From 787b4769eda705a7807014e18f0ae8d51a4a5c8f Mon Sep 17 00:00:00 2001
From: Antoine Hoffmann <antoine.hoffmann@epfl.ch>
Date: Fri, 11 Aug 2023 13:43:11 +0200
Subject: [PATCH] save scripts
---
matlab/plot/quick_lin_gene_plot.m | 112 ++++++++++++++++++++++++++++++
wk/lin_run_script.m | 27 +++----
wk/lin_scan_script.m | 5 +-
wk/load_and_replot.m | 23 ++++++
wk/load_metadata_scan.m | 2 +-
5 files changed, 153 insertions(+), 16 deletions(-)
create mode 100644 matlab/plot/quick_lin_gene_plot.m
create mode 100644 wk/load_and_replot.m
diff --git a/matlab/plot/quick_lin_gene_plot.m b/matlab/plot/quick_lin_gene_plot.m
new file mode 100644
index 00000000..2a5a4219
--- /dev/null
+++ b/matlab/plot/quick_lin_gene_plot.m
@@ -0,0 +1,112 @@
+%% gyroLES plot
+% genepath = '/misc/gene_results';
+% % simpath = '/NL_Zpinch_Kn_1.7_eta_0.25_nuSG_1e-1_gyroLES/';
+% simpath = '/NL_Zpinch_Kn_1.8_eta_0.25_nuSG_5e-2_gyroLES/';
+% filename = 'GyroLES_ions.dat';
+% toload = [genepath simpath filename];
+% data = readtable(toload);
+% t = data.Var1;
+% mu_x = data.Var2;
+% mu_y = data.Var3;
+% figure;
+% plot(t,mu_x); hold on
+% plot(t,mu_y);
+% legend('mu_x','mu_y'); xlabel('time'); ylabel('Hyper-diff');
+% title('gyroLES results for H&P fig. 2c')
+
+%% Plot linear results
+% path = '/home/ahoffman/gene/linear_zpinch_results/';
+% fname ='tmp.txt';
+% fname ='GENE_LIN_Kn_1.8_KT_0.45_nuSG_0.047_32x16.txt';
+% fname ='GENE_LIN_Kn_1.5_KT_0.325_nuSG_0.047_32x16.txt';
+% fname ='GENE_LIN_Kn_1.5_KT_0.325_nuSG_0.0235_32x16.txt';
+% fname ='GENE_LIN_Kn_1.5_KT_0.325_nuSG_0.0047_32x16.txt';
+% fname ='GENE_LIN_Kn_1.5_KT_0.325_nuSG_0.0047_64x32.txt';
+% fname ='GENE_LIN_Kn_1.4_KT_0.35_nuSG_0.0047_64x32.txt';
+% fname ='GENE_LIN_Kn_1.6_KT_0.4_nuSG_0.0047_64x32.txt';
+% fname ='GENE_LIN_Kn_1.6_KT_0.4_nuSGDK_0.0047_64x32.txt';
+% fname ='GENE_LIN_Kn_1.6_KT_0.4_nuLDDK_0.0047_64x32.txt';
+% fname ='GENE_LIN_Kn_1.8_KT_0.4_nuLDDK_0.0047_64x32.txt';
+% fname ='GENE_LIN_Kn_1.8_KT_0.45_nu_0_32x16.txt';
+% fname ='GENE_LIN_Kn_1.8_KT_0.45_nuSG_0.0235_64x32.txt';
+% fname ='GENE_LIN_Kn_1.9_KT_0.475_nuSG_0.047_64x32.txt';
+% fname ='GENE_LIN_Kn_1.9_KT_0.475_nuSG_0.235_64x32.txt';
+% fname ='GENE_LIN_Kn_1.7_KT_0.425_nuSG_0.235_64x32.txt';
+% fname ='GENE_LIN_Kn_1.8_KT_0.45_nuSGDK_0.047_32x16.txt';
+% fname ='GENE_LIN_Kn_1.8_KT_0.475_nu_0_mu_5e-2.txt';
+% fname ='GENE_LIN_Kn_1.8_KT_0.45_nuSGDK_0.0235_64x32.txt';
+% fname ='GENE_LIN_Kn_1.8_KT_0.45_nuSGDK_0.0235_32x16.txt';
+% fname ='GENE_LIN_Kn_2.0_KT_0.5_nu_0_32x16.txt';
+% fname ='GENE_LIN_Kn_2.0_KT_0.5_nuSGDK_0.0235_32x16.txt';
+% fname ='GENE_LIN_Kn_1.6_KT_0.4_nu_0_32x16.txt';
+% fname ='GENE_LIN_Kn_2.5_KT_0.625_nu_0_32x16.txt';
+path = '/home/ahoffman/gene/linear_CBC_results/';
