From ab81f3e047fa39e1af8b858a74ff1202aafc773a Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Wed, 4 Aug 2021 09:54:14 +0200
Subject: [PATCH] scripts update
---
matlab/setup.m | 19 +++++++------
wk/HD_study.m | 7 +++++
wk/analysis_3D.m | 12 +++++---
wk/linear_study.m | 39 +++++++++++++-------------
wk/local_run.m | 8 +++---
wk/marconi_run.m | 16 +++++------
wk/plot_cosol_mat.m | 68 +++++++++++++++++++++++++++++++--------------
7 files changed, 104 insertions(+), 65 deletions(-)
diff --git a/matlab/setup.m b/matlab/setup.m
index 0f6ded1f..821068bd 100644
--- a/matlab/setup.m
+++ b/matlab/setup.m
@@ -54,19 +54,22 @@ if (abs(CO) == 2) %Sugama operator
elseif (abs(CO) == 3) %pitch angle operator
INITIAL.mat_file = ['''../../../iCa/gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5'''];
elseif (CO == 4) % Full Coulomb GK
- disp('Warning, FCGK not implemented yet')
+ INITIAL.mat_file = ['''../../../iCa/gk_coulomb_P_6_J_3_N_150_kpm_8.0.h5'''];
elseif (CO == -1) % DGDK
disp('Warning, DGDK not debugged')
end
% Naming and creating input file
-if (CO == -3); CONAME = 'PADK';
-elseif(CO == -2); CONAME = 'SGDK';
-elseif(CO == -1); CONAME = 'DGDK';
-elseif(CO == 0); CONAME = 'LBDK';
-elseif(CO == 1); CONAME = 'DGGK';
-elseif(CO == 2); CONAME = 'SGGK';
-elseif(CO == 3); CONAME = 'PAGK';
+switch abs(CO)
+ case 0; CONAME = 'LB';
+ case 1; CONAME = 'DG';
+ case 2; CONAME = 'SG';
+ case 3; CONAME = 'PA';
+ case 4; CONAME = 'FC';
+ otherwise; CONAME ='UK';
+end
+if (CO <= 0); CONAME = [CONAME,'DK'];
+else; CONAME = [CONAME,'GK'];
end
if (CLOS == 0); CLOSNAME = 'Trunc.';
elseif(CLOS == 1); CLOSNAME = 'Clos. 1';
diff --git a/wk/HD_study.m b/wk/HD_study.m
index dbf3f4e2..7ec342c5 100644
--- a/wk/HD_study.m
+++ b/wk/HD_study.m
@@ -34,6 +34,7 @@ rp_=[...
5e-2, 1e-3;...
1e-2, 1e-3;...
1e-2, 1e-4;...
+ 1e-2, 5e-4;...
];
figure; set(gcf, 'Position', [100, 100, 900, 400])
grid on; xlim([5e-4,5e0]); ylim([5e-5,5e+0]);
@@ -72,6 +73,12 @@ mu_ = [3e-3 1e-3 1e-4];
nu_ = [1e-2 1e-2 1e-2];
plot(nu_,mu_,'x--','DisplayName','N=150, L=100, P,J=2,1');
+% HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e-02_DGGK_CLOS_0_mu_3e-02/
+mu_ = [3e-3 5e-4];
+nu_ = [1e-2 1e-2];
+plot(nu_,mu_,'x--','DisplayName','N=150, L=100, P,J=4,2');
+
+
% HD_study/150x75_L_100_P_2_J_1_eta_0.6_nu_5e-02_DGGK_CLOS_0_mu_3e-02/
mu_ = [3e-3 1e-3];
nu_ = [5e-2 5e-2];
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index 5300342d..083fd6e3 100644
--- a/wk/analysis_3D.m
+++ b/wk/analysis_3D.m
@@ -7,8 +7,10 @@ outfile ='';
outfile ='';
outfile ='';
outfile ='';
-outfile ='HD_study/300x150_L_100_P_2_J_1_eta_0.6_nu_5e-01_DGGK_mu_2e-03';
-% outfile ='HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e-02_DGGK_mu_3e-03';
+outfile ='';
+outfile ='';
+outfile ='';
+outfile ='HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e-02_DGGK_mu_3e-03';
BASIC.RESDIR = ['../results/',outfile,'/'];
BASIC.MISCDIR = ['/misc/HeLaZ_outputs/results/',outfile,'/'];
CMD = ['cp ', BASIC.RESDIR,'outputs* ',BASIC.MISCDIR]; disp(CMD);
@@ -19,7 +21,9 @@ outfile ='';
outfile ='';
outfile ='';
outfile ='';
-outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/test_3D_marconi/100x50_L_60_P_2_J_1_eta_Inf_nu_1e-01_DGGK_mu_0e+00/out.txt';
+outfile ='';
+outfile ='';
+outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/test_3D_marconi/100x50x20_L_60_q0_1_P_2_J_1_eta_0.6_nu_1e-01_DGGK_mu_2e-02/out.txt';
BASIC.RESDIR = ['../',outfile(46:end-8),'/'];
BASIC.MISCDIR = ['/misc/HeLaZ_outputs/',outfile(46:end-8),'/'];
end
@@ -74,7 +78,7 @@ t0 =00; iz = 1; ix = 1; iy = 1;
skip_ = 1; DELAY = 1e-2*skip_;
[~, it03D] = min(abs(Ts3D-t0)); FRAMES_3D = it03D:skip_:numel(Ts3D);
[~, it05D] = min(abs(Ts5D-t0)); FRAMES_5D = it05D:skip_:numel(Ts5D);
-INTERP = 0; T = Ts3D; FRAMES = FRAMES_3D;
+INTERP = 1; T = Ts3D; FRAMES = FRAMES_3D;
% Field to plot
% FIELD = dens_e; NAME = 'ne'; FIELDNAME = 'n_e';
% FIELD = dens_i; NAME = 'ni'; FIELDNAME = 'n_i';
diff --git a/wk/linear_study.m b/wk/linear_study.m
index 223568a4..81d50007 100644
--- a/wk/linear_study.m
+++ b/wk/linear_study.m
@@ -1,6 +1,6 @@
-for NU = [0.01]
+for NU = [0.1]
for ETAN = [2.0]
-for CO = [3]
+for CO = [1]
%clear all;
addpath(genpath('../matlab')) % ... add
default_plots_options
@@ -33,12 +33,10 @@ SPSCP = 0; % Sampling per time unit for checkpoints
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 00;
%% OPTIONS
-% SIMID = 'v2.7_lin_analysis'; % Name of the simulation
-SIMID = 'kobayashi_2015_fig2'; % Name of the simulation
-% SIMID = 'v2.6_lin_analysis'; % Name of the simulation
+SIMID = 'v3.1_lin_analysis'; % Name of the simulation
NON_LIN = 0 *(1-KXEQ0); % activate non-linearity (is cancelled if KXEQ0 = 1)
% Collision operator
-% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Full Couloumb ; +/- for GK/DK)
+% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle, 4 : Full Couloumb ; +/- for GK/DK)
% CO = 2;
INIT_ZF = 0; ZF_AMP = 0.0;
CLOS = 0; % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
@@ -63,15 +61,18 @@ JOBNUM = 00;
KPAR = 0.0; % Parellel wave vector component
HD_CO = 0.5; % Hyper diffusivity cutoff ratio
kmax = N*pi/L;% Highest fourier mode
-MU = NU_HYP/(HD_CO*kmax)^4 % Hyperdiffusivity coefficient
-
+MU = NU_HYP/(HD_CO*kmax)^4; % Hyperdiffusivity coefficient
+Nz = 1; % number of perpendicular planes (parallel grid)
+q0 = 1.0; % safety factor
+shear = 0.0; % magnetic shear
+eps = 0.0; % inverse aspect ratio
%% PARAMETER SCANS
if 1
%% Parameter scan over PJ
% PA = [2 4 6 10];
% JA = [1 2 3 5];
-PA = [2];
-JA = [1];
+PA = [6];
+JA = [3];
DTA= DT*ones(size(JA));%./sqrt(JA);
% DTA= DT;
mup_ = MU_P;
@@ -87,23 +88,21 @@ for i = 1:Nparam
PMAXE = PA(i); PMAXI = PA(i);
JMAXE = JA(i); JMAXI = JA(i);
DT = DTA(i);
-% MU_P = mup_/PMAXE^2;
-% MU_J = muj_/JMAXE^3;
setup
% Run linear simulation
-% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ./../../../bin/helaz 1 1; cd ../../../wk'])
- system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ./../../../bin/helaz 1 6; cd ../../../wk'])
-% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ./../../../bin/helaz 2 3; cd ../../../wk'])
+% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ./../../../bin/helaz_3 1 1; cd ../../../wk'])
