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SCOPE.m
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%% SCOPE.m (script)
% SCOPE is a coupled radiative transfer and energy balance model.
% Option 'lite' runs a computationally lighter variation of the model,
% with the net radiation and leaf temperatures of leaf
% inclination classes are averaged. SCOPE_lite is developed by C. van
% der Tol of the Ts_sunlitUniversity of Twente, under subcontract of Magellium,
% funded by the Europan Space Agency under contract FLEXL2-PFT-CCN2
%
% Copyright (C) 2021 Christiaan van der Tol
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
% any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program. If not, see <http://www.gnu.org/licenses/>.
clear all %#ok<CLALL>
restoredefaultpath
addpath src/RTMs
addpath src/supporting
addpath src/fluxes
addpath src/IO
%% 1. define constants
constants = define_constants;
%% 2. paths
path_input = 'input/'; % path of all inputs
path_of_code = cd;
%% 3. simulation options
fid = fopen('set_parameter_filenames.csv','r');
parameter_file = textscan(fid,'%s','Delimiter', ',');
fclose(fid);
fid = fopen([path_input parameter_file{1}{1}],'r');
Ni = textscan(fid,'%d%s','Delimiter',',');%,'Whitespace','');
fclose(fid);
N = double(Ni{1});
options.lite = N(1); % lite version
options.calc_fluor = N(2); % calculate chlorophyll fluorescence in observation direction
options.calc_planck = N(3); % calculate spectrum of thermal radiation
options.calc_xanthophyllabs = N(4); % include simulation of reflectance dependence on de-epoxydation state
options.soilspectrum = N(5); % 0: use soil reflectance from file; 1: calculate soil reflectance with BSM
options.Fluorescence_model = N(6); %0: empirical, with sustained NPQ (fit to Flexas' data); 1: empirical, with sigmoid for Kn; 2: Magnani 2012 model
options.apply_T_corr = N(7); % correct Vcmax and rate constants for temperature in biochemical.m
options.verify = N(8);
options.saveCSV = N(9);
options.mSCOPE = N(10);
options.simulation = N(11); % 0: individual runs (specify all input in a this file)
% 1: time series (uses text files with meteo input as time series)
% 2: Lookup-Table (specify the values to be included)
% 3: Lookup-Table with random input (specify the ranges of values)
options.dynamic_azimuth = N(18); % 0; calculate the relative azimuth (psi) each time step given a fixed observation azimuth angle
options.calc_directional = N(12); % 0: calculate full BRDF (many angles)
options.calc_vert_profiles = N(13);
options.soil_heat_method = N(14); % 0 - GAM=Soil_Inertia0(lambdas), 1 - GAM=Soil_Inertia1(SMC), 2 - G=0.35*Rn (always in no TS)
options.calc_rss_rbs = N(15); % 0 - fixed, 1 calc
options.MoninObukhov = N(16);
options.save_spectral = N(17);
if options.simulation>2 || options.simulation<0, fprintf('\n simulation option should be between 0 and 2 \r'); return, end
options.Cca_function_of_Cab = 0; % this will change to 1 if Cca is not provided in the input.
switch options.lite
case 0, integr = 'angles_and_layers';
otherwise, integr = 'layers';
end
%% 3. file names
f_names = {'Simulation_Name','soil_file','optipar_file','atmos_file', 'Dataset_dir',...
'meteo_ec_csv', 'vegetation_retrieved_csv', 'LIDF_file', 'verification_dir', ...
