diff --git a/matlab/load/load_gene_data.m b/matlab/load/load_gene_data.m
index 4ef290a3ac5cc5d74272ca516e341442a8c66928..af55df0c97085e5dbc8e0f02edcd908429caec7a 100644
--- a/matlab/load/load_gene_data.m
+++ b/matlab/load/load_gene_data.m
@@ -48,14 +48,14 @@ for jt = 1:numel(DATA.Ts3D)
t = DATA.Ts3D(jt);
[~, it] = min(abs(DATA.Ts3D-t));
%
-% tmp = h5read([folder,momfile],['/mom_ions/dens/',sprintf('%10.10d',it-1)]);
-% DATA.DENS_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
+ tmp = h5read([folder,momfile],['/mom_ions/dens/',sprintf('%10.10d',it-1)]);
+ DATA.DENS_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
%
-% tmp = h5read([folder,momfile],['/mom_ions/T_par/',sprintf('%10.10d',it-1)]);
-% DATA.TPAR_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
+ tmp = h5read([folder,momfile],['/mom_ions/T_par/',sprintf('%10.10d',it-1)]);
+ DATA.TPAR_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
%
-% tmp = h5read([folder,momfile],['/mom_ions/T_perp/',sprintf('%10.10d',it-1)]);
-% DATA.TPER_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
+ tmp = h5read([folder,momfile],['/mom_ions/T_perp/',sprintf('%10.10d',it-1)]);
+ DATA.TPER_I(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
tmp = h5read([folder,phifile],['/field/phi/',sprintf('%10.10d',it-1)]);
DATA.PHI(:,:,:,it) = tmp.real + 1i*tmp.imaginary;
diff --git a/matlab/plot/spectrum_1D.m b/matlab/plot/spectrum_1D.m
index 7288fe1764d4cf00576da25b73dc4f33d587b394..6591df1634c111a4632f7bdc928aac7cacb8db72 100644
--- a/matlab/plot/spectrum_1D.m
+++ b/matlab/plot/spectrum_1D.m
@@ -1,7 +1,7 @@
function [ FIGURE ] = spectrum_1D( data, options )
options.PLAN = 'kxky';
-options.COMP = 'avg';
+options.COMP = 1;
options.INTERP = 0;
options.POLARPLOT = 0;
options.AXISEQUAL = 1;
diff --git a/wk/CBC_nu_CO_scan.m b/wk/CBC_nu_CO_scan.m
index 7f69c6072b02dea69c0264feb9cba4ad639328ff..9a07ac6e5d6b8359fda849fcc37634b31c10ebae 100644
--- a/wk/CBC_nu_CO_scan.m
+++ b/wk/CBC_nu_CO_scan.m
@@ -1,12 +1,15 @@
gyacomodir = '/home/ahoffman/gyacomo/';
-% EXECNAME = 'gyacomo_1.0';
+addpath(genpath([gyacomodir,'matlab'])) % ... add
+addpath(genpath([gyacomodir,'matlab/plot'])) % ... add
+addpath(genpath([gyacomodir,'matlab/compute'])) % ... add
+addpath(genpath([gyacomodir,'matlab/load'])) % ... add% EXECNAME = 'gyacomo_1.0';
% EXECNAME = 'gyacomo_dbg';
EXECNAME = 'gyacomo';
%%
NU_a = [0.005 0.01:0.01:0.1];
% P_a = [2 4 6 8 10 12 16];
-% NU_a = 0.05;
-P_a = [10];
+% NU_a = 0.1;
+P_a = [2 4 8 10 12 16 20];
CO = 'SG';
@@ -19,7 +22,7 @@ kymin = 0.05;
Ny = 40;
SIMID = 'linear_CBC_nu+PJ_scan_kT_6.96_SGGK'; % Name of the simulation
% SIMID = 'linear_CBC_nu_scan_kT_11_ky_0.3_DGGK'; % Name of the simulation
