benchmark_linear_1D_entropy_mode.m
db9967c54b20half_ky_plane

benchmark_linear_1D_entropy_mode.m
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			addpath(genpath('../matlab')) % ... add
			default_plots_options
			SIMDIR = '../results/benchmarks/1D_linear_entropy_mode/';
			% Compile HeLaZ
			cd ..
			system('make');
			cd wk
			% Run HeLaZ in sequential
			system(['cd ',SIMDIR,';',' ./../../../bin/helaz3.03 0; cd ../../../wk']);
			% Run HeLaZ in parallel (discrepencies can occur at marginal growth rate)
			% since the random seed will not be the same)
			% system(['cd ',SIMDIR,';',' mpirun -np 6 ./../../../bin/helaz 1 6 0; cd ../../../wk'])
			% system(['cd ',SIMDIR,';',' mpirun -np 6 ./../../../bin/helaz 2 3 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_nadiab.fig']); hold on;
			plot(kx,gamma_phi,'-x','DisplayName','new results');
			hold on;
			legend('show');