'mSCOPE_csv', 'nly'}; % must be in this order
cols = {'t', 'year', 'Rin','Rli', 'p','Ta','ea','u','RH', 'VPD', 'tts','tto', 'psi' ... % expected from EC file as well as ('Ca','SMC')
'Cab','Cca','Cdm','Cw','Cs','Cant','N'... % leaf
'SMC','BSMBrightness', 'BSMlat', 'BSMlon',... % soil
'LAI', 'hc', 'LIDFa', 'LIDFb',... % canopy
'z','Ca', ... % meteo
'Vcmax25', 'BallBerrySlope',... % biochemistry;
'atmos_names'
};
fnc = [f_names, cols];
F = struct('FileID', fnc);
fid = fopen([path_input parameter_file{1}{2}],'r');
while ~feof(fid)
line = fgetl(fid);
if ~isempty(line)
charline = char(line);
if ~(charline(1) == '%')
X = textscan(line,'%s%s','Delimiter', ',', 'Whitespace','\t');
x = X{1}; y = X{2};
k = find(strcmp(fnc,x{:}));
if ~isempty(k) && ~isempty(y)
F(k).FileName = y{:};
end
end
end
end
fclose(fid);
%% 4. input data
k = 1;
fid = fopen([path_input parameter_file{1}{3}], 'r');
clear('X')
while ~feof(fid)
line = fgetl(fid);
y = textscan(line,'%s', 'Delimiter', ',', 'TreatAsEmpty', ' ');
varnames(k) = y{1}(1); %#ok<SAGROW>
X(k).Val = str2double(y{:});
k = k+1;
end
fclose(fid);
V = assignvarnames();
for i = 1:length(V)
j = find(strcmp(varnames,V(i).Name));
if isempty(j)
if i==2
fprintf(1,'%s %s %s \n','warning: input "', V(i).Name, '" not provided in input data...');
fprintf(1,'%s %s %s\n', 'I will use 0.25*Cab instead');
options.Cca_function_of_Cab = 1;
else
if ~(options.simulation==1) && (i==30 || i==32)
fprintf(1,'%s %s %s \n','warning: input "', V(i).Name, '" not provided in input data...');
fprintf(1,'%s %s %s\n', 'I will use the MODTRAN spectrum as it is');
else
if (options.simulation == 1 || (~options.simulation && (i<46 || i>50 )))
fprintf(1,'%s %s %s \n','warning: input "', V(i).Name, '" not provided in input data');
if (options.simulation ==1)% && (i==1 ||i==9||i==22||i==23||i==54 || (i>29 && i<37)))
fprintf(1,'%s %s %s\n', 'I will look for the values in Dataset Directory "',F(5).FileName,'"');
else
if (i== 24 || i==25)
fprintf(1,'%s %s %s\n', 'will estimate it from LAI, CR, CD1, Psicor, and CSSOIL');
options.calc_zo = 1;
else
if (i>38 && i<44)
fprintf(1,'%s %s %s\n', 'will use the provided zo and d');
options.calc_zo = 0;
else
if ~((options.simulation ==1 && (i==30 ||i==32)))
fprintf(1,'%s \n', 'this input is required: SCOPE ends');
return
elseif (options.simulation ==1 && (i==30 ||i==32))
fprintf(1,'%s %s %s\n', '... no problem, I will find it in Dataset Directory "',F(5).FileName, '"');
end
end
end
end
end
end
end
else
k = find(~isnan(X(j).Val));
if ~isempty(k)
V(i).Val = X(j).Val(k);
else
V(i).Val = -999;
end
end
end
%% 6. Load spectral data for leaf and soil
load([path_input,'fluspect_parameters/', F(3).FileName]);
if options.soilspectrum ==0
rsfile = load([path_input,'soil_spectra/', F(2).FileName]); % file with soil reflectance spectra
end
%% 8. Define canopy structure and other 'fixed' parameters
