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benchmark_kperp_scan.m
5b5157b79b2fdivided_output

benchmark_kperp_scan.m
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			SIMID = 'benchmark_kperp_scan'; % Name of the simulations
			addpath(genpath('../matlab')) % ... add
			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
			%% outputs options
			OUTPUTS.nsave_0d = 0;
			OUTPUTS.nsave_1d = 0;
			OUTPUTS.nsave_2d = 1;
			OUTPUTS.nsave_5d = 0;
			OUTPUTS.write_Ni00 = '.true.';
			OUTPUTS.write_moments = '.true.';
			OUTPUTS.write_phi = '.true.';
			OUTPUTS.write_non_lin = '.false.';
			OUTPUTS.write_doubleprecision = '.true.';
			OUTPUTS.resfile0 = '''results''';
			%% Grid parameters
			GRID.pmaxe = 15;
			GRID.jmaxe = 6;
			GRID.pmaxi = 15;
			GRID.jmaxi = 6;
			GRID.nkr = 1;
			GRID.krmin = 0.;
			GRID.krmax = 0.;
			GRID.nkz = 20;
			GRID.kzmin = 0.1;
			GRID.kzmax = 1.5;
			%% Model parameters
			MODEL.CO = -1; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
			MODEL.NON_LIN = 0; % Non linear term
			MODEL.nu = 0.01; % collisionality nu*L_perp/Cs0
			% temperature ratio T_a/T_e
			MODEL.tau_e = 1.0;
			MODEL.tau_i = 1.0;
			% mass ratio sqrt(m_a/m_i)
			MODEL.sigma_e = 0.0233380;
			MODEL.sigma_i = 1.0;
			% charge q_a/e
			MODEL.q_e =-1.0;
			MODEL.q_i = 1.0;
			% gradients L_perp/L_x
			MODEL.eta_n = 1.0; % Density
			MODEL.eta_T = 0.0; % Temperature
			MODEL.eta_B = 0.5; % Magnetic
			% Debye length
			MODEL.lambdaD = 0.0;
			%% Time integration and intialization parameters
			TIME_INTEGRATION.numerical_scheme = '''RK4''';
			BASIC.nrun = 100000;
			BASIC.dt = 0.05;
			BASIC.tmax = 50.0;
			INITIAL.initback_moments = 0.01;
			INITIAL.initnoise_moments = 0.;
			INITIAL.iseed = 42;
			INITIAL.selfmat_file = ...
			['''../iCa/self_Coll_GKE_0_GKI_0_ESELF_1_ISELF_1_Pmaxe_',num2str(GRID.pmaxe),...
			'_Jmaxe_',num2str(GRID.jmaxe),'_Pmaxi_',num2str(GRID.pmaxi),'_Jmaxi_',...
			num2str(GRID.jmaxi),'_pamaxx_10.h5'''];
			INITIAL.eimat_file = ...
			['''../iCa/ei_Coll_GKE_0_GKI_0_ETEST_1_EBACK_1_Pmaxe_',num2str(GRID.pmaxe),...
			'_Jmaxe_',num2str(GRID.jmaxe),'_Pmaxi_',num2str(GRID.pmaxi),'_Jmaxi_',...
			num2str(GRID.jmaxi),'_pamaxx_10_tau_1.0000_mu_0.0233.h5'''];
			INITIAL.iemat_file = ...
			['''../iCa/ie_Coll_GKE_0_GKI_0_ITEST_1_IBACK_1_Pmaxe_',num2str(GRID.pmaxe),...
			'_Jmaxe_',num2str(GRID.jmaxe),'_Pmaxi_',num2str(GRID.pmaxi),'_Jmaxi_',...
			num2str(GRID.jmaxi),'_pamaxx_10_tau_1.0000_mu_0.0233.h5'''];
			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
			%% Write input file
			INPUT = write_fort90(OUTPUTS,GRID,MODEL,INITIAL,TIME_INTEGRATION,BASIC);

			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
			%% Run HeLaZ
			nproc = 1;
			EXEC = ' ../bin/helaz ';
			RUN = ['mpirun -np ' num2str(nproc)];
			CMD = [RUN, EXEC, INPUT];
			system(CMD);

			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
			%% Run MOLI with same input parameters
			params.RK4 = 1;
			run ../matlab/MOLI_kperp_scan
			if params.RK4; MOLIsolvername = 'RK4';
			else; MOLIsolvername = 'ode15i';
			end
			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
			%% Analysis and basic figures
			SAVEFIG = 1;
			filename = 'results_00.h5';
			default_plots_options

			%% Growth rate analysis
			moment = 'Ni00';

			kr = h5read(filename,['/data/var2d/' moment '/coordkr']);
			kz = h5read(filename,['/data/var2d/' moment '/coordkz']);
			timeNi = squeeze(h5read(filename,'/data/var2d/time'));
			Ni00 = zeros(numel(kr),numel(kz),numel(timeNi));

			for it = 1:numel(timeNi)
			tmp = h5read(filename,['/data/var2d/', moment,'/', num2str(it,'%06d')]);
			Ni00(:,:,it) = tmp.real + 1i * tmp.imaginary;
			end

			% Amplitude ratio method
			ikr = 1;
			gammas = zeros(numel(kr),numel(kz));
			Napj = ones(numel(timeNi),(GRID.pmaxe+1)(GRID.jmaxe+1)+(GRID.pmaxi+1)(GRID.jmaxi+1));
			for ikz = 1:numel(kz)
			gammas(ikr,ikz) = LinearFit_s(squeeze(timeNi), squeeze(abs(Ni00(ikr,ikz,:))));
			end

			%% Plot
			fig = figure;

			X = kz*sqrt(1+MODEL.tau_i); % Convert to Ricci 2006 Normalization

			subplot(121) % growth rate
			%HeLaZ results
			Y1 = gammas(1,:);
			plot(X,Y1,'-','DisplayName','HeLaZ')
			hold on

			%MOLI results
			Y2 = results.kperp.Maxgammas;
			plot(X,Y2,'--','DisplayName','MOLI');
			title(TITLE);
			grid on
			legend('show')
			xlabel('$k_\perp * (1+\tau)^{1/2}$')
			ylabel('$\gamma L_\perp/c_{s} $')

			subplot(122) % Error
			ERR = abs(gammas(1,:)' - results.kperp.Maxgammas);

			plot(X,ERR,'-','DisplayName','MOLI relative error');
			grid on
			legend('show')
			xlabel('$k_\perp * (1+\tau)^{1/2}$')
			ylabel('$\epsilon_\gamma $')

			if SAVEFIG; FIGNAME = 'g_vs_kz'; save_figure; end;

			%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

gyacomo/wk/benchmark_kperp_scan.m5b5157b79b2fdivided_output

benchmark_kperp_scan.mView Options

gyacomo/wk/benchmark_kperp_scan.m
5b5157b79b2fdivided_output

benchmark_kperp_scan.m
View Options