From 264438f6ab33d5b814f06dd7fe6e52be8503eac0 Mon Sep 17 00:00:00 2001
From: Antoine Hoffmann <antoine.hoffmann@epfl.ch>
Date: Tue, 31 Jan 2023 17:22:08 +0100
Subject: [PATCH] Save the scripts
---
matlab/compile_results.m | 23 ++++++-
matlab/extract_fig_data.m | 2 +-
matlab/load/load_3D_data.m | 32 +++-------
matlab/load/load_gene_data.m | 2 +-
matlab/plot/photomaton.m | 4 +-
.../plot_radial_transport_and_spacetime.m | 9 ++-
matlab/plot/show_moments_spectrum.m | 29 ++++++---
matlab/plot/statistical_transport_averaging.m | 15 +++--
wk/analysis_gene.m | 48 +++++++++-----
wk/analysis_gyacomo.m | 38 ++++++-----
wk/header_3D_results.m | 20 ++++--
wk/p2_heatflux_salpha_convergence.m | 64 +++++++++++++++----
12 files changed, 190 insertions(+), 96 deletions(-)
diff --git a/matlab/compile_results.m b/matlab/compile_results.m
index f6ccd44b..fccc7ee8 100644
--- a/matlab/compile_results.m
+++ b/matlab/compile_results.m
@@ -13,6 +13,7 @@ DATA.DT_EVOL = []; %
% FIELDS
Nipj_ = []; Nepj_ = [];
Ni00_ = []; Ne00_ = [];
+Nipjz_ = []; Nepjz_ = [];
HFLUXI_ = [];
HFLUXE_ = [];
GGAMMAI_ = [];
@@ -154,6 +155,18 @@ while(CONTINUE)
end
[Ni00, Ts3D, ~] = load_3D_data(filename, 'Ni00');
Ni00_ = cat(4,Ni00_,Ni00); clear Ni00
+ if KIN_E
+ try
+ Nepjz = load_3D_data(filename, 'Nepjz');
+ Nepjz_ = cat(4,Nepjz_,Nepjz); clear Nepjz
+ catch
+ end
+ end
+% try
+ [Nipjz, Ts3D, ~] = load_3D_data(filename, 'Nipjz');
+ Nipjz_ = cat(4,Nipjz_,Nipjz); clear Nipjz
+% catch
+% end
end
if W_DENS
if KIN_E
@@ -195,7 +208,9 @@ while(CONTINUE)
Ts5D = [];
if W_NAPJ
[Nipj, Ts5D, ~] = load_5D_data(filename, 'moments_i');
+ tic
Nipj_ = cat(6,Nipj_,Nipj); clear Nipj
+ toc
if KIN_E
Nepj = load_5D_data(filename, 'moments_e');
Nepj_ = cat(6,Nepj_,Nepj); clear Nepj
@@ -274,9 +289,11 @@ else
DATA.scale = 1;%(1/Nx/Ny)^2;
% Fields
DATA.GGAMMA_RI = GGAMMAI_; DATA.PGAMMA_RI = PGAMMAI_; DATA.HFLUX_X = HFLUXI_;
- DATA.Nipj = Nipj_; DATA.Ni00 = Ni00_; DATA.DENS_I = DENS_I_; DATA.TEMP_I = TEMP_I_;
+ DATA.Nipj = Nipj_; DATA.Ni00 = Ni00_; DATA.Nipjz = Nipjz_;
+ DATA.DENS_I = DENS_I_; DATA.TEMP_I = TEMP_I_;
if(KIN_E)
- DATA.Nepj = Nepj_; DATA.Ne00 = Ne00_; DATA.DENS_E = DENS_E_; DATA.TEMP_E = TEMP_E_;
+ DATA.Nepj = Nepj_; DATA.Ne00 = Ne00_; DATA.Nepjz = Nepjz_;
+ DATA.DENS_E = DENS_E_; DATA.TEMP_E = TEMP_E_;
DATA.HFLUX_XE = HFLUXE_;
end
DATA.Ts5D = Ts5D_; DATA.Ts3D = Ts3D_; DATA.Ts0D = Ts0D_;
@@ -299,6 +316,8 @@ else
num2str(DATA.Nx),'$, $(P,J)=(',num2str(DATA.PMAXI),',',...
num2str(DATA.JMAXI),')$,',' $\mu_{hd}=$(',num2str(DATA.MUx),...
