From 37685bde400162315af2d80533fedc76d59ae8bf Mon Sep 17 00:00:00 2001
From: Antoine Hoffmann <antoine.hoffmann@epfl.ch>
Date: Thu, 9 Jun 2022 11:01:53 +0200
Subject: [PATCH] small scripts changes
---
.../plot_radial_transport_and_spacetime.m | 4 +-
wk/analysis_HeLaZ.m | 10 +--
wk/analysis_gbms.m | 17 +++++-
wk/header_3D_results.m | 4 +-
wk/quick_run.m | 61 +++++++++++--------
5 files changed, 60 insertions(+), 36 deletions(-)
diff --git a/matlab/plot/plot_radial_transport_and_spacetime.m b/matlab/plot/plot_radial_transport_and_spacetime.m
index d052fc15..7e31997c 100644
--- a/matlab/plot/plot_radial_transport_and_spacetime.m
+++ b/matlab/plot/plot_radial_transport_and_spacetime.m
@@ -84,8 +84,8 @@ mvm = @(x) movmean(x,OPTIONS.NMVA);
OPTIONS.POLARPLOT = 0;
toplot = process_field(DATA,OPTIONS);
f2plot = toplot.FIELD;
-
- clim = max(max(max(abs(plt(f2plot(:,:,its3D:ite3D))))));
+ dframe = ite3D - its3D;
+ clim = max(max(max(abs(plt(f2plot(:,:,:))))));
subplot(313)
[TY,TX] = meshgrid(DATA.x,DATA.Ts3D(toplot.FRAMES));
pclr = pcolor(TX,TY,squeeze(plt(f2plot))');
diff --git a/wk/analysis_HeLaZ.m b/wk/analysis_HeLaZ.m
index 4a06a7a1..fbe4b779 100644
--- a/wk/analysis_HeLaZ.m
+++ b/wk/analysis_HeLaZ.m
@@ -10,7 +10,7 @@ system(['mkdir -p ',MISCDIR]);
CMD = ['rsync ', LOCALDIR,'outputs* ',MISCDIR]; disp(CMD);
system(CMD);
% Load outputs from jobnummin up to jobnummax
-JOBNUMMIN = 15; JOBNUMMAX = 16;
+JOBNUMMIN = 00; JOBNUMMAX = 20;
data = compile_results(MISCDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
data.localdir = LOCALDIR;
data.FIGDIR = LOCALDIR;
@@ -49,12 +49,12 @@ options.NAME = '\phi';
% options.NAME = 'n_i^{NZ}';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
-options.PLAN = 'xy';
+options.PLAN = 'xz';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
options.COMP = 9;
% options.TIME = dat.Ts5D;
-options.TIME = [1800:1:2000];
+options.TIME = [0:1:2000];
data.EPS = 0.1;
data.a = data.EPS * 2000;
create_film(data,options,'.gif')
@@ -119,7 +119,7 @@ options.ST = 0;
options.PLOT_TYPE = 'space-time';
options.NORMALIZED = 1;
options.JOBNUM = 0;
-options.TIME = [1300 1400];
+options.TIME = [50];
options.specie = 'i';
options.compz = 'avg';
fig = show_moments_spectrum(data,options);
@@ -165,7 +165,7 @@ if 0
%% Mode evolution
options.NORMALIZED = 0;
options.K2PLOT = 1;
-options.TIME = 1800:2000;
+options.TIME = 0:90;
options.NMA = 1;
options.NMODES = 15;
options.iz = 'avg';
diff --git a/wk/analysis_gbms.m b/wk/analysis_gbms.m
index f3a35be5..1e3d2958 100644
--- a/wk/analysis_gbms.m
+++ b/wk/analysis_gbms.m
@@ -5,6 +5,7 @@
%%
resdir = '/home/ahoffman/Documents/gbms/benchmark_HeLaZ/shearless_linear_cyclone/';
+resdir = '/home/ahoffman/Documents/gbms/benchmark_HeLaZ/RH_test/';
% resdir = '/home/ahoffman/Documents/gbms/benchmark_HeLaZ/linear_cyclone/';
% resdir = '/home/ahoffman/molix/';
outfile = [resdir,'field.dat.h5'];
