Wrote two benchmarks scripts, data for benchmark should be uploaded

wk/benchmark_HeLaZ_molix.m

+addpath(genpath('../matlab')) % ... add
+default_plots_options
+
+%% KINETIC ELECTRON TEST
+% Run HeLaZ
+cd ..
+system('make');
+cd wk
+SIMDIR = '../results/benchmarks/shearless_molix_Kin_e/';
+system(['cd ',SIMDIR,';',' ./../../../bin/helaz 0; cd ../../../wk'])
+
+% Run molix
+% cd ../../molix
+% system('make');
+% system('./bin/molix > out.txt');
+% cd ../HeLaZ/wk
+% Compare the results with molix at a given time
+time_2_plot = 5.0;
+[Y_,X_]=molix_plot_phi([SIMDIR,'molix_phi.h5'],time_2_plot);
+[ PHI, Ts3D, dt3D] = load_3D_data([SIMDIR,'outputs_00.h5'], 'phi');
+[Pe, Je, Pi, Ji, kx, ky, z] = load_grid_data(filename);
+
+plot_phi_ballooning; hold on
+plot(X_/pi,real(Y_),'ob');
+plot(X_/pi,imag(Y_),'or');
+plot(X_/pi,abs(Y_) ,'ok');
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% ADIABATIC ELECTRON TEST
+% Run HeLaZ
+cd ..
+system('make');
+cd wk
+SIMDIR = '../results/benchmarks/shearless_molix_Adiab_e/';
+system(['cd ',SIMDIR,';',' ./../../../bin/helaz 0; cd ../../../wk'])
+% Run molix
+% cd ../../molix
+% system('make');
+% system('./bin/molix > out.txt');
+% cd ../HeLaZ/wk
+% Compare the results with molix at a given time
+time_2_plot = 5.0;
+[Y_,X_]=molix_plot_phi([SIMDIR,'molix_phi.h5'],time_2_plot);
+[ PHI, Ts3D, dt3D] = load_3D_data([SIMDIR,'outputs_00.h5'], 'phi');
+[Pe, Je, Pi, Ji, kx, ky, z] = load_grid_data([SIMDIR,'outputs_00.h5']);
+
+plot_phi_ballooning; hold on
+plot(X_/pi,real(Y_),'ob');
+plot(X_/pi,imag(Y_),'or');
+plot(X_/pi,abs(Y_) ,'ok');

wk/benchmark_linear_1D_entropy_mode.m

+addpath(genpath('../matlab')) % ... add
+default_plots_options
+SIMDIR = '../results/benchmarks/1D_linear_entropy_mode/';
+% Compile HeLaZ
+cd ..
+system('make');
+cd wk
+% Run HeLaZ
+system(['cd ',SIMDIR,';',' ./../../../bin/helaz 0; cd ../../../wk'])
+%compute growth rate
+%%
+filename = [SIMDIR,'/outputs_00.h5'];
+[ PHI, Ts3D, dt3D] = load_3D_data(filename, 'phi');
+[Pe, Je, Pi, Ji, kx, ky, z] = load_grid_data(filename);   
+gamma_phi  = kx;
+for ikx = 2:size(kx)
+    tend   = max(Ts3D(abs(PHI(ikx,1,1,:))~=0));
+    tstart   = 0.6*tend;
+    [~,itstart] = min(abs(Ts3D-tstart));
+    [~,itend]   = min(abs(Ts3D-tend));
+    trange = itstart:itend;
+    % exp fit on phi
+    X_ = Ts3D(trange); Y_ = squeeze(abs(PHI(ikx,1,1,trange)));
+    gamma_phi (ikx) = LinearFit_s(X_,Y_);
+end
+
+%% Plot
+SCALE = 1;%sqrt(2);
+openfig([SIMDIR,'/benchmark_data.fig']); hold on;
+plot(kx,gamma_phi,'-x','DisplayName','new results');
+hold on;
+legend('show');
+

wk/molix_helaz_benchmark.m

-%%
-
-cd ..
-system('make');
-cd wk
-
-shearless_linear_fluxtube
-
-
-cd ../../molix
-system('make');
-system('./bin/molix');
-cd ../HeLaZ/wk
-%%
-time_2_plot = 5.0;
-[Y_,X_]=molix_plot_phi('../../molix/field.dat.h5',time_2_plot);
-
-plot_phi_ballooning; hold on
-plot(X_/pi,real(Y_),'ob');
-plot(X_/pi,imag(Y_),'or');
-plot(X_/pi,abs(Y_) ,'ok');
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