scripts update

matlab/compile_results.m

@@ -72,9 +72,11 @@ while(CONTINUE)
                 tmp = Nipj_; sz = size(tmp);
                 Nipj_ = zeros(cat(1,[Pi_new,Ji_new]',sz(3:end)')');
                 Nipj_(1:Pi_old,1:Ji_old,:,:,:,:) = tmp;
+                if(KIN_E) 
                 tmp = Nepj_; sz = size(tmp);
-%                 Nepj_ = zeros(cat(1,[Pe_new,Je_new]',sz(3:end)')');
-%                 Nepj_(1:Pe_old,1:Je_old,:,:,:,:) = tmp;
+                Nepj_ = zeros(cat(1,[Pe_new,Je_new]',sz(3:end)')');
+                Nepj_(1:Pe_old,1:Je_old,:,:,:,:) = tmp;
+                end
             end
             if W_SAPJ
                 tmp = Sipj_; sz = size(tmp);

matlab/compute/compute_fluxtube_growth_rate.m

@@ -41,9 +41,9 @@ linear_gr.ce     = abs(ce);
 linear_gr.ky     = kys;
 if PLOT >0
        figure
-       plot(linear_gr.ky,linear_gr.g_ky(:,end),'DisplayName','$Re(\omega_{k_y})$'); hold on;
-       plot(linear_gr.ky,linear_gr.w_ky(:,end),'DisplayName','$Im(\omega_{k_y})$'); hold on;
-       plot(linear_gr.ky,linear_gr.ce  (:,end),'DisplayName','$\epsilon$'); hold on;
+       plot(linear_gr.ky,linear_gr.g_ky(:,end),'-o','DisplayName','$Re(\omega_{k_y})$'); hold on;
+       plot(linear_gr.ky,linear_gr.w_ky(:,end),'-o','DisplayName','$Im(\omega_{k_y})$'); hold on;
+       plot(linear_gr.ky,linear_gr.ce  (:,end),'-o','DisplayName','$\epsilon$'); hold on;
        xlim([min(linear_gr.ky) max(linear_gr.ky)]);
        xlabel('$k_y$');
        legend('show');

wk/analysis_HeLaZ.m

@@ -50,7 +50,7 @@ options.NAME      = '\phi';
 % options.NAME      = 'n_i^{NZ}';
 % options.NAME      = '\Gamma_x';
 % options.NAME      = 'n_i';
-options.PLAN      = 'kxky';
+options.PLAN      = 'xz';
 % options.NAME      = 'f_i';
 % options.PLAN      = 'sx';
 options.COMP      = 'avg';
@@ -78,7 +78,7 @@ options.PLAN      = 'kxky';
 % options.NAME      = 'f_i';
 % options.PLAN      = 'sx';
 options.COMP      = 'avg';
-options.TIME      = [300 400 600];
+options.TIME      = [100];
 data.a = data.EPS * 2e3;
 fig = photomaton(data,options);
 % save_figure(data,fig)

wk/cbc_qx_results.m

@@ -23,19 +23,19 @@ xlabel('CBC drive [\%]'); ylabel('Radial Heat Flux $Q_x^\infty$');
 
 KN       = 2.22;
 KT       = [1.00 0.90 0.80 0.70 0.60 0.50]*6.96;
-gm42     = [32.2 16.8 0.00 0.00 1.74 0.00];
-gm42_err = [05.2 02.8 0.00 0.00 0.53 0.00];
-gm84     = [0.00 0.00 0.00 0.00 0.00 0.00];
-gm84_err = [0.00 0.00 0.00 0.00 0.00 0.00];
+gm42     = [32.2 18.8 10.5 5.89 1.74 0.00];
+gm42_err = [05.2 03.8 2.10 1.66 0.53 0.00];
+gm84     = [0.00 13.2 7.66 3.20 0.00 0.00];
+gm84_err = [0.00 2.79 1.93 0.98 0.00 0.00];
 gne      = [0.00 0.00 0.00 0.00 0.00 0.00];
 gne_err  = [0.00 0.00 0.00 0.00 0.00 0.00];
 
 figure
-errorbar(KT./KN,gm42,gm42_err,'o-', 'LineWidth',1.5); hold on;
-errorbar(KT./KN,gm84,gm84_err,'o-', 'LineWidth',1.5);
-errorbar(KT./KN, gne, gne_err,'x-k','LineWidth',1.5);
+errorbar(KT,gm42./KT,gm42_err./KT,'o-', 'LineWidth',1.5); hold on;
+errorbar(KT,gm84./KT,gm84_err./KT,'o-', 'LineWidth',1.5);
+errorbar(KT, gne./KT, gne_err./KT,'x-k','LineWidth',1.5);
 