@@ -18,7 +19,7 @@ gbms_dat.Nx = numel(gbms_dat.kx); gbms_dat.Nkx = numel(gbms_dat.kx);
gbms_dat.Ny = numel(gbms_dat.ky); gbms_dat.Nky = numel(gbms_dat.ky);
gbms_dat.Nz = numel(gbms_dat.z);
-dky = min(gbms_dat.ky(gbms_dat.ky>0)); Ly = 2*pi/dky;
+dky = min(gbms_dat.ky(gbms_dat.ky>0)); Ly =0;% 2*pi/dky;
gbms_dat.y = linspace(-Ly/2,Ly/2,gbms_dat.Ny+1); gbms_dat.y = gbms_dat.y(1:end-1);
gbms_dat.x = 0;
gbms_dat.PHI = zeros(gbms_dat.Ny,gbms_dat.Nx,gbms_dat.Nz,gbms_dat.Nt);
@@ -50,7 +51,7 @@ end
if 0
%% 2D snapshots
% Options
-options.INTERP = 0;
+options.INTERP = 0;
options.POLARPLOT = 0;
options.AXISEQUAL = 1;
options.NAME = '\phi';
@@ -70,7 +71,7 @@ nplots = 1;
lg = compute_fluxtube_growth_rate(gbms_dat,trange,nplots);
end
-if 1
+if 0
%% Ballooning plot
options.time_2_plot = data.Ts3D(end);
options.kymodes = [0.5];
@@ -78,4 +79,14 @@ options.normalized = 1;
options.sheared = 0;
options.field = 'phi';
fig = plot_ballooning(gbms_dat,options);
+end
+
+if 1
+%% RH TEST
+ikx = 1;
+plt = @(x) squeeze(mean(real(x(1,ikx,:,:)),3))./squeeze(mean(real(x(1,ikx,:,1)),3));
+figure
+plot(gbms_dat.Ts3D, plt(gbms_dat.PHI));
+xlabel('$t$'); ylabel('$\phi_z(t)/\phi_z(0)$')
+title(sprintf('$k_x=$%2.2f, $k_y=0.00$',gbms_dat.kx(ikx)))
end
\ No newline at end of file
diff --git a/wk/header_3D_results.m b/wk/header_3D_results.m
index 9b790c18..b028f6c0 100644
--- a/wk/header_3D_results.m
+++ b/wk/header_3D_results.m
@@ -5,7 +5,9 @@ helazdir = '/home/ahoffman/HeLaZ/';
outfile ='';
outfile ='';
outfile ='';
-outfile ='shearless_cyclone/128x128x16x5x3_start';
+% outfile ='shearless_cyclone/128x128x16x5x3_start';
+% outfile ='shearless_cyclone/128x128x16_CBC_100';
+outfile ='shearless_cyclone/128x128x16_CBC_120';
% outfile ='shearless_cyclone/128x128x16xdmax_6_L_120_CBC_1.0';
% outfile ='shearless_cyclone/128x128x16xdmax_L_120_CBC_1.0';
% outfile ='shearless_cyclone/180x180x20x4x2_L_120_CBC_0.8_to_1.0';
diff --git a/wk/quick_run.m b/wk/quick_run.m
index 8165d782..77df8c3c 100644
--- a/wk/quick_run.m
+++ b/wk/quick_run.m
@@ -13,23 +13,23 @@ EXECNAME = 'helaz3';
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 0.2; % Collision frequency
+NU = 0.1; % Collision frequency
TAU = 1.0; % e/i temperature ratio
-K_N = 2.22; % Density gradient drive
-K_T = 6.96; % Temperature '''
+K_N = 0;%2.22; % Density gradient drive
+K_T = 0;%6.96; % Temperature '''
K_E = 0.0; % Electrostat '''
-SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
+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 = 1; % real space x-gridpoints
-NY = 64; % '' y-gridpoints
+PMAXE = 6; % Hermite basis size of electrons
+JMAXE = 3; % Laguerre "
+PMAXI = 6; % " ions
+JMAXI = 3; % "
+NX = 2; % real space x-gridpoints
+NY = 1; % '' y-gridpoints
LX = 100; % Size of the squared frequency domain
LY = 60; % Size of the squared frequency domain
-NZ = 16; % number of perpendicular planes (parallel grid)
+NZ = 32; % number of perpendicular planes (parallel grid)
NPOL = 1;
