diff --git a/matlab/load_results.m b/matlab/load_results.m
index c4489bc0c1c7f62f0ac015c575b5a841b287a594..412b92a4f9862867bef8bbc5da1c99e33587f4a0 100644
--- a/matlab/load_results.m
+++ b/matlab/load_results.m
@@ -11,6 +11,8 @@ W_PHI = strcmp(h5readatt(filename,'/data/input','write_phi') ,'y');
W_NA00 = strcmp(h5readatt(filename,'/data/input','write_Na00') ,'y');
W_NAPJ = strcmp(h5readatt(filename,'/data/input','write_Napj') ,'y');
W_SAPJ = strcmp(h5readatt(filename,'/data/input','write_Sapj') ,'y');
+W_DENS = strcmp(h5readatt(filename,'/data/input','write_dens') ,'y');
+W_TEMP = strcmp(h5readatt(filename,'/data/input','write_temp') ,'y');
if W_GAMMA
@@ -37,3 +39,13 @@ if W_SAPJ
[Sipj, Ts5D, dt5D] = load_5D_data(filename, 'Sipj');
Sepj = load_5D_data(filename, 'Sepj');
end
+
+if W_DENS
+ [DENS_E, Ts2D, dt2D] = load_2D_data(filename, 'dens_e');
+ [DENS_I, Ts2D, dt2D] = load_2D_data(filename, 'dens_i');
+end
+
+if W_TEMP
+ [TEMP_E, Ts2D, dt2D] = load_2D_data(filename, 'temp_e');
+ [TEMP_I, Ts2D, dt2D] = load_2D_data(filename, 'temp_i');
+end
\ No newline at end of file
diff --git a/matlab/photomaton.m b/matlab/photomaton.m
index d5508bfc87b4f3311e722c3f50656325b67f3e91..1d3d0db4701cd97c50d45a5c8d830d7f974da15c 100644
--- a/matlab/photomaton.m
+++ b/matlab/photomaton.m
@@ -1,13 +1,13 @@
if 0
%% Photomaton : real space
-% FIELD = ni00; FNAME = 'ni'; FIELDLTX = '$N_i^{00}$'; XX = RR; YY = ZZ;
+FIELD = ni00; FNAME = 'ni'; FIELDLTX = '$N_i^{00}$'; XX = RR; YY = ZZ;
% FIELD = ne00; FNAME = 'ne'; FIELDLTX = '$N_e^{00}$'; XX = RR; YY = ZZ;
-FIELD = phi; FNAME = 'phi'; FIELDLTX = '$\phi$'; XX = RR; YY = ZZ;
-% FIELD = dr2phi; FNAME = 'dr2phi'; XX = RR; YY = ZZ;
-tf = 100; [~,it1] = min(abs(Ts2D-tf));
-tf = 285; [~,it2] = min(abs(Ts2D-tf));
-tf = 350; [~,it3] = min(abs(Ts2D-tf));
-tf = 1100; [~,it4] = min(abs(Ts2D-tf));
+% FIELD = phi; FNAME = 'phi'; FIELDLTX = '$\phi$'; XX = RR; YY = ZZ;
+% FIELD = dr2phi; FNAME = 'dr2phi'; FIELDLTX = '$\partial_r^2\phi$'; XX = RR; YY = ZZ;
+tf = 10; [~,it1] = min(abs(Ts2D-tf));
+tf = 40; [~,it2] = min(abs(Ts2D-tf));
+tf = 80; [~,it3] = min(abs(Ts2D-tf));
+tf = 100; [~,it4] = min(abs(Ts2D-tf));
fig = figure; FIGNAME = [FNAME,'_snaps','_',PARAMS]; set(gcf, 'Position', [100, 100, 1500, 350])
plt = @(x) x;%./max(max(x));
subplot(141)
diff --git a/matlab/setup.m b/matlab/setup.m
index dd1765268c914e2234c2c0027f90f1efb103f96c..270c8db0341c6a80a2fb27b7d78298269f71b52b 100644
--- a/matlab/setup.m
+++ b/matlab/setup.m
@@ -163,6 +163,8 @@ if W_PHI; OUTPUTS.write_phi = '.true.'; else; OUTPUTS.write_phi = '.false
if W_NA00; OUTPUTS.write_Na00 = '.true.'; else; OUTPUTS.write_Na00 = '.false.';end;
if W_NAPJ; OUTPUTS.write_Napj = '.true.'; else; OUTPUTS.write_Napj = '.false.';end;
if W_SAPJ; OUTPUTS.write_Sapj = '.true.'; else; OUTPUTS.write_Sapj = '.false.';end;
+if W_DENS; OUTPUTS.write_dens = '.true.'; else; OUTPUTS.write_dens = '.false.';end;
+if W_TEMP; OUTPUTS.write_temp = '.true.'; else; OUTPUTS.write_temp = '.false.';end;
OUTPUTS.resfile0 = '''outputs''';
OUTPUTS.rstfile0 = '''checkpoint''';
OUTPUTS.job2load = JOB2LOAD;
@@ -176,8 +178,8 @@ end
%% Compile and WRITE input file
INPUT = write_fort90(OUTPUTS,GRID,MODEL,INITIAL,TIME_INTEGRATION,BASIC);
nproc = 1;
-% MAKE = 'cd ..; make; cd wk';
-% system(MAKE);
+MAKE = 'cd ..; make; cd wk';
+system(MAKE);
%%
disp(['Set up ',SIMID]);
disp([resolution,gridname,degngrad]);
diff --git a/matlab/write_fort90.m b/matlab/write_fort90.m
index ed9b721d09c438e4dc578d75f634ba614beac0dc..97dc7b07f807c87d91470109e2bcf21e01e4f196 100644
