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calibration_routine_O_P.m
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function x = calibration_routine()
tic
format shortEng
format compact
% parpool
% gaoptions = optimoptions('ga','UseParallel',true);
% x = [0.032; 0.3627];
% lb = x0*0.1;
% ub = x0*10;
[lake_params, sediment_params] = load_params();
% x(1) = lake_params{47}; % 47 settling velocity for Chl1 a (m day-1)
% x(2) = lake_params{49}; % 49 loss rate (1/day) at 20 deg C
% x(3) = lake_params{50}; % 50 specific growth rate (1/day) at 20 deg C
% x(4) = lake_params{53}; % 53 Half saturation growth P level (mg/m3)
% x(5) = lake_params{56}; % 56 Settling velocity for Chl2 a (m day-1)
% x(6) = lake_params{57}; % 57 Loss rate (1/day) at 20 deg C
% x(7) = lake_params{58}; % 58 Specific growth rate (1/day) at 20 deg C
% x(8) = lake_params{59}; % 59 Half saturation growth P level (mg/m3)
% x(9) = lake_params{46}; % % 46 settling velocity for S (m day-1)
% x(10) = lake_params{23}; % 23 scaling factor for inflow concentration of DOC (-)
% x(11) = lake_params{19}; % 19 scaling factor for inflow concentration of POC (-)
% x(12) = lake_params{34}; % 34 Scaling factor for inflow concentration of Fe3 (-)
% x(13) = lake_params{10}; % 10 PAR saturation level for phytoplankton growth (mol(quanta) m-2 s-1)
% x(14) = lake_params{54}; % 16 PAR saturation level for phytoplankton growth (mol(quanta) m-2 s-1)
% x(15) = lake_params{12}; % 12 Optical cross_section of chlorophyll (m2 mg-1)
% x(16) = lake_params{55}; % 17 Optical cross_section of chlorophyll (m2 mg-1)
% x(17) = sediment_params{23}; % 38 R16 sorption of P on Fe k
% x(18) = sediment_params{52}; % accel
% x(19) = lake_params{24}; % % 24 scaling factor for inflow concentration of POP (-)
x = [50.0000e-003, 110.6689e-003, 1.0000e+000, 638.9222e-003, 204.8121e-003, 167.6746e-003, 1.0985e+000, 1.5525e+000, 53.9466e-003, 521.8961e-003, 1, 84.3021e-003, 24.5705e-006, 75.5867e-006, 45.0000e-003, 29.6431e-003, 4.9321e+003, 65.1237e+000, 390.1162e-003];
lb = [0.05, 0.1, 1, 0.2, 0.05, 0.1, 1, 0.2, 0.01, 0, 0, 0, 1e-5, 1e-5, 0.005, 0.005, 1, 1, 0];
ub = [0.5, 0.3, 1.5, 2, 0.5, 0.3, 1.5, 2, 1, 10, 100, 100, 1e-4, 1e-4, 0.045, 0.045, 1e5, 100, 1];
fcns = {@gaplotscorediversity, @gaplotstopping, @gaplotgenealogy, @gaplotscores, @gaplotdistance, @gaplotselection, @gaplotmaxconstr, @gaplotbestf, @gaplotbestindiv, @gaplotexpectation, @gaplotrange, @gaplotpareto, @gaplotparetodistance, @gaplotrankhist, @gaplotspread};
population_size = 72; % Populations size for each generation of the genetic algorithm
max_generations = 7; % How many generations to run the genetic algorithm for
parallelize = true; % 15 generation takes 12 hours on 24 cores
% options = gaoptimset('Display','iter','UseParallel', true, 'TolFun', 1e-2, 'PlotFcns', fcns);
options = optimoptions('ga', 'MaxGenerations', max_generations, 'PopulationSize', population_size, 'UseParallel', parallelize);
x = ga(@opt_fun,length(x),[],[],[],[],lb,ub, @nonlcon, options)
%% opt_fun: function which we are going to minimize
function [res] = opt_fun(x)
[lake_params, sediment_params] = load_params();
lake_params{47} = x(1); % 47 settling velocity for Chl1 a (m day-1)
lake_params{49} = x(2); % 49 loss rate (1/day) at 20 deg C
lake_params{50} = x(3); % 50 specific growth rate (1/day) at 20 deg C
lake_params{53} = x(4); % 53 Half saturation growth P level (mg/m3)
lake_params{56} = x(5); % 56 Settling velocity for Chl2 a (m day-1)
lake_params{57} = x(6); % 57 Loss rate (1/day) at 20 deg C
lake_params{58} = x(7); % 58 Specific growth rate (1/day) at 20 deg C
lake_params{59} = x(8); % 59 Half saturation growth P level (mg/m3)
lake_params{46} = x(9); % % 46 settling velocity for S (m day-1)
lake_params{23} = x(10); % 23 scaling factor for inflow concentration of DOC (-)