+ system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ./../../../bin/helaz_3 1 6; cd ../../../wk'])
+% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ./../../../bin/helaz_3 2 3; cd ../../../wk'])
% Load and process results
%%
filename = ['../results/',SIMID,'/',PARAMS,'/outputs_00.h5'];
load_results
- tend = Ts2D(end); tstart = 0.4*tend;
- [~,itstart] = min(abs(Ts2D-tstart));
- [~,itend] = min(abs(Ts2D-tend));
+ tend = Ts3D(end); tstart = 0.4*tend;
+ [~,itstart] = min(abs(Ts3D-tstart));
+ [~,itend] = min(abs(Ts3D-tend));
for ikx = 1:N/2+1
- gamma_Ni00(i,ikx) = (LinearFit_s(Ts2D(itstart:itend)',(squeeze(abs(Ni00(ikx,1,itstart:itend))))));
- Ni00_ST(i,ikx,1:numel(Ts2D)) = squeeze((Ni00(ikx,1,:)));
+ gamma_Ni00(i,ikx) = (LinearFit_s(Ts3D(itstart:itend)',(squeeze(abs(Ni00(ikx,1,itstart:itend))))));
+ Ni00_ST(i,ikx,1:numel(Ts3D)) = squeeze((Ni00(ikx,1,:)));
end
tend = Ts5D(end); tstart = 0.4*tend;
[~,itstart] = min(abs(Ts5D-tstart));
diff --git a/wk/local_run.m b/wk/local_run.m
index c588c465..f6f67373 100644
--- a/wk/local_run.m
+++ b/wk/local_run.m
@@ -6,10 +6,10 @@ CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%% PHYSICAL PARAMETERS
NU = 0.1; % Collision frequency
ETAN = 1.0/0.6; % Density gradient drive (R/Ln)
-NU_HYP = 0.1;
+NU_HYP = 1.0;
%% GRID AND GEOMETRY PARAMETERS
-N = 100; % Frequency gridpoints (Nkx = N/2)
-L = 60; % Size of the squared frequency domain
+N = 50; % Frequency gridpoints (Nkx = N/2)
+L = 30; % Size of the squared frequency domain
Nz = 10; % number of perpendicular planes (parallel grid)
q0 = 1.0; % safety factor
shear = 0.0; % magnetic shear
@@ -17,7 +17,7 @@ eps = 0.0; % inverse aspect ratio
P = 2;
J = 1;
%% TIME PARAMETERS
-TMAX = 200; % Maximal time unit
+TMAX = 500; % Maximal time unit
DT = 1e-2; % Time step
SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1; % Sampling per time unit for 2D arrays
diff --git a/wk/marconi_run.m b/wk/marconi_run.m
index 236dc473..f93e63cf 100644
--- a/wk/marconi_run.m
+++ b/wk/marconi_run.m
@@ -18,13 +18,13 @@ NP_P = 2; % MPI processes along p
NP_KX = 24; % MPI processes along kx
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 0.05; % Collision frequency
+NU = 0.1; % Collision frequency
ETAN = 1.0/0.6; % Density gradient drive (R/Ln)
-NU_HYP = 10.0;
+NU_HYP = 1.0;
%% GRID PARAMETERS
-N = 300; % Frequency gridpoints (Nkx = N/2)
-L = 100; % Size of the squared frequency domain
-Nz = 1; % number of perpendicular planes (parallel grid)
+N = 100; % Frequency gridpoints (Nkx = N/2)
+L = 60; % Size of the squared frequency domain
+Nz = 20; % number of perpendicular planes (parallel grid)
q0 = 1.0; % q factor ()
shear = 0.0; % magnetic shear
eps = 0.0; % inverse aspect ratio
@@ -43,11 +43,11 @@ JOB2LOAD= 0;
%% OPTIONS AND NAMING
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle ; +/- for GK/DK)
-CO = 2;
+CO = 1;
CLOS = 0; % Closure model (0: =0 truncation)
NL_CLOS = 0; % 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 = 'test_3D_marconi'; % Name of the simulation
+% SIMID = 'HD_study'; % 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
