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gyacomo/matlab/molix_plot_phi.m
f42bbe611b46gather_output

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molix_plot_phi.m
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function [phib, b_angle] = molix_plot_phi(resfile,varargin)
% plot ballooning representation at the specified iput by time2plot for
% each ky modes
set(0,'defaulttextInterpreter','latex')
set(0, 'defaultAxesTickLabelInterpreter','latex');
set(0, 'defaultLegendInterpreter','latex');
set(0,'defaultAxesFontSize',16);
set(0, 'DefaultLineLineWidth', 1.5);
% read data and attributes
coordkx = h5read(resfile,'/data/var2d/phi/coordkx');
dimskx = size(coordkx);
Nkx = (dimskx(1) - 1)/2;
% Nkx = (length(coordkx)-1)/2
coordz = h5read(resfile,'/data/var2d/phi/coordz');
coordky = h5read(resfile,'/data/var2d/phi/coordky');
Nky = length(coordky);
Nz = length(coordz);
coordtime =h5read(resfile,'/data/var2d/time');
Nt = length(coordtime);
pmax = double(h5readatt(resfile,'/data/input','pmaxi'));
jmax = double(h5readatt(resfile,'/data/input','jmaxi'));
epsilon = double(h5readatt(resfile,'/data/input','inv. aspect ratio'));
safety_fac = double(h5readatt(resfile,'/data/input','safety factor'));
nu = double(h5readatt(resfile,'/data/input','nu'));
shear = double(h5readatt(resfile,'/data/input','magnetic shear'));
RTi= double(h5readatt(resfile,'/data/input','RTi'));
RTe= double(h5readatt(resfile,'/data/input','RTe'));
Rn= double(h5readatt(resfile,'/data/input','Rni'));
% read electrostatic pot.
if(nargin == 1 )
% plot end of the simulation
if( Nt >1)
[~,idxte] = min(abs(coordtime -coordtime(end-1)));
else
idxte =0;
end
elseif(nargin ==2)
time2plot = varargin{1};
[~,idxte] = min(abs(coordtime -time2plot));
end
iframe = idxte-1;
dataset = ['/data/var2d/phi/',num2str(iframe,'%06d')];
phi = h5read(resfile,dataset);
% read eigenvalu
% dataset = ['/data/var2d/eig/growth_rate'];
% growth_rate = h5read(resfile,dataset);
% dataset = ['/data/var2d/eig/freq'];
% frequency = h5read(resfile,dataset);
dataset = ['/data/var2d/time'];
time2d= h5read(resfile,dataset);
% Apply baollooning tranform
for iky=1:Nky
dims = size(phi.real);
phib_real = zeros( dims(1)*Nz ,1);
phib_imag= phib_real;
b_angle = phib_real;
midpoint = floor((dims(1)*Nz )/2)+1;
for ip =1: dims(1)
start_ = (ip -1)*Nz +1;
end_ = ip*Nz;
phib_real(start_:end_) = phi.real(ip,iky,:);
phib_imag(start_:end_) = phi.imaginary(ip,iky, :);
end
% Define ballooning angle
idx = -Nkx:1:Nkx;
for ip =1: dims(1)
for iz=1:Nz
ii = Nz*(ip -1) + iz;
b_angle(ii) =coordz(iz) + 2*pi*idx(ip);
end
end
% normalize real and imaginary parts at chi =0
[~,idxLFS] = min(abs(b_angle -0));
phib = phib_real(:) + 1i * phib_imag(:);
% Normalize to the outermid plane
phib_norm = phib(:);% / phib( idxLFS) ;
phib_real_norm(:) = real( phib_norm);%phib_real(:)/phib_real(idxLFS);
phib_imag_norm(:) = imag( phib_norm);%phib_imag(:)/ phib_imag(idxLFS);
%
%
% figure; hold all;
% plot(b_angle/pi, phib_real_norm,'-b');
% plot(b_angle/pi, phib_imag_norm ,'-r');
% plot(b_angle/pi, sqrt(phib_real_norm .^2 + phib_imag_norm.^2),'--k');
% legend('real','imag','norm')
% xlabel('$\chi / \pi$')
% ylabel('$\phi_B (\chi)$');
% % title(['$(P,J) =(',num2str(pmax),', ', num2str(jmax),'$), $\nu =',num2str(nu),...
% % '$, $\epsilon = ',num2str(epsilon),'$, $k_y = ', num2str(coordky( iky)),'$, $q =',num2str(safety_fac),'$, $s = ', num2str(shear),'$, $R_N = ', ...
% % num2str(Rn),'$, $R_{T_i} = ', num2str(RTi),'$, $N_z =',num2str(Nz),'$']);
% title(['molix, t=',num2str(coordtime(idxte))]);
% %set(gca,'Yscale','log')
%
% %Check symmetry of the mode at the outter mid plane
% figure; hold all;
% right = phib_real(midpoint+1:end);
% left = fliplr(phib_real(1:midpoint-1)');
% up_down_symm = right(1:end) - left(1:end-1)';
% %plot(b_angle(midpoint+1:end)/pi,phib_real(midpoint+1:end),'-xb');
% plot(b_angle(midpoint+1:end)/pi,up_down_symm ,'-xb');
%plot(abs(b_angle(1:midpoint-1))/pi,phib_real(1:midpoint-1),'-xb');
%
%
% figure; hold all
% plot(b_angle/pi, phib_imag.^2 + phib_real.^2 ,'xk');
% %set(gca,'Yscale','log')
% xlabel('$\chi / \pi$')
% ylabel('$\phi_B (\chi)$');
% title(['$(P,J) =(',num2str(pmax),', ', num2str(jmax),'$), $\nu =',num2str(nu),'$, $\epsilon = ',num2str(epsilon),'$, $q =',num2str(safety_fac),'$, $s = ', num2str(shear),'$, $k_y =',num2str(ky),'$']);
end
end
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