--- a/matlab/write_fort90.m
+++ b/matlab/write_fort90.m
@@ -35,6 +35,8 @@ fprintf(fid,[' write_phi = ', OUTPUTS.write_phi,'\n']);
fprintf(fid,[' write_Na00 = ', OUTPUTS.write_Na00,'\n']);
fprintf(fid,[' write_Napj = ', OUTPUTS.write_Napj,'\n']);
fprintf(fid,[' write_Sapj = ', OUTPUTS.write_Sapj,'\n']);
+fprintf(fid,[' write_dens = ', OUTPUTS.write_dens,'\n']);
+fprintf(fid,[' write_temp = ', OUTPUTS.write_temp,'\n']);
fprintf(fid,[' resfile0 = ', OUTPUTS.resfile0,'\n']);
fprintf(fid,[' rstfile0 = ', OUTPUTS.rstfile0,'\n']);
fprintf(fid,[' job2load = ', num2str(OUTPUTS.job2load),'\n']);
diff --git a/wk/analysis_2D.m b/wk/analysis_2D.m
index ee087aa66a141d78d88500acac76412b78239509..6eebb675dd4de2161d381a755f8ec9be83573389 100644
--- a/wk/analysis_2D.m
+++ b/wk/analysis_2D.m
@@ -5,18 +5,17 @@ if 1 % Local results
outfile ='';
outfile ='';
outfile ='';
-outfile ='kobayashi/100x50_L_50_P_4_J_2_eta_0.71429_nu_5e-03_DGGK_CLOS_0_mu_1e-02';
-% outfile ='kobayashi/100x50_L_50_P_4_J_2_eta_0.71429_nu_5e-03_SGGK_CLOS_0_mu_1e-02';
-% outfile ='v2.6_P_6_J_3/200x100_L_120_P_6_J_3_eta_0.5_nu_1e-01_DGGK_CLOS_0_mu_2e-02';
-
+outfile ='test_diagnostics/100x50_L_50_P_2_J_1_eta_0.5_nu_5e-03_DGGK_CLOS_0_mu_1e-02';
BASIC.RESDIR = ['../results/',outfile,'/'];
BASIC.MISCDIR = ['../results/',outfile,'/'];
end
if 0 % Marconi results
outfile ='';
outfile ='';
-outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/kobayashi/100x50_L_50_P_6_J_3_eta_0.71429_nu_5e-03_DGGK_CLOS_0_mu_1e-02/out.txt';
-% outfile =['/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_',num2str(ETA_),'_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt'];
+outfile ='';
+outfile ='';
+% outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.7_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt';
+% outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt';
% load_marconi(outfile);
BASIC.RESDIR = ['../',outfile(46:end-8),'/'];
BASIC.MISCDIR = ['/misc/HeLaZ_outputs/',outfile(46:end-8),'/'];
@@ -24,7 +23,7 @@ end
%%
% JOBNUM = 1; load_results;
-JOBNUMMAX = 0; compile_results %Compile the results from first output found to JOBNUMMAX if existing
+JOBNUMMAX = 20; compile_results %Compile the results from first output found to JOBNUMMAX if existing
%% Retrieving max polynomial degree and sampling info
Npe = numel(Pe); Nje = numel(Je); [JE,PE] = meshgrid(Je,Pe);
@@ -60,16 +59,26 @@ dzni00 = zeros(Nr,Nz,Ns2D);
np_i = zeros(Nr,Nz,Ns5D); % Ion particle density
si00 = zeros(Nr,Nz,Ns5D);
phi = zeros(Nr,Nz,Ns2D);
+dens_e = zeros(Nr,Nz,Ns2D);
+dens_i = zeros(Nr,Nz,Ns2D);
+temp_e = zeros(Nr,Nz,Ns2D);
+temp_i = zeros(Nr,Nz,Ns2D);
drphi = zeros(Nr,Nz,Ns2D);
dzphi = zeros(Nr,Nz,Ns2D);
dr2phi = zeros(Nr,Nz,Ns2D);
for it = 1:numel(Ts2D)
NE_ = Ne00(:,:,it); NI_ = Ni00(:,:,it); PH_ = PHI(:,:,it);
- ne00(:,:,it) = real(fftshift(ifft2((NE_),Nr,Nz)));
- ni00(:,:,it) = real(fftshift(ifft2((NI_),Nr,Nz)));
- dzni00(:,:,it) = real(fftshift(ifft2(1i*KZ.*(NI_),Nr,Nz)));
- phi (:,:,it) = real(fftshift(ifft2((PH_),Nr,Nz)));
+ DENS_E_ = DENS_E(:,:,it); DENS_I_ = DENS_I(:,:,it);
+ TEMP_E_ = TEMP_E(:,:,it); TEMP_I_ = TEMP_I(:,:,it);
+ ne00(:,:,it) = real(fftshift(ifft2((NE_),Nr,Nz)));
+ ni00(:,:,it) = real(fftshift(ifft2((NI_),Nr,Nz)));
+ dzni00(:,:,it) = real(fftshift(ifft2(1i*KZ.*(NI_),Nr,Nz)));
+ phi (:,:,it) = real(fftshift(ifft2((PH_),Nr,Nz)));
+ dens_e (:,:,it) = real(fftshift(ifft2((DENS_E_),Nr,Nz)));
+ dens_i (:,:,it) = real(fftshift(ifft2((DENS_I_),Nr,Nz)));
