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gyacomo/matlab/load/load_gene_data.m
3f25a0efc43cdivided_output

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load_gene_data.m
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function [ DATA ] = load_gene_data( folder )
%to load gene data as for HeLaZ results
namelist = read_namelist([folder,'parameters.dat']);
DATA.namelist = namelist;
%% Grid
file = 'coord.dat.h5';
DATA.vp = h5read([folder,file],'/coord/vp');
DATA.Nvp = numel(DATA.vp);
DATA.mu = h5read([folder,file],'/coord/mu');
DATA.Nmu = numel(DATA.mu);
DATA.kx = h5read([folder,file],'/coord/kx');
DATA.Nkx = numel(DATA.kx);
DATA.Nx = DATA.Nkx;
DATA.ky = h5read([folder,file],'/coord/ky');
DATA.Nky = numel(DATA.ky);
DATA.Ny = DATA.Nky*2-1;
DATA.z = h5read([folder,file],'/coord/z');
DATA.Nz = numel(DATA.z);
dkx = DATA.kx(2); dky = DATA.ky(2);
Lx = 2*pi/dkx; Ly = 2*pi/dky;
x = linspace(-Lx/2,Lx/2,DATA.Nx+1); x = x(1:end-1);
y = linspace(-Ly/2,Ly/2,DATA.Ny+1); y = y(1:end-1);
DATA.x = x; DATA.y = y; DATA.Lx = Lx; DATA.Ly = Ly;
%% Transport
file = 'nrg.dat.h5';
DATA.Ts0D = h5read([folder,file],'/nrgions/time');
DATA.PGAMMA_RI = h5read([folder,file],'/nrgions/Gamma_es');
DATA.HFLUX_X = h5read([folder,file],'/nrgions/Q_es');
%% fields and moments
file = 'mom_ions.dat.h5';
DATA.Ts3D = h5read([folder,file],'/mom_ions/time');
DATA.DENS_I = zeros(DATA.Nkx,DATA.Nky,DATA.Nz,numel(DATA.Ts3D));
DATA.TPER_I = zeros(DATA.Nkx,DATA.Nky,DATA.Nz,numel(DATA.Ts3D));
DATA.TPAR_I = zeros(DATA.Nkx,DATA.Nky,DATA.Nz,numel(DATA.Ts3D));
DATA.PHI = zeros(DATA.Nkx,DATA.Nky,DATA.Nz,numel(DATA.Ts3D));
for jt = 1:numel(DATA.Ts3D)
t = DATA.Ts3D(jt);
[~, it] = min(abs(DATA.Ts3D-t));
tmp = h5read([folder,file],['/mom_ions/dens/',sprintf('%10.10d',it-1)]);
DATA.DENS_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
tmp = h5read([folder,file],['/mom_ions/T_par/',sprintf('%10.10d',it-1)]);
DATA.TPAR_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
tmp = h5read([folder,file],['/mom_ions/T_perp/',sprintf('%10.10d',it-1)]);
DATA.TPER_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
tmp = h5read([folder,'field.dat.h5'],['/field/phi/',sprintf('%10.10d',it-1)]);
DATA.PHI(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
end
DATA.TEMP_I = (DATA.TPAR_I + 2*DATA.TPER_I)/3.0 - DATA.DENS_I;
DATA.scale = 1;
DATA.PARAMS = ['GENE'];
DATA.param_title = 'GENE';
DATA.localdir = folder;
%% Geometry
CMD = ['tail -n ',num2str(namelist.box.nz0),' ',folder,namelist.geometry.magn_geometry{1},'.dat > tmp.txt'];
system(CMD);
DATA.geo_arrays = load('tmp.txt');
system('rm tmp.txt');
end
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