000E-10 # minimum buoyancy variance [m^2/s^4; min=0.0; default=1.00000000E-10]
epsb_min: 1.00000000E-14 # minimum buoyancy variance destruction rate [m^2/s^5; min=0.0; default=1.00000000E-14]
generic: # generic length scale (GLS) model
gen_m: 1.5 # exponent for k [dimensionless; default=1.5]
gen_n: -1.0 # exponent for l [dimensionless; default=-1.0]
cpsi1: 1.44 # empirical coefficient cpsi1 in psi equation [dimensionless; default=1.44]
cpsi2: 1.92 # empirical coefficient cpsi2 in psi equation [dimensionless; default=1.92]
cpsi3minus: 0.0 # cpsi3 for stable stratification [dimensionless; default=0.0]
sig_kpsi: 1.0 # Schmidt number for TKE diffusivity [dimensionless; default=1.0]
sig_psi: 1.3 # Schmidt number for psi diffusivity [dimensionless; default=1.3]
keps: # k-epsilon model
ce3minus: 0.0 # ce3 for stable stratification [dimensionless; default=0.0]
my: # Mellor-Yamada model
length: 1 # barotropic length scale in q^2 l equation [1=parabolic, 2=triangular, 3=linear from surface; default=1]
scnd: # second-order model
method: 2 # method [1=quasi-equilibrium, 2=weak equilibrium with algebraic buoyancy variance; default=2]
scnd_coeff: 5 # coefficients of second-order model [0=custom, 1=Gibson and Launder (1978), 2=Mellor and Yamada (1982), 3=Kantha and Clayson (1994), 4=Luyten et al. (1996), 5=Canuto et al. (2001) (version A), 6=Canuto et al. (2001) (version B), 7=Cheng et al. (2002); default=5]
iw: # internal wave mixing
alpha: 0.0 # coefficient for Mellor internal wave model [dimensionless; default=0.0]
mimic_3d: # effects of horizontal gradients
ext_pressure: # external pressure
mode: 0 # formulation [0=horizontal gradient in surface elevation, 1=horizontal velocities at given height above bed, 2=vertically averaged horizontal velocities; default=0]
dpdx: # pressure in West-East direction
method: 0 # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
AmpM: 0.0 # amplitude of 1st harmonic [dimensionless; default=0.0]
PhaseM: 0.0 # phase of 1st harmonic [s; min=0.0; default=0.0]
AmpS: 0.0 # amplitude of 2nd harmonic [dimensionless; default=0.0]
PhaseS: 0.0 # phase of 2nd harmonic [s; min=0.0; default=0.0]
dpdy: # pressure in South-North direction
method: 0 # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
AmpM: 0.0 # amplitude of 1st harmonic [dimensionless; default=0.0]
PhaseM: 0.0 # phase of 1st harmonic [s; min=0.0; default=0.0]
AmpS: 0.0 # amplitude of 2nd harmonic [dimensionless; default=0.0]
PhaseS: 0.0 # phase of 2nd harmonic [s; min=0.0; default=0.0]
h: # height above bed
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [m; min=0.0; default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
PeriodM: 44714.0 # period of 1st tidal harmonic (eg. M2-tide) [s; default=44714.0]
PeriodS: 43200.0 # period of 2nd tidal harmonic (eg. S2-tide) [s; default=43200.0]
int_press: # internal pressure
dtdx: # temperature gradient in West-East direction
method: 0 # method [0=off, 1=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [Celsius/m; default=0.0]
file: # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
dtdy: # temperature gradient in South-North direction
method: 0 # method [0=off, 1=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [Celsius/m; default=0.0]
file: # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
dsdx: # salinity gradient in West-East direction
method: 0 # method [0=off, 1=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [psu/m; default=0.0]
file: # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
dsdy: # salinity gradient in South-North direction
method: 0 # method [0=off, 1=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [psu/m; default=0.0]
file: # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
t_adv: false # horizontally advect temperature [default=false]
s_adv: false # horizontally advect salinity [default=false]
zeta: # surface elevation
method: 3 # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [m; default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
offset: -10.312 # offset to be added to values read from file [m; default=0.0]
period_1: 44714.0 # period of 1st harmonic (eg. M2-tide) [s; default=44714.0]
amp_1: 0.0 # amplitude of 1st harmonic [m; default=0.0]
phase_1: 0.0 # phase of 1st harmonic [s; min=0.0; default=0.0]
period_2: 43200.0 # period of 2nd harmonic (eg. S2-tide) [s; default=43200.0]
amp_2: 0.0 # amplitude of 2nd harmonic [m; default=0.0]
phase_2: 0.0 # phase of 2nd harmonic [s; min=0.0; default=0.0]
w: # vertical velocity
max: # maximum velocity
method: 0 # method [0=off, 1=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [m/s; default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
height: # height of maximum velocity
method: 1 # method [1=constant, 2=from file; default=1]
constant_value: 0.0 # value to use throughout the simulation [m; default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