+ temp_e (:,:,it) = real(fftshift(ifft2((TEMP_E_),Nr,Nz)));
+ temp_i (:,:,it) = real(fftshift(ifft2((TEMP_I_),Nr,Nz)));
drphi(:,:,it) = real(fftshift(ifft2(1i*KR.*(PH_),Nr,Nz)));
dr2phi(:,:,it)= real(fftshift(ifft2(-KR.^2.*(PH_),Nr,Nz)));
dzphi(:,:,it) = real(fftshift(ifft2(1i*KZ.*(PH_),Nr,Nz)));
@@ -329,7 +338,7 @@ fig = figure; FIGNAME = ['space_time','_',PARAMS];set(gcf, 'Position', [100, 10
save_figure
end
-if 1
+if 0
%% Averaged shear and Reynold stress profiles
figure;
plt = @(x) squeeze(mean(mean(real(x(:,:,its2D:ite2D)),2),3))/max(abs(squeeze(mean(mean(real(x(:,:,its2D:ite2D)),2),3))));
@@ -340,8 +349,37 @@ plot(r,plt(-drphi.*dzphi-drphi.*dzni00),'--','DisplayName','$\Pi_\phi+\Pi_{ni00}
xlim([-60,60]); xlabel('$r/\rho_s$');
end
+if 0
+%% |phi_k|^2 spectra (Kobayashi 2015 fig 3)
+tstart = 500; tend = 5000;
+[~,itstart] = min(abs(Ts2D-tstart));
+[~,itend] = min(abs(Ts2D-tend));
+trange = itstart:itend;
+%full kperp points
+phi_k_2 = reshape(mean((abs(PHI(:,:,trange))).^2,3),[numel(KR),1]);
+kperp = reshape(sqrt(KR.^2+KZ.^2),[numel(KR),1]);
+%interpolated kperps
+nk_noAA = floor(2/3*numel(kr));
+kp_ip = kr(1:nk_noAA);
+[thg, rg] = meshgrid(linspace(-pi/2,pi/2,2*nk_noAA),kp_ip);
+[xn,yn] = pol2cart(thg,rg);
+[xc,yc] = meshgrid(sort(kz),kr);
+Z_rth = interp2(xc,yc,mean((abs(PHI(:,:,trange))).^2,3),xn,yn);
+z_k = mean(Z_rth,2);
+%for theorical trends
+kp_1d = linspace(0.1,5,100);
+figure;
+scatter(kperp,phi_k_2,'.'); hold on; grid on;
+plot(kp_ip,z_k);
+plot(kp_1d,1e4*kp_1d.^(-13/3));
+plot(kp_1d,1e4*kp_1d.^(-3)./(1+kp_1d.^2).^2);
+set(gca, 'XScale', 'log');set(gca, 'YScale', 'log');
+xlabel('$k_\perp \rho_s$'); ylabel('$|\phi_k|^2$');
+xlim([0.1,10]);
+end
+
%%
-t0 = 00;
+t0 = 000;
[~, it02D] = min(abs(Ts2D-t0));
[~, it05D] = min(abs(Ts5D-t0));
skip_ = 1;
@@ -350,18 +388,34 @@ FRAMES_2D = it02D:skip_:numel(Ts2D);
FRAMES_5D = it05D:skip_:numel(Ts5D);
%% GIFS %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if 0
-%% Density ion
+%% part density ion
GIFNAME = ['ni',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
-FIELD = real(ni00); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
+FIELD = real(dens_i); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
FIELDNAME = '$n_i$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
% create_gif
create_mov
end
if 0
-%% Density electrons
-GIFNAME = ['ne',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
+%% part temperature ion
+GIFNAME = ['Ti',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
+FIELD = real(temp_i); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
+FIELDNAME = '$T_i$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
+% create_gif
+create_mov
+end
+if 0
+%% GC Density ion
+GIFNAME = ['ni00',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
+FIELD = real(ni00); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
+FIELDNAME = '$n_i^{00}$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
+% create_gif
+create_mov
+end
+if 0
+%% GC Density electrons
+GIFNAME = ['ne00',sprintf('_%.2d',JOBNUM),'_',PARAMS]; INTERP = 0;
FIELD = real(ne00); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
-FIELDNAME = '$n_e$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
+FIELDNAME = '$n_e^{00}$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
% create_gif
create_mov
end
diff --git a/wk/linear_study.m b/wk/linear_study.m
index 671fa975bddd50a377bd8dfd1ce34ab4c190c37d..5885586127607258e999f38d51f7429a39b8af86 100644
--- a/wk/linear_study.m
+++ b/wk/linear_study.m