',',num2str(DATA.MUy),')'];
+ DATA.paramshort = [num2str(DATA.Pmaxi),'x',num2str(DATA.Jmaxi),'x',...
+ num2str(DATA.Nkx),'x',num2str(DATA.Nky),'x',num2str(DATA.Nz)];
JOBNUM = LASTJOB;
filename = sprintf([DIRECTORY,'outputs_%.2d.h5'],JOBNUM);
diff --git a/matlab/extract_fig_data.m b/matlab/extract_fig_data.m
index 4be8de84..2e19518e 100644
--- a/matlab/extract_fig_data.m
+++ b/matlab/extract_fig_data.m
@@ -4,7 +4,7 @@
% tw = [3000 4000];
% tw = [4000 4500];
% tw = [4500 5000];
-tw = [400 40000];
+tw = [450 650];
fig = gcf;
axObjs = fig.Children;
diff --git a/matlab/load/load_3D_data.m b/matlab/load/load_3D_data.m
index 37b54548..9c9df71d 100644
--- a/matlab/load/load_3D_data.m
+++ b/matlab/load/load_3D_data.m
@@ -1,31 +1,19 @@
function [ data, time, dt ] = load_3D_data( filename, variablename )
-%LOAD_2D_DATA load a 2D variable stored in a hdf5 result file from HeLaZ
+%LOAD_3D_DATA load a 3D variable stored in a hdf5 result file from HeLaZ
time = h5read(filename,'/data/var3d/time');
- kx = h5read(filename,'/data/grid/coordkx');
- ky = h5read(filename,'/data/grid/coordky');
- z = h5read(filename,'/data/grid/coordz');
dt = h5readatt(filename,'/data/input','dt');
cstart= h5readatt(filename,'/data/input','start_iframe3d');
- data = zeros(numel(ky),numel(kx),numel(z),numel(time));
- [KX,KY] = meshgrid(kx,ky);
+ % Find array size by loading the first output
+ tmp = h5read(filename,['/data/var3d/',variablename,'/', num2str(cstart+1,'%06d')]);
+ sz = size(tmp.real);
+ % add time dimension
+ sz = [sz numel(time)];
+ data = zeros(sz);
- switch variablename
- case 'vEx'
- for it = 1:numel(time)
- tmp = h5read(filename,['/data/var3d/phi/', num2str(cstart+it,'%06d')]);
- data(:,:,:,it) = 1i.*KY.*(tmp.real + 1i * tmp.imaginary);
- end
- case 'vEy'
- for it = 1:numel(time)
- tmp = h5read(filename,['/data/var3d/phi/', num2str(cstart+it,'%06d')]);
- data(:,:,:,it) = -1i.*KX.*(tmp.real + 1i * tmp.imaginary);
- end
- otherwise
- for it = 1:numel(time)
- tmp = h5read(filename,['/data/var3d/',variablename,'/', num2str(cstart+it,'%06d')]);
- data(:,:,:,it) = tmp.real + 1i * tmp.imaginary;
- end
+ for it = 1:numel(time)
+ tmp = h5read(filename,['/data/var3d/',variablename,'/', num2str(cstart+it,'%06d')]);
+ data(:,:,:,it) = tmp.real + 1i * tmp.imaginary;
end
end
diff --git a/matlab/load/load_gene_data.m b/matlab/load/load_gene_data.m
index 63554d8a..2fdff459 100644
--- a/matlab/load/load_gene_data.m
+++ b/matlab/load/load_gene_data.m
@@ -1,6 +1,6 @@
