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gotm.yaml.gsw
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gotm.yaml.gsw
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# This file was created with only commonly used settings, plus those that differ from the default specified by GOTM.
# You can generate a configuration with every possible setting with: gotm --write_yaml <OUTFILE> --detail full
# To see only the settings that differ from the default, use: gotm --write_yaml <OUTFILE> --detail minimal
version: 7 # version of configuration file [default=7]
title: GOTM Simulation # simulation title used in output [default=GOTM simulation]
location:
name: PROVESS Northern Experiment 1998 # station name used in output [default=GOTM site]
latitude: 5.93333300E+01 # latitude [degrees North; min=-90.0; max=90.0; default=0.0]
longitude: 1.28333300E+00 # longitude [degrees East; min=-360.0; max=360.0; default=0.0]
depth: 110.0 # water depth [m; min=0.0; default=100.0]
time:
start: 1998-01-01 00:00:00 # start date and time [yyyy-mm-dd HH:MM:SS; default=2017-01-01 00:00:00]
stop: 1999-01-01 00:00:00 # stop date and time [yyyy-mm-dd HH:MM:SS; default=2018-01-01 00:00:00]
dt: 3600.0 # time step for integration [s; min=0.0; default=3600.0]
grid:
nlev: 110 # number of layers [min=1; default=100]
method: analytical # layer thickness specification [analytical=equal by default with optional zooming, file_sigma=prescribed relative fractions, file_h=prescribed thicknesses; default=analytical]
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: # path to file with layer thicknesses [default=]
temperature: # temperature profile used for initialization and optionally relaxation [Celsius]
method: file # method [off, file=from file, constant, two_layer=two layers with linear gradient in between, buoyancy=from salinity and buoyancy frequency; default=off]
constant_value: 20.0 # value to use throughout the simulation [Celsius; default=0.0]
file: t_prof_file.dat # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
two_layer:
z_s: 30.0 # depth where upper layer ends [m; min=0.0; default=0.0]
t_s: 20.0 # upper layer temperature [Celsius; min=0.0; max=40.0; default=0.0]
z_b: 40.0 # depth where lower layer begins [m; min=0.0; default=0.0]
t_b: 15.0 # lower layer temperature [Celsius; min=0.0; max=40.0; default=0.0]
NN: 2.56000000E-04 # square of 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]
salinity: # salinity profile used for initialization and optionally relaxation [psu]
method: file # method [off, file=from file, constant, two_layer=two layers with linear gradient in between, buoyancy=from temperature and buoyancy frequency; default=off]
constant_value: 20.0 # value to use throughout the simulation [psu; min=0.0; default=0.0]
file: s_prof_file.dat # path to file with series of profiles [default=]
column: 1 # index of column to read from [default=1]
two_layer:
z_s: 30.0 # depth where upper layer ends [m; min=0.0; default=0.0]
s_s: 20.0 # upper layer salinity [psu; min=0.0; max=40.0; default=0.0]
z_b: 40.0 # depth where lower layer begins [m; min=0.0; default=0.0]
s_b: 15.0 # lower layer salinity [psu; min=0.0; max=40.0; default=0.0]
NN: 2.56000000E-04 # square of buoyancy frequency [s^-2; min=0.0; default=0.0]
relax: # relax model salinity to observed/prescribed value
tau: 86400.0 # time scale for interior layer [s; min=0.0; default=1.00000000E+15]
tau_s: 86400.0 # time scale for surface layer [s; min=0.0; default=1.00000000E+15]
tau_b: 86400.0 # time scale for bottom layer [s; min=0.0; default=1.00000000E+15]
surface:
fluxes: # heat and momentum fluxes
method: kondo # method to calculate fluxes from meteorological conditions [off=use prescribed fluxes, kondo=Kondo (1975), fairall=Fairall et al. (1996); default=off]
heat: # prescribed total heat flux (sensible, latent and net back-radiation) [W/m^2]
method: constant # method [constant, file=from file; default=constant]
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]
tx: # prescribed momentum flux in West-East direction [Pa]
method: constant # method [constant, file=from file; default=constant]
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 [Pa]
method: constant # method [constant, file=from file; default=constant]
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]
u10: # wind speed in West-East direction @ 10 m [m/s]
method: file # method [constant, file=from file; default=constant]
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]
v10: # wind speed in South-North direction @ 10 m [m/s]
method: file # method [constant, file=from file; default=constant]
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]
ssuv_method: absolute # wind treatment [absolute=use absolute wind speed, relative=use wind speed relative to current velocity; default=relative]
