Skip to content
Snippets Groups Projects
Commit 01dcbfc3 authored by Antoine Cyril David Hoffmann's avatar Antoine Cyril David Hoffmann
Browse files

scripts updates

parent 8787f7ea
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
Showing
with 47 additions and 50 deletions
matlab/plots/plot_radial_transport_and_shear.m
+ 6
− 6
View file @ 01dcbfc3
......@@ -15,10 +15,10 @@ shear_infty_std = std (mean(shear_maxx_avgy(:,its2D:ite2D),1));
fig = figure; FIGNAME = ['ZF_transport_drphi','_',PARAMS];set(gcf, 'Position', [100, 100, 1200, 600])
subplot(311)
% yyaxis left
plot(Ts0D,PGAMMA_RI*SCALE,'DisplayName','$\langle n_i d\phi/dz \rangle_z$'); hold on;
plot(Ts0D,PGAMMA_RI*SCALE,'DisplayName','$\langle n_i \partial_y\phi \rangle_y$'); hold on;
plot(Ts0D(its0D:ite0D),ones(ite0D-its0D+1,1)*gamma_infty_avg, '-k',...
'DisplayName',['$\Gamma^{\infty} = $',num2str(gamma_infty_avg),'$\pm$',num2str(gamma_infty_std)]);
grid on; set(gca,'xticklabel',[]); ylabel('$\Gamma_r$')
grid on; set(gca,'xticklabel',[]); ylabel('$\Gamma_x$')
ylim([0,5*abs(gamma_infty_avg)]); xlim([Ts0D(1),Ts0D(end)]);
title(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta=$',num2str(ETAB/ETAN),...
', $L=',num2str(L),'$, $N=',num2str(Nx),'$, $(P,J)=(',num2str(PMAXI),',',num2str(JMAXI),')$,',...
......@@ -29,10 +29,10 @@ fig = figure; FIGNAME = ['ZF_transport_drphi','_',PARAMS];set(gcf, 'Position',
lstyle = line_styles(1);
% plt = @(x_) mean(x_,1);
plt = @(x_) x_(1,:);
plot(Ts3D,plt(shear_maxx_maxy),'DisplayName','$\max_{x,y}(s_\phi)$'); hold on;
plot(Ts3D,plt(shear_maxx_avgy),'DisplayName','$\max_{x}\langle s_\phi\rangle_y$'); hold on;
plot(Ts3D,plt(shear_avgx_maxy),'DisplayName','$\max_{y}\langle s_\phi\rangle_x$'); hold on;
plot(Ts3D,plt(shear_avgx_avgy),'DisplayName','$\langle s_\phi\rangle_{x,y}$'); hold on;
plot(Ts3D,plt(shear_maxx_maxy),'DisplayName','$\max_{x,y}(\partial^2_x\phi)$'); hold on;
plot(Ts3D,plt(shear_maxx_avgy),'DisplayName','$\max_{x}\langle \partial^2_x\phi\rangle_y$'); hold on;
plot(Ts3D,plt(shear_avgx_maxy),'DisplayName','$\max_{y}\langle \partial^2_x\phi\rangle_x$'); hold on;
plot(Ts3D,plt(shear_avgx_avgy),'DisplayName','$\langle \partial^2_x\phi\rangle_{x,y}$'); hold on;
plot(Ts3D(its2D:ite2D),ones(ite2D-its2D+1,1)*shear_infty_avg, '-k',...
'DisplayName',['$s^{\infty} = $',num2str(shear_infty_avg),'$\pm$',num2str(shear_infty_std)]);
ylim([0,shear_infty_avg*5.0]); xlim([Ts0D(1),Ts0D(end)]);
......
matlab/plots/plot_space_time_diagrams.m
+ 3
− 3
View file @ 01dcbfc3
......@@ -4,9 +4,9 @@ trange = itstart:itend;
[TY,TX] = meshgrid(x,Ts3D(trange));
fig = figure; FIGNAME = ['space_time','_',PARAMS];set(gcf, 'Position', [100, 100, 1200, 600])
subplot(211)
% pclr = pcolor(TX,TY,squeeze(mean(dens_i(:,:,trange).*dyphi(:,:,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
pclr = pcolor(TX,TY,squeeze(mean(ni00(:,:,1,trange).*dyphi(:,:,1,trange),2))'); set(pclr, 'edgecolor','none',...