diff --git a/wk/plot_cosol_mat.m b/wk/plot_cosol_mat.m
index 876a233a..a6f583a9 100644
--- a/wk/plot_cosol_mat.m
+++ b/wk/plot_cosol_mat.m
@@ -1,29 +1,29 @@
-MAT = results.iCa;
-figure
-suptitle('DGGK,P=6,J=3');
-subplot(221)
- imagesc(log(abs(MAT)));
- title('log abs')
-subplot(222)
- imagesc(imag(MAT)); colormap(bluewhitered)
- title('imag'); colorbar
-subplot(223)
- imagesc(imag(MAT)>0);
- title('imag$>$0');
-subplot(224)
- imagesc(imag(MAT)<0);
- title('imag$<$0');
-
-
+% MAT = results.iCa;
+% figure
+% suptitle('FCGK,P=6,J=3');
+% subplot(221)
+% imagesc(log(abs(MAT)));
+% title('log abs')
+% subplot(222)
+% imagesc(imag(MAT)); colormap(bluewhitered)
+% title('imag'); colorbar
+% subplot(223)
+% imagesc(imag(MAT)>0);
+% title('imag$>$0');
+% subplot(224)
+% imagesc(imag(MAT)<0);
+% title('imag$<$0');
+%
+%
%% SGGK
P_ = 20; J_ = 10;
mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_sugama_P_20_J_10_N_150_kpm_8.0.h5';
-SGGK_self = h5read(mat_file_name,'/00149/Caapj/Ciipj');
+SGGK_self = h5read(mat_file_name,'/00000/Caapj/Ciipj');
SGGK_ei = h5read(mat_file_name,'/00000/Ceipj/CeipjF')+h5read(mat_file_name,'/00000/Ceipj/CeipjT');
SGGK_ie = h5read(mat_file_name,'/00000/Ciepj/CiepjF')+h5read(mat_file_name,'/00000/Ciepj/CiepjT');
figure
-MAT = 1i*SGGK_self; suptitle('SGGK ii,P=20,J=10, k=8');
+MAT = 1i*SGGK_self; suptitle('SGGK ii,P=20,J=10, k=0');
% MAT = 1i*SGGK_ei; suptitle('SGGK ei,P=20,J=10');
% MAT = 1i*SGGK_ie; suptitle('SGGK ie,P=20,J=10');
subplot(221)
@@ -42,13 +42,38 @@ subplot(224)
%% PAGK
P_ = 20; J_ = 10;
mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5';
-PAGK_self = h5read(mat_file_name,'/00149/Caapj/Ceepj');
+PAGK_self = h5read(mat_file_name,'/00000/Caapj/Ceepj');
% PAGK_ei = h5read(mat_file_name,'/00000/Ceipj/CeipjF')+h5read(mat_file_name,'/00000/Ceipj/CeipjT');
% PAGK_ie = h5read(mat_file_name,'/00000/Ciepj/CiepjF')+h5read(mat_file_name,'/00000/Ciepj/CiepjT');
figure
-MAT = 1i*PAGK_self; suptitle('PAGK ii,P=20,J=10, k=8');
+MAT = 1i*PAGK_self; suptitle('PAGK ii,P=20,J=10, k=0');
+
+subplot(221)
+ imagesc(abs(MAT));
+ title('log abs')
+subplot(222)
+ imagesc(imag(MAT)); colormap(bluewhitered)
+ title('imag'); colorbar
+subplot(223)
+ imagesc(imag(MAT)>0);
+ title('imag$>$0');
+subplot(224)
+ imagesc(imag(MAT)<0);
+ title('imag$<$0');
+
+ %% SGGK
+P_ = 6; J_ = 3;
+mat_file_name = '/home/ahoffman/HeLaZ/iCa/gk_coulomb_P_6_J_3_N_150_kpm_8.0.h5';
+FCGK_self = h5read(mat_file_name,'/00000/Caapj/Ciipj');
+FCGK_ei = h5read(mat_file_name,'/00000/Ceipj/CeipjF')+h5read(mat_file_name,'/00000/Ceipj/CeipjT');
+FCGK_ie = h5read(mat_file_name,'/00000/Ciepj/CiepjF')+h5read(mat_file_name,'/00000/Ciepj/CiepjT');
+
+figure
+MAT = 1i*FCGK_self; suptitle('FCGK ii,P=20,J=10, k=0');
+% MAT = 1i*SGGK_ei; suptitle('FCGK ei,P=20,J=10');
+% MAT = 1i*SGGK_ie; suptitle('FCGK ie,P=20,J=10');
subplot(221)
imagesc(abs(MAT));
title('log abs')
@@ -61,3 +86,4 @@ subplot(223)
subplot(224)
imagesc(imag(MAT)<0);
title('imag$<$0');
+
\ No newline at end of file
--
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