evolve moments on a 2D k grid

wk/kr_kz_time_evolution.m

+%% Run linear simulation on a kr,kz grid and compute the non linear term afterwards
+clear all; close all;
+BASIC.SIMID = 'kr_kz_time_evolution'; % 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_doubleprecision = '.true.';
+OUTPUTS.resfile0      = '''results''';
+%% Grid parameters
+GRID.pmaxe = 8;
+GRID.jmaxe = 4;
+GRID.pmaxi = 8;
+GRID.jmaxi = 4;
+GRID.nkr   = 16;
+GRID.krmin = 0.1;
+GRID.krmax = 1.;
+GRID.nkz   = 16;
+GRID.kzmin = 0.1;
+GRID.kzmax = 1.0;
+%% Model parameters
+MODEL.CO      = -2;  % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
+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   = 0.0;        % Density
+MODEL.eta_T   = 0.0;        % Temperature
+MODEL.eta_B   = 1.0;        % Magnetic
+% Debye length
+MODEL.lambdaD = 0.0;
+%% Time integration and intialization parameters
+TIME_INTEGRATION.numerical_scheme  = '''RK4''';
+BASIC.nrun                = 100000;
+BASIC.dt                  = 0.01;
+BASIC.tmax                = 100.0;
+INITIAL.initback_moments  = 0.01;
+INITIAL.initnoise_moments = 0.0;
+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 and run HeLaZ
+INPUT = write_fort90(OUTPUTS,GRID,MODEL,INITIAL,TIME_INTEGRATION,BASIC);
+nproc = 1;
+EXEC  = ' ../bin/helaz ';
+RUN   = ['mpirun -np ' num2str(nproc)];
+CMD   = [RUN, EXEC, INPUT];
+system(CMD);
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Analysis and basic figures
+default_plots_options
+SAVEFIG = 1;
+filename = 'results_00.h5';
+default_plots_options
+TITLE  = [TITLE,', $k_z=',num2str(GRID.kzmin),'$'];
+
+%% Load HeLaZ moments
+
+moment = 'Ni00';
+
+kr     = h5read(filename,['/data/var2d/' moment '/coordkr']);
+kz     = h5read(filename,['/data/var2d/' moment '/coordkz']);
+time   = h5read(filename,'/data/var2d/time');
+Ni00   = zeros(numel(kr),numel(kz),numel(time));
+for it = 1:numel(time)
+    tmp          = h5read(filename,['/data/var2d/', moment,'/', num2str(it,'%06d')]);
+    Ni00(:,:,it) = tmp.real + 1i * tmp.imaginary;
+end
+
+%% Gif creation
+disp('Creating gif..');
+skip    = 50;    % To skip some frames
+delay   = 0.05; % Speed of the movie (smaller for faster)
+t       = time(1:skip:end);
+N       = squeeze(Ni00(:,:,1:skip:end));
+H       = zeros(GRID.nkr, GRID.nkz, numel(t));
+h       = zeros(GRID.nkr, GRID.nkz, numel(t));
+Pad = 1.0; % Padding
+for it = 1:numel(t)
+    H(:,:,it) = abs(N(:,:,it));
+    F         = abs(ifft2(H,floor(Pad*GRID.nkr),floor(Pad*GRID.nkz)));
+    h(:,:,it) = F(1:GRID.nkr, 1:GRID.nkr);
+end
+GIFNAME = 'Ni00';
+create_gif(kr, kz, t, H, BASIC, GRID, MODEL, delay, GIFNAME)
+% GIFNAME = 'Mi00';
+% create_gif(kr, kz, t, h, BASIC, GRID, MODEL, delay, GIFNAME)
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%