diff --git a/matlab/compute/mode_growth_meter.m b/matlab/compute/mode_growth_meter.m
index b8c229d8494c65de226361e3ac394799fd1bfee3..8c2bce8f4647749a20dd9267ef10f2ece623caff 100644
--- a/matlab/compute/mode_growth_meter.m
+++ b/matlab/compute/mode_growth_meter.m
@@ -3,8 +3,12 @@ function [FIGURE] = mode_growth_meter(DATA,OPTIONS)
NORMALIZED = OPTIONS.NORMALIZED;
Nma = OPTIONS.NMA; %Number moving average
-iz = OPTIONS.iz;
-[~,ikzf] = max(squeeze(mean(abs(squeeze(DATA.PHI(1,:,iz,:))),2)));
+switch OPTIONS.iz
+ case 'avg'
+ field = squeeze(mean(DATA.PHI,3));
+ otherwise
+ field = squeeze(DATA.PHI(:,:,OPTIONS.iz,:));
+end
FRAMES = zeros(size(OPTIONS.TIME));
for i = 1:numel(OPTIONS.TIME)
@@ -13,6 +17,8 @@ end
FRAMES = unique(FRAMES);
t = DATA.Ts3D(FRAMES);
+[~,ikzf] = max(mean(squeeze(abs(field(1,:,FRAMES))),2));
+
FIGURE.fig = figure; set(gcf, 'Position', [100 100 1200 700])
FIGURE.FIGNAME = 'mode_growth_meter';
for i = 1:2
@@ -20,27 +26,27 @@ for i = 1:2
if MODES_SELECTOR == 2
if NORMALIZED
- plt = @(x,ik) movmean(abs(squeeze(x(1,ik,iz,FRAMES)))./max(abs(squeeze(x(1,ik,iz,FRAMES)))),Nma);
+ plt = @(x,ik) movmean(abs(squeeze(x(1,ik,FRAMES)))./max(abs(squeeze(x(1,ik,FRAMES)))),Nma);
else
- plt = @(x,ik) movmean(abs(squeeze(x(1,ik,iz,FRAMES))),Nma);
+ plt = @(x,ik) movmean(abs(squeeze(x(1,ik,FRAMES))),Nma);
end
kstr = 'k_x';
k = DATA.kx;
MODESTR = 'Zonal modes';
elseif MODES_SELECTOR == 1
if NORMALIZED
- plt = @(x,ik) movmean(abs(squeeze(x(ik,1,iz,FRAMES)))./max(abs(squeeze(x(ik,1,iz,FRAMES)))),Nma);
+ plt = @(x,ik) movmean(abs(squeeze(x(ik,1,FRAMES)))./max(abs(squeeze(x(ik,1,FRAMES)))),Nma);
else
- plt = @(x,ik) movmean(abs(squeeze(x(ik,1,iz,FRAMES))),Nma);
+ plt = @(x,ik) movmean(abs(squeeze(x(ik,1,FRAMES))),Nma);
end
kstr = 'k_y';
k = DATA.ky;
MODESTR = 'NZ modes';
elseif MODES_SELECTOR == 3
if NORMALIZED
- plt = @(x,ik) movmean(abs(squeeze(x(ik,ik,iz,FRAMES)))./max(abs(squeeze(x(ik,ik,iz,FRAMES)))),Nma);
+ plt = @(x,ik) movmean(abs(squeeze(x(ik,ik,FRAMES)))./max(abs(squeeze(x(ik,ik,FRAMES)))),Nma);
else
- plt = @(x,ik) movmean(abs(squeeze(x(ik,ik,iz,FRAMES))),Nma);
+ plt = @(x,ik) movmean(abs(squeeze(x(ik,ik,FRAMES))),Nma);
end
kstr = 'k_y=k_x';
k = DATA.ky;
@@ -60,7 +66,7 @@ for i = 1:2
amp = MODES;
i_=1;
for ik = MODES
- gr = polyfit(t,log(plt(DATA.PHI,ik)),1);
+ gr = polyfit(t,log(plt(field,ik)),1);
gamma(i_) = gr(1);
amp(i_) = gr(2);
i_=i_+1;
@@ -69,7 +75,7 @@ for i = 1:2
%plot
subplot(2,3,1+3*(i-1))
[YY,XX] = meshgrid(t,fftshift(k));
