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Commit 70aca9ca authored by Antoine Cyril David Hoffmann's avatar Antoine Cyril David Hoffmann :seedling:
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matlab/evolve_tracers.m
+ 13
− 9
View file @ 70aca9ca
% Options
SHOW_FILM = 0;
SHOW_FILM = 1;
field2plot ='phi';
INIT = 'lin'; % lin (for a line)/ round (for a small round)/ gauss for random
U_TIME = 1000; % >0 for frozen velocity at a given time, -1 for evolving field
Evolve_U = 1; % 0 for frozen velocity at a given time, 1 for evolving field
Tfin = 100;
Tfin = 500;
dt_ = 0.1;
Nstep = ceil(Tfin/dt_);
% Init tracers
......@@ -181,8 +181,7 @@ while(t_<Tfin && it <= Nstep)
u___ = linterp(u__0,u__1,a__i);
% push the particle
% q = sign(-u___(3));
q = 1;%-u___(3);
q = sign(-u___(3));
% q =1;
x_ = x_ + dt_*u___(1)*q;
y_ = y_ + dt_*u___(2)*q;
......@@ -224,19 +223,20 @@ while(t_<Tfin && it <= Nstep)
end
scale = max(max(abs(F2P))); % Scaling to normalize
pclr = pcolor(XX_,YY_,F2P/scale);
caxis([-1 1]); colormap(bluewhitered); colorbar;
caxis([-1 1]); colormap(bluewhitered); %colorbar;
set(pclr, 'edgecolor','none'); hold on; caxis([-1+dimmed,1+dimmed]); shading interp
for ip = 1:Np
ia0 = max(1,it-Na);
plot(Traj_x(ip,ia0:it),Traj_y(ip,ia0:it),'.','Color',color(ip,:)); hold on
end
for ip = 1:Np
plot(Traj_x(ip, 1),Traj_y(ip, 1),'xk'); hold on
% plot(Traj_x(ip, 1),Traj_y(ip, 1),'xk'); hold on
plot(Traj_x(ip,it),Traj_y(ip,it),'ok','MarkerFaceColor',color(ip,:)); hold on
end
title(['$t \approx$', sprintf('%.3d',ceil(data.Ts3D(itu_)))]);
axis equal
xlim([xmin xmax]); ylim([ymin ymax]);
xlabel('$x/\rho_s$'); ylabel('$y/\rho_s$');
drawnow
% Capture the plot as an image
frame = getframe(fig);
......@@ -303,10 +303,14 @@ xlim(U_TIME + [0 Tfin]);
subplot(222);
itf = floor(Nt/2); %fit end time
% x^2 displacement
plot(time_,mean(xtot.^2,1),'DisplayName','$\langle x.^2\rangle_p$'); hold on
x2tot = mean(xtot.^2,1);
plot(time_-time_(1),x2tot,'DisplayName','$\langle x.^2\rangle_p$'); hold on
fit = polyfit(time_(1:itf),mean(xtot(:,1:itf).^2,1),1);
plot(time_,fit(1)*time_+fit(2),'--k'); hold on
ylabel('$\langle x^2 \rangle_p$');
plot(time_-time_(1),fit(1)*time_+fit(2),'--k'); hold on
% Put a linear growth from the first point to check if it super/sub
% diffusive
% loglog(time_-time_(1),(time_-time_(1))*x2tot(2)/(time_(2)-time_(1)),'--k'); hold on
% ylabel('$\langle x^2 \rangle_p$');
% % y^2 displacement
% fit = polyfit(time_(1:itf),mean(ytot(:,1:itf).^2,1),1);
......
matlab/extract_fig_data.m
+ 5
− 5
View file @ 70aca9ca
......@@ -4,7 +4,7 @@
% tw = [3000 4000];
% tw = [4000 4500];
% tw = [4500 5000];
tw = [500 1000];
tw = [00 5000];
fig = gcf;
axObjs = fig.Children;
......@@ -19,13 +19,13 @@ end
% n1 = numel(X_);
[~,n0] = min(abs(X_-tw(1)));
[~,n1] = min(abs(X_-tw(2)));
mvm = @(x) movmean(x,50);
shift = X_(n0);
mvm = @(x) movmean(x,1);
shift = 0;%X_(n0);
% shift = 0;
skip = 50;
figure;
plot(X_(n0:end),Y_(n0:end));
plot(mvm(X_(n0:n1)-shift),mvm(Y_(n0:n1))); hold on;
plot(mvm(X_(n0:skip:n1)-shift),mvm(Y_(n0:skip:n1))); hold on;
% t0 = ceil(numel(X_)*0.2); t1 = numel(X_);
avg= mean(Y_(n0:n1)); dev = std(Y_(n0:n1));
......