 % set(gca, 'YScale', 'log')
 
 legend('GM (4,2)','GM (8,4)','Gene')
-xlabel('$\eta=\kappa_T/\kappa_N$'); ylabel('Radial Heat Flux $Q_x^\infty$');
+xlabel('$\eta=\kappa_T/\kappa_N$'); ylabel('$\chi_i$');

wk/header_3D_results.m

@@ -2,21 +2,26 @@
 helazdir = '/home/ahoffman/HeLaZ/';
 % Directory of the simulation (from results)
 % if 1% Local results
-outfile ='';
+% outfile ='volcokas/64x32x16x5x3_kin_e_npol_1';
 
 %% Dimits
 % outfile ='shearless_cyclone/128x64x16x5x3_Dim_90';
-outfile ='shearless_cyclone/64x32x16x5x3_Dim_50';
+% outfile ='shearless_cyclone/128x64x16x9x5_Dim_scan/128x64x16x9x5_Dim_60';
+% outfile ='shearless_cyclone/128x64x16x5x3_Dim_scan/128x64x16x5x3_Dim_70';
+% outfile ='shearless_cyclone/64x32x16x5x3_Dim_scan/64x32x16x5x3_Dim_70';
 %% AVS
 % outfile = 'volcokas/64x32x16x5x3_kin_e_npol_1';
-
-%% Bechmark
+% outfile = 'volcokas/64x32x16x5x3_kin_e_npol_1';
+outfile = 'shearless_cyclone/64x32x160x5x3_CBC_Npol_10_kine';
+%% CBC
 % outfile ='shearless_cyclone/64x32x16x5x3_CBC_080';
-% outfile ='shearless_cyclone/64x32x16x5x3_CBC_100';
+% outfile ='shearless_cyclone/64x32x16x5x3_CBC_scan/64x32x16x5x3_CBC_100';
 % outfile ='shearless_cyclone/64x32x16x5x3_CBC_120';
 
 % outfile ='shearless_cyclone/64x32x16x9x5_CBC_080';
 % outfile ='shearless_cyclone/64x32x16x9x5_CBC_100';
 % outfile ='shearless_cyclone/64x32x16x9x5_CBC_120';
 
+% outfile = 'shearless_cyclone/64x32x16x5x3_CBC_CO/64x32x16x5x3_CBC_LRGK';
+
 run analysis_HeLaZ

wk/heat_flux_postproc.m

 % Hflux_x = 0;
 % Hflux_x = 0 * data.Ts5D;
-filename = '/home/ahoffman/HeLaZ/results/shearless_cyclone/64x32x16x5x3_CBC_100/outputs_00.h5';
-kernel_i = h5read(filename,'/data/metric/kernel_i');
+% filename = '/home/ahoffman/HeLaZ/results/shearless_cyclone/64x32x16x5x3_CBC_100/outputs_00.h5';
+filename = '/misc/HeLaZ_outputs/results/shearless_cyclone/64x32x160x5x3_CBC_Npol_10_kine/outputs_00.h5';
+kernel_i = h5read(filename,'/data/metric/kernel_i'); sigma = 0.0738;
 Jacobian = h5read(filename,'/data/metric/Jacobian');
 STEPS = 1:numel(data.Ts5D);
 Hflux_x = 1:numel(STEPS);
@@ -35,9 +36,9 @@ for it = STEPS
     correct_op = zeros(Nky,Nkx,Nz);
     for in = 1:Nj
         n = in-1;
-        Kn    = squeeze(kernel_i(in,:,:,:,1));
-        N2n   = squeeze(data.Nipj(3,in  ,:,:,:,it5d));
-        N0n   = squeeze(data.Nipj(1,in  ,:,:,:,it5d));
+        Kn    = squeeze(kernel_i(in,:,:,:,1))*sigma^(2*n);
+        N2n   = squeeze(data.Nepj(3,in  ,:,:,:,it5d));
+        N0n   = squeeze(data.Nepj(1,in  ,:,:,:,it5d));
         sumkernmom = sumkernmom + ...
             Kn.* (c2n(n) .* N2n + c0n(n) .* N0n);
         