function [ DATA ] = load_gene_data( folder )
%to load gene data as for HeLaZ results
-namelist = read_namelist([folder,'parameters.dat']);
+namelist = read_namelist([folder,'parameters']);
DATA.namelist = namelist;
DATA.folder = folder;
%% Grid
diff --git a/matlab/plot/photomaton.m b/matlab/plot/photomaton.m
index e60fd8cc..2e7ccdcf 100644
--- a/matlab/plot/photomaton.m
+++ b/matlab/plot/photomaton.m
@@ -15,8 +15,8 @@ Ncols = ceil(Nframes/Nrows);
%
TNAME = [];
FIGURE.fig = figure; set(gcf, 'Position', toplot.DIMENSIONS.*[1 1 Ncols Nrows])
- frame_max = max(max(max(abs(toplot.FIELD(:,:,:)))));
for i_ = 1:numel(FRAMES)
+ frame_max = max(max(max(abs(toplot.FIELD(:,:,i_)))));
subplot(Nrows,Ncols,i_); TNAME = [TNAME,'_',sprintf('%.0f',DATA.Ts3D(FRAMES(i_)))];
if OPTIONS.NORMALIZE
scale = frame_max; % Scaling to normalize
@@ -43,7 +43,7 @@ FIGURE.fig = figure; set(gcf, 'Position', toplot.DIMENSIONS.*[1 1 Ncols Nrows])
end
xlabel(toplot.XNAME); ylabel(toplot.YNAME);
% if i_ > 1; set(gca,'ytick',[]); end;
- title([sprintf('$t c_s/R=%.0f$',tshot),', max = ',sprintf('%.1e',scale)]);
+ title([sprintf('$t c_s/R=%.0f$',tshot),', max = ',sprintf('%.1e',frame_max)]);
end
legend(['$',toplot.FIELDNAME,'$']);
diff --git a/matlab/plot/plot_radial_transport_and_spacetime.m b/matlab/plot/plot_radial_transport_and_spacetime.m
index e37e1073..884a919e 100644
--- a/matlab/plot/plot_radial_transport_and_spacetime.m
+++ b/matlab/plot/plot_radial_transport_and_spacetime.m
@@ -61,11 +61,16 @@ function [FIGURE] = plot_radial_transport_and_spacetime(DATA, OPTIONS,CODE)
end
%% Figure
+clr_ = lines(20);
mvm = @(x) movmean(x,OPTIONS.NMVA);
FIGURE.fig = figure; FIGURE.FIGNAME = ['ZF_transport_drphi','_',DATA.PARAMS]; %set(gcf, 'Position', [500, 1000, 1000, 600])
FIGURE.ax1 = subplot(3,1,1,'parent',FIGURE.fig);
- plot(mvm(DATA.Ts0D),mvm(DATA.PGAMMA_RI*SCALE),'DisplayName','$\langle n_i \partial_y\phi \rangle_y$'); hold on;
- plot(mvm(DATA.Ts0D),mvm(DATA.HFLUX_X*SCALE),'DisplayName','$\langle n_i \partial_y\phi \rangle_y$'); hold on;
+ plot(mvm(DATA.Ts0D),mvm(DATA.PGAMMA_RI*SCALE),'--',...
+ 'color',clr_((DATA.Pmaxi-1)/2-1,:),...
+ 'DisplayName',['$\Gamma_x$ ',DATA.paramshort]); hold on;
+ plot(mvm(DATA.Ts0D),mvm(DATA.HFLUX_X*SCALE),'-',...
+ 'color',clr_((DATA.Pmaxi-1)/2-1,:),...
+ 'DisplayName',['$Q_x$ ',DATA.paramshort]); hold on;
ylabel('Transport')
if(~isnan(Qx_infty_avg))
plot(DATA.Ts0D(its0D:ite0D),ones(ite0D-its0D+1,1)*Qx_infty_avg, '-k',...