wk/analysis_gene.m
+ 10
− 10
View file @ 70aca9ca
......@@ -12,9 +12,9 @@ addpath(genpath([helazdir,'matlab/load'])) % ... add
% folder = '/misc/gene_results/shearless_cyclone/s_alpha_output_0.5/';
% 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/HP_fig_2a_mu_1e-2/';
% folder = '/misc/gene_results/HP_fig_2b_mu_5e-2/';
% folder = '/misc/gene_results/HP_fig_2c_mu_5e-2/';
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_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/';
......@@ -29,7 +29,7 @@ addpath(genpath([helazdir,'matlab/load'])) % ... add
% folder = '/misc/gene_results/CBC/KT_13_large_box_128x64x16x24x12/';
% folder = '/misc/gene_results/CBC/Lapillone_Fig6/';
% folder = '/misc/gene_results/Z-pinch/HP_kN_1.6_adapt_mu_01/';
folder = '/misc/gene_results/miller/';
% folder = '/misc/gene_results/miller/';
gene_data = load_gene_data(folder);
gene_data = invert_kxky_to_kykx_gene_results(gene_data);
if 1
......@@ -76,9 +76,9 @@ if 0
% Options
options.INTERP = 1;
options.POLARPLOT = 0;
options.NAME = '\phi';
% options.NAME = '\phi';
% options.NAME = 'v_y';
% options.NAME = 'n_i^{NZ}';
options.NAME = 'n_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
options.PLAN = 'xy';
......@@ -131,15 +131,15 @@ end
if 0
%% Time averaged spectrum
options.TIME = 300:600;
options.TIME = [4000 8000];
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;
options.COMPXY = 'zero';
options.COMPXY = 'avg'; % avg/sum/max/zero/ 2D plot otherwise
options.COMPT = 'avg';
options.PLOT = 'semilogy';
fig = spectrum_1D(gene_data,options);
......
wk/analysis_gyacomo.m
+ 5
− 5
View file @ 70aca9ca
......@@ -34,7 +34,7 @@ disp([num2str(data.NU_EVOL(i_)),' ',num2str(data.NU_EVOL(i_+1))])
options.TAVG_0 = data.TJOB_SE(i_);%0.4*data.Ts3D(end);
options.TAVG_1 = data.TJOB_SE(i_+1);%0.9*data.Ts3D(end); % Averaging times duration
options.NCUT = 4; % Number of cuts for averaging and error estimation
options.NMVA = 1; % Moving average for time traces
options.NMVA = 100; % Moving average for time traces
% options.ST_FIELD = '\Gamma_x'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
options.ST_FIELD = '\phi'; % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
options.INTERP = 0;
......@@ -59,13 +59,13 @@ if 0
% Options
options.INTERP = 1;
options.POLARPLOT = 0;
options.NAME = '\phi';
% options.NAME = '\phi';
% options.NAME = '\omega_z';
% options.NAME = 'N_i^{00}';
% options.NAME = 'v_y';
% options.NAME = 'n_i^{NZ}';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
options.NAME = 'n_i';
options.PLAN = 'xy';
% options.NAME = 'f_i';
% options.PLAN = 'sx';
......@@ -154,9 +154,9 @@ if 0
%% Time averaged spectrum
options.TIME = [2000 3000];
options.NORM =1;
options.NAME = '\phi';
% options.NAME = '\phi';
% options.NAME = 'N_i^{00}';
% options.NAME ='\Gamma_x';
options.NAME ='\Gamma_x';
options.PLAN = 'kxky';
options.COMPZ = 'avg';
options.OK = 0;
......
