Scripts adaptations

matlab/compute/ifourier_GENE.m

@@ -5,16 +5,16 @@ function [ field_r ] = ifourier_GENE( field_c )
 %   comparison purpose.
 
 %% Original
-[nx,nky,nz]=size(field_c);
+[nky,nx,nz]=size(field_c);
 %extend to whole ky by imposing reality condition
 ny=2*nky-1;
 
 if ny~=1
     %note, we need one extra point which we set to zero for the ifft 
-    spectrumKxKyZ=zeros(nx,ny,nz);
-    spectrumKxKyZ(:,1:nky,:)=field_c(:,:,:);
-    spectrumKxKyZ(1,(nky+1):(ny),:)=conj(field_c(1,nky:-1:2,:));
-    spectrumKxKyZ(2:nx,(nky+1):(ny),:)=conj(field_c(nx:-1:2,nky:-1:2,:));
+    spectrumKxKyZ=zeros(ny,nx,nz);
+    spectrumKxKyZ(1:nky,:,:)=field_c(:,:,:);
+    spectrumKxKyZ((nky+1):(ny),1,:)=conj(field_c(nky:-1:2,1,:));
+    spectrumKxKyZ((nky+1):(ny),2:nx,:)=conj(field_c(nky:-1:2,nx:-1:2,:));
 else
     %pad with zeros to interpolate on fine scale
     ny=20;

matlab/plot/plot_radial_transport_and_spacetime.m

@@ -26,7 +26,7 @@ function [FIGURE] = plot_radial_transport_and_spacetime(DATA, TAVG_0, TAVG_1,stf
     end
     Gx_t_mtlb = squeeze(mean(mean(Gx,1),2)); 
     % Compute Heat flux from ifft matlab
-    Qx = zeros(DATA.Nx,DATA.Ny,numel(DATA.Ts3D));
+    Qx = zeros(DATA.Ny,DATA.Nx,numel(DATA.Ts3D));
     for it = 1:numel(DATA.Ts3D)
         for iz = 1:DATA.Nz
             Qx(:,:,it)  = Qx(:,:,it) + ifourier_GENE(-1i*KY.*(DATA.PHI(:,:,iz,it)))...
@@ -71,7 +71,7 @@ mvm = @(x) movmean(x,Nmvm);
         % computation
     Ns3D = numel(DATA.Ts3D);
     [KY, KX] = meshgrid(DATA.ky, DATA.kx);
-    plt = @(x) mean(x(:,:,1,:),2);
+    plt = @(x) mean(x(:,:,1,:),1);
     kycut = max(DATA.ky);
     kxcut = max(DATA.kx);
     LP = (abs(KY)<kycut).*(abs(KX)<kxcut); %Low pass filter
@@ -87,7 +87,7 @@ mvm = @(x) movmean(x,Nmvm);
     end
     switch stfname
         case 'phi'
-                phi            = zeros(DATA.Nx,DATA.Ny,1,Ns3D);
+                phi            = zeros(DATA.Ny,DATA.Nx,1,Ns3D);
                 for it = 1:numel(DATA.Ts3D)
                     phi(:,:,1,it)  = ifourier_GENE(compz(DATA.PHI(:,:,:,it)));
                 end