canopy.nlincl = 13;
canopy.nlazi = 36;
canopy.litab = [ 5:10:75 81:2:89 ]'; % a column, never change the angles unless 'ladgen' is also adapted
canopy.lazitab = ( 5:10:355 ); % a row
soilemp.SMC = 25; % empirical parameter (fixed) for BSM
soilemp.film = 0.015; % empirical parameter (fixed) for BMS
LIDF_file = F(8).FileName;
if ~isempty(LIDF_file)
canopy.lidf = dlmread([path_input,'leafangles/',LIDF_file],'',3,0);
end
%% 10. Define spectral regions
[spectral] = define_bands;
%% 11. load time series data
if options.simulation == 1
vi = ones(length(V),1);
for k = 1:length(V)
if ~strcmp(V(k).Name, 'Tparam') && length(V(k).Val) > 1
warning('%s value from the first column of input_data will be used, time series mode', V(k).Name)
V(k).Val = V(k).Val(1);
end
end
[soil,leafbio,canopy,meteo,angles,xyt] = select_input(V,vi,canopy,options,constants);
[V, xyt, mly_ts, atmo_paths] = load_timeseries(V, F, xyt, path_input,options);
else
soil = struct;
end
%% 12. preparations
%% soil heat
if options.simulation==1
if options.soil_heat_method<2
if (isempty(meteo.Ta) || meteo.Ta<-273), meteo.Ta = 20; end
soil.Tsold = meteo.Ta*ones(12,2);
end
end
%% temperature sensitivity of photosynthesis parameters
leafbio.TDP = define_temp_response_biochem; % temperature response C3 and C4 according to CLM4 model
%% variables
nvars = length(V);
vmax = cellfun(@length, {V.Val})';
vmax(27,1) = 1; % these are Tparam and LIDFb
vi = ones(nvars,1);
switch options.simulation
case 0, telmax = max(vmax); [xyt.t,xyt.year]= deal(zeros(telmax,1));
case 1, telmax = size(xyt.t,1);
case 2, telmax = prod(double(vmax)); [xyt.t,xyt.year]= deal(zeros(telmax,1));
end
% [rad,thermal,fluxes] = initialize_output_structures(spectral);
if options.calc_directional
anglesfile = load([path_input,'directional/brdf_angles2.dat']); % Multiple observation angles in case of BRDF calculation
directional.tto = anglesfile(:,1); % [deg] Observation zenith Angles for calcbrdf
directional.psi = anglesfile(:,2); % [deg] Observation zenith Angles for calcbrdf
directional.noa = length(directional.tto); % Number of Observation Angles
else
directional = NaN;
end
%% irradiance
atmfile = fullfile(path_input, 'radiationdata', F(4).FileName);
if options.simulation == 1 && ~isempty(atmo_paths)
atmfile = atmo_paths{1};
end
atmo = load_atmo(atmfile, spectral.SCOPEspec);
%% 13. create output files
[Output_dir, f, fnames] = create_output_files_binary(parameter_file, F, path_of_code, path_input, spectral,options);
%% 14. Run the models
fprintf('\n The calculations start now \r')
calculate = 1;
tic
for k = 1:telmax
if options.simulation == 1, vi(vmax>1) = k; end
if options.simulation == 0, vi(vmax==telmax) = k; end
[soil,leafbio,canopy,meteo,angles,xyt] = select_input(V,vi,canopy,options,constants,xyt,soil,leafbio);