@@ -18,8 +18,8 @@ NU_HYP = 0.0; % Hyperdiffusivity coefficient
LAMBDAD = 0.0;
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
-N = 66; % Frequency gridpoints (Nkr = N/2)
-L = 150; % Size of the squared frequency domain
+N = 100; % Frequency gridpoints (Nkr = N/2)
+L = 100; % Size of the squared frequency domain
KREQ0 = 1; % put kr = 0
MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
diff --git a/wk/load_multiple_outputs_marconi.m b/wk/load_multiple_outputs_marconi.m
index 16b333b5f8297bb31bc7776e944c38368b123343..0c7c81ea1bc891dec07de5b14676a8ba96333bdc 100644
--- a/wk/load_multiple_outputs_marconi.m
+++ b/wk/load_multiple_outputs_marconi.m
@@ -1,7 +1,8 @@
addpath(genpath('../matlab')) % ... add
%% Paste the list of simulation results to load
-load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.5_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.7_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.8_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.9_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.5_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt')
+load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/kobayashi/100x50_L_50_P_10_J_5_eta_0.71429_nu_5e-03_DGGK_CLOS_0_mu_1e-02/out.txt')
diff --git a/wk/local_run.m b/wk/local_run.m
index 8d3c7ac35a2cc058fe605cbd8fe63531bc2a65fa..7d099685f584cb6f85498a335fdcde0a47d48d8d 100644
--- a/wk/local_run.m
+++ b/wk/local_run.m
@@ -5,19 +5,19 @@ CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 5.0e-3; % Collision frequency
-ETAB = 1/1.4; % Magnetic gradient
+ETAB = 0.5;%1/1.4; % Magnetic gradient
ETAN = 1.0; % Density gradient
NU_HYP = 1.0;
%% GRID PARAMETERS
N = 100; % Frequency gridpoints (Nkr = N/2)
L = 50; % Size of the squared frequency domain
-P = 4;
-J = 2;
+P = 2;
+J = 1;
MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARAMETERS
-TMAX = 2000; % Maximal time unit
-DT = 1e-2; % Time step
+TMAX = 500; % Maximal time unit
+DT = 2e-2; % Time step
SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1; % Sampling per time unit for 2D arrays
SPS5D = 1/50; % Sampling per time unit for 5D arrays
@@ -27,12 +27,12 @@ JOB2LOAD= 0;
%% OPTIONS AND NAMING
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Full Couloumb ; +/- for GK/DK)
-CO = 2;
+CO =1;
CLOS = 0; % Closure model (0: =0 truncation)
NL_CLOS = -1; % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
-% SIMID = 'test'; % Name of the simulation
-SIMID = 'kobayashi'; % Name of the simulation
-% SIMID = ['v2.6_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
+SIMID = 'test_diagnostics'; % Name of the simulation
+% SIMID = 'kobayashi'; % Name of the simulation
+% SIMID = ['v2.7_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
NON_LIN = 1; % activate non-linearity (is cancelled if KREQ0 = 1)
INIT_ZF = 0; ZF_AMP = 0.0;
%% OUTPUTS
@@ -42,6 +42,8 @@ W_PHI = 1;
W_NA00 = 1;
W_NAPJ = 1;
W_SAPJ = 0;
+W_DENS = 1;
+W_TEMP = 1;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% unused
diff --git a/wk/marconi_run.m b/wk/marconi_run.m
index 92dda8fe6122e835b5660acec9b2dc3a193138bb..eab3af94e0a1a4a21fc3aed82936a24ac2b88140 100644
--- a/wk/marconi_run.m
+++ b/wk/marconi_run.m
@@ -1,9 +1,9 @@
clear all;
addpath(genpath('../matlab')) % ... add
-SUBMIT = 0; % To submit the job automatically
+SUBMIT = 1; % To submit the job automatically
% EXECNAME = 'helaz_dbg';
- EXECNAME = 'helaz_2.62';
-for ETAB = [0.5]
+ EXECNAME = 'helaz_2.71';
+for ETAB = [0.6]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -28,22 +28,22 @@ INIT_ZF = 0; ZF_AMP = 0.0;
