Options

Effectively this are (almost 1 2) all capabilities of the SCOPE model.

This is an input structure that controls the workflow.

The values have binary (or tertiary) logic thus equal to 0 or 1 (or 2).

Influence on the output files is highlighted in the corresponding section Output files

Note

Not all combinations can bring to the desired result

Initialized

SCOPE.m: read from input_data.xlsx or setoptions.m

Rules of input reading

simulation

Defines rules of input reading

Switch in SCOPE.m (multiple)

0

individual run(s): specify one value for fixed input parameters, and an equal number (> 1) of values for all parameters that vary between the runs.

1
time series (uses text files with meteo input as time series from “../data/input/dataset X” with files similar to ../data/input/dataset for_verification specified on the filenames sheet of input_data.xslx
load_timeseries()
2

Lookup-Table: specify a number of values in the row of input parameters. All possible combinations of inputs will be used.

Let us illustrate what the difference is in details.

It is possible to specify several values in a row on inputdata sheet of input_data.xslx. Suppose we have an the following combination of input parameters. Notice, we provide two values for Cab and Cca parameters.

_images/simulation.bmp

If individual run(s) (options.simulation == 0) was chosen the given combination will end up in two simulations:

  • Cab=80, Cca=20

  • Cab=40, Cca=10

If Lookup-Table (options.simulation == 2) was chosen the given combination will end up in four simulations:

  • Cab=80, Cca=20

  • Cab=80, Cca=10

  • Cab=40, Cca=20

  • Cab=40, Cca=10

Variations in input

rt_thermal

Leaf and soil emissivity in thermal range

Switch in SCOPE.m

0

provide emissivity values as input leafbio (rho_thermal, tau_thermal), soil.rs_thermal

1

use values from fluspect and soil at 2400 nm for the TIR range

calc_zo

roughness length for momentum of the canopy (zo) and displacement height (d)

Switch in select_input() load_timeseries()

0

zo and d values provided in the inputdata canopy

1

calculate zo and d from the LAI, canopy height, CD1, CR, CSSOIL (recommended if LAI changes in time series) zo_and_d()

soilspectrum

Calculate soil reflectance or use from a file in ../data/input/soil_spectrum

Switch in SCOPE.m

0

use soil spectrum from the file with soil.spectrum
default file is soilnew.txt, can be changed on the filenames sheet soil_file cell
variable name is rsfile
1

simulate soil spectrum with the BSM model (BSM()) parameters are fixed in code

soil_heat_method

Method of ground heat flux (G) calculation

Switch in SCOPE.m, select_input(), ebal()

0

standard calculation of thermal inertia from soil characteristic
Soil_Inertia0() in select_input()
1
empirically calibrated formula from soil moisture content Soil_Inertia1() in select_input()
2
as constant fraction (0.35) of soil net radiation
Soil_Inertia0() in select_input()

calc_rss_rbs

soil resistance for evaporation from the pore space (rss) and soil boundary layer resistance (rbs)

Switch in select_input()

0

use resistance rss and rbs as provided in inputdata soil

1

calculate rss from soil moisture content and correct rbs for LAI calc_rssrbs()

Variations in output

RTMo() (SAIL) is executed in any valid run. Other functions may be included with these options.

calc_ebal

Switch in SCOPE.m

0

Only RTMo() is run (with RTMf() if options.calc_fluor)

1

Calculate the complete energy balance.

Warning

required for calc_planck, calc_directional, calc_xanthophyllabs

calc_planck

Calculate spectrum of thermal radiation with spectral emissivity instead of broadband

Warning

only effective with calc_ebal == 1

Switch in SCOPE.m, calc_brdf()

0

RTMt_sb() - broadband brightness temperature is calculated in accordance to Stefan-Boltzman’s equation.

1
RTMt_planck() is launched in SCOPE.m and calc_brdf() (if calc_directional).
Calculation is done per each wavelength thus takes more time than Stefan-Boltzman.

calc_directional

Calculate BRDF and directional temperature for many angles specified in the file: directional.

Warning

  • only effective with calc_ebal == 1

  • Be patient, this takes some time

Switch in SCOPE.m, calc_brdf()

0

1
struct directional is loaded from the file directional
calc_brdf() is launched in SCOPE.m

calc_xanthophyllabs

Calculate dynamic xanthopyll absorption (zeaxanthin) for simulating PRI (photochemical reflectance index)

Warning

  • only effective with calc_ebal == 1

Switch in SCOPE.m

0

1

RTMz() is launched in SCOPE.m and calc_brdf() (if calc_directional)

calc_vert_profiles

Calculation of vertical profiles (per 60 canopy layers).

Corresponding structure profiles

Switch in SCOPE.m, RTMo() and ebal()

0

Profiles are not calculated

1
Photosynthetically active radiation (PAR) per layer is calculated in RTMo()
Energy, temperature and photosynthesis fluxes per layer are calculated in ebal()
Fluorescence fluxes are calculated in RTMf() if (calc_fluor)

calc_fluor

Calculation of fluorescence

Switch in SCOPE.m, calc_brdf()

0

No fluorescence

1
RTMf() is launched in SCOPE.m and calc_brdf() (if calc_directional)
total emitted fluorescence is calculated by SCOPE.m

calc_PSI

Separate fluorescence of photosystems I and II (PSI, PSII) or not

Switch in SCOPE.m, select_input()

0

recommended
treat the whole fluorescence spectrum as one spectrum (new calibrated optipar)
fluspect version fluspect_B_CX_PSI_PSII_combined()
1
differentiate PSI and PSII with Franck et al. spectra (of SCOPE 1.62 and older)
fluspect version fluspect_B_CX()
fluorescence quantum efficiency of PSI is set to 0.2 of PSII in select_input()

Fluorescence_model

Fluorescence model

Switch in ebal()

0

empirical, with sustained NPQ (fit to Flexas’ data)

1

empirical, with sigmoid for Kn: biochemical() (Berry-Van der Tol)

2

biochemical_MD12() (von Caemmerer-Magnani)

apply_T_corr

correct Vcmax and rate constants for temperature

Warning

only effective with Fluorescence_model != 2 i.e. for biochemical()

Switch in ebal()

0
1

correction in accordance to Q10 rule

For users’ comfort

verify

verify the results (compare to saved ‘standard’ output) to test the code for the first time

Switch in SCOPE.m

0
1

runs output_verification()

save_headers

write header lines in output files

Switch in create_output_files()

0
1

runs additional section in create_output_files() which writes two lines (names, units) in output files

makeplots

plot the results

Switch in SCOPE.m

0
1

launches plots() for the results of the last run

1

extra output variables that are not saved to files (see Structs) are available in the workspace after the model run.

2

model can be varied by user, please, consult API to learn signatures of functions