canopy.nlayers = ceil(10*canopy.LAI) + ((meteo.Rin < 200) & options.MoninObukhov)*60;
canopy.nlayers = max(2, canopy.nlayers); % patch for LAI < 0.1
nl = canopy.nlayers;
x = (-1/nl : -1/nl : -1)'; % a column vector
canopy.xl = [0; x]; % add top level
% canopy.xl(1:end-1) = canopy.xl(1:end-1)+canopy.xl(1:end-1)-1/(2*nl); % middle of the thin layer
if options.simulation ~=1
fprintf('simulation %i ', k );
fprintf('of %i \n', telmax);
else
calculate = ~isnan(meteo.p*meteo.Ta*meteo.ea*meteo.u.*meteo.Rin.*meteo.Rli);
fprintf('time = %s: %i / %i\n', datestr(xyt.t(k)), k, telmax)
if isnan(meteo.p*meteo.Ta*meteo.ea*meteo.u.*meteo.Rin.*meteo.Rli)
warning('run is invalid: there is NaN somewhere in meteo input [p, Ta, ea, u, Rin, Rli]')
end
end
if calculate
if isempty(LIDF_file)
canopy.lidf = leafangles(canopy.LIDFa,canopy.LIDFb); % This is 'ladgen' in the original SAIL model,
end
%% leaf radiative transfer model FLUSPECT
leafbio.emis = 1-leafbio.rho_thermal-leafbio.tau_thermal;
leafbio.V2Z = 0;
if options.simulation == 1 && ~isempty(fieldnames(mly_ts)) % means that options.simulation == 1
mly.nly = mly_ts.nly;
mly.pLAI = mly_ts.pLAI(k, :);
mly.totLAI = sum(mly.pLAI);
mly.pCab = mly_ts.pCab(k, :);
mly.pCca = mly_ts.pCca(k, :);
mly.pCdm = mly_ts.pCw(k, :);
mly.pCw = mly_ts.pCw(k, :);
mly.pCs = mly_ts.pCs(k, :);
mly.pN = mly_ts.pN(k, :);
elseif k == 1 && options.mSCOPE
mly = input_mSCOPE(fullfile('input', 'mSCOPE.csv'));
else
if options.mSCOPE
warning('I do not know how to use mSCOPE layers with multiple but non time series runs, so I will not use it')
end
mly.nly = 1;
mly.pLAI = canopy.LAI;
mly.totLAI = canopy.LAI;
mly.pCab = leafbio.Cab;
mly.pCca = leafbio.Cca;
mly.pCdm = leafbio.Cdm;
mly.pCw = leafbio.Cw;
mly.pCs = leafbio.Cs;
mly.pN = leafbio.N;
end
if options.simulation == 1 && ~isempty(atmo_paths) && k > 1
atmfile_k = atmo_paths{k};
if ~strcmp(atmfile_k, atmo_paths{k-1})
atmo = load_atmo(atmfile_k, spectral.SCOPEspec);
end
end
leafopt = fluspect_mSCOPE(mly,spectral,leafbio,optipar, nl);
leafopt.refl(:, spectral.IwlT) = leafbio.rho_thermal;
leafopt.tran(:, spectral.IwlT) = leafbio.tau_thermal;
if options.calc_xanthophyllabs
leafbio.V2Z = 1;
leafoptZ = fluspect_mSCOPE(mly,spectral,leafbio,optipar, nl);
leafopt.reflZ = leafopt.refl;
leafopt.tranZ = leafopt.tran;
leafopt.reflZ(:, spectral.IwlP) = leafoptZ.refl(:, spectral.IwlP);
leafopt.tranZ(:, spectral.IwlP) = leafoptZ.tran(:, spectral.IwlP);
end
%% soil reflectance model BSM
if options.soilspectrum == 0
soil.refl = rsfile(:,soil.spectrum+1);
else
soil.refl = BSM(soil,optipar,soilemp);
end
soil.refl(spectral.IwlT) = soil.rs_thermal;
%% four stream canopy radiative transfer model for incident radiation
[rad,gap,profiles] = RTMo(spectral,atmo,soil,leafopt,canopy,angles,constants,meteo,options);
%% energy balance
[iter,rad,thermal,soil,bcu,bch,fluxes,resistance,meteo] ...