-RUN = 1;
+RUN = 0;
g_ky = zeros(numel(NU_a),numel(P_a),Ny/2);
g_avg= g_ky*0;
@@ -56,7 +59,7 @@ for NU = NU_a
ZETA = 0.0; % squareness
NEXC = 1; % To extend Lx if needed (Lx = Nexc/(kymin*shear))
EPS = 0.18; % inverse aspect ratio
- SPS0D = 1; SPS2D = 0; SPS3D = 1;SPS5D= 1/5; SPSCP = 0;
+ SPS0D = 1; SPS2D = -1; SPS3D = 1;SPS5D= 1/5; SPSCP = 0;
JOB2LOAD= -1;
LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
GKCO = 1; % gyrokinetic operator
@@ -65,7 +68,7 @@ for NU = NU_a
CLOS = 0; % Closure model (0: =0 truncation, 1: v^Nmax closure (p+2j<=Pmax))s
NL_CLOS = 0; % nonlinear closure model (-2:nmax=jmax; -1:nmax=jmax-j; >=0:nmax=NL_CLOS)
KERN = 0; % Kernel model (0 : GK)
- INIT_OPT= 'phi'; % Start simulation with a noisy mom00/phi/allmom
+ INIT_OPT= 'mom00'; % Start simulation with a noisy mom00/phi/allmom
W_DOUBLE = 1;
W_GAMMA = 1; W_HF = 1;
W_PHI = 1; W_NA00 = 1;
@@ -86,6 +89,7 @@ for NU = NU_a
setup
if RUN
system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 2 3 1 0; cd ../../../wk'])
+% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0; cd ../../../wk'])
end
% Load results
@@ -130,24 +134,28 @@ for i = 1:numel(idx_)
e_ = g_std(:,:,idx_(i));
end
+colors_ = summer(numel(NU_a));
subplot(121)
for i = 1:numel(NU_a)
errorbar(P_a,y_(i,:),e_(i,:),...
'LineWidth',1.2,...
- 'DisplayName',['$\nu=$',num2str(NU_a(i))]);
+ 'DisplayName',['$\nu=$',num2str(NU_a(i))],...
+ 'color',colors_(i,:));
hold on;
end
title(['$\kappa_T=$',num2str(K_Ti),' $k_y=k_y^{max}$']);
legend('show'); xlabel('$P$, $J=P/2$'); ylabel('$\gamma$');
+colors_ = jet(numel(P_a));
subplot(122)
for j = 1:numel(P_a)
errorbar(NU_a,y_(:,j),e_(:,j),...
'LineWidth',1.2,...
- 'DisplayName',['(',num2str(P_a(j)),',',num2str(P_a(j)/2),')']);
+ 'DisplayName',['(',num2str(P_a(j)),',',num2str(P_a(j)/2),')'],...
+ 'color',colors_(j,:));
hold on;
end
-title(['$\kappa_T=$',num2str(K_Ti),' $k_y=$',num2str(data.ky(idx_))]);
+title(['$\kappa_T=$',num2str(K_Ti),' $k_y=k_y^{max}$']);
legend('show'); xlabel(['$\nu_{',CO,'}$']); ylabel('$\gamma$');
end
diff --git a/wk/analysis_gene.m b/wk/analysis_gene.m
index a35d30f9177c74c15d487f65329441deef8ecdd0..48a6d16062264b56782e49bbe682c15404661e32 100644
--- a/wk/analysis_gene.m
+++ b/wk/analysis_gene.m
@@ -13,15 +13,15 @@ addpath(genpath([gyacomodir,'matlab/load'])) % ... add
% folder = '/misc/gene_results/shearless_cyclone/LD_s_alpha_output_1.0/';
% folder = '/misc/gene_results/shearless_cyclone/LD_s_alpha_output_0.8/';
% folder = '/misc/gene_results/Z-pinch/HP_fig_2a_mu_1e-2/';
-folder = '/misc/gene_results/Z-pinch/HP_fig_2b_mu_5e-2/';
+% folder = '/misc/gene_results/Z-pinch/HP_fig_2b_mu_5e-2/';
% folder = '/misc/gene_results/Z-pinch/HP_fig_2c_mu_5e-2/';