lake_params{19} = x(11); % 19 scaling factor for inflow concentration of POC (-)
lake_params{34} = x(12); % 34 Scaling factor for inflow concentration of Fe3 (-)
lake_params{10} = x(13); % 10 PAR saturation level for phytoplankton growth (mol(quanta) m-2 s-1)
lake_params{54} = x(14); % 16 PAR saturation level for phytoplankton growth (mol(quanta) m-2 s-1)
lake_params{12} = x(15); % 12 Optical cross_section of chlorophyll (m2 mg-1)
lake_params{55} = x(16); % 17 Optical cross_section of chlorophyll (m2 mg-1)
sediment_params{23} = x(17); % 38 R16 sorption of P on Fe k
sediment_params{52} = x(18); % accel
lake_params{24} = x(19); % 24 scaling factor for inflow concentration of POP (-)
run_ID = 'Vansjo_Hist_M0' ; % CALIBRATION RUN
clim_ID = run_ID
m_start=[2000, 1, 1]; %
m_stop=[2009, 12, 31]; %
run_INCA = 0; % 1- MyLake will run INCA, 0- No run
use_INCA = 0; % 1- MyLake will take written INCA input, either written just now or saved before, and prepare inputs from them. 0- MyLake uses hand-made input files
is_save_results = false;
% sediment_params{56} = 1; % Only for preliminary calibration: coarse time step for chemical and sediment modules
disp(datetime('now'));
try
[MyLake_results, Sediment_results] = fn_MyL_application(m_start, m_stop, sediment_params, lake_params, use_INCA, run_INCA, run_ID, clim_ID, is_save_results); % runs the model and outputs obs and sim
load('Postproc_code/Vansjo/VAN1_data_2017_02_28_10_55.mat')
depths = [5;10;15;20;25;30;35;40];
rmsd_O2 = 0;
for i=1:size(depths,1)
d = depths(i);
zinx=find(MyLake_results.basin1.z == d);
O2_measured = res.T(res.depth1 == d);
day_measured = res.date(res.depth1 == d);
day_measured = day_measured(~isnan(O2_measured));
O2_measured = O2_measured(~isnan(O2_measured));
O2_mod = MyLake_results.basin1.concentrations.O2(zinx,:)'/1000;
[T_date,loc_sim, loc_obs] = intersect(MyLake_results.basin1.days, day_measured);
rmsd_O2 = rmsd_O2 + RMSE(O2_mod(loc_sim, 1), O2_measured(loc_obs, 1));
% rmsd_O2 = rmsd_O2 + sqrt(mean((O2_mod(loc_sim, 1)-O2_measured(loc_obs, 1)).^2));
end
zinx=find(MyLake_results.basin1.z<4);
TP_mod = mean((MyLake_results.basin1.concentrations.P(zinx,:)+MyLake_results.basin1.concentrations.PP(zinx,:) + MyLake_results.basin1.concentrations.DOP(zinx,:) + MyLake_results.basin1.concentrations.POP(zinx,:))', 2);
Chl_mod = mean((MyLake_results.basin1.concentrations.Chl(zinx,:)+MyLake_results.basin1.concentrations.C(zinx,:))', 2);
P_mod = mean((MyLake_results.basin1.concentrations.P(zinx,:))', 2);
POP_mod = mean((MyLake_results.basin1.concentrations.POP(zinx,:) + MyLake_results.basin1.concentrations.PP(zinx,:))', 2);
load 'obs/store_obs/TOTP.dat' % measured
% load 'obs/store_obs/Cha.dat' % measured
load 'obs/store_obs/Cha_aquaM_march_2017.dat' % measured
load 'obs/store_obs/PO4.dat' % measured
load 'obs/store_obs/Part.dat' % measured
[TP_date,loc_sim, loc_obs] = (intersect(MyLake_results.basin1.days, TOTP(:,1)));
rmsd_TOTP = RMSE(TP_mod(loc_sim, 1), TOTP(loc_obs, 2));
[TP_date,loc_sim, loc_obs] = (intersect(MyLake_results.basin1.days, Cha_aquaM_march_2017(:,1)));
rmsd_Chl = RMSE(Chl_mod(loc_sim, 1), Cha_aquaM_march_2017(loc_obs, 2));
[TP_date,loc_sim, loc_obs] = (intersect(MyLake_results.basin1.days, PO4(:,1)));
rmsd_PO4 = RMSE(P_mod(loc_sim, 1), PO4(loc_obs, 2));
[TP_date,loc_sim, loc_obs] = (intersect(MyLake_results.basin1.days, Part(:,1)));
rmsd_PP = RMSE(POP_mod(loc_sim, 1), Part(loc_obs, 2));
x'
res = sum([3*rmsd_TOTP, 5*rmsd_Chl, 5*rmsd_PO4, 3*rmsd_PP, rmsd_O2])
catch ME
fprintf('\tID: %s\n', ME.identifier)
fprintf('\tMessage: %s\n', ME.message)
fprintf('\tStack::\n')
for k=1:length(ME.stack)
disp(ME.stack(k))
end
res = NaN
end
function r = RMSE(y, yhat)
r = sqrt(mean((y-yhat).^2));
function [c,ceq] = nonlcon(x)
c = -x;
ceq = [];