adv_discr: 6 # vertical advection scheme [1=first-order upstream, 3=third-order upstream-biased polynomial, 4=third-order TVD with Superbee limiter, 5=third-order TVD with MUSCL limiter, 6=third-order TVD with ULTIMATE QUICKEST limiter; default=6]
water_balance_method: 3 # 0=none, 1=surface, 2=all layers, 3=free surface, default=0
velocities: # observed/prescribed horizontal velocities
u: # velocity in West-East direction
method: 0 # method [0=off, 2=from file; default=0]
file: # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
v: # velocity in South-North direction
method: 0 # method [0=off, 2=from file; default=0]
file: # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
relax: # relax model velocities towards observed/prescribed value
tau: 1.00000000E+15 # time scale [s; min=0.0; default=1.00000000E+15]
ramp: 1.00000000E+15 # duration of initial relaxation period [s; min=0.0; default=1.00000000E+15]
o2: # oxygen
scale_factor: 1.0 # scale factor to be applied to values read from file [default=1.0]
offset: 0.0 # offset to be added to values read from file [default=0.0]
streams:
inflow: # stream configuration
method: 1 # inflow method [default=1]
zu: 0.0 # upper limit [m; default=0.0]
zl: 0.0 # lower limit [m; default=0.0]
flow: # water flow
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [m^3/s; default=0.0]
file: inflow_file_1.dat # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
temp: # flow temperature
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: -1.0 # value to use throughout the simulation [Celcius; default=-1.0]
file: inflow_file_1.dat # path to file with time series [default=]
column: 2 # index of column to read from [default=1]
salt: # flow salinity
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: -1.0 # value to use throughout the simulation [PSU; default=-1.0]
file: inflow_file_1.dat # path to file with time series [default=]
column: 3 # index of column to read from [default=1]
outflow: # stream configuration
method: 1 # inflow method [default=1]
zu: -25.5 # upper limit [m; default=0.0]
zl: -26.5 # lower limit [m; default=0.0]
flow: # water flow
method: 2 # method [0=constant, 2=from file; default=0]
constant_value: 0.0 # value to use throughout the simulation [m^3/s; default=0.0]
file: outflow_file_1.dat # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
temp: # flow temperature
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: -1.0 # value to use throughout the simulation [Celcius; default=-1.0]
file: outflow_file_1.dat # path to file with time series [default=]
column: 2 # index of column to read from [default=1]
salt: # flow salinity
method: 0 # method [0=constant, 2=from file; default=0]
constant_value: -1.0 # value to use throughout the simulation [PSU; default=-1.0]
file: outflow_file_1.dat # path to file with time series [default=]
column: 3 # index of column to read from [default=1]
physical_constants:
rho_0: 1000.0 # reference density [kg/m^3; min=0.0; default=1027.0]
buoyancy:
NN_ini: 1.00000000E-04 # initial value of NN (=buoyancy gradient) [s^-2; default=0.0]
fabm: # Framework for Aquatic Biogeochemical Models
use: true # enable FABM [default=false]
freshwater_impact: true # enable dilution/concentration by precipitation/evaporation [default=true]
feedbacks: # feedbacks to physics
bottom_everywhere: true # apply benthic/pelagic coupling at every layer [default=false]
shade: true # interior light absorption [default=false]
albedo: false # surface albedo [default=false]
surface_drag: false # surface drag [default=false]
repair_state: true # clip state to minimum/maximum boundaries [default=false]
numerics:
ode_method: 1
split_factor: 1
eq_state: # equation of state
mode: 2 # formula [1=UNESCO, 2=Jackett et al. (2005); default=2]
method: 2 # implementation [1=full with in-situ temperature/density, 2=full with potential temperature/density, 3=linearized at T0,S0,p0, 4=linearized at T0,S0,p0,dtr0,dsr0; default=1]
T0: 10.0 # reference temperature [Celsius; min=-2.0; default=10.0]
S0: 35.0 # reference salinity [psu; min=0.0; default=35.0]
p0: 0.0 # reference pressure [Pa; default=0.0]
dtr0: -0.17 # thermal expansion coefficient [kg/m^3/K; default=-0.17]
dsr0: 0.78 # saline expansion coefficient [kg/m^3/psu; default=0.78]
restart:
load: false # initialize simulation with state stored in restart.nc [default=false]
output:
output/output: # path of output file, excluding extension
format: netcdf # format [text, netcdf; default=netcdf]
time_unit: hour # time unit [second, hour, day, month, year, dt=model time step; default=day]
time_step: 24 # number of time units between output [min=1; default=1]
time_method: mean # treatment of time dimension [point=instantaneous, mean, integrated; default=point]
sync_interval: 0 # number of output steps between sychronization to disk (<= 0: sync on close only) [default=1]
variables:
- source: /* # variable name in model