N = 200; % Frequency gridpoints (Nkr = N/2)
L = 120; % Size of the squared frequency domain
P = 10; % Electron and Ion highest Hermite polynomial degree
-J = 05; % Electron and Ion highest Laguerre polynomial degree
+J = 5; % Electron and Ion highest Laguerre polynomial degree
MU_P = 0.0;% Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0.0;% Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARAMETERS
-TMAX = 10000; % Maximal time unit
-DT = 1e-3; % Time step
+TMAX = 5000; % Maximal time unit
+DT = 1e-5; % Time step
SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1/4; % Sampling per time unit for 2D arrays
SPS5D = 1/100; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints
-RESTART = 1; % To restart from last checkpoint
+RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 0;
%% Naming
% SIMID = 'kobayashi'; % Name of the simulation
% SIMID = 'test'; % Name of the simulation
-SIMID = ['v2.6_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
+SIMID = ['v2.7_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
PREFIX =[];
% PREFIX = sprintf('%d_%d_',NP_P, NP_KR);
%% Options
diff --git a/wk/open_figure_script.m b/wk/open_figure_script.m
index c69ae0c029dd87801dcffa4cc5ab0e2a61a10bf6..947dcf31ba1b5f4b907bcc3290f202d63811350f 100644
--- a/wk/open_figure_script.m
+++ b/wk/open_figure_script.m
@@ -2,16 +2,15 @@ simname_ = '';
fname_='';
%% Marconi output file
% fname_='';
-% fname_='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-02/out.txt';
-fname_='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_6_J_3/200x100_L_120_P_6_J_3_eta_0.7_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt';
+% fname_='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt';
+fname_='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/v2.6_P_6_J_3/200x100_L_120_P_6_J_3_eta_0.6_nu_1e-03_DGGK_CLOS_0_mu_2e-02/out.txt';
simname_ = fname_(54:end-8);
%%
-simname_ = '';
-simname_ = '';
-simname_ = '';
-simname_ = '';
-simname_ = 'kobayashi/100x50_L_50_P_2_J_1_eta_0.71429_nu_5e-03_DGGK_CLOS_0_mu_1e-02';
+% simname_ = '';
+% simname_ = '';
+% simname_ = '';
+% simname_ = 'v2.7_P_4_J_2/100x50_L_50_P_4_J_2_eta_0.7_nu_5e-02_DGGK_CLOS_0_mu_1e-02';
% simname_ = 'v2.6_P_2_J_1/200x100_L_120_P_2_J_1_eta_0.6_nu_1e-02_SGGK_CLOS_0_mu_1e-01';
% simname_ = 'v2.5_P_10_J_5/200x100_L_120_P_10_J_5_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-02';
@@ -21,9 +20,9 @@ simname_ = 'kobayashi/100x50_L_50_P_2_J_1_eta_0.71429_nu_5e-03_DGGK_CLOS_0_mu_1e
%%
-figname_ = '/fig/ZF_transport_drphi_';
+% figname_ = '/fig/ZF_transport_drphi_';
% figname_ = '/fig/space_time_';
-% figname_ = '/fig/phi_shear_phase_space_';
+figname_ = '/fig/phi_shear_phase_space_';
path_ = '../results/';
diff --git a/wk/transport_results_2_6.m b/wk/transport_results_2_6.m
index 47e78c83ad20133d8d3e16ede258488b725edb21..b329b17403c51339512d9d3c488628eac2396157 100644
--- a/wk/transport_results_2_6.m
+++ b/wk/transport_results_2_6.m
@@ -1,156 +1,146 @@
default_plots_options
%% nuDGGK = 0.1
figure; set(gcf, 'Position', [100, 100, 1200, 350])
-% 6,3 nuDGGK=1.0
-eta = [0.5,0.6,0.7,0.8];
-gamma = [32.6443 3.6895 0.3744 0.056];
-std_g = [6.1529 0.7986 0.0493 0.0134];
+% 6,3 nuDGGK=0.1
+eta = [0.5,0.6,0.7];
+gamma = [116 24.396 3.684];
+std_g = [23 3 0.4];
subplot(121)
-errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=1.0$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(1,:)); hold on;
+errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=0.1$',...