SG = 0; % Staggered z grids option
%% GEOMETRY
@@ -40,15 +40,15 @@ SHEAR = 0.0; % magnetic shear (Not implemented yet)
EPS = 0.18; % inverse aspect ratio
%% TIME PARMETERS
TMAX = 30; % Maximal time unit
-DT = 2*5e-3; % Time step
-SPS0D = 1; % Sampling per time unit for 2D arrays
+DT = 1e-2; % Time step
+SPS0D = 20; % Sampling per time unit for 2D arrays
SPS2D = 0; % Sampling per time unit for 2D arrays
-SPS3D = 1; % Sampling per time unit for 2D arrays
+SPS3D = 20; % Sampling per time unit for 2D arrays
SPS5D = 1; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints
JOB2LOAD= -1;
%% OPTIONS
-SIMID = 'dbg'; % Name of the simulation
+SIMID = 'Ros_Hin_test'; % 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)
@@ -56,10 +56,10 @@ CO = 'DG';
GKCO = 0; % gyrokinetic operator
ABCO = 1; % interspecies collisions
INIT_ZF = 0; ZF_AMP = 0.0;
-CLOS = 1; % Closure model (0: =0 truncation, 1: gyrofluid closure (p+2j<=Pmax))s
+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= 'phi'; % Start simulation with a noisy mom00/phi/allmom
+INIT_OPT= 'mom00'; % Start simulation with a noisy mom00/phi/allmom
%% OUTPUTS
W_DOUBLE = 1;
W_GAMMA = 1; W_HF = 1;
@@ -75,12 +75,12 @@ MU = 0.0; % Hyperdiffusivity coefficient
INIT_BLOB = 0; WIPE_TURB = 0; ACT_ON_MODES = 0;
MU_X = MU; %
MU_Y = MU; %
-MU_Z = 0.2; %
+MU_Z = 0.0; %
MU_P = 0.0; %
MU_J = 0.0; %
LAMBDAD = 0.0;
-NOISE0 = 1.0e-5; % Init noise amplitude
-BCKGD0 = 0.0; % Init background
+NOISE0 = 0.0e-5; % Init noise amplitude
+BCKGD0 = 1.0; % Init background
GRADB = 1.0;
CURVB = 1.0;
%%-------------------------------------------------------------------------
@@ -91,8 +91,8 @@ system(['rm fort*.90']);
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 2 2 0; cd ../../../wk'])
- system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',HELAZDIR,'bin/',EXECNAME,' 1 6 1 0; cd ../../../wk'])
+ system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 2 2 0; cd ../../../wk'])
+% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',HELAZDIR,'bin/',EXECNAME,' 1 6 1 0; cd ../../../wk'])
end
%% Load results
@@ -111,7 +111,7 @@ nplots = 1;
lg = compute_fluxtube_growth_rate(data,trange,nplots);
end
-if 1
+if 0
%% Ballooning plot
options.time_2_plot = [0.9 1]*data.Ts3D(end);
options.kymodes = [0.5];
@@ -150,14 +150,25 @@ options.kzky = 0;
save_figure(data,fig)
end
-if 1
+if 0
%% Mode evolution
options.NORMALIZED = 1;
options.K2PLOT = 1;
options.TIME = [0.8 1]*data.Ts3D(end);
options.NMA = 1;
-options.NMODES = 5;
+options.NMODES = 2;
options.iz = 9;
fig = mode_growth_meter(data,options);
save_figure(gbms_dat,fig)
end
+
+
+if 1
+%% RH TEST
+ikx = 2;
+plt = @(x) squeeze(mean(real(x(1,ikx,:,:)),3))./squeeze(mean(real(x(1,ikx,:,1)),3));
+figure
+plot(data.Ts3D, plt(data.PHI));
+xlabel('$t$'); ylabel('$\phi_z(t)/\phi_z(0)$')
+title(sprintf('$k_x=$%2.2f, $k_y=0.00$',data.kx(ikx)))
+end
--
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