+% fname = 'CBC_100_20x1x32x30x14_Lv_3_Lw_12_circ.txt';
+% fname = 'CBC_100_20x1x32x32x12_Lv_3_Lw_12.txt';
+% fname = 'CBC_KT_4_20x1x32x32x12_Lv_3_Lw_12.txt';
+% fname = 'CBC_KT_4_20x1x32x64x24_Lv_6_Lw_24.txt';
+% fname = 'CBC_KT_5.3_20x1x32x32x12_Lv_3_Lw_12.txt';
+% fname = 'CBC_KT_5.3_32x1x48x40x16_Lv_3_Lw_12.txt';
+% fname = 'CBC_ky_0.3_20x1x32x32x12_Lv_3_Lw_12.txt';
+% fname = 'CBC_ky_0.3_20x1x32x32x12_Lv_3_Lw_12_nuv_1e-3.txt';
+% fname = 'CBC_KT_11_20x1x16x24x10_Lv_3_Lw_12.txt';
+% fname = 'CBC_KT_11_20x1x32x30x14_Lv_3_Lw_12.txt';
+% fname = 'CBC_ky_0.3_20x1x16x24x10_Lv_3_Lw_12_nuv_1e-3.txt';
+%----------Shearless CBC
+% fname = 'CBC_salpha_s0_nz_24_nv_48_nw_16_adiabe.txt';
+% fname = 'CBC_salpha_s0_nz_24_nv_48_nw_16_kine.txt';
+% fname = 'CBC_salpha_s0_nz_24_nv_48_nw_16_kine_beta_1e-4.txt';
+% fname = 'CBC_miller_s0_nz_24_nv_48_nw_16_adiabe.txt';
+% fname = 'CBC_miller_s0_nz_24_nv_48_nw_16_kine.txt';
+%----------Shearless pITG
+% fname = 'pITG_salpha_s0_nz_24_nv_48_nw_16_adiabe.txt';
+% fname = 'pITG_miller_s0_nz_24_nv_48_nw_16_adiabe.txt';
+% fname = 'pITG_salpha_s0_nz_24_nv_48_nw_16_kine.txt';
+% fname = 'pITG_miller_s0_nz_24_nv_48_nw_16_kine.txt';
+%----------Convergence nvpar shearless pITG
+% fname = 'pITG_salpha_s0_nz_24_nv_scan_nw_16_adiabe.txt';
+% fname = 'pITG_miller_s0_nz_24_nv_scan_nw_16_adiabe.txt';
+% fname = 'pITG_salpha_s0_nz_24_nv_scan_nw_16_kine.txt';
+% fname = 'pITG_miller_s0_nz_24_nv_scan_nw_16_kine.txt';
+% fname = 'pITG_salpha_s0_nz_24_nv_scan_nw_24_adiabe.txt';
+% fname = 'pITG_miller_s0_nz_24_nv_scan_nw_24_adiabe.txt';
+%----------Convergence nvpar shearless CBC
+% fname = 'CBC_salpha_nz_24_nv_scan_nw_16_adiabe.txt';
+% fname = 'CBC_miller_nz_24_nv_scan_nw_16_adiabe.txt';
+% fname = 'CBC_salpha_nz_24_nv_scan_nw_16_kine.txt';
+% fname = 'CBC_miller_nz_24_nv_scan_nw_16_kine.txt';
+%---------- CBC
+% fname = 'CBC_salpha_nx_8_nz_18_nv_12_nw_8_adiabe.txt';
+% fname = 'CBC_salpha_nx_8_nz_18_nv_18_nw_8_adiabe.txt';
+
+% fname = 'CBC_salpha_nx_8_nz_24_nv_6_nw_4_adiabe.txt';
+% fname = 'CBC_salpha_nx_8_nz_24_nv_6_nw_4_adiabe_0.5L.txt';
+% fname = 'CBC_salpha_nx_8_nz_24_nv_8_nw_4_adiabe.txt';
+% fname = 'CBC_salpha_nx_8_nz_24_nv_8_nw_4_adiabe_0.5L.txt';
+fname = 'CBC_salpha_nx_8_nz_24_nv_8_nw_4_adiabe_0.2L.txt';
+% fname = 'CBC_salpha_nx_8_nz_24_nv_16_nw_8_adiabe.txt';
+% fname = 'CBC_salpha_nx_8_nz_24_nv_16_nw_8_adiabe_0.5L.txt';
+% fname = 'CBC_salpha_nx_8_nz_24_nv_36_nw_16_adiabe.txt';
+% fname = 'CBC_salpha_nx_8_nz_24_nv_36_nw_16_adiabe_0.5L.txt';
+% fname = 'CBC_salpha_nx_8_nz_24_nv_48_nw_16_adiabe.txt';
+
+% fname = 'kT_5.3_salpha_nx_8_nz_24_nv_60_nw_30_adiabe.txt';
+
+% fname = 'CBC_salpha_nx_8_nz_24_nv_36_nw_16_kine.txt';
+% fname = 'CBC_miller_nx_20_nz_32_nv_32_nw_12_adiabe.txt';