= ebal(constants,options,rad,gap, ...
meteo,soil,canopy,leafbio, k, xyt,integr);
%% fluorescence radiative transfer model
if options.calc_fluor
[rad] = RTMf(constants,spectral,rad,soil,leafopt,canopy,gap,angles,bcu.eta,bch.eta);
end
%% radiative transfer model for PRI effects
if options.calc_xanthophyllabs
[rad] = RTMz(constants,spectral,rad,soil,leafopt,canopy,gap,angles,bcu.Kn,bch.Kn);
end
rad = RTMt_sb(constants,rad,soil,leafbio,canopy,gap,thermal.Tcu,thermal.Tch,thermal.Tsu,thermal.Tsh,1,spectral);
if options.calc_planck
rad = RTMt_planck(spectral,rad,soil,leafopt,canopy,gap,thermal.Tcu,thermal.Tch,thermal.Tsu,thermal.Tsh);
end
%% computation of data products
% aPAR, LST, NPQ, ETR, photosynthesis, SIF-reabsorption correction
% aPAR [umol m-2 s-1, total canopy and total chlorphyll]
Ps = gap.Ps(1:nl);
Ph = (1-Ps);
canopy.LAIsunlit = canopy.LAI*mean(Ps);
canopy.LAIshaded = canopy.LAI-canopy.LAIsunlit;
canopy.Pnsun_Cab = canopy.LAI*meanleaf(canopy,rad.Pnu_Cab,integr,Ps); % net PAR Cab sunlit leaves (photons)
canopy.Pnsha_Cab = canopy.LAI*meanleaf(canopy,rad.Pnh_Cab,'layers',Ph); % net PAR Cab shaded leaves (photons)
canopy.Pntot_Cab = canopy.Pnsun_Cab+canopy.Pnsha_Cab; % net PAR Cab leaves (photons)
canopy.Pnsun_Car = canopy.LAI*meanleaf(canopy,rad.Pnu_Car,integr,Ps); % net PAR Cab sunlit leaves (photons)
canopy.Pnsha_Car = canopy.LAI*meanleaf(canopy,rad.Pnh_Car,'layers',Ph); % net PAR Cab shaded leaves (photons)
canopy.Pntot_Car = canopy.Pnsun_Car+canopy.Pnsha_Car; % net PAR Cab leaves (photons)
canopy.Pnsun = canopy.LAI*meanleaf(canopy,rad.Pnu,integr,Ps); % net PAR sunlit leaves (photons)
canopy.Pnsha = canopy.LAI*meanleaf(canopy,rad.Pnh,'layers',Ph); % net PAR shaded leaves (photons)
canopy.Pntot = canopy.Pnsun+canopy.Pnsha; % net PAR leaves (photons)
canopy.Rnsun_Cab = canopy.LAI*meanleaf(canopy,rad.Rnu_Cab,integr,Ps); % net PAR Cab sunlit leaves (radiance)
canopy.Rnsha_Cab = canopy.LAI*meanleaf(canopy,rad.Rnh_Cab,'layers',Ph); % net PAR Cab sunlit leaves (radiance)
canopy.Rntot_Cab = canopy.Rnsun_Cab+canopy.Rnsha_Cab; % net PAR Cab leaves (radiance)
canopy.Rnsun_Car = canopy.LAI*meanleaf(canopy,rad.Rnu_Car,integr,Ps); % net PAR Cab sunlit leaves (radiance)
canopy.Rnsha_Car = canopy.LAI*meanleaf(canopy,rad.Rnh_Car,'layers',Ph); % net PAR Cab sunlit leaves (radiance)
canopy.Rntot_Car = canopy.Rnsun_Car+canopy.Rnsha_Car; % net PAR Cab leaves (radiance)
canopy.Rnsun_PAR = canopy.LAI*meanleaf(canopy,rad.Rnu_PAR,integr,Ps); % net PAR sunlit leaves (radiance)
canopy.Rnsha_PAR = canopy.LAI*meanleaf(canopy,rad.Rnh_PAR,'layers',Ph); % net PAR sunlit leaves (radiance)
canopy.Rntot_PAR = canopy.Rnsun_PAR+canopy.Rnsha_PAR; % net PAR leaves (radiance)
% LST [K] (directional, but assuming black-body surface!)
canopy.LST = (pi*(rad.Lot+rad.Lote)./(constants.sigmaSB*rad.canopyemis)).^0.25;
canopy.emis = rad.canopyemis;
% photosynthesis [mumol m-2 s-1]
canopy.A = canopy.LAI*(meanleaf(canopy,bch.A,'layers',Ph)+meanleaf(canopy,bcu.A,integr,Ps)); % photosynthesis
% electron transport rate [mumol m-2 s-1]
canopy.Ja = canopy.LAI*(meanleaf(canopy,bch.Ja,'layers',Ph)+meanleaf(canopy,bcu.Ja,integr,Ps)); % electron transport
% non-photochemical quenching (energy) [W m-2]
canopy.ENPQ = canopy.LAI*(meanleaf(canopy,rad.Rnh_Cab.*bch.Phi_N,'layers',Ph)+meanleaf(canopy,rad.Rnu_Cab.*bcu.Phi_N,integr,Ps)); % NPQ energy;
canopy.PNPQ = canopy.LAI*(meanleaf(canopy,rad.Pnh_Cab.*bch.Phi_N,'layers',Ph)+meanleaf(canopy,rad.Pnu_Cab.*bcu.Phi_N,integr,Ps)); % NPQ energy;
% computation of re-absorption corrected fluorescence
% Yang and Van der Tol (2019); Van der Tol et al. (2019)
%aPAR_Cab_eta = canopy.LAI*(meanleaf(canopy,bch.eta .* rad.Rnh_Cab,'layers',Ph)+meanleaf(canopy,bcu.eta .* rad.Rnu_Cab,integr,Ps)); %
aPAR_Cab_eta = canopy.LAI*(meanleaf(canopy,bch.eta .* rad.Pnh_Cab,'layers',Ph)+meanleaf(canopy,bcu.eta .* rad.Pnu_Cab,integr,Ps)); %
if options.calc_fluor
ep = constants.A*ephoton(spectral.wlF'*1E-9,constants);
rad.PoutFrc = leafbio.fqe*aPAR_Cab_eta;
rad.EoutFrc_ = 1E-3*ep.*(rad.PoutFrc*optipar.phi(spectral.IwlF)); %1E-6: umol2mol, 1E3: nm-1 to um-1
rad.EoutFrc = 1E-3*Sint(rad.EoutFrc_,spectral.wlF);
sigmaF = pi*rad.LoF_./rad.EoutFrc_;
rad.sigmaF = interp1(spectral.wlF(1:4:end),sigmaF(1:4:end),spectral.wlF);
canopy.fqe = rad.PoutFrc./canopy.Pntot_Cab;
else
canopy.fqe = nan;
end
rad.Lotot_ = rad.Lo_+rad.Lot_;
rad.Eout_ = rad.Eout_+rad.Eoutte_;
if options.calc_fluor
rad.Lototf_ = rad.Lotot_;
rad.Lototf_(spectral.IwlF') = rad.Lototf_(spectral.IwlF)+rad.LoF_;
rad.reflapp = rad.refl;
rad.reflapp(spectral.IwlF) =pi*rad.Lototf_(spectral.IwlF)./(rad.Esun_(spectral.IwlF)+rad.Esky_(spectral.IwlF));
end
if options.calc_directional
directional = calc_brdf(constants,options,directional,spectral,angles,atmo,soil,leafopt,canopy,meteo,thermal,bcu,bch);
savebrdfoutput(options,directional,angles,spectral,Output_dir)
end
rad.Lo = 0.001 * Sint(rad.Lo_(spectral.IwlP),spectral.wlP);
%% write output
n_col = output_data_binary(f, k, xyt, rad, canopy, V, vi, vmax, options, fluxes, meteo, iter,resistance);
%% update input
if options.simulation==2 && telmax>1, vi = count_k(nvars,vi,vmax,1); end
end
end
toc
if options.saveCSV
bin_to_csv(fnames, V, vmax, n_col, telmax)
end
fclose('all');
if options.verify
output_verification_csv(Output_dir, F(9).FileName)
end