'DisplayName','$\langle n_i\partial_z\phi\rangle_z$'); colorbar;
pclr = pcolor(TX,TY,squeeze(mean(dens_i(:,:,1,trange).*dyphi(:,:,1,trange),2))'); set(pclr, 'edgecolor','none'); colorbar;
% pclr = pcolor(TX,TY,squeeze(mean(ni00(:,:,1,trange).*dyphi(:,:,1,trange),2))'); set(pclr, 'edgecolor','none',...
% 'DisplayName','$\langle n_i\partial_z\phi\rangle_z$'); colorbar;
shading interp
colormap hot;
% caxis([0.0,0.05*max(max(mean(ni00(:,:,its2D:ite2D).*dyphi(:,:,1,its2D:ite2D),2)))]);
......
wk/analysis_3D.m
+ 14
− 9
View file @ 01dcbfc3
......@@ -6,7 +6,13 @@ outfile ='';
outfile ='';
outfile ='';
outfile ='';
outfile ='simulation_A/cw_SGGK_mu_1e-2';
outfile ='';
outfile ='';
outfile ='HD_study/200x100_L_200_P_2_J_1_eta_0.6_nu_1e+00_DGGK_CLOS_0_mu_0e+00';
% outfile ='simulation_B/cw_DGGK'; % to analyse
% outfile ='simulation_B/cw_SGGK_mu_1e-1';
% outfile ='simulation_B/cw_DGGK';
% outfile ='simulation_A/cw_DGGK_eta_0.5';
% outfile ='simulation_A/LBDK_damping_150x75_L_100_P_4_J_2_eta_0.6_nu_1e-01_SGGK_mu_0e+00';
BASIC.RESDIR = ['../results/',outfile,'/'];
BASIC.MISCDIR = ['/misc/HeLaZ_outputs/results/',outfile,'/'];
......@@ -17,15 +23,14 @@ else% Marconi results
outfile ='';
outfile ='';
outfile ='';
outfile ='';
outfile ='';
outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_B/300x150_L_120_P_8_J_4_eta_0.6_nu_5e-01_SGGK_mu_0e+00/out.txt';
BASIC.RESDIR = ['../',outfile(46:end-8),'/'];
BASIC.MISCDIR = ['/misc/HeLaZ_outputs/',outfile(46:end-8),'/'];
end
%% Load the results
% Load outputs from jobnummin up to jobnummax
JOBNUMMIN = 06; JOBNUMMAX = 20;
JOBNUMMIN = 00; JOBNUMMAX = 20;
% JOBNUMMIN = 07; JOBNUMMAX = 20; % For CO damping sim A
compile_results %Compile the results from first output found to JOBNUMMAX if existing
......@@ -44,13 +49,13 @@ end
if 1
%% Space time diagramm (fig 11 Ivanov 2020)
TAVG_0 = 1.4e4; TAVG_1 = 1.5e4; % Averaging times duration
TAVG_0 = 1.2e4; TAVG_1 = 1.3e4; % Averaging times duration
plot_radial_transport_and_shear
end
if 0
%% Space time diagramms
cmax = 0.0001 % max of the colorbar for transport
cmax = 0.00001 % max of the colorbar for transport
tstart = 0; tend = Ts3D(end); % time window
plot_space_time_diagrams
end
......@@ -72,7 +77,7 @@ end
if 0
%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Options
t0 =10950; iz = 1; ix = 1; iy = 1;
t0 =0; iz = 1; ix = 1; iy = 1;
skip_ =1; DELAY = 2e-3*skip_;
[~, it03D] = min(abs(Ts3D-t0)); FRAMES_3D = it03D:skip_:numel(Ts3D);
[~, it05D] = min(abs(Ts5D-t0)); FRAMES_5D = it05D:skip_:numel(Ts5D);
......@@ -88,7 +93,7 @@ INTERP = 0; T = Ts3D; FRAMES = FRAMES_3D;
% FIELD = temp_i-Z_T_i; NAME = 'Ti_NZ';FIELDNAME = 'T_i^{NZ}';
% FIELD = ne00; NAME = 'ne00'; FIELDNAME = 'n_e^{00}';
% FIELD = ni00; NAME = 'ni00'; FIELDNAME = 'n_i^{00}';
% FIELD = phi; NAME = 'phi'; FIELDNAME = '\phi';
FIELD = phi; NAME = 'phi'; FIELDNAME = '\phi';
% FIELD = Gamma_x; NAME = 'Gamma_x'; FIELDNAME = '\Gamma_x';
% Sliced
......@@ -129,7 +134,7 @@ FIELD = phi; FNAME = 'phi'; FIELDLTX = '\phi';
% FIELD = dens_e-Z_n_e-(Z_phi-phi); FNAME = 'Non_adiab_part'; FIELDLTX = 'n_e^{NZ}-\phi^{NZ}';
% Chose when to plot it
tf = 11000:50:11300;
tf = 128:1:133;
% Sliced
ix = 1; iy = 1; iz = 1;
......