+% fname = 'CBC_miller_nx_8_nz_24_nv_36_nw_16_adiabe.txt';
+% fname = 'CBC_miller_nx_20_nz_32_nv_32_nw_12_kine.txt';
+% fname = 'CBC_miller_nx_8_nz_24_nv_36_nw_16_kine.txt';
+%----------Convergence nv CBC
+% fname = 'CBC_ky_0.3_nv_scan_8x1x24_nw_8_Lv_3_Lw_6.txt';
+% fname = 'CBC_ky_0.3_nv_scan_8x1x24_nw_16_Lv_3_Lw_6.txt';
+% fname = 'CBC_ky_0.3_nv_scan_8x1x24_nw_24_Lv_3_Lw_6.txt';
+
+data_ = load([path,fname]);
+
+figure
+% plot(data_(:,2),data_(:,3),'-dk','DisplayName',fname); hold on;
+% plot(data_(:,2),data_(:,4),'--*k','DisplayName',fname);
+
+plot(data_(:,2),data_(:,3)./data_(:,2).^2,'-dk','DisplayName',fname); hold on;
+legend show
diff --git a/wk/lin_run_script.m b/wk/lin_run_script.m
index aad2bfd6..b4832e7d 100644
--- a/wk/lin_run_script.m
+++ b/wk/lin_run_script.m
@@ -15,7 +15,7 @@ addpath(genpath([gyacomodir,'matlab/load'])) % Add load folder
addpath(genpath([gyacomodir,'wk/parameters'])) % Add parameters folder
%% Setup run or load an executable
-RUN = 1; % To run or just to load
+RUN = 0; % To run or just to load
default_plots_options
% EXECNAME = 'gyacomo23_sp_save'; % single precision
EXECNAME = 'gyacomo23_sp'; % single precision
@@ -32,15 +32,15 @@ EXECNAME = 'gyacomo23_sp'; % single precision
run lin_ITG
% run lin_KBM
%% Change parameters
-% EXBRATE = 0.001; % Background ExB shear flow
-% NY = 2;
-% NX = 4;
-% PMAX = 2;
-% JMAX = PMAX/2;
-% ky = 0.5;
-% LY = 2*pi/ky;
-% DT = 1e-3;
-% TMAX = 10;
+EXBRATE = 0.0; % Background ExB shear flow
+NY = 40;
+NX = 8;
+PMAX = 16;
+JMAX = PMAX/2;
+ky = 0.05;
+LY = 2*pi/ky;
+DT = 5e-3;
+TMAX = 50;
% % SIGMA_E = 0.04;
% TMAX = 10;
% DTSAVE0D = 200*DT;
@@ -52,9 +52,9 @@ setup
% Run linear simulation
if RUN
MVIN =['cd ../results/',SIMID,'/',PARAMS,'/;'];
- RUN =['time ',mpirun,' -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0;'];
+ % RUN =['time ',mpirun,' -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0;'];
% RUN =['time ',mpirun,' -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0;'];
- % RUN =['time ',mpirun,' -np 8 ',gyacomodir,'bin/',EXECNAME,' 2 2 2 0;'];
+ RUN =['time ',mpirun,' -np 8 ',gyacomodir,'bin/',EXECNAME,' 2 2 2 0;'];
% RUN =['time ',mpirun,' -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0;'];
% RUN = ['./../../../bin/gyacomo23_sp 0;'];
MVOUT='cd ../../../wk;';
@@ -86,8 +86,9 @@ options.NMA = 1; % Set NMA option to 1
options.NMODES = 999; % Set how much modes we study
options.iz = 'avg'; % Compressing z
options.ik = 1; %
+options.GOK2 = 0; % plot gamma/k^2
options.fftz.flag = 0; % Set fftz.flag option to 0
-fig = mode_growth_meter(data,options); % Call the function mode_growth_meter with data and options as input arguments, and store the result in fig