- pclr = pcolor(XX,YY,abs(plt(fftshift(DATA.PHI,MODES_SELECTOR),1:numel(k))));set(pclr, 'edgecolor','none'); hold on;
+ pclr = pcolor(XX,YY,abs(plt(fftshift(field,MODES_SELECTOR),1:numel(k))));set(pclr, 'edgecolor','none'); hold on;
set(gca,'YDir','normal')
% xlim([t(1) t(end)]); %ylim([1e-5 1])
xlabel(['$',kstr,'\rho_s$']); ylabel('$t c_s /\rho_s$');
@@ -78,11 +84,11 @@ for i = 1:2
subplot(2,3,2+3*(i-1))
mod2plot = [2:OPTIONS.NMODES+1];
for i_ = mod2plot
- semilogy(t,plt(DATA.PHI,MODES(i_))); hold on;
+ semilogy(t,plt(field,MODES(i_))); hold on;
% semilogy(t,exp(gamma(i_).*t+amp(i_)),'--k')
end
if MODES_SELECTOR == 2
- semilogy(t,plt(DATA.PHI,ikzf),'--k');
+ semilogy(t,plt(field,ikzf),'--k');
end
xlim([t(1) t(end)]); %ylim([1e-5 1])
xlabel('$t c_s /\rho_s$'); ylabel(['$|\phi_{',kstr,'}|$']);
diff --git a/matlab/plot/plot_radial_transport_and_spacetime.m b/matlab/plot/plot_radial_transport_and_spacetime.m
index 93e0c5cb2ea39338bdead42162b7b7d422339701..d052fc151287e70892c385601da4e2430ec8fbc4 100644
--- a/matlab/plot/plot_radial_transport_and_spacetime.m
+++ b/matlab/plot/plot_radial_transport_and_spacetime.m
@@ -3,12 +3,15 @@ function [FIGURE] = plot_radial_transport_and_spacetime(DATA, OPTIONS)
tend = OPTIONS.TAVG_1; tstart = OPTIONS.TAVG_0;
[~,its0D] = min(abs(DATA.Ts0D-tstart));
[~,ite0D] = min(abs(DATA.Ts0D-tend));
+ [~,its3D] = min(abs(DATA.Ts3D-tstart));
+ [~,ite3D] = min(abs(DATA.Ts3D-tend));
SCALE = DATA.scale;%(1/DATA.Nx/DATA.Ny)^2;
Gx_infty_avg = mean(DATA.PGAMMA_RI(its0D:ite0D))*SCALE;
Gx_infty_std = std (DATA.PGAMMA_RI(its0D:ite0D))*SCALE;
Qx_infty_avg = mean(DATA.HFLUX_X(its0D:ite0D))*SCALE;
Qx_infty_std = std (DATA.HFLUX_X(its0D:ite0D))*SCALE;
- [~,ikzf] = max(squeeze(mean(abs(squeeze(DATA.PHI(:,1,1,:))),2)));
+ f_avg_z = squeeze(mean(DATA.PHI(:,:,:,:),3));
+ [~,ikzf] = max(squeeze(mean(abs(f_avg_z(1,:,its3D:ite3D)),3)));
Ns3D = numel(DATA.Ts3D);
[KX, KY] = meshgrid(DATA.kx, DATA.ky);
@@ -16,34 +19,33 @@ function [FIGURE] = plot_radial_transport_and_spacetime(DATA, OPTIONS)
% Compute Gamma from ifft matlab
Gx = zeros(DATA.Ny,DATA.Nx,numel(DATA.Ts3D));
- for it = 1:numel(DATA.Ts3D)
- for iz = 1:DATA.Nz
- Gx(:,:,it) = Gx(:,:,it) + ifourier_GENE(-1i*KY.*(DATA.PHI(:,:,iz,it)))...
- .*ifourier_GENE(DATA.DENS_I(:,:,iz,it));
- end
- Gx(:,:,it) = Gx(:,:,it)/DATA.Nz;
- end
+% for it = 1:numel(DATA.Ts3D)
+% for iz = 1:DATA.Nz
+% Gx(:,:,it) = Gx(:,:,it) + ifourier_GENE(-1i*KY.*(DATA.PHI(:,:,iz,it)))...