wk/quick_run.m

@@ -13,22 +13,22 @@ EXECNAME = 'helaz3';
 CLUSTER.TIME  = '99:00:00'; % allocation time hh:mm:ss
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% PHYSICAL PARAMETERS
-NU      = 0.05;   % Collision frequency
+NU      = 0.1;   % Collision frequency
 TAU     = 1.0;    % e/i temperature ratio
-K_N     = 0;%2.22;   % Density gradient drive
-K_T     = 0;%6.96;   % Temperature '''
+K_N     = 2.22;   % Density gradient drive
+K_T     = 6.96;   % Temperature '''
 K_E     = 0.0;   % Electrostat '''
 SIGMA_E = 0.05196152422706632;%0.0233380;   % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
 KIN_E   = 0;     % 1: kinetic electrons, 2: adiabatic electrons
 %% GRID PARAMETERS
-PMAXE   = 8;     % Hermite basis size of electrons
-JMAXE   = 4;     % Laguerre "
-PMAXI   = 8;     % " ions
-JMAXI   = 4;     % "
-NX      = 2;    % real space x-gridpoints
-NY      = 1;     %     ''     y-gridpoints
+PMAXE   = 4;     % Hermite basis size of electrons
+JMAXE   = 2;     % Laguerre "
+PMAXI   = 4;     % " ions
+JMAXI   = 2;     % "
+NX      = 20;    % real space x-gridpoints
+NY      = 2;     %     ''     y-gridpoints
 LX      = 100;   % Size of the squared frequency domain
-LY      = 60;     % Size of the squared frequency domain
+LY      = 20;     % Size of the squared frequency domain
 NZ      = 32;     % number of perpendicular planes (parallel grid)
 NPOL    = 1;
 SG      = 0;     % Staggered z grids option
@@ -36,11 +36,11 @@ SG      = 0;     % Staggered z grids option
 % GEOMETRY= 'Z-pinch'; % Z-pinch overwrites q0, shear and eps
 GEOMETRY= 's-alpha';
 Q0      = 1.4;    % safety factor
-SHEAR   = 0.0;    % magnetic shear (Not implemented yet)
+SHEAR   = 0.8;    % magnetic shear (Not implemented yet)
 EPS     = 0.18;    % inverse aspect ratio
 %% TIME PARMETERS
 TMAX    = 50;  % Maximal time unit
-DT      = 2e-2;   % Time step
+DT      = 1e-2;   % Time step
 SPS0D   = 20;      % Sampling per time unit for 2D arrays
 SPS2D   = 0;      % Sampling per time unit for 2D arrays
 SPS3D   = 20;      % Sampling per time unit for 2D arrays
@@ -48,7 +48,7 @@ SPS5D   = 1;    % Sampling per time unit for 5D arrays
 SPSCP   = 0;    % Sampling per time unit for checkpoints
 JOB2LOAD= -1;
 %% OPTIONS
-SIMID   = 'Ros_Hin_test';  % Name of the simulation
+SIMID   = 'linear_CBC';  % Name of the simulation
 LINEARITY = 'linear';   % activate non-linearity (is cancelled if KXEQ0 = 1)
 % Collision operator
 % (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
@@ -59,7 +59,7 @@ INIT_ZF = 0; ZF_AMP = 0.0;
 CLOS    = 0;   % Closure model (0: =0 truncation, 1: gyrofluid 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= 'mom00';   % Start simulation with a noisy mom00/phi/allmom
+INIT_OPT= 'phi';   % Start simulation with a noisy mom00/phi/allmom
 %% OUTPUTS
 W_DOUBLE = 1;
 W_GAMMA  = 1; W_HF     = 1;
@@ -90,8 +90,8 @@ system(['rm fort*.90']);
 % Run linear simulation
 if RUN
 %     system(['cd ../results/',SIMID,'/',PARAMS,'/; time mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 4 1 0; cd ../../../wk'])
-%     system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ',HELAZDIR,'bin/',EXECNAME,' 1 1 1 0; cd ../../../wk'])
-    system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 1 4 0; cd ../../../wk'])
+    system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ',HELAZDIR,'bin/',EXECNAME,' 1 1 1 0; cd ../../../wk'])
+%     system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 1 4 0; cd ../../../wk'])
 %     system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',HELAZDIR,'bin/',EXECNAME,' 1 6 1 0; cd ../../../wk'])
 end
 
@@ -104,7 +104,7 @@ JOBNUMMIN = 00; JOBNUMMAX = 00;
 data = compile_results(LOCALDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
 
 %% Short analysis
-if 0
+if 1
 %% linear growth rate (adapted for 2D zpinch and fluxtube)
 trange = [0.5 1]*data.Ts3D(end);
 nplots = 1;