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gyacomo/wk/analysis_gene.m
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analysis_gene.m
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gyacomodir = '/home/ahoffman/gyacomo/';
addpath(genpath([gyacomodir,'matlab'])) % ... add
addpath(genpath([gyacomodir,'matlab/plot'])) % ... add
addpath(genpath([gyacomodir,'matlab/compute'])) % ... add
addpath(genpath([gyacomodir,'matlab/load'])) % ... add
% folder = '/misc/gene_results/shearless_cyclone/miller_output_1.0/';
% folder = '/misc/gene_results/shearless_cyclone/miller_output_0.8/';
% folder = '/misc/gene_results/shearless_cyclone/s_alpha_output_1.0/';
% folder = '/misc/gene_results/shearless_cyclone/rm_corrections_HF/';
% folder = '/misc/gene_results/shearless_cyclone/linear_s_alpha_CBC_100/';
% folder = '/misc/gene_results/shearless_cyclone/s_alpha_output_0.5/';
% folder = '/misc/gene_results/shearless_cyclone/LD_s_alpha_output_1.0/';
% folder = '/misc/gene_results/shearless_cyclone/LD_s_alpha_output_0.8/';
% folder = '/misc/gene_results/Z-pinch/HP_fig_2a_mu_1e-2/';
folder = '/misc/gene_results/Z-pinch/HP_fig_2a_gyroLES/';
% folder = '/misc/gene_results/Z-pinch/HP_fig_2b_mu_5e-2/';
% folder = '/misc/gene_results/Z-pinch/HP_fig_2c_mu_5e-2/';
% folder = '/misc/gene_results/Z-pinch/HP_fig_2c_gyroLES/';
% folder = '/misc/gene_results/Z-pinch/HP_fig_2c_mu_1e-2_muv_1e-1/';
% folder = '/misc/gene_results/LD_zpinch_1.6/';
% folder = '/misc/gene_results/ZP_HP_kn_1.6_nuv_3.2/';
% folder = '/misc/gene_results/ZP_HP_kn_1.6_nuv_3.2/';
% folder = '/misc/gene_results/Z-pinch/ZP_HP_kn_1.6_HRES/';
% folder = '/misc/gene_results/ZP_kn_2.5_large_box/';
% folder = '/misc/gene_results/Z-pinch/kN_2.0_HD_transport_spectrum_01/';
% folder = '/misc/gene_results/Z-pinch/kN_2.5_HD_transport_spectrum_01/';
% folder = '/misc/gene_results/CBC/128x64x16x24x12/';
% folder = '/misc/gene_results/CBC/196x96x20x32x16_02/';
% folder = '/misc/gene_results/CBC/128x64x16x6x4/';
% folder = '/misc/gene_results/CBC/KT_5.3_128x64x16x24x12_01/';
% folder = '/misc/gene_results/CBC/KT_4.5_128x64x16x24x12_01/';
% folder = '/misc/gene_results/CBC/KT_9_128x64x16x24x12/';
% folder = '/misc/gene_results/CBC/KT_13_large_box_128x64x16x24x12/';
% folder = '/misc/gene_results/CBC/Lapillone_Fig6/';
% folder = '/misc/gene_results/Z-pinch/HP_kN_1.6_adapt_mu_01/';
% folder = '/misc/gene_results/miller/';
% folder = '/misc/gene_results/CBC/KT_4.5_192x96x24x30x16_00/';
% folder = '/misc/gene_results/CBC/KT_5.0_192x96x24x30x16_00/';
% folder = '/misc/gene_results/CBC/KT_5.3_192x96x24x30x16_00/';
% folder = '/misc/gene_results/CBC/KT_6.96_64x32x32x24x12_Nexc_5/';
gene_data = load_gene_data(folder);
gene_data = invert_kxky_to_kykx_gene_results(gene_data);
if 1
%% Space time diagramm (fig 11 Ivanov 2020)
options.TAVG_0 = 0.1*gene_data.Ts3D(end);
options.TAVG_1 = gene_data.Ts3D(end); % Averaging times duration
options.NMVA = 1; % Moving average for time traces
options.ST_FIELD = '\phi'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x, Q_x)
options.INTERP = 1;
options.NCUT = 4; % Number of cuts for averaging and error estimation
options.RESOLUTION = 256;
gene_data.FIGDIR = folder;
fig = plot_radial_transport_and_spacetime(gene_data,options);
save_figure(gene_data,fig,'.png')
end
if 0
%% statistical transport averaging
options.T = [100 500];
fig = statistical_transport_averaging(gene_data,options);
end
if 0
%% 2D snapshots
% Options
options.INTERP = 1;
options.POLARPLOT = 0;
options.AXISEQUAL = 0;
% options.NAME = 'Q_x';
% options.NAME = '\phi';
options.NAME = 'n_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
options.PLAN = 'xy';
% options.NAME ='f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
options.TIME = [1:10];
gene_data.a = data.EPS * 2000;
fig = photomaton(gene_data,options);
save_figure(gene_data,fig,'.png')
end
if 0
%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Options
options.INTERP = 1;
options.POLARPLOT = 0;
% options.NAME = '\phi';
% options.NAME = 'v_y';
% options.NAME = '\Gamma_x';
options.NAME = 'n_i';
options.PLAN = 'xy';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
options.TIME = gene_data.Ts3D;
options.RESOLUTION= 256;
gene_data.a = data.EPS * 2000;
create_film(gene_data,options,'.gif')
end
if 0
%% Geometry
names = {'$g^{xx}$','$g^{xy}$','$g^{xz}$','$g^{yy}$','$g^{yz}$','$g^{zz}$',...
'$B_0$','$\partial_x B_0$','$\partial_y B_0$','$\partial_z B_0$',...
'$J$','$R$','$\phi$','$Z$','$\partial_R x$','$\partial_Z x$'};
figure;
subplot(311)
for i = 1:6
plot(gene_data.z, gene_data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
end
xlim([min(gene_data.z),max(gene_data.z)]); legend('show'); title('GENE geometry');
subplot(312)
for i = 7:10
plot(gene_data.z, gene_data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
end
xlim([min(gene_data.z),max(gene_data.z)]); legend('show');
subplot(313)
for i = 11:16
plot(gene_data.z, gene_data.geo_arrays(:,i),'DisplayName',names{i}); hold on;
end
xlim([min(gene_data.z),max(gene_data.z)]); legend('show');
end
if 0
%% Show f_i(vpar,mu)
options.times = 100:200;
options.specie = 'i';
options.PLT_FCT = 'contour';
options.folder = folder;
options.iz = 'avg';
options.FIELD = '<f_>';
options.ONED = 0;
% options.FIELD = 'Q_es';
plot_fa_gene(options);
end
if 0
%% Time averaged spectrum
options.TIME = [4000 5000];
options.NORM =1;
% options.NAME = '\phi';
% options.NAME = 'n_i';
options.NAME ='\Gamma_x';
options.PLAN = 'kxky';
options.COMPZ = 'avg';
options.OK = 0;
options.COMPXY = 'avg'; % avg/sum/max/zero/ 2D plot otherwise
options.COMPT = 'avg';
options.PLOT = 'semilogy';
fig = spectrum_1D(gene_data,options);
% save_figure(data,fig)
end
if 0
%% Mode evolution
options.NORMALIZED = 0;
options.K2PLOT = 1;
options.TIME = 1:700;
options.NMA = 1;
options.NMODES = 15;
options.iz = 'avg';
fig = mode_growth_meter(gene_data,options);
save_figure(gene_data,fig)
end
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