diff --git a/matlab/plot/show_moments_spectrum.m b/matlab/plot/show_moments_spectrum.m
index 2fc32fa4..3f000729 100644
--- a/matlab/plot/show_moments_spectrum.m
+++ b/matlab/plot/show_moments_spectrum.m
@@ -1,16 +1,25 @@
function [ FIGURE ] = show_moments_spectrum( DATA, OPTIONS )
-
Pi = DATA.Pi;
Ji = DATA.Ji;
-Nipj = sum(sum(sum(abs(DATA.Nipj),3),4),5);
+if (isempty(DATA.Nipjz))
+ Time_ = DATA.Ts3D;
+ Nipj = sum(abs(DATA.Nipjz),3);
+else
+ Time_ = DATA.Ts5D;
+ Nipj = sum(sum(sum(abs(DATA.Nipj),3),4),5);
+end
Nipj = squeeze(Nipj);
if DATA.KIN_E
Pe = DATA.Pe;
Je = DATA.Je;
-Nepj = sum(sum(sum(abs(DATA.Nepj),3),4),5);
-Nepj = squeeze(Nepj);
+ if ~(isempty(DATA.Nepjz))
+ Nepj = sum(abs(DATA.Nepjz),3);
+ else
+ Nepj = sum(sum(sum(abs(DATA.Nepj),3),4),5);
+ end
+ Nepj = squeeze(Nepj);
end
FIGURE.fig = figure; FIGURE.FIGNAME = ['mom_spectrum_',DATA.PARAMS];
@@ -19,8 +28,8 @@ set(gcf, 'Position', [100 50 1000 400])
if ~OPTIONS.ST
t0 = OPTIONS.TIME(1);
t1 = OPTIONS.TIME(end);
- [~,it0] = min(abs(t0-DATA.Ts5D));
- [~,it1] = min(abs(t1-DATA.Ts5D));
+ [~,it0] = min(abs(t0-Time_));
+ [~,it1] = min(abs(t1-Time_));
Nipj = mean(Nipj(:,:,it0:it1),3);
if DATA.KIN_E
Nepj = mean(Nepj(:,:,it0:it1),3);
@@ -87,7 +96,7 @@ else
% weights to average
weights = zeros(size(p2ji));
% space time of moments amplitude wrt to p+2j degree
- Ni_ST = zeros(numel(p2ji),numel(DATA.Ts5D));
+ Ni_ST = zeros(numel(p2ji),numel(Time_));
% fill the st diagramm by averaging every p+2j=n moments together
for ip = 1:numel(Pi)
for ij = 1:numel(Ji)
@@ -109,7 +118,7 @@ else
% weights to average
weights = zeros(size(p2je));
% space time of moments amplitude wrt to p+2j degree
- Ne_ST = zeros(numel(p2je),numel(DATA.Ts5D));
+ Ne_ST = zeros(numel(p2je),numel(Time_));
% fill the st diagramm by averaging every p+2j=n moments together
for ip = 1:numel(Pe)
for ij = 1:numel(Je)
@@ -134,7 +143,7 @@ else
if DATA.KIN_E
subplot(2,1,1)
end
- imagesc(DATA.Ts5D,p2ji,plt(Ni_ST,1:numel(p2ji)));
+ imagesc(Time_,p2ji,plt(Ni_ST,1:numel(p2ji)));
set(gca,'YDir','normal')
% pclr = pcolor(XX,YY,plt(Ni_ST));
% set(pclr, 'edgecolor','none'); hold on;
@@ -142,7 +151,7 @@ else
title('$\langle\sum_k |N_i^{pj}|\rangle_{p+2j=const}$')
if DATA.KIN_E
subplot(2,1,2)
- imagesc(DATA.Ts5D,p2je,plt(Ne_ST,1:numel(p2ji)));
+ imagesc(Time_,p2je,plt(Ne_ST,1:numel(p2ji)));
set(gca,'YDir','normal')
% pclr = pcolor(XX,YY,plt(Ne_ST));
% set(pclr, 'edgecolor','none'); hold on;
diff --git a/matlab/plot/statistical_transport_averaging.m b/matlab/plot/statistical_transport_averaging.m
index ffc0395e..af463893 100644
--- a/matlab/plot/statistical_transport_averaging.m
+++ b/matlab/plot/statistical_transport_averaging.m
@@ -1,5 +1,5 @@
-function [ fig, Gx_infty_avg, Gx_infty_std ] = statistical_transport_averaging( data, options )
+function [ fig, res ] = statistical_transport_averaging( data, options )
scale = data.scale;
Trange = options.T;
[~,it0] = min(abs(Trange(1)-data.Ts0D));
@@ -21,7 +21,7 @@ dt_const = numel(unique(round(diff(data.Ts0D(it0:it1))*100)))==1;
transp_seg_std(Np) = std(gamma(1:Np));
end
- time_seg = (data.Ts0D(it0:it1)-data.Ts0D(it0));
+ time_seg = (data.Ts0D(it0:it1));
