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gyacomo/matlab/plot/gene_transport_spectrum.m
5e48668823b53D_parallel

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gene_transport_spectrum.m
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% folder = '/misc/gene_results/NL_Zpinch_Kn_1.8_eta_0.25_nuSG_5e-2_mu_1e-2_SGDK_36x20/';
% folder = '/misc/gene_results/HP_fig_2c_mu_5e-2/';
% folder = '/misc/gene_results/HP_fig_2b_mu_5e-2/';
% folder = '/misc/gene_results/HP_fig_2c_gyroLES/';
% folder = '/misc/gene_results/NL_Zpinch_Kn_1.8_eta_0.25_nuSG_5e-2_mu_1e-2_SGDK_128x32x48x32/';
folder = '/misc/gene_results/shearless_cyclone/output/';
file = 'coord.dat.h5';
vp = h5read([folder,file],'/coord/vp');
mu = h5read([folder,file],'/coord/mu');
kx = h5read([folder,file],'/coord/kx');
ky = h5read([folder,file],'/coord/ky');
z = h5read([folder,file],'/coord/z');
[KY,~] = meshgrid(ky,kx);
file = 'field.dat.h5';
time = h5read([folder,file],'/field/time');
KDIM = 'ky';
TIMES = time;
switch KDIM
case 'kx'
sdim = 2;
k = kx;
xname = '$k_x$';
yname = '$\sum_{k_y}|\Gamma_k|$';
shiftx = @(x) x(1:numel(kx)/2);
shifty = @(x) x(1:numel(kx)/2);
case 'ky'
sdim = 1;
k = ky;
xname = '$k_y$';
yname = '$\sum_{k_x}|\Gamma_k|$';
shiftx = @(x) x;
shifty = @(x) x(1:numel(ky));
end
colors = jet(numel(TIMES));
i_ = 1;
figure
for T = TIMES
[~, it] = min(abs(time-T));
v_x = h5read([folder, 'field.dat.h5'],[ '/field/phi/',sprintf('%10.10d',it-1)]);
v_x = v_x.real + 1i*v_x.imaginary; v_x = squeeze(v_x(:,:,1));
v_x = -1i*KY.*v_x;
n_i = h5read([folder,'mom_ions.dat.h5'],['/mom_ions/dens/',sprintf('%10.10d',it-1)]);
n_i = n_i.real + 1i*n_i.imaginary; n_i = squeeze(n_i(:,:,1));
% topclr_ = abs(n_i);
% v_x = computeFXYZ(v_x);
% n_i = computeFXYZ(n_i);
v_x = real(ifft2(v_x));
n_i = real(ifft2(n_i));
Gx = n_i.*v_x;
Gx = fft2(Gx);
% topclr_ = abs(Gx);
end
[~, it0] = min(abs(time-T(1)));
[~, it1] = min(abs(time-T(end)));
Gx = mean(Gx,3);
subplot(1,2,1)
sdim = 2;
k = kx;
shiftx = @(x) x;%(1:numel(kx)/2);
shifty = @(x) x;%(1:numel(kx)/2);
Y = abs(Gx(:,ky==0));
Y = Y/max(Y);
semilogy(shiftx(k),shifty(Y),'DisplayName',['$t=',num2str(time(it)),'$'],...
'Color',colors(i_,:)); hold on;
subplot(1,2,2)
sdim = 1;
k = ky;
shiftx = @(x) x;
shifty = @(x) x;%(1:numel(ky));
Y = abs(Gx(kx==0,:));
Y = Y/max(Y);
semilogy(shiftx(k),shifty(Y),'DisplayName',['$t=',num2str(time(it)),'$'],...
'Color',colors(i_,:)); hold on;
i_ = i_+1;
subplot(1,2,1)
xname = '$k_x$';
yname = '$\sum_{k_y}|\Gamma_k|$';
title('Gene $k_x$ transport spectrum'); legend('show','Location','eastoutside');
xlabel(xname); ylabel(yname)
subplot(1,2,2)
xname = '$k_y$';
yname = '$\sum_{k_x}|\Gamma_k|$';
title('Gene $k_y$ transport spectrum'); legend('show','Location','eastoutside');
xlabel(xname); ylabel(yname)
figure; pclr = pcolor(topclr_); set(pclr,'EdgeColor','none');
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