airp: # air pressure [Pa]
method: file # method [constant, file=from file; default=constant]
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: 100.0 # scale factor to be applied to values read from file [default=1.0]
airt: # air temperature @ 2 m [Celsius or K]
method: file # method [constant, file=from file; default=constant]
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]
hum: # humidity @ 2 m
method: file # method [constant, file=from file; default=constant]
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: relative # humidity metric [relative=relative humidity (%), wet_bulb=wet-bulb temperature, dew_point=dew point temperature, specific=specific humidity (kg/kg); default=relative]
cloud: # cloud cover [1]
method: file # method [constant, file=from file; default=constant]
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]
precip: # precipitation [m/s]
method: constant # method [constant, file=from file; default=constant]
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]
flux_impact: false # include effect on fluxes of sensible heat and momentum [default=false]
calc_evaporation: false # calculate evaporation from meteorological conditions [default=false]
swr: # shortwave radiation [W/m^2]
method: calculate # method [constant, file=from file, calculate=from time, location and cloud cover; default=constant]
constant_value: 0.0 # value to use throughout the simulation [W/m^2; min=0.0; default=0.0]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
longwave_radiation: # net longwave radiation [W/m^2]
method: clark # method [file=from file, clark=Clark et al. (1974), hastenrath_lamb=Hastenrath and Lamb (1978), bignami=Bignami et al. (1995), berliand_berliand=Berliand and Berliand (1952), josey1=Josey et al. (2003) - 1, josey2=Josey et al. (2003) - 2; default=clark]
file: # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
albedo:
method: payne # method to compute albedo [constant, payne=Payne (1972), cogley=Cogley (1979); default=payne]
constant_value: 0.0 # constant value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.0]
sst: # observed surface temperature [Celsius]
method: file # method [constant, file=from file; default=constant]
file: sst_file.dat # path to file with time series [default=]
roughness:
charnock: true # 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: 0.03 # physical bottom roughness [m; min=0.0; default=0.05]
light_extinction:
method: jerlov-i # water type [jerlov-i=Jerlov type I, jerlov-1-50m=Jerlov type 1 (upper 50 m), jerlov-ia=Jerlov type IA, jerlov-ib=Jerlov type IB, jerlov-ii=Jerlov type II, jerlov-iii=Jerlov type III, custom; default=jerlov-i]
A: # non-visible fraction of shortwave radiation [1]
method: constant # method [constant, file=from file; default=constant]
constant_value: 0.7 # 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 [m]
method: constant # method [constant, file=from file; default=constant]
constant_value: 0.4 # 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 [m]
method: constant # method [constant, file=from file; default=constant]
constant_value: 8.0 # 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: second_order # turbulence closure [convective=convective adjustment, first_order=first-order, second_order=second-order, cvmix; default=second_order]
tke_method: tke # turbulent kinetic energy equation [local_eq=algebraic length scale equation, tke=differential equation for tke (k-epsilon style), mellor_yamada=differential equation for q^2/2 (Mellor-Yamada style); default=tke]
len_scale_method: dissipation # dissipative length scale [parabolic, triangular, xing_davies=Xing and Davies (1995), robert_ouellet=Robert and Ouellet (1987), blackadar=Blackadar (two boundaries) (1962), bougeault_andre=Bougeault and Andre (1986), eifler_schrimpf=Eifler and Schrimpf (ISPRAMIX) (1992), dissipation=dynamic dissipation rate equation, mellor_yamada=dynamic Mellor-Yamada q^2 l-equation, gls=generic length scale (GLS); default=dissipation]
stab_method: schumann_gerz # stability functions [constant, munk_anderson=Munk and Anderson (1954), schumann_gerz=Schumann and Gerz (1995), eifler_schrimpf=Eifler and Schrimpf (1992); default=constant]
turb_param:
cm0_fix: 5.47700000E-01 # value of the stability function in the log-law [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: 0.53 # 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: 1.00000000E-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: 1.0 # exponent for k [dimensionless; default=1.5]
gen_n: -0.67 # exponent for l [dimensionless; default=-1.0]
cpsi1: 1.0 # empirical coefficient cpsi1 in psi equation [dimensionless; default=1.44]
cpsi2: 1.22 # empirical coefficient cpsi2 in psi equation [dimensionless; default=1.92]