fig = 0;
if options.NPLOTS > 0
@@ -43,8 +43,13 @@ if options.NPLOTS > 0
xlabel('Averaging time'); ylabel('$\langle Q_x\rangle_{\tau}$');
legend(['$Q_x^\infty=$',sprintf('%2.2e',transp_seg_avg(end))])
end
-Gx_infty_avg = mean(gamma);
-Gx_infty_std = std (gamma);
-disp(['G_x=',sprintf('%2.2e',Gx_infty_avg),'+-',sprintf('%2.2e',Gx_infty_std)]);
+res.time_seg = time_seg;
+res.Qx_t =
+res.Gx_avg = mean(gamma);
+res.Gx_std = std (gamma);
+disp(['G_x=',sprintf('%2.2e',res.Gx_avg),'+-',sprintf('%2.2e',res.Gx_std)]);
+res.Qx_avg = mean(Qx);
+res.Qx_std = std (Qx);
+disp(['G_x=',sprintf('%2.2e',res.Qx_avg),'+-',sprintf('%2.2e',res.Qx_std)]);
end
diff --git a/wk/analysis_gene.m b/wk/analysis_gene.m
index 0c3c014d..11c0b16a 100644
--- a/wk/analysis_gene.m
+++ b/wk/analysis_gene.m
@@ -29,7 +29,7 @@ addpath(genpath([gyacomodir,'matlab/load'])) % ... add
% folder = '/misc/gene_results/CBC/128x64x16x24x12/';
% folder = '/misc/gene_results/CBC/196x96x20x32x16_01/';
% folder = '/misc/gene_results/CBC/256x96x24x32x12/';
-folder = '/misc/gene_results/CBC/128x64x16x6x4/';
+% folder = '/misc/gene_results/CBC/128x64x16x6x4/';
% folder = '/misc/gene_results/CBC/KT_5.3_128x64x16x24x12_01/';
% folder = '/misc/gene_results/CBC/KT_4.5_128x64x16x24x12_01/';
% folder = '/misc/gene_results/CBC/KT_9_128x64x16x24x12/';
@@ -46,10 +46,17 @@ folder = '/misc/gene_results/CBC/128x64x16x6x4/';
%Paper 2
% folder = '/misc/gene_results/CBC/KT_6.96_64x32x32x24x12_Nexc_5/';
+% folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x8x4_Nexc_5_00/';
+% folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x16x8_Nexc_5_00/';
% folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x32x16_Nexc_5_00/';
% folder = '/misc/gene_results/CBC/KT_6.96_128x64x24x32x16_Nexc_5_01/';
+
% folder = '/misc/gene_results/CBC/KT_5.3_128x64x24x32x16_Nexc_5_00/';
% folder = '/misc/gene_results/CBC/KT_5.3_128x64x24x32x16_Nexc_5_01/';
+% folder = '/misc/gene_results/CBC/new_sim/KT_5.3_128x64x24x16x8_Nexc_5/';
+% folder = '/misc/gene_results/CBC/new_sim/KT_5.3_128x64x24x8x4_Nexc_5/';
+folder = '/misc/gene_results/CBC/new_sim/KT_6.96_128x64x24x8x4_Nexc_5_smallvbox/';
+% folder = '/misc/gene_results/CBC/new_sim/KT_6.96_128x64x24x16x8_Nexc_5_largexbox/';
gene_data = load_gene_data(folder);
gene_data.FIGDIR = folder;
@@ -82,24 +89,31 @@ fig = statistical_transport_averaging(gene_data,options);
end
if 0
-%% 2D snapshots
+%% fields snapshots
% Options
-options.INTERP = 1;
+options.INTERP = 0;
options.POLARPLOT = 0;
options.AXISEQUAL = 0;
+options.NORMALIZE = 0;
+% options.NAME = '\phi';
+% options.NAME = '\psi';
+% options.NAME = '\omega_z';
+options.NAME = 'n_i';
+% options.NAME = 'n_i-n_e';
+% options.NAME = '\phi^{NZ}';
+% options.NAME = 'N_i^{00}';
+% options.NAME = 'N_i^{00}-N_e^{00}';
+% options.NAME = 's_{Ex}';
% options.NAME = 'Q_x';
-options.NAME = '\phi';
-% options.NAME = 'n_i';
-% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'kxz';
-% options.NAME ='f_e';
-% options.PLAN = 'sx';
-options.COMP = 'avg';
-options.TIME = [40 55 70];
-gene_data.a = data.EPS * 2000;
+options.PLAN = 'xy';
+options.COMP = 1;
+options.TIME = [0];