+[fig, kykx, wkykx, ekykx] = mode_growth_meter(data,options); % Call the function mode_growth_meter with data and options as input arguments, and store the result in fig
end
if (1 && NZ>4)
diff --git a/wk/lin_scan_script.m b/wk/lin_scan_script.m
index fa4b3509..5497c8e2 100644
--- a/wk/lin_scan_script.m
+++ b/wk/lin_scan_script.m
@@ -18,8 +18,8 @@ addpath(genpath([gyacomodir,'wk/parameters'])) % Add parameters folder
RUN = 1; % To run or just to load
RERUN = 0; % rerun if the data does not exist
default_plots_options
-EXECNAME = 'gyacomo23_sp'; % single precision
-% EXECNAME = 'gyacomo23_dp'; % double precision
+% EXECNAME = 'gyacomo23_sp'; % single precision
+EXECNAME = 'gyacomo23_dp'; % double precision
%% Setup parameters
% run lin_DTT_AB_rho85
@@ -30,6 +30,7 @@ run lin_JET_rho97
%% Change parameters
NY = 2;
+EXBRATE = 0;
% SIGMA_E = 0.023;
%% Scan parameters
SIMID = [SIMID,'_scan'];
diff --git a/wk/load_and_replot.m b/wk/load_and_replot.m
new file mode 100644
index 00000000..3d0e7ee5
--- /dev/null
+++ b/wk/load_and_replot.m
@@ -0,0 +1,23 @@
+% Load the .fig file
+figFile = '/home/ahoffman/paper2_fig/31_CBC_linear_convergence.fig'; % Replace with the actual path to your .fig file
+% figFile = 'tmp.fig'; % Replace with the actual path to your .fig file
+figHandle = openfig(figFile);
+
+%% Extract data from the figure
+% Here, we assume that the plotted data is stored in a single line plot
+lineHandle = findobj(figHandle, 'Type', 'line');
+xData = get(lineHandle, 'XData');
+yData = get(lineHandle, 'YData');
+% Extract legend labels
+legendHandle = findobj(figHandle, 'Type', 'legend');
+legendEntries = flip(get(legendHandle, 'String'));
+% legendEntries = legendEntries{end:-1:1};
+% Close the loaded figure
+close(figHandle);
+%%
+ figure
+for i = numel(xData):-1:1
+ % plot(xData{i},yData{i},'DisplayName',legendEntries{i}); hold on
+ plot(xData{i},yData{i}./xData{i}.^2,'DisplayName',legendEntries{i}); hold on
+end
+legend show
\ No newline at end of file
diff --git a/wk/load_metadata_scan.m b/wk/load_metadata_scan.m
index 6615ee53..f15aee8a 100644
--- a/wk/load_metadata_scan.m
+++ b/wk/load_metadata_scan.m
@@ -19,7 +19,7 @@ addpath(genpath([gyacomodir,'matlab/load'])) % ... add% EXECNAME = 'gyacomo_1.0'
% datafname = 'lin_JET_rho97_scan/4x32_ky_0.01_10_P_2_8_kN_10_DGGK_0.05_be_0.0031.mat';
% datafname = 'lin_JET_rho97_scan/8x32_ky_0.01_10_P_2_8_kN_10_DGGK_0.05_be_0.0031.mat';
% datafname = 'lin_JET_rho97_scan/8x32_ky_0.01_10_P_2_2_kN_10_DGGK_0.05_be_0.0031.mat';
-datafname = 'lin_JET_rho97_scan/8x32_ky_0.031623_31.6228_P_2_2_kN_10_DGGK_0.1_be_0.0031.mat';
+datafname = 'lin_JET_rho97_scan/8x32_ky_0.031623_31.6228_P_2_8_kN_10_DGGK_0.1_be_0.0031.mat';
%% Chose if we filter gamma>0.05
FILTERGAMMA = 0;
--
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