wk/continue_multiple_runs_marconi.m
+ 3
− 4
View file @ 01dcbfc3
%% Paste the list of continue_run calls
continue_run('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_7e-02_SGGK_mu_0e+00/out.txt')
continue_run('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_B/300x150_L_120_P_8_J_4_eta_0.6_nu_5e-01_SGGK_mu_0e+00/out.txt')
%% Functions to modify preexisting fort.90 input file and launch on marconi
function [] = continue_run(outfilename)
......@@ -51,7 +50,7 @@ function [] = continue_run(outfilename)
A{39} = [' job2load = ',num2str(J2L)];
disp(A{39})
% Change time step
A{3} = [' dt = 0.005'];
A{3} = [' dt = 0.01'];
% Increase endtime
A{4} = [' tmax = 20000'];
% Change collision operator
......@@ -63,7 +62,7 @@ function [] = continue_run(outfilename)
% change HD
line_= A{47};
mu_old = str2num(line_(13:end));
A{47} = [' mu = ',num2str(mu_old)];
A{47} = [' mu = ',num2str(0)];
% change L
line_= A{14};
L_old = str2num(line_(12:end));
......
wk/linear_study.m
+ 5
− 5
View file @ 01dcbfc3
for CO = [1]
for CO = [2]
RUN = 1; % To run or just to load
addpath(genpath('../matlab')) % ... add
default_plots_options
......@@ -7,12 +7,12 @@ default_plots_options
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 1.0; % Collision frequency
NU = 0.1; % Collision frequency
TAU = 1.0; % e/i temperature ratio
ETAB = 1.0;
ETAN = 1/0.6; % Density gradient
ETAT = 0.0; % Temperature gradient
NU_HYP = 0.0; % Hyperdiffusivity coefficient
NU_HYP = 3.0; % Hyperdiffusivity coefficient
LAMBDAD = 0.0;
NOISE0 = 1.0e-5; % Init noise amplitude
BCKGD0 = 0.0; % Init background
......@@ -111,8 +111,8 @@ for i = 1:Nparam
[~,itend] = min(abs(Ts3D-tend));
gamma_Ni00(i,ikx) = (LinearFit_s(Ts3D(itstart:itend)',(squeeze(abs(Ni00(ikx,1,1,itstart:itend))))));
gamma_phi (i,ikx) = (LinearFit_s(Ts3D(itstart:itend)',(squeeze(abs(PHI (ikx,1,1,itstart:itend))))));
Ni00_ST(i,ikx,:) = squeeze((Ni00(ikx,1,1,1:TMAX/SPS3D)));
PHI_ST(i,ikx,:) = squeeze((PHI (ikx,1,1,1:TMAX/SPS3D)));
% Ni00_ST(i,ikx,:) = squeeze((Ni00(ikx,1,1,1:TMAX/SPS3D)));
% PHI_ST(i,ikx,:) = squeeze((PHI (ikx,1,1,1:TMAX/SPS3D)));
end
tend = Ts5D(end); tstart = 0.4*tend;
[~,itstart] = min(abs(Ts5D-tstart));
......