% folder = '/misc/gene_results/LD_zpinch_1.6/';
% folder = '/misc/gene_results/ZP_HP_kn_1.6_nuv_3.2/';
% folder = '/misc/gene_results/ZP_HP_kn_1.6_nuv_3.2/';
% folder = '/misc/gene_results/Z-pinch/ZP_HP_kn_1.6_HRES/';
% folder = '/misc/gene_results/ZP_kn_2.5_large_box/';
-% folder = '/misc/gene_results/Z-pinch/kN_2.0_HD_transport_spectrum_00/';
-% folder = '/misc/gene_results/Z-pinch/kN_2.5_HD_transport_spectrum_00/';
+folder = '/misc/gene_results/Z-pinch/kN_2.0_HD_transport_spectrum_01/';
+% folder = '/misc/gene_results/Z-pinch/kN_2.5_HD_transport_spectrum_01/';
% folder = '/misc/gene_results/CBC/128x64x16x24x12/';
% folder = '/misc/gene_results/CBC/196x96x20x32x16_02/';
@@ -43,6 +43,7 @@ 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;
options.NCUT = 4; % Number of cuts for averaging and error estimation
+options.RESOLUTION = 256;
gene_data.FIGDIR = folder;
fig = plot_radial_transport_and_spacetime(gene_data,options);
save_figure(gene_data,fig,'.png')
@@ -80,15 +81,16 @@ if 0
% Options
options.INTERP = 1;
options.POLARPLOT = 0;
-options.NAME = '\phi';
+% options.NAME = '\phi';
% options.NAME = 'v_y';
% options.NAME = '\Gamma_x';
-% options.NAME = 'n_i';
-options.PLAN = 'kxky';
+options.NAME = 'n_i';
+options.PLAN = 'xy';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
options.TIME = gene_data.Ts3D;
+options.RESOLUTION= 256;
gene_data.a = data.EPS * 2000;
create_film(gene_data,options,'.gif')
end
@@ -134,7 +136,7 @@ end
if 0
%% Time averaged spectrum
-options.TIME = [60 10000];
+options.TIME = [600 5000];
options.NORM =1;
% options.NAME = '\phi';
% options.NAME = 'n_i';
diff --git a/wk/gene_data.FIGDIR b/wk/gene_data.FIGDIR
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/wk/header_3D_results.m b/wk/header_3D_results.m
index 63cb0bf33d953ee2f8636517e5faaf903fc35339..8a872def7c8ecc1c43bf6be710d72542bbaf9a4c 100644
--- a/wk/header_3D_results.m
+++ b/wk/header_3D_results.m
@@ -35,7 +35,7 @@ gyacomodir = '/home/ahoffman/gyacomo/';
% resdir = 'CBC/96x96x16x3x2_Nexc_6';
% resdir = 'CBC/128x96x16x3x2';
% resdir = 'CBC/192x96x16x3x2';
-% resdir = 'CBC/192x96x24x13x7';
+resdir = 'CBC/192x96x24x13x7';
% resdir = 'CBC/kT_11_128x64x16x5x3';
% resdir = 'CBC/kT_9_256x128x16x3x2';
% resdir = 'CBC/kT_4.5_128x64x16x13x3';
@@ -60,7 +60,7 @@ gyacomodir = '/home/ahoffman/gyacomo/';
%% Linear CBC
% resdir = 'linear_CBC/20x2x32_21x11_Lx_62.8319_Ly_31.4159_q0_1.4_e_0.18_s_0.8_kN_2.22_kT_5.3_nu_1e-02_DGDK_adiabe';
% resdir = 'testcases/miller_example';
-resdir = 'Miller/128x256x3x2_CBC_dt_5e-3';
-% resdir = ['results/',resdir];
+% resdir = 'Miller/128x256x3x2_CBC_dt_5e-3';
+resdir = ['results/',resdir];
JOBNUMMIN = 00; JOBNUMMAX = 10;
run analysis_gyacomo