+options.RESOLUTION = 256;
+
+data.a = data.EPS * 2e3;
fig = photomaton(gene_data,options);
-save_figure(gene_data,fig,'.png')
+% save_figure(data,fig)
end
if 0
@@ -111,7 +125,7 @@ options.NAME = '\phi';
% options.NAME = 'v_{Ey}';
% options.NAME = 'G_x';
% options.NAME = 'n_i';
-options.PLAN = 'xz';
+options.PLAN = 'xy';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
@@ -168,11 +182,11 @@ end
if 0
%% Time averaged spectrum
-options.TIME = [100 500];
+options.TIME = [1];
options.NORM =1;
-% options.NAME = '\phi';
+options.NAME = '\phi';
% options.NAME = 'n_i';
-options.NAME ='\Gamma_x';
+% options.NAME ='\Gamma_x';
options.PLAN = 'kxky';
options.COMPZ = 'avg';
options.OK = 0;
diff --git a/wk/analysis_gyacomo.m b/wk/analysis_gyacomo.m
index a7f93e8a..000f5022 100644
--- a/wk/analysis_gyacomo.m
+++ b/wk/analysis_gyacomo.m
@@ -11,12 +11,13 @@ addpath(genpath([gyacomodir,'matlab/load'])) % ... add
%% Load the results
LOCALDIR = [gyacomodir,resdir,'/'];
MISCDIR = ['/misc/gyacomo_outputs/',resdir,'/']; %For long term storage
+DATADIR = [PARTITION,resdir,'/'];
system(['mkdir -p ',MISCDIR]);
system(['mkdir -p ',LOCALDIR]);
% CMD = ['rsync ', LOCALDIR,'outputs* ',MISCDIR]; disp(CMD);
% system(CMD);
% Load outputs from jobnummin up to jobnummax
-data = compile_results(MISCDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
+data = compile_results(DATADIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
data.localdir = LOCALDIR;
data.FIGDIR = LOCALDIR;
data.folder = LOCALDIR;
@@ -46,17 +47,22 @@ end
if 0
%% statistical transport averaging
-gavg =[]; gstd = [];
+Gavg =[]; Gstd = [];
+Qavg =[]; Qstd = [];
+figure; hold on;
+plot(data.Ts0D,data.Qx);
for i_ = 1:2:numel(data.TJOB_SE)
% i_ = 3;
disp([num2str(data.TJOB_SE(i_)),' ',num2str(data.TJOB_SE(i_+1))])
disp([num2str(data.NU_EVOL(i_)),' ',num2str(data.NU_EVOL(i_+1))])
-options.T = [data.TJOB_SE(i_) data.TJOB_SE(i_+1)];
+options.T = [data.TJOB_SE(i_)*1.2 data.TJOB_SE(i_+1)];
options.NPLOTS = 0;
-[fig, gavg_, gstd_] = statistical_transport_averaging(data,options);
-gavg = [gavg gavg_]; gstd = [gstd gstd_];
+[fig, res] = statistical_transport_averaging(data,options);
+Gavg = [Gavg res.Gx_avg]; Gstd = [Gstd res.Gx_std];
+Qavg = [Qavg res.Qx_avg]; Qstd = [Qstd res.Qx_std];
end
-disp(gavg); disp(gstd);
+% disp(Gavg); disp(Gstd);
+disp(Qavg); disp(Qstd);
end
if 0
%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -66,18 +72,18 @@ options.POLARPLOT = 0;
options.NAME = '\phi';
% options.NAME = '\omega_z';
% options.NAME = 'N_i^{00}';
-% options.NAME = 'v_x';
+% options.NAME = 's_{Ey}';
% options.NAME = 'n_i^{NZ}';
-% options.NAME = '\Gamma_x';
+% options.NAME = 'G_x';
% options.NAME = 'n_i';
% options.NAME = 'n_i-n_e';
options.PLAN = 'xy';
-options.NAME = 'f_i';
-options.PLAN = 'sx';
+% options.NAME = 'f_i';
+% options.PLAN = 'sx';
options.COMP = 'avg';
% options.TIME = data.Ts5D(end-30:end);
-% options.TIME = data.Ts3D;
-options.TIME = [0:10000];
+options.TIME = data.Ts3D;
+% options.TIME = [0:10000];
data.EPS = 0.1;
data.a = data.EPS * 2000;
options.RESOLUTION = 256;
@@ -94,7 +100,7 @@ options.NORMALIZE = 0;
options.NAME = '\phi';