cpsi3minus: 0.05 # cpsi3 for stable stratification [dimensionless; default=0.0]
sig_kpsi: 0.8 # Schmidt number for TKE diffusivity [dimensionless; default=1.0]
sig_psi: 1.07 # Schmidt number for psi diffusivity [dimensionless; default=1.3]
keps: # k-epsilon model
ce3minus: -0.4 # ce3 for stable stratification [dimensionless; default=0.0]
my: # Mellor-Yamada model
length: linear # barotropic length scale in q^2 l equation [parabolic, triangular, linear=linear from surface; default=parabolic]
scnd: # second-order model
method: quasi_eq # method [quasi_eq=quasi-equilibrium, weak_eq_kb_eq=weak equilibrium with algebraic buoyancy variance; default=weak_eq_kb_eq]
scnd_coeff: cheng # coefficients of second-order model [custom, gibson_launder=Gibson and Launder (1978), mellor_yamada=Mellor and Yamada (1982), kantha_clayson=Kantha and Clayson (1994), luyten=Luyten et al. (1996), canuto-a=Canuto et al. (2001) (version A), canuto-b=Canuto et al. (2001) (version B), cheng=Cheng et al. (2002); default=canuto-a]
iw: # internal wave mixing
alpha: 0.7 # coefficient for Mellor internal wave model [dimensionless; default=0.0]
mimic_3d: # effects of horizontal gradients
ext_pressure: # external pressure
type: elevation # pressure metric [elevation=horizontal gradient in surface elevation, velocity=horizontal velocities at given height above bed, average_velocity=vertically averaged horizontal velocities; default=elevation]
dpdx: # pressure in West-East direction
method: file # method [constant, tidal=from tidal constituents, file=from file; default=constant]
constant_value: 0.0 # value to use throughout the simulation [default=0.0]
file: ext_press_file.dat # path to file with time series [default=]
column: 2 # index of column to read from [default=1]
tidal: # tidal constituents
amp_1: 0.0 # amplitude of 1st harmonic [default=0.0]
phase_1: 0.0 # phase of 1st harmonic [s; default=0.0]
amp_2: 0.0 # amplitude of 2nd harmonic [default=0.0]
phase_2: 0.0 # phase of 2nd harmonic [s; default=0.0]
dpdy: # pressure in South-North direction
method: file # method [constant, tidal=from tidal constituents, file=from file; default=constant]
constant_value: 0.0 # value to use throughout the simulation [default=0.0]
file: ext_press_file.dat # path to file with time series [default=]
column: 3 # index of column to read from [default=1]
tidal: # tidal constituents
amp_1: 0.0 # amplitude of 1st harmonic [default=0.0]
phase_1: 0.0 # phase of 1st harmonic [s; default=0.0]
amp_2: 0.0 # amplitude of 2nd harmonic [default=0.0]
phase_2: 0.0 # phase of 2nd harmonic [s; default=0.0]
h: # height above bed [m]
method: file # method [constant, file=from file; default=constant]
constant_value: 0.0 # value to use throughout the simulation [m; min=0.0; default=0.0]
file: ext_press_file.dat # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
period_1: 44714.0 # period of 1st tidal harmonic (eg. M2-tide) [s; default=44714.0]
period_2: 43200.0 # period of 2nd tidal harmonic (eg. S2-tide) [s; default=43200.0]
int_pressure: # internal pressure
type: none # method [none, gradients=prescribed horiztonal gradients of T and S, plume=surface or bottom plume; default=none]
gradients: # horizontal salinity and temperature gradients
dtdx: # temperature gradient in West-East direction [Celsius/m]
method: off # method [off, constant, file=from file; default=off]
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 [Celsius/m]
method: off # method [off, constant, file=from file; default=off]
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 [psu/m]
method: off # method [off, constant, file=from file; default=off]
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 [psu/m]
method: off # method [off, constant, file=from file; default=off]
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]
plume: # surface or bottom plume
type: bottom # plume type [surface=buoyant surface-attached, bottom=dense bottom-attached; default=bottom]
x_slope: 0.0 # plume slope in West-East direction [dimensionless; default=0.0]
y_slope: 0.0 # plume slope in South-North direction [dimensionless; default=0.0]
t_adv: false # horizontally advect temperature [default=false]
s_adv: false # horizontally advect salinity [default=false]
zeta: # surface elevation [m]
method: constant # method [constant, tidal=from tidal constituents, file=from file; default=constant]
constant_value: 0.0 # value to use throughout the simulation [m; default=0.0]
file: zeta_file.dat # path to file with time series [default=]
column: 1 # index of column to read from [default=1]
tidal: # tidal constituents
period_1: 44714.0 # period of 1st harmonic (eg. M2-tide) [s; default=44714.0]
amp_1: 1.0 # amplitude of 1st harmonic [m; default=0.0]
phase_1: 0.0 # phase of 1st harmonic [s; default=0.0]
period_2: 43200.0 # period of 2nd harmonic (eg. S2-tide) [s; default=43200.0]