+% .*ifourier_GENE(DATA.DENS_I(:,:,iz,it));
+% end
+% Gx(:,:,it) = Gx(:,:,it)/DATA.Nz;
+% end
Gx_t_mtlb = squeeze(mean(mean(Gx,1),2));
% Compute Heat flux from ifft matlab
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)))...
- .*ifourier_GENE(DATA.TEMP_I(:,:,iz,it));
- end
- Qx(:,:,it) = Qx(:,:,it)/DATA.Nz;
- end
+% for it = 1:numel(DATA.Ts3D)
+% for iz = 1:DATA.Nz
+% Qx(:,:,it) = Qx(:,:,it) + ifourier_GENE(-1i*KY.*(DATA.PHI(:,:,iz,it)))...
+% .*ifourier_GENE(DATA.TEMP_I(:,:,iz,it));
+% end
+% Qx(:,:,it) = Qx(:,:,it)/DATA.Nz;
+% end
Qx_t_mtlb = squeeze(mean(mean(Qx,1),2));
% zonal vs nonzonal energies for phi(t)
E_Zmode_SK = zeros(1,Ns3D);
E_NZmode_SK = zeros(1,Ns3D);
for it = 1:numel(DATA.Ts3D)
- E_Zmode_SK(it) = squeeze(DATA.ky(ikzf).^2.*abs(DATA.PHI(ikzf,1,1,it))^2);
- E_NZmode_SK(it) = squeeze(sum(sum(((1+KX.^2+KY.^2).*abs(DATA.PHI(:,:,1,it)).^2.*(KY~=0)))));
+ E_Zmode_SK(it) = squeeze(DATA.ky(ikzf).^2.*abs(squeeze(f_avg_z(ikzf,1,it))).^2);
+ E_NZmode_SK(it) = squeeze(sum(sum(((1+KX.^2+KY.^2).*abs(squeeze(f_avg_z(:,:,it))).^2.*(KY~=0)))));
end
- [~,its3D] = min(abs(DATA.Ts3D-tstart));
- [~,ite3D] = min(abs(DATA.Ts3D-tend));
+
%% Figure
mvm = @(x) movmean(x,OPTIONS.NMVA);
@@ -83,7 +85,7 @@ mvm = @(x) movmean(x,OPTIONS.NMVA);
toplot = process_field(DATA,OPTIONS);
f2plot = toplot.FIELD;
- clim = max(max(max(abs(plt(f2plot(:,:,:))))));
+ clim = max(max(max(abs(plt(f2plot(:,:,its3D:ite3D))))));
subplot(313)
[TY,TX] = meshgrid(DATA.x,DATA.Ts3D(toplot.FRAMES));
pclr = pcolor(TX,TY,squeeze(plt(f2plot))');
diff --git a/wk/analysis_HeLaZ.m b/wk/analysis_HeLaZ.m
index 6fba72bd9f2be417996e03e67ffc39fb58ad3511..4a06a7a1b4c80c537454a27cffeb7a053f94f07a 100644
--- a/wk/analysis_HeLaZ.m
+++ b/wk/analysis_HeLaZ.m
@@ -10,7 +10,7 @@ system(['mkdir -p ',MISCDIR]);
CMD = ['rsync ', LOCALDIR,'outputs* ',MISCDIR]; disp(CMD);
system(CMD);
% Load outputs from jobnummin up to jobnummax
-JOBNUMMIN = 10; JOBNUMMAX = 20;
+JOBNUMMIN = 15; JOBNUMMAX = 16;
data = compile_results(MISCDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
data.localdir = LOCALDIR;
data.FIGDIR = LOCALDIR;
@@ -49,12 +49,12 @@ options.NAME = '\phi';
% options.NAME = 'n_i^{NZ}';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
-options.PLAN = 'xz';
+options.PLAN = 'xy';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
-options.COMP = 'avg';
+options.COMP = 9;
% options.TIME = dat.Ts5D;
-options.TIME = 1250:1:1500;
+options.TIME = [1800:1:2000];
data.EPS = 0.1;
data.a = data.EPS * 2000;
create_film(data,options,'.gif')
@@ -63,7 +63,7 @@ end
if 0
%% 2D snapshots
% Options
-options.INTERP = 0;
+options.INTERP = 1;
options.POLARPLOT = 0;
options.AXISEQUAL = 1;
options.NAME = '\phi';
@@ -72,11 +72,11 @@ options.NAME = '\phi';
% options.NAME = 'T_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'kxky';