% options.NAME = '\psi';
% options.NAME = '\omega_z';
-% options.NAME = 'n_e';
+% options.NAME = 'n_i';
% options.NAME = 'n_i-n_e';
% options.NAME = '\phi^{NZ}';
% options.NAME = 'N_i^{00}';
@@ -103,8 +109,8 @@ options.NAME = '\phi';
% options.NAME = 'Q_x';
% options.NAME = 'k^2n_e';
options.PLAN = 'xy';
-options.COMP = 'avg';
-options.TIME = [500];
+options.COMP = 1;
+options.TIME = [29.5 30 30.5];
options.RESOLUTION = 256;
data.a = data.EPS * 2e3;
@@ -150,7 +156,7 @@ if 0
%% Hermite-Laguerre spectrum
% options.TIME = 'avg';
options.P2J = 0;
-options.ST = 1;
+options.ST = 0;
options.PLOT_TYPE = 'space-time';
options.NORMALIZED = 0;
options.JOBNUM = 0;
diff --git a/wk/header_3D_results.m b/wk/header_3D_results.m
index 9a860e05..9d8b87fe 100644
--- a/wk/header_3D_results.m
+++ b/wk/header_3D_results.m
@@ -1,9 +1,8 @@
% Directory of the code "mypathtoHeLaZ/HeLaZ/"
gyacomodir = '/home/ahoffman/gyacomo/';
-% Directory of the simulation (from results)
-% if 1% Local results
-% resdir ='volcokas/64x32x16x5x3_kin_e_npol_1';
-
+% Partition of the computer where the data have to be searched
+PARTITION = '/misc/gyacomo_outputs/';
+% PARTITION = gyacomodir;
%% Dimits
% resdir ='shearless_cyclone/128x64x16x5x3_Dim_90';
% resdir ='shearless_cyclone/128x64x16x9x5_Dim_scan/128x64x16x9x5_Dim_60';
@@ -79,6 +78,7 @@ gyacomodir = '/home/ahoffman/gyacomo/';
% resdir = 'GCM_CBC/daint/Miller_GX_comparison';
% resdir = 'GCM_CBC/daint/Salpha_GX_comparison';
%% Paper 2 simulations
+% convergence CBC and Dimits regime
% resdir = 'paper_2_nonlinear/kT_6.96/CBC_7x4x128x64x24';
% resdir = 'paper_2_nonlinear/kT_6.96/CBC_3x2x128x64x24_Nexc_5';
% resdir = 'paper_2_nonlinear/kT_6.96/CBC_5x3x128x64x24_Nexc_5';
@@ -90,9 +90,17 @@ gyacomodir = '/home/ahoffman/gyacomo/';
% resdir = 'paper_2_nonlinear/kT_5.3/CBC_kT_5.3_7x4x128x64x24_Nexc_5';
% resdir = 'paper_2_nonlinear/kT_5.3/CBC_kT_5.3_9x5x128x64x24_Nexc_5';
% resdir = 'paper_2_nonlinear/kT_5.3/CBC_kT_5.3_11x6x128x64x24_Nexc_5';
+% resdir = 'paper_2_nonlinear/kT_5.3/CBC_kT_5.3_13x7x128x64x24_Nexc_5';
% resdir = 'paper_2_nonlinear/kT_5.3/CBC_kT_5.3_15x8x128x64x24_Nexc_5';
-resdir = 'paper_2_nonlinear/kT_5.3/CBC_kT_5.3_17x9x128x64x24_Nexc_5';
+% resdir = 'paper_2_nonlinear/kT_5.3/CBC_kT_5.3_17x9x128x64x24_Nexc_5';
+% Scan in kT
+% resdir = 'paper_2_nonlinear/kT_scan_DGGK_0.05/9x5x128x64x24';
+
+% resdir = 'paper_2_nonlinear/CBC_rerun/rerun_CBC_3x2x128x64x16';
+% resdir = 'dev/init_ppj';
+% resdir = 'dev/hatB_NL';
+resdir = 'dev/CBC_wave_study';
resdir = ['results/',resdir];
-JOBNUMMIN = 00; JOBNUMMAX = 10;
+JOBNUMMIN = 04; JOBNUMMAX = 10;
run analysis_gyacomo
diff --git a/wk/p2_heatflux_salpha_convergence.m b/wk/p2_heatflux_salpha_convergence.m
index 2d850670..49773c32 100644
--- a/wk/p2_heatflux_salpha_convergence.m
+++ b/wk/p2_heatflux_salpha_convergence.m
@@ -1,19 +1,59 @@
+%% Heat flux convergence for kt=6.96 and 5.3
figure
-%% KT 6.96, nuDGDK = 0.05, 128x64x24, Nexc 5
+title('s-$\alpha$ turb. heat flux conv.');
+% KT 6.96, nuDGDK = 0.05, 128x64x16, Nexc 1
+P = [2 4 12];
+Qx = [50.00 46.00 41.00];
+std_= [6.600 2.300 6.600];
+ errorbar(P,Qx,std_/2,'o-.r',...
