scripts save

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;

matlab/plot/spectrum_1D.m

 function [ FIGURE ] = spectrum_1D( data, options )
 
 options.PLAN      = 'kxky';
-options.COMP      = 'avg';
+options.COMP      = 1;
 options.INTERP    = 0;
 options.POLARPLOT = 0;
 options.AXISEQUAL = 1;

wk/CBC_nu_CO_scan.m

 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
 

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';

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