wk/header_2DZP_results.m
+ 17
− 2
View file @ 70aca9ca
......@@ -200,10 +200,25 @@ resdir ='';
%% Convergence cases kN = (1.6 2.2) nu = (0.01 1.0)
% resdir = 'Zpinch_rerun/convcoll_Kn_1.6_200x32x3x2_mu_0.01';
% resdir = 'Zpinch_rerun/convcoll_Kn_1.6_200x32x5x3_mu_0.01';
% resdir = 'Zpinch_rerun/convcoll_Kn_1.6_200x32x7x4_mu_0.01';
% resdir = 'Zpinch_rerun/convcoll_Kn_1.6_200x32x9x5_mu_0.01';
% resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x3x2_mu_0.01';
resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x7x4_mu_0.01';
% resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x5x3_mu_0.01';
% resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x7x4_mu_0.01';
resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x9x5_mu_0.01';
JOBNUMMIN = 00; JOBNUMMAX = 10;
% resdir = 'Zpinch_rerun/convcoll_Kn_1.6_200x32x3x2_nu_0.1';
% resdir = 'Zpinch_rerun/convcoll_Kn_1.6_200x32x5x3_nu_0.1';
% resdir = 'Zpinch_rerun/convcoll_Kn_1.6_200x32x7x4_nu_0.1';
% resdir = 'Zpinch_rerun/convcoll_Kn_1.6_200x32x9x5_nu_0.1';
% resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x3x2_nu_0.1';
% resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x5x3_nu_0.1';
% resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x7x4_nu_0.1';
% resdir = 'Zpinch_rerun/convcoll_Kn_2.2_200x32x9x5_nu_0.1';
JOBNUMMIN = 00; JOBNUMMAX = 03;
resdir = ['results/',resdir];
run analysis_gyacomo
\ No newline at end of file
wk/lin_EPY.m
+ 13
− 13
View file @ 70aca9ca
......@@ -4,21 +4,21 @@
% for benchmark and debugging purpose since it makes matlab "busy"
%
SIMID = 'lin_EPY'; % Name of the simulation
SIMID = 'dbg'; % Name of the simulation
RUN = 1; % To run or just to load
% SIMID = 'dbg'; % Name of the simulation
RUN = 0; % To run or just to load
addpath(genpath('../matlab')) % ... add
default_plots_options
PROGDIR = '/home/ahoffman/gyacomo/';
EXECNAME = 'gyacomo_dbg';
% EXECNAME = 'gyacomo';
% EXECNAME = 'gyacomo_dbg';
EXECNAME = 'gyacomo';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 0.01; % Collision frequency
NU = 0.1; % Collision frequency
TAU = 1.0; % e/i temperature ratio
K_Ne = 2.2; % ele Density '''
K_Ne = 1.6; % ele Density '''
K_Te = K_Ne/4; % ele Temperature '''
K_Ni = K_Ne; % ion Density gradient drive
K_Ti = K_Ni/4; % ion Temperature '''
......@@ -33,7 +33,7 @@ JMAXE = J; % Laguerre "
PMAXI = P; % " ions
JMAXI = J; % "
NX = 2; % real space x-gridpoints
NY = 2; % '' y-gridpoints
NY = 100; % '' y-gridpoints
LX = 2*pi/0.8; % Size of the squared frequency domain
LY = 120;%2*pi/0.05; % Size of the squared frequency domain
NZ = 1; % number of perpendicular planes (parallel grid)
......@@ -46,11 +46,11 @@ SHEAR = 0.8; % magnetic shear
NEXC = 1; % To extend Lx if needed (Lx = Nexc/(kymin*shear))
EPS = 0.18; % inverse aspect ratio
%% TIME PARMETERS
TMAX = 200; % Maximal time unit
TMAX = 500; % Maximal time unit
DT = 1e-2; % Time step
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = 0; % Sampling per time unit for 2D arrays
SPS3D = 2; % Sampling per time unit for 2D arrays
SPS3D = 1/5; % Sampling per time unit for 2D arrays
SPS5D = 1/5; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints
JOB2LOAD= -1;
......@@ -111,7 +111,7 @@ data = compile_results(LOCALDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from
if 1
%% linear growth rate (adapted for 2D zpinch and fluxtube)
options.TRANGE = [0.5 1]*data.Ts3D(end);
options.NPLOTS = 1; % 1 for only growth rate and error, 2 for omega local evolution, 3 for plot according to z
options.NPLOTS = 2; % 1 for only growth rate and error, 2 for omega local evolution, 3 for plot according to z
options.GOK = 0; %plot 0: gamma 1: gamma/k 2: gamma^2/k^3
lg = compute_fluxtube_growth_rate(data,options);
[gmax, kmax] = max(lg.g_ky(:,end));
......@@ -157,13 +157,13 @@ options.kzky = 0;
[lg, fig] = compute_3D_zpinch_growth_rate(data,trange,options);
save_figure(data,fig)
end
if 0
if 1
%% Mode evolution
options.NORMALIZED = 0;
options.K2PLOT = 1;
options.K2PLOT = 10;
options.TIME = [0:1000];
options.NMA = 1;
options.NMODES = 1;
options.NMODES = 10;
options.iz = 'avg';
fig = mode_growth_meter(data,options);
save_figure(data,fig,'.png')
......
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