+ 'LineWidth',2.0,'MarkerSize',8,...
+ 'DisplayName','KT 6.9, nuDGDK 0.05'); hold on
+xlabel('$P$, $J=P/2$'); ylabel('$Q_x$');
+% KT 6.96, nuDGDK = 0.05, 128x64x24, Nexc 5
P = [4 6 8 10 ];
Qx = [67.62 67.50 59.21 64.17];
-std = [15.42 20.32 17.25 16.05];
- errorbar(P,Qx,std/2,'s-',...
- 'LineWidth',2.0,...
- 'DisplayName','KT 6.96, nuDGDK 0.05'); hold on
+std_= [15.42 20.32 17.25 16.05];
+ errorbar(P,Qx,std_/2,'o-r',...
+ 'LineWidth',2.0,'MarkerSize',8,...
+ 'DisplayName','KT 6.9, nuDGDK 0.05'); hold on
xlabel('$P$, $J=P/2$'); ylabel('$Q_x$');
-%% KT 5.3, nuDGDK = 0.05, 128x64x24, Nexc 5
-P = [4 6 8 10 ];
-Qx = [44.10 21.61 16.04 0.489];
-std = [10.61 6.952 4.166 0.061];
- errorbar(P,Qx,std/2,'s-',...
- 'LineWidth',2.0,...
+% KT 5.3, nuDGDK = 0.05, 128x64x24, Nexc 5
+P = [4 6 8 10 12 ];
+Qx = [44.10 21.61 16.04 0.558 0.901];
+std_= [10.61 6.952 4.166 0.025 0.122];
+errorbar(P,Qx,std_/2,'o-b',...
+ 'LineWidth',2.0,'MarkerSize',8,...
'DisplayName','KT 5.3, nuDGDK 0.05');
xlabel('$P$, $J=P/2$'); ylabel('$Q_x$');
-title('GYAC, turb. heat flux conv.');
\ No newline at end of file
+% GENE RESULTS 6.96 128x64x24, Nexc 5
+Nvp = [32 16 8 8];
+Qx = [34.53 37.96 1.948 13.0];
+std_= [7.830 6.048 0.629 3.09];
+errorbar(Nvp,Qx,std_/2,'s--r',...
+ 'LineWidth',2.0,'MarkerSize',8,...
+ 'DisplayName','KT 6.9 GENE');
+xlabel('$P=N_{v\parallel}$, $J=P/2=N_\mu$'); ylabel('$Q_x$');
+
+% GENE RESULTS 5.3 128x64x24, Nexc 5
+% Comment: the result with nvp = 8 is not trusworthy as GENE does not have
+% a linear instability with this resolution.. It is then hard to draw
+% any conclusion from it.
+Nvp = [32 16 8];
+Qx = [0.284 0.000 0.370];
+std_= [0.177 0.000 0.140];
+errorbar(Nvp,Qx,std_/2,'s--b',...
+ 'LineWidth',2.0,'MarkerSize',8,...
+ 'DisplayName','KT 5.3 GENE');
+xlabel('$P=N_{v\parallel}$, $J=P/2=N_\mu$'); ylabel('$Q_x$');
+
+%% KT scans 9x5x128x64x24
+clrs = lines(10);
+figure
+kT_ = [6.96 6.3 5.8 5.3 4.8];
+Qx_ = [59.21 40.1740 31.3627 16.04 1.0900];
+std_= [6.7880 7.5513 9.7815 4.166 0.4995];
+errorbar(kT_,Qx_,std_/2,'s--','color',clrs(4,:),...
+ 'LineWidth',2.0,'MarkerSize',8,...
+ 'DisplayName','(8,4)');
+xlabel('$K_T$'); ylabel('$Q_x$');
--
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