wk/load_multiple_outputs_marconi.m
+ 4
− 8
View file @ 01dcbfc3
addpath(genpath('../matlab')) % ... add
%% Paste the list of simulation results to load
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_5e-01_SGGK_mu_3e-02/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e-01_SGGK_mu_3e-02/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_5e-01_SGGK_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e-01_SGGK_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_2e-01_SGGK_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_7e-02_SGGK_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e-02_SGGK_mu_3e-02/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e+00_SGGK_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_A/300x150_L_120_P_8_J_4_eta_0.6_nu_1e-01_DGGK_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_A/300x150_L_120_P_8_J_4_eta_0.6_nu_1e-01_SGGK_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_B/300x150_L_120_P_8_J_4_eta_0.6_nu_5e-01_DGGK_mu_0e+00/out.txt')
load_marconi('/marconi_scratch/userexternal/ahoffman/HeLaZ/results/simulation_B/300x150_L_120_P_8_J_4_eta_0.6_nu_5e-01_SGGK_mu_0e+00/out.txt')
wk/marconi_run.m
+ 9
− 8
View file @ 01dcbfc3
......@@ -18,28 +18,28 @@ NP_P = 2; % MPI processes along p
NP_KX = 24; % MPI processes along kx
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 1.0; % Collision frequency
NU = 0.5; % Collision frequency
ETAN = 1.0/0.6; % Density gradient drive (R/Ln)
NU_HYP = 0.0;
%% GRID PARAMETERS
N = 150; % Frequency gridpoints (Nkx = N/2)
L = 100; % Size of the squared frequency domain
N = 300; % Frequency gridpoints (Nkx = N/2)
L = 120; % Size of the squared frequency domain
Nz = 1; % number of perpendicular planes (parallel grid)
q0 = 1.0; % q factor ()
shear = 0.0; % magnetic shear
eps = 0.0; % inverse aspect ratio
P = 4;
J = 2;
P = 8;
J = 4;
%% TIME PARAMETERS
TMAX = 10000; % Maximal time unit
DT = 5e-3; % Time step
SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1; % Sampling per time unit for 2D arrays
SPS3D = 1/2; % Sampling per time unit for 3D arrays
SPS5D = 1/500; % Sampling per time unit for 5D arrays
SPS5D = 1/100; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints/10
RESTART = 1; % To restart from last checkpoint
JOB2LOAD= 3;
JOB2LOAD= 0;
%% OPTIONS AND NAMING
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle ; +/- for GK/DK)
......@@ -47,7 +47,7 @@ CO = 2;
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_3D_marconi'; % Name of the simulation
SIMID = 'HD_study'; % Name of the simulation
SIMID = 'simulation_B'; % Name of the simulation
% SIMID = ['v3.0_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
NON_LIN = 1; % activate non-linearity (is cancelled if KXEQ0 = 1)
% INIT options
......@@ -79,6 +79,7 @@ HD_CO = 0.5; % Hyper diffusivity cutoff ratio
% kmaxcut = 2.5;
MU = NU_HYP/(HD_CO*kmax)^4; % Hyperdiffusivity coefficient
NOISE0 = 1.0e-5;
BCKGD0 = 0.0; % Init background
TAU = 1.0; % e/i temperature ratio
ETAT = 0.0; % Temperature gradient
ETAB = 1.0; % Magnetic gradient (1.0 to set R=LB)
......
wk/open_figure_script.m
+ 1
− 1
View file @ 01dcbfc3
......@@ -15,7 +15,7 @@ simname_ = fname_(54:end-8);
% simname_ = '';
% simname_ = '';
% simname_ = '';
simname_ = 'simulation_A/DGGK_damping_150x75_L_100_P_4_J_2_eta_0.6_nu_1e-01_SGGK_mu_0e+00';
simname_ = 'simulation_A/cw_SGGK_mu_1e-2';
......
wk/plot_cosol_mat.m
+ 2
− 6
View file @ 01dcbfc3
......@@ -92,12 +92,8 @@ subplot(224)
%% Single eigenvalue analysis
% mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_coulomb_P_2_J_1_N_1_kpm_4.0_NFLR_5.h5';
% mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_coulomb_P_6_J_3_N_150_kpm_8.0_NFLR_8.h5';
% mat_file_name = '/home/ahoffman/cosolver/gk.coulomb.NFLR/k.4/self.NFLR.8.0.h5';
% mat_file_name = '/home/ahoffman/cosolver/gk.coulomb_6_3_NFLR_8_kp_4_npiflr_8_sigma_3e-3/scanfiles_00000/self.0.h5';
% mat_file_name = '/home/ahoffman/cosolver/gk.coulomb_6_3_NFLR_8_kp_4_npiflr_0_sigma_5e-4/scanfiles_00000/self.0.h5';
mat_file_name = '/home/ahoffman/cosolver/gk.coulomb_6_3_NFLR_8_kp_4_bjf/scanfiles_00000/self.0.h5';
% mat_file_name = '/home/ahoffman/cosolver/gk.coulomb_6_3_NFLR_8_kp_4_bjf/scanfiles_00000/self.0.h5';
mat_file_name = '/home/ahoffman/cosolver/gk.coulomb_6_3_NFLR_8_kp_4_new_Tljpmf_fort_bjf/scanfiles_00000/self.0.h5';
matidx = 74;
matidx = sprintf('%5.5i',matidx);disp(matidx);
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment