diff --git a/matlab/compute/ifourier_GENE.m b/matlab/compute/ifourier_GENE.m
index df01e5fdbb1bb86a1e823b73d211f194ba456afd..3c3a454a2032a384d73508347e8301d7f618454e 100644
--- a/matlab/compute/ifourier_GENE.m
+++ b/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;
diff --git a/matlab/plot/plot_radial_transport_and_spacetime.m b/matlab/plot/plot_radial_transport_and_spacetime.m
index 6e5444cda4e448e122301db10e76a75d2118ae7f..1957f424a2f33896164166879060e516f13ef60c 100644
--- a/matlab/plot/plot_radial_transport_and_spacetime.m
+++ b/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
diff --git a/matlab/process_field.m b/matlab/process_field.m
index 5762fc84b51c6057ac03c95b353644ae0c11827a..5258ef7cdc949185f2d72f9d52af005053424220 100644
--- a/matlab/process_field.m
+++ b/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
diff --git a/src/srcinfo.h b/src/srcinfo.h
index 690578d034de2e4a918e524c06036ee19d822ba9..b83013358773aa2ce9b86a1293b2fef8beedfeda 100644
--- a/src/srcinfo.h
+++ b/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')
diff --git a/src/srcinfo/srcinfo.h b/src/srcinfo/srcinfo.h
index 690578d034de2e4a918e524c06036ee19d822ba9..b83013358773aa2ce9b86a1293b2fef8beedfeda 100644
--- a/src/srcinfo/srcinfo.h
+++ b/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')
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index a0c6cd14c80963e5e89f7e294ccc7f9f1b2f9987..a96dc88198026b2ff5e33b8e8281dfbfbf3837e6 100644
--- a/wk/analysis_3D.m
+++ b/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')
diff --git a/wk/analysis_header.m b/wk/analysis_header.m
index afc69d88664dd754ceeeea603745ba28b18be58b..98f1b8b7a164ab3bd71b5aa6dac631c4b8a64ef6 100644
--- a/wk/analysis_header.m
+++ b/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/';