+ 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(6,:)); hold on;
subplot(122)
-% 10,5 nuDGGK = 1.0
-eta = [0.5 0.6,0.7,0.8];
-gamma = [32.6 3.5546 0.3917 0.0500];
-std_g = [7.7 0.5846 0.0486 0.0088];
-shear = [1.8505 0.60866 0.048249];
-std_s = [0.1599 0.00614 0.0061403];
+% 10,5 nuDGGK = 0.1
+eta = [0.5 0.6,0.7];
+gamma = [110 24.9 4.1];
+std_g = [23 4 0.38];
+shear = [4.6 4.0 1.35];
+std_s = [0.5 0.41 0.12];
subplot(121)
-errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=1.0$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(2,:)); hold on;
+errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.1$',...
+ 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(6,:)); hold on;
subplot(122)
-errorbar(eta(2:end),shear,std_s,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=1.0$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(2,:)); hold on;
+errorbar(eta,shear,std_s,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.1$',...
+ 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(6,:)); hold on;
-% 12,6 nuDGGK = 1.0
-eta = [0.6];
-gamma = [4.064];
-std_g = [0.7964];
+kmax = [0.576 0.5236 0.314];
+gmax = [0.305 0.20 0.06];
subplot(121)
-errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=12,06$, $\nu_{DGGK}=1.0$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(3,:)); hold on;
-subplot(122)
-
-
% Mix len Ricci 2006
-subplot(121)
semilogy([0.5 1.0],[10 1e-1],'--','color',[0,0,0]+0.6, 'DisplayName','Mix. Length');
+% Bohm transport :
+btransp = gmax./kmax.^2;
+semilogy(.5:.1:.7,btransp','--','color',[0.4,0,0]+0.6, 'DisplayName','$\gamma/k^2$');
set(gca, 'YScale', 'log'); grid on; legend('show')
xlabel('$L_n/R$'); ylabel('$\Gamma^\infty_{part}$')
subplot(122)
-grate = [0.2131 0.106 0.02021];
-semilogy([0.6 0.7 0.8],grate,'--','color',[0,0,0]+0.6, 'DisplayName','Lin. Max Growth');
+semilogy([0.5 0.6 0.7],gmax,'--','color',[0,0,0]+0.6, 'DisplayName','Lin. Max Growth');
set(gca, 'YScale', 'log'); grid on; legend('show')
xlabel('$L_n/R$'); ylabel('$V_E$''')
-%% nuDGGK = 0.5
+%% nuDGGK = 0.01
figure; set(gcf, 'Position', [100, 100, 1200, 350])
-% 6,3 nuDGGK=0.5
+% 6,3 nuDGGK=0.01
eta = [0.5,0.6,0.7,0.8];
-gamma = [20.511 2.6292 0.2353 0.057];
-std_g = [3.67 1.2 0.055 0.004];
-shear = [nan 1.7417 0.57345 0.25155];
-std_s = [nan 0.35991 0.041 0.00913];
+gamma = [30.2 4.3 0.37 0.06];
+std_g = [4 0.7 0.05 0.008];
+shear = [5.0 2.0 0.6 0.16];
+std_s = [0.37 0.17 0.03 0.012];
subplot(121)
-errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=0.5$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(4,:)); hold on;
+errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=0.01$',...
+ 'LineWidth',2.0,'MarkerSize',5, 'Color', 'b'); hold on;
subplot(122)
-errorbar(eta,shear,std_s,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=0.5$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(4,:)); hold on;
+errorbar(eta,shear,std_s,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=0.01$',...