+options.PLAN = 'xy';
% options.NAME = 'f_i';
% options.PLAN = 'sx';
options.COMP = 'avg';
-options.TIME = [1200 1300 1400 1500];
+options.TIME = [1600 1800 2000];
data.a = data.EPS * 2e3;
fig = photomaton(data,options);
save_figure(data,fig)
@@ -165,10 +165,10 @@ if 0
%% Mode evolution
options.NORMALIZED = 0;
options.K2PLOT = 1;
-options.TIME = 1200:1300;
+options.TIME = 1800:2000;
options.NMA = 1;
options.NMODES = 15;
-options.iz = 9;
+options.iz = 'avg';
fig = mode_growth_meter(data,options);
save_figure(data,fig)
end
diff --git a/wk/analysis_gene.m b/wk/analysis_gene.m
index 281885dec2b0d23f1c5263e81273452e2035fa17..86e064c561aa6b39a9b9086478f451dd12a62ed5 100644
--- a/wk/analysis_gene.m
+++ b/wk/analysis_gene.m
@@ -16,7 +16,7 @@ options.TAVG_1 = gene_data.Ts3D(end); % Averaging times duration
options.NMVA = 1; % Moving average for time traces
options.ST_FIELD = '\phi'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x, Q_x)
options.INTERP = 1;
-gene_data.FIGDIR = folder;;
+gene_data.FIGDIR = folder;
fig = plot_radial_transport_and_spacetime(gene_data,options);
save_figure(gene_data,fig)
end
@@ -32,11 +32,11 @@ options.NAME = '\phi';
% options.NAME = 'T_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'kxky';
+options.PLAN = 'xy';
% options.NAME ='f_e';
% options.PLAN = 'sx';
-options.COMP = 9;
-options.TIME = [0 50 100 200 300];
+options.COMP = 'avg';
+options.TIME = [500];
gene_data.a = data.EPS * 2000;
fig = photomaton(gene_data,options);
save_figure(gene_data,fig)
@@ -52,11 +52,11 @@ options.NAME = '\phi';
% options.NAME = 'n_i^{NZ}';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
-options.PLAN = 'xz';
+options.PLAN = 'xy';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
-options.TIME = 000:300;
+options.TIME = gene_data.Ts3D;
gene_data.a = data.EPS * 2000;
create_film(gene_data,options,'.gif')
end
@@ -104,10 +104,10 @@ if 0
%% Mode evolution
options.NORMALIZED = 0;
options.K2PLOT = 1;
-options.TIME = 100:200;
+options.TIME = 100:700;
options.NMA = 1;
options.NMODES = 15;
-options.iz = 9;
+options.iz = 'avg';
fig = mode_growth_meter(gene_data,options);
save_figure(gene_data,fig)
end
diff --git a/wk/header_3D_results.m b/wk/header_3D_results.m
index 05a07248e807018a60b0b34822d654440f0369b5..9b790c181e5874996ac1f7b8a0153924b88da44c 100644
--- a/wk/header_3D_results.m
+++ b/wk/header_3D_results.m
@@ -5,7 +5,8 @@ helazdir = '/home/ahoffman/HeLaZ/';
outfile ='';
outfile ='';
outfile ='';
-outfile ='shearless_cyclone/128x128x16xdmax_6_L_120_CBC_1.0';
+outfile ='shearless_cyclone/128x128x16x5x3_start';
+% outfile ='shearless_cyclone/128x128x16xdmax_6_L_120_CBC_1.0';
% outfile ='shearless_cyclone/128x128x16xdmax_L_120_CBC_1.0';
% outfile ='shearless_cyclone/180x180x20x4x2_L_120_CBC_0.8_to_1.0';
% outfile ='quick_run/CLOS_1_64x64_5x3_L_120_kN_2.0_kT_0.5_nu_1e-01_SGGK';