matlab/process_field.m

@@ -17,28 +17,28 @@ LTXNAME = OPTIONS.NAME;
 switch OPTIONS.PLAN
     case 'xy'
         XNAME = '$x$'; YNAME = '$y$';
-        [Y,X] = meshgrid(DATA.y,DATA.x);
+        [X,Y] = meshgrid(DATA.x,DATA.y);
         REALP = 1; COMPDIM = 3; POLARPLOT = 0; SCALE = 1;
     case 'xz'
         XNAME = '$x$'; YNAME = '$z$';
         [Y,X] = meshgrid(DATA.z,DATA.x);
-        REALP = 1; COMPDIM = 2; SCALE = 0;
+        REALP = 1; COMPDIM = 1; SCALE = 0;
     case 'yz'
         XNAME = '$y$'; YNAME = '$z$'; 
         [Y,X] = meshgrid(DATA.z,DATA.y);
-        REALP = 1; COMPDIM = 1; SCALE = 0;
+        REALP = 1; COMPDIM = 2; SCALE = 0;
     case 'kxky'
         XNAME = '$k_x$'; YNAME = '$k_y$';
-        [Y,X] = meshgrid(DATA.ky,DATA.kx);
+        [X,Y] = meshgrid(DATA.kx,DATA.ky);
         REALP = 0; COMPDIM = 3; POLARPLOT = 0; SCALE = 1;
     case 'kxz'
         XNAME = '$k_x$'; YNAME = '$z$';
         [Y,X] = meshgrid(DATA.z,DATA.kx);
-        REALP = 0; COMPDIM = 2; POLARPLOT = 0; SCALE = 0;
+        REALP = 0; COMPDIM = 1; POLARPLOT = 0; SCALE = 0;
     case 'kyz'
         XNAME = '$k_y$'; YNAME = '$z$';
         [Y,X] = meshgrid(DATA.z,DATA.ky);
-        REALP = 0; COMPDIM = 1; POLARPLOT = 0; SCALE = 0;
+        REALP = 0; COMPDIM = 2; POLARPLOT = 0; SCALE = 0;
     case 'sx'
         XNAME = '$v_\parallel$'; YNAME = '$\mu$';
         [Y,X] = meshgrid(OPTIONS.XPERP,OPTIONS.SPAR);
@@ -110,7 +110,7 @@ end
 switch REALP
     case 1 % Real space plot
         INTERP = OPTIONS.INTERP;
-        process = @(x) real(fftshift(ifft2(x,Nx,Ny)));
+        process = @(x) real(fftshift(ifft2(x,Ny,Nx)));
         shift_x = @(x) x;
         shift_y = @(x) x;
     case 0 % Frequencies plot

src/srcinfo.h

@@ -3,8 +3,8 @@ character(len=40) BRANCH
 character(len=20) AUTHOR
 character(len=40) EXECDATE
 character(len=40) HOST
-parameter (VERSION='e4c9228-dirty')
+parameter (VERSION='38a4f6e-dirty')
 parameter (BRANCH='kx_pos_plane')
 parameter (AUTHOR='ahoffman')
-parameter (EXECDATE='Mon May 2 09:30:54 CEST 2022')
+parameter (EXECDATE='Mon May 2 14:23:17 CEST 2022')
 parameter (HOST ='spcpc606')

src/srcinfo/srcinfo.h

@@ -3,8 +3,8 @@ character(len=40) BRANCH
 character(len=20) AUTHOR
 character(len=40) EXECDATE
 character(len=40) HOST
-parameter (VERSION='e4c9228-dirty')
+parameter (VERSION='38a4f6e-dirty')
 parameter (BRANCH='kx_pos_plane')
 parameter (AUTHOR='ahoffman')
-parameter (EXECDATE='Mon May 2 09:30:54 CEST 2022')
+parameter (EXECDATE='Mon May 2 14:23:17 CEST 2022')
 parameter (HOST ='spcpc606')

wk/analysis_3D.m

@@ -39,18 +39,18 @@ if 0
 % Options
 options.INTERP    = 1;
 options.POLARPLOT = 0;
-options.NAME      = '\phi';
-% options.NAME      = 'N_i^{00}';
+% options.NAME      = '\phi';
+options.NAME      = 'N_i^{00}';
 % options.NAME      = 'v_y';
 % options.NAME      = 'n_i^{NZ}';
 % options.NAME      = '\Gamma_x';
 % options.NAME      = 'n_i';
-options.PLAN      = 'kxky';
+options.PLAN      = 'xy';
 % options.NAME      = 'f_e';
 % options.PLAN      = 'sx';
 options.COMP      = 'avg';
 % options.TIME      = dat.Ts5D;
-options.TIME      = 0:0.1:10;
+options.TIME      = 0:1:100;
 data.EPS          = 0.1;
 data.a = data.EPS * 2000;
 create_film(data,options,'.gif')

wk/analysis_header.m

@@ -3,7 +3,7 @@ helazdir = '/home/ahoffman/HeLaZ/';
 % Directory of the simulation
 % if 1% Local results
 outfile ='';
-outfile ='quick_run/1x32_5x3_L_120_kN_2_kT_0.5_nu_1e-01_DGGK';
+outfile ='quick_run/64x64_5x3_L_120_kN_2.0_kT_0.5_nu_1e-01_SGGK';
 % outfile ='pedestal/64x64x16x2x1_L_300_LnT_20_nu_0.1';
 % outfile ='quick_run/32x32x16_5x3_L_300_q0_2.5_e_0.18_kN_20_kT_20_nu_1e-01_DGGK';
 % outfile ='shearless_cyclone/128x128x16x4x2_L_120_CTC_1.0/';