+ 'LineWidth',2.0,'MarkerSize',5, 'Color', 'b'); hold on;
-% 10,5 nuDGGK=0.5
-eta = [0.6,0.7,0.8 0.9];
-gamma = [2.4949 0.23368 0.057792 0.023572];
-std_g = [0.8696 0.085267 0.0060463 0.0046137];
-shear = [1.7094 0.55278 0.2054 0.085678];
-std_s = [0.2428 0.068223 0.012734 0.012291];
-subplot(121)
-errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.5$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(5,:)); hold on;
-subplot(122)
-errorbar(eta,shear,std_s,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.5$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(5,:)); hold on;
+% % 10,5 nuDGGK=0.01
+% eta = [0.6,0.7,0.8 0.9];
+% gamma = [2.4949 0.23368 0.057792 0.023572];
+% std_g = [0.8696 0.085267 0.0060463 0.0046137];
+% shear = [1.7094 0.55278 0.2054 0.085678];
+% std_s = [0.2428 0.068223 0.012734 0.012291];
+% subplot(121)
+% errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.5$',...
+% 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(5,:)); hold on;
+% subplot(122)
+% errorbar(eta,shear,std_s,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.5$',...
+% 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(5,:)); hold on;
-% Mix len Ricci 2006
+kmax = [0.733 0.63 0.52 0.47];
+gmax = [0.32 0.22 0.11 0.027];
subplot(121)
+% Mix len Ricci 2006
semilogy([0.5 1.0],[10 1e-1],'--','color',[0,0,0]+0.6, 'DisplayName','Mix. Length');
+% Bohm transport :
+btransp = gmax./kmax.^2;
+semilogy(.5:.1:.8,btransp','--','color',[0.4,0,0]+0.6, 'DisplayName','$\gamma/k^2$');
set(gca, 'YScale', 'log'); grid on; legend('show')
xlabel('$L_n/R$'); ylabel('$\Gamma^\infty_{part}$')
subplot(122)
-grate = [0.2194 0.129 0.05084 0.01346];
-semilogy([0.6 0.7 0.8 0.9],grate,'--','color',[0,0,0]+0.6, 'DisplayName','Lin. Max Growth');
+semilogy([0.5:0.1:0.8],gmax,'--','color',[0,0,0]+0.6, 'DisplayName','Lin. Max Growth');
set(gca, 'YScale', 'log'); grid on; legend('show')
xlabel('$L_n/R$'); ylabel('$V_E$''')
-%% nuDGGK = 0.1
+%% nuDGGK = 0.001
figure; set(gcf, 'Position', [100, 100, 1200, 350])
% 6,3
-eta = [0.6 0.7 0.8];
-gamma = [0.24321 0.085 0.0367];
-std_g = [0.295 0.05 0.0023];
-gbmax = [1.0 0.21 0.0367];
-gbmin = [0.02 0.04 0.0367];
-% errorbar(eta,gamma,std_,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=0.1$',...
-% 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(6,:)); hold on;
+eta = [0.6 0.7 0.8 0.9];
+gamma = [0.26 0.088 0.042 0.0156];
+std_g = [0.4 0.06 0.003 0.0014];
+gbmax = [1.2 0.33 0.042 0.0156];
+gbmin = [0.015 0.035 0.003 0.0156];
+shear = [0.75 0.55 0.34 0.19];
+std_s = [0.33 0.12 0.012];
+sbmax = [1.4 0.796 0.34 0.19];
+sbmin = [0.4 0.4 0.34 0.19];
+
subplot(121)
-plot(eta,gamma,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.1$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(6,:)); hold on;
-plot(eta,gbmax,'-.','DisplayName',' ','Color',line_colors(6,:)); hold on;
-plot(eta,gbmin,'-.','DisplayName',' ','Color',line_colors(6,:)); hold on;
+plot(eta,gamma,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=0.001$',...
+ 'LineWidth',2.0,'MarkerSize',5, 'Color', 'k'); hold on;
+subplot(122)
+plot(eta,shear,'-','DisplayName','$P,J=06,03$, $\nu_{DGGK}=0.001$',...
+ 'LineWidth',2.0,'MarkerSize',5, 'Color', 'k'); hold on;
% 10,5
-eta = [0.5 0.6 0.7 0.8 0.9];
-gamma = [12.2 0.19761 0.088 0.04253 0.026037];
-std_g = [4.7 0.21328 0.065 0.009 0.00118];
-gbmax = [12.2 0.8 0.25 0.04253 0.026037];
-gbmin = [12.2 0.02 0.03 0.04253 0.026037];
-shear = [0.65361 0.46548 0.30645 0.21123 ];
-std_s = [0.21288 0.10233 0.02886 0.0044664 ];
-sbmax = [1 0.7 0.30645 0.21123 ];
-sbmin = [0.4 0.35 0.30645 0.21123 ];
+% eta = [0.5 0.6 0.7 0.8 0.9];
+% gamma = [12.2 0.19761 0.088 0.04253 0.026037];
+% std_g = [4.7 0.21328 0.065 0.009 0.00118];
+% gbmax = [12.2 0.8 0.25 0.04253 0.026037];
+% gbmin = [12.2 0.02 0.03 0.04253 0.026037];
+% shear = [0.65361 0.46548 0.30645 0.21123 ];
+% std_s = [0.21288 0.10233 0.02886 0.0044664 ];
+% sbmax = [1 0.7 0.30645 0.21123 ];
+% sbmin = [0.4 0.35 0.30645 0.21123 ];
% errorbar(eta,gamma,std_,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.1$',...
