Script to run linear analysis

wk/linear_study.m

+clear all;
+addpath(genpath('../matlab')) % ... add
+default_plots_options
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Set Up parameters
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% PHYSICAL PARAMETERS
+NU      = 1e-2;   % Collision frequency
+TAU     = 1.0;    % e/i temperature ratio
+ETAB    = 1.0;
+ETAN    = 1.0;    % Density gradient
+ETAT    = 0.0;    % Temperature gradient
+MU      = 1e-4;   % Hyper diffusivity coefficient
+LAMBDAD = 0.0; 
+NOISE0  = 1.0e-5;
+%% GRID PARAMETERS
+N       = 50;     % Frequency gridpoints (Nkr = N/2)
+L       = 30;     % Size of the squared frequency domain
+PMAXE   = 20;
+JMAXE   = 10; 
+PMAXI   = 20;
+JMAXI   = 10;
+KREQ0   = 1;      % put kr = 0
+KPAR    = 0.0;    % Parellel wave vector component
+%% TIME PARAMETERS 
+TMAX    = 150;  % Maximal time unit
+DT      = 5e-3;   % Time step
+SPS2D   = 1;      % Sampling per time unit for 2D arrays
+SPS5D   = 0;    % Sampling per time unit for 5D arrays
+RESTART = 0;      % To restart from last checkpoint
+JOB2LOAD= 00;
+%% OPTIONS
+SIMID   = 'linear_study';  % Name of the simulation
+NON_LIN = 1 *(1-KREQ0);   % activate non-linearity (is cancelled if KREQ0 = 1)
+CO      = -2;  % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% unused
+KR0KH   = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
+NO_E    = 0;  % Remove electrons dynamic
+% DK    = 0;  % Drift kinetic model (put every kernel_n to 0 except n=0 to 1)
+JOBNUM = 00;
+
+setup
+
+
+%% PARAMETER SCANS
+if 0
+%% Parameter scan over PJ
+ETAB  = 1.0;
+TMAX  = 150;
+PA = [2,3,4,5,6,8,10,12,14,16,20];
+JA = [1,1,2,2,3,4,5,6,7,8,10];
+% PA = [40];
+% JA = [20];
+Nparam = numel(PA);
+param_name = 'PJ';
+
+gamma_Ni = zeros(Nparam,N);
+
+for i = 1:Nparam
+    % Change scan parameter
+    PMAXE = PA(i); PMAXI = PA(i);
+    JMAXE = JA(i); JMAXI = JA(i);
+    setup
+    % Run linear simulation
+    run
+    % Load and process results
+    load_results
+    tend   = Ts2D(end); tstart   = 0.6*tend; 
+    for ikz = 1:N
+        gamma_Ni(i,ikz) = LinearFit_s(Ts2D,squeeze(abs(Ni00(1,ikz,:))),tstart,tend);
+    end
+    gamma_Ni(i,:) = real(gamma_Ni(i,:) .* (gamma_Ni(i,:)>=0.0));
+    % Clean output
+    system(['rm -r ',BASIC.RESDIR])
+end
+
+if 1
+%% Plot
+fig = figure; FIGNAME = 'linear_study';
+plt = @(x) circshift(x,N/2-1);
+for i = 1:Nparam
+    clr       = line_colors(mod(i-1,numel(line_colors(:,1)))+1,:);
+    linestyle = line_styles(floor((i-1)/numel(line_colors(:,1)))+1);
+    plot(plt(kz),plt(gamma_Ni(i,:)),...
+        'Color',clr,...
+        'LineStyle',linestyle{1},...
+        'DisplayName',['$P=$',num2str(PA(i)),', $J=$',num2str(JA(i))]);
+    hold on;
+end
+grid on; xlabel('$k_z$'); ylabel('$\gamma(N_i^{00})$'); xlim([0.0,max(kz)]);
+title(['$\eta_B=',num2str(ETAB),'$'])
+legend('show')
+saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
+end
+end
+if 0
+%% Parameter scan over eta_B
+PMAXE = 20; PMAXI = 20;
+JMAXE = 10; JMAXI = 10;
+TMAX  = 50;
+eta_B = [0.1, 0.33, 0.5, 0.67, 1.0];
+Nparam = numel(eta_B);
+param_name = 'etaB';
+
+gamma_Ni = zeros(Nparam,N);
+
+for i = 1:Nparam
+    % Change scan parameter
+    ETAB = eta_B(i);
+    setup
+    % Run linear simulation
+    run
+    % Load and process results
+    load_results
+    tend   = Ts2D(end); tstart   = 0.6*tend; 
+    for ikz = 1:N
+        gamma_Ni(i,ikz) = LinearFit_s(Ts2D,squeeze(abs(Ni00(1,ikz,:))),tstart,tend);
+    end
+    gamma_Ni(i,:) = real(gamma_Ni(i,:) .* (gamma_Ni(i,:)>=0.0));
+    % Clean output
+    system(['rm -r ',BASIC.RESDIR])
+end
+
+if 1
+%% Plot
+fig = figure; FIGNAME = 'linear_study';
+plt = @(x) circshift(x,N/2-1);
+for i = 1:Nparam
+    clr       = line_colors(mod(i-1,numel(line_colors(:,1)))+1,:);
+    linestyle = line_styles(floor((i-1)/numel(line_colors(:,1)))+1);
+    plot(plt(kz),plt(gamma_Ni(i,:)),...
+        'Color',clr,...
+        'LineStyle',linestyle{1},...
+        'DisplayName',['$\eta_B=$',num2str(eta_B(i))]);
+    hold on;
+end
+grid on; xlabel('$k_z$'); ylabel('$\gamma(N_i^{00})$'); xlim([0.0,max(kz)]);
+title(['$P_e=',num2str(PMAXE),'$',', $J_e=',num2str(JMAXE),'$',...
+       ', $P_i=',num2str(PMAXE),'$',', $J_i=',num2str(JMAXI),'$'])
+legend('show')
+saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
+end
+end
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