amp_2: 0.5 # amplitude of 2nd harmonic [m; default=0.0]
phase_2: 0.0 # phase of 2nd harmonic [s; default=0.0]
w: # vertical velocity
max: # maximum velocity [m/s]
method: off # method [off, constant, file=from file; default=off]
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 [m]
method: constant # method [constant, file=from file; default=constant]
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: p2_pdm # vertical advection scheme [upstream=first-order upstream, p2=third-order upstream-biased polynomial, superbee=third-order TVD with Superbee limiter, muscl=third-order TVD with MUSCL limiter, p2_pdm=third-order TVD with ULTIMATE QUICKEST limiter; default=p2_pdm]
o2: # oxygen
scale_factor: 31.25 # scale factor to be applied to values read from file [default=1.0]
cvmix:
surface_layer: # surface layer mixing
use: true # compute surface layer mixing coefficients [default=true]
kpp: # K-Profile Parameterization
use: true # use the K-Profile Parameterization [default=true]
langmuir_method: none # method of Langmuir turbulence pararmeterization [none, lwf16=Li et al. (2016), lf17=Li and Fox-Kemper (2017), rwh16=Reichl et al. (2016); default=none]
surface_layer_extent: 0.1 # extent of surface layer in fraction of the boundary layer [dimensionless; min=0.0; max=1.0; default=0.1]
Ri_c: 0.3 # critical Richardson number [dimensionless; min=0.0; default=0.3]
check_Ekman_length: false # limit the OBL by the Ekman depth [default=false]
check_MonOb_length: false # limit the OBL by the Monin-Obukhov depth [default=false]
use_enhanced_diff: true # enhance diffusivity at OBL [default=true]
use_noDGat1: true # zero gradient of the shape function at OBL [default=true]
match_technique: simple # matching technique of shape functions with the ocean interior [simple=simple shapes, gradient=gradient term, both=both gradient and nonlocal terms, parabolic=parabolic nonlocal term; default=simple]
bulk_Ri_interp_type: quadratic # interpolation type for the bulk Richardson number [linear, quadratic, cubic; default=quadratic]
OBL_interp_type: lmd94 # interpolation type for diffusivity and viscosity at OBL [linear, quadratic, cubic, lmd94=Large et al. (1994); default=lmd94]
interior: # interior mixing
use: false # compute interior mixing coefficients [default=false]
background:
use: false # use interior background mixing coefficients [default=false]
diffusivity: 1.00000000E-05 # background diffusivity [m^2/s; default=1.00000000E-05]
viscosity: 1.00000000E-04 # background viscosity [m^2/s; default=1.00000000E-04]
shear:
use: false # compute interior shear mixing coefficients [default=false]
num_smooth_Ri: 1 # number of iterations to smooth the gradient Richardson number [default=1]
mix_scheme: kpp # shear mixing scheme [pp=Pacanowski and Philander (1981), kpp=Large et al. (1994); default=kpp]
PP_nu_zero: 0.005 # numerator in viscosity term in PP [m^2/s; default=0.005]
PP_alpha: 5.0 # coefficient of Ri in denominator of visc / diff terms [dimensionless; default=5.0]
PP_exp: 2.0 # exponent of denominator in viscosity term [dimensionless; default=2.0]
KPP_nu_zero: 0.005 # leading coefficient of the KPP shear mixing formula [m^2/s; default=0.005]
KPP_Ri_zero: 0.7 # critical Richardson number for KPP shear mixing [dimensionless; default=0.7]
KPP_exp: 3.0 # exponent of unitless factor of diffusivity [dimensionless; default=3.0]
convection:
use: false # compute interior convective mixing coefficients [default=false]
diffusivity: 1.0 # convective diffusivity [m^2/s; default=1.0]
viscosity: 1.0 # convective viscosity [m^2/s; default=1.0]
basedOnBVF: true # triger convection based on the squared Brunt-Vaisala frequency [default=true]
triggerBVF: 0.0 # threshold of squared Brunt-Vaisala frequency [1/s^2; default=0.0]
tidal_mixing:
use: false # compute interior tidal mixing coefficients [default=false]
double_diffusion:
use: false # compute interior double diffusion mixing coefficients [default=false]
buoyancy:
NN_ini: 1.00000000E-04 # initial buoyancy gradient (squared buoyancy frequency) [s^-2; default=0.0]
equation_of_state: # equation of state
method: full_teos-10 # density formulation [full_teos-10=TEOS-10, linear_teos-10=linearized at T0, S0, p0 (rho0 is calculated), linear_custom=linearized at T0, S0, rho0, dtr0, dsr0; default=full_teos-10]
rho0: 1027.0 # reference density [kg/m3; default=1027.0]
linear:
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:
nns_annual: # path of output file, excluding extension
time_unit: hour # time unit [second, hour, day, month, year, dt=model time step; default=day]
time_step: 1 # number of time units between output [min=1; default=1]
time_method: point # treatment of time dimension [point=instantaneous, mean, integrated; default=point]
variables:
- source: * # variable name in model