-
Notifications
You must be signed in to change notification settings - Fork 4
/
calibration_routine_O_P_Chl.m
171 lines (121 loc) · 8.5 KB
/
calibration_routine_O_P_Chl.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
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) = 58.3842e-003; % 50.0000e-003 % 47 settling velocity for Chl1 a (m day-1)
x(2) = 128.2949e-003; % 110.6689e-003 % 49 loss rate (1/day) at 20 deg C
x(3) = 1.4988e+000; % 1.0000e+000 % 50 specific growth rate (1/day) at 20 deg C
x(4) = 1.6945e+000; % 638.9222e-003 % 53 Half saturation growth P level (mg/m3)
x(5) = 208.3324e-003; % 204.8121e-003 % 56 Settling velocity for Chl2 a (m day-1)
x(6) = 201.6135e-003; % 167.6746e-003 % 57 Loss rate (1/day) at 20 deg C
x(7) = 1.2687e+000; % 1.0985e+000 % 58 Specific growth rate (1/day) at 20 deg C
x(8) = 1.6142e+000; % 1.5525e+000 % 59 Half saturation growth P level (mg/m3)
x(9) = 31.3665e-003; % 53.9466e-003 % % 46 settling velocity for S (m day-1)
x(10) = 14.4699e-006; % 24.5705e-006 % 10 PAR saturation level for phytoplankton growth (mol(quanta) m-2 s-1)
x(11) = 30.5827e-006; % 75.5867e-006 % 16 PAR saturation level for phytoplankton growth (mol(quanta) m-2 s-1)
x(12) = 37.9560e-003; % 45.0000e-003 % 12 Optical cross_section of chlorophyll (m2 mg-1)
x(13) = 34.7141e-003; % 29.6431e-003 % 17 Optical cross_section of chlorophyll (m2 mg-1)
x(14) = 21.5114e+000; % 65.1237e+000 % accel
x(15) = 373.1228e-003; % 390.1162e-003 % 24 scaling factor for inflow concentration of POP (-)
% Ecomac-2 results "-RMSD*(R^2 - 1) = 42" % ====================================================
x = [0.0509799553636229; 0.112442493655332; 1.28362330332034; 1.36809570914136; 0.0501864460452149; 0.108370399688849; 1.46968213451174; 1.53127867204317; 0.0473597449781419; 2.37096381881603e-05; 3.26782527521984e-05; 0.0449499936004535; 0.0403445049032881; 20.3036606042011; 0.622744575375964];
lb = [0.05 , 0.1 , 1 , 0.2 , 0.05 , 0.1 , 1 , 0.2 , 0.01 , 1e-5 , 1e-5 , 0.005 , 0.005 , 1 , 0];
ub = [0.5 , 0.3 , 1.5 , 2 , 0.5 , 0.3 , 1.5 , 2 , 1 , 1e-4 , 1e-4 , 0.045 , 0.045 , 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); % 50.0000e-003 % 47 settling velocity for Chl1 a (m day-1)
lake_params{49} = x(2); % 110.6689e-003 % 49 loss rate (1/day) at 20 deg C
lake_params{50} = x(3); % 1.0000e+000 % 50 specific growth rate (1/day) at 20 deg C
lake_params{53} = x(4); % 638.9222e-003 % 53 Half saturation growth P level (mg/m3)
lake_params{56} = x(5); % 204.8121e-003 % 56 Settling velocity for Chl2 a (m day-1)
lake_params{57} = x(6); % 167.6746e-003 % 57 Loss rate (1/day) at 20 deg C
lake_params{58} = x(7); % 1.0985e+000 % 58 Specific growth rate (1/day) at 20 deg C
lake_params{59} = x(8); % 1.5525e+000 % 59 Half saturation growth P level (mg/m3)
lake_params{46} = x(9); % 53.9466e-003 % % 46 settling velocity for S (m day-1)
lake_params{10} = x(10); % 24.5705e-006 % 10 PAR saturation level for phytoplankton growth (mol(quanta) m-2 s-1)
lake_params{54} = x(11); % 75.5867e-006 % 16 PAR saturation level for phytoplankton growth (mol(quanta) m-2 s-1)
lake_params{12} = x(12); % 45.0000e-003 % 12 Optical cross_section of chlorophyll (m2 mg-1)
lake_params{55} = x(13); % 29.6431e-003 % 17 Optical cross_section of chlorophyll (m2 mg-1)
sediment_params{52} = x(14); % 65.1237e+000 % accel
lake_params{24} = x(15); % 390.1162e-003 % 24 scaling factor for inflow concentration of POP (-)
sediment_params{73} = 48;
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;
rsquared_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(i) = rmsd(O2_mod(loc_sim, 1), O2_measured(loc_obs, 1));
rsquared_O2(i) = rsquared(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, :) + MyLake_results.basin1.concentrations.POP(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 = rmsd(TP_mod(loc_sim, 1), TOTP(loc_obs, 2));
rsquared_TOTP = rsquared(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 = rmsd(Chl_mod(loc_sim, 1), Cha_aquaM_march_2017(loc_obs, 2));
rsquared_Chl = rsquared(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 = rmsd(P_mod(loc_sim, 1), PO4(loc_obs, 2));
rsquared_PO4 = rsquared(P_mod(loc_sim, 1), PO4(loc_obs, 2));
[TP_date,loc_sim, loc_obs] = (intersect(MyLake_results.basin1.days, Part(:,1)));
rmsd_PP = rmsd(POP_mod(loc_sim, 1), Part(loc_obs, 2));
rsquared_PP = rsquared(POP_mod(loc_sim, 1), Part(loc_obs, 2));
x'
% res = sum([3*rmsd_TOTP, 3*rmsd_Chl, 3*rmsd_PO4, 3*rmsd_PP, rmsd_O2])
% res = sum([- (rsquared_TOTP - 1), - (rsquared_Chl - 1), - (rsquared_PO4 - 1), - (rsquared_PP - 1), mean(- (rsquared_O2 + 1))])
res = sum([- (rsquared_TOTP - 1) .* rmsd_TOTP, - (rsquared_Chl - 1) .* rmsd_Chl, - (rsquared_PO4 - 1) .* rmsd_PO4, - (rsquared_PP - 1) .* rmsd_PP, mean(- (rsquared_O2 - 1) .* 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 [c,ceq] = nonlcon(x)
c = -x;
ceq = [];