% 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(7,:)); hold on;
-subplot(121)
-plot(eta,gamma,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.1$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(7,:)); hold on;
-plot(eta,gbmax,'-.','DisplayName',' ','Color',line_colors(7,:)); hold on;
-plot(eta,gbmin,'-.','DisplayName',' ','Color',line_colors(7,:)); hold on;
-subplot(122)
-plot(eta(2:end),shear,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.1$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(7,:)); hold on;
-plot(eta(2:end),sbmax,'-.','DisplayName',' ','Color',line_colors(7,:)); hold on;
-plot(eta(2:end),sbmin,'-.','DisplayName',' ','Color',line_colors(7,:)); hold on;
+% subplot(121)
+% plot(eta,gamma,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.1$',...
+% 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(7,:)); hold on;
+% plot(eta,gbmax,'-.','DisplayName',' ','Color',line_colors(7,:)); hold on;
+% plot(eta,gbmin,'-.','DisplayName',' ','Color',line_colors(7,:)); hold on;
+% subplot(122)
+% plot(eta(2:end),shear,'-','DisplayName','$P,J=10,05$, $\nu_{DGGK}=0.1$',...
+% 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(7,:)); hold on;
+% plot(eta(2:end),sbmax,'-.','DisplayName',' ','Color',line_colors(7,:)); hold on;
+% plot(eta(2:end),sbmin,'-.','DisplayName',' ','Color',line_colors(7,:)); hold on;
-% Mix len Ricci 2006
+kmax = [0.27 0.68 0.52 0.31];
+gmax = [0.838 0.195 0.109 0.029];
subplot(121)
+% Mix len Ricci 2006
semilogy([0.5 1.0],[10 1e-1],'--','color',[0,0,0]+0.6, 'DisplayName','Mix. Length');
+% Bohm transport :
+btransp = gmax./kmax.^2;
+semilogy(.6:.1:.9,btransp','--','color',[0.4,0,0]+0.6, 'DisplayName','$\gamma/k^2$');
set(gca, 'YScale', 'log'); grid on; legend('show')
xlabel('$L_n/R$'); ylabel('$\Gamma^\infty_{part}$')
subplot(122)
-grate = [0.236 0.174 0.112 0.053];
-semilogy([0.6 0.7 0.8 0.9],grate,'--','color',[0,0,0]+0.6, 'DisplayName','Lin. Max Growth');
+semilogy([.6:.1:.9],gmax,'--','color',[0,0,0]+0.6, 'DisplayName','Lin. Max Growth');
set(gca, 'YScale', 'log'); grid on; legend('show')
xlabel('$L_n/R$'); ylabel('$V_E$''')
-
-%% nuSGGK = 1.0
-figure
-% 6,3 nuDGGK=1.0
-eta = [0.5 0.6,0.7,0.8];
-gamma = [2.3 0.2215 0.0133 0.0032];
-std_g = [3.1 0.22 0.0019 0.0006];
-errorbar(eta,gamma,std_g,'-','DisplayName','$P,J=06,03$, $\nu_{SGGK}=1.0$',...
- 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(8,:)); hold on;
-
-
-% 10,5 nuDGGK = 1.0
-eta = [0.5 0.6,0.7,0.8];
-gamma = [10 0.319 0.009 0.0026];
-std_g = [1.34 0.228 0.001 0.001];
-% errorbar(eta,gamma,err,'-.','DisplayName','$P,J=10,5$, $\nu_{SGGK}=1.0$',...
-% 'LineWidth',2.0,'MarkerSize',5, 'Color', line_colors(1,:)); hold on;
-
-% Mix len Ricci 2006
-semilogy([0.5 1.0],[10 1e-1],'--','color',[0,0,0]+0.6, 'DisplayName','Mix. Length');
-set(gca, 'YScale', 'log'); grid on; legend('show')
-xlabel('$L_n/R$'); ylabel('$\Gamma^\infty_{part}$')
+subplot(121)
+plot(eta,gbmax,'-.','DisplayName',' ','Color','k'); hold on;
+plot(eta,gbmin,'-.','DisplayName',' ','Color','k'); hold on;
+subplot(122)
+plot(eta,sbmax,'-.','DisplayName',' ','Color','k'); hold on;
+plot(eta,sbmin,'-.','DisplayName',' ','Color','k'); hold on;