From 5caf879b882ac86b156963f026e04200b3040fab Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Wed, 3 Mar 2021 11:24:38 +0100
Subject: [PATCH] update scripts
---
wk/analysis_2D.m | 81 +++++++++++++++++-------------------------------
wk/daint_run.m | 24 +++++++-------
wk/local_run.m | 43 +++++++++++++------------
wk/marconi_run.m | 15 +++++----
wk/untitled.m | 32 +++++++++++++++++++
5 files changed, 102 insertions(+), 93 deletions(-)
create mode 100644 wk/untitled.m
diff --git a/wk/analysis_2D.m b/wk/analysis_2D.m
index 8a1cb01e..00306a61 100644
--- a/wk/analysis_2D.m
+++ b/wk/analysis_2D.m
@@ -1,12 +1,20 @@
%% Load results
+outfile ='';
if 0
- %%
+ %% Load from Marconi
outfile ='';
outfile ='';
- outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_DGGK_eta_0.6_nu_1e+00/150x75_L_70_P_10_J_5_eta_0.6_nu_1e+00_DGGK_CLOS_0_mu_8e-04/out.txt';
-
+ outfile ='/marconi_scratch/userexternal/ahoffman/HeLaZ/results/Marconi_DGGK_eta_0.6_nu_1e+00/300x150_L_70_P_10_J_5_eta_0.6_nu_1e+00_DGGK_CLOS_0_mu_1e-04/out.txt';
BASIC.RESDIR = load_marconi(outfile);
end
+if 0
+ %% Load from Daint
+ outfile ='';
+ outfile ='';
+ outfile ='/scratch/snx3000/ahoffman/HeLaZ/results/Daint_eta_0.6_nu_1e-01/200x100_L_70_P_12_J_6_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_1e-03/out.txt';
+% outfile ='/scratch/snx3000/ahoffman/HeLaZ/results/Daint_eta_0.6_nu_1e-01/150x75_L_70_P_12_J_6_eta_0.6_nu_1e-01_DGGK_CLOS_0_mu_2e-03/out.txt';
+ BASIC.RESDIR = load_daint(outfile);
+end
%%
% JOBNUM = 0; load_results;
% JOBNUM = 1; load_results;
@@ -143,7 +151,6 @@ disp('- growth rate')
[~,itmax] = max(GFlux_ri);
tstart = 0.1 * Ts2D(itmax); tend = 0.9 * Ts2D(itmax);
g_ = zeros(Nkr,Nkz);
-[~,ikr0KH] = min(abs(kr-KR0KH));
for ikr = 1:Nkr
for ikz = 1:Nkz
g_(ikr,ikz) = LinearFit_s(Ts2D,squeeze(abs(Ni00(ikr,ikz,:))),tstart,tend);
@@ -206,22 +213,17 @@ end
if 1
%% Particle fluxes
+SCALING = Nkr*dkr * Nkz*dkz;
fig = figure; FIGNAME = ['gamma',sprintf('_%.2d',JOBNUM)];
-set(gcf, 'Position', [100, 100, 1200, 400])
- subplot(211)
- plot(Ts2D,GFlux_ri); hold on
- plot(Ts5D,PFlux_ri,'--'); hold on
- ylabel('$\Gamma_r$'); grid on
+set(gcf, 'Position', [100, 100, 800, 300])
+ plot(Ts2D,GFLUX_RI, 'color', line_colors(2,:)); hold on
+ plot(Ts5D,PFLUX_RI,'.', 'color', line_colors(2,:)); hold on
+ plot(Ts2D,SCALING*GFlux_ri, 'color', line_colors(1,:)); hold on
+ plot(Ts5D,SCALING*PFlux_ri,'.', 'color', line_colors(1,:)); hold on
+ xlabel('$tc_{s0}/\rho_s$'); ylabel('$\Gamma_r$'); grid on
title(['$\eta=',num2str(ETAB),'\quad',...
- '\nu_{',CONAME,'}=',num2str(NU),'$'])
- legend(['$P=',num2str(PMAXI),'$, $J=',num2str(JMAXI),'$'],'Particle flux')%'$\eta\gamma_{max}/k_{max}^2$')
- subplot(212)
- plot(Ts2D,GFLUX_RI); hold on
- plot(Ts5D,PFLUX_RI,'--'); hold on
- ylabel('$\Gamma_r$'); grid on
- title(['$\eta=',num2str(ETAB),'\quad',...
- '\nu_{',CONAME,'}=',num2str(NU),'$'])
- legend(['$P=',num2str(PMAXI),'$, $J=',num2str(JMAXI),'$'],'Particle flux')%'$\eta\gamma_{max}/k_{max}^2$')
+ '\nu_{',CONAME,'}=',num2str(NU),'$', ' $P=',num2str(PMAXI),'$, $J=',num2str(JMAXI),'$'])
+ legend('Gyro Flux','Particle flux', 'iFFT GFlux', 'iFFT PFlux')%'$\eta\gamma_{max}/k_{max}^2$')
save_figure
end
@@ -229,9 +231,8 @@ if 1
%% Space time diagramm (fig 11 Ivanov 2020)
fig = figure; FIGNAME = 'space_time_drphi';set(gcf, 'Position', [100, 100, 1200, 600])
subplot(311)
- plot(Ts2D,GFlux_ri); hold on
- plot(Ts5D,PFlux_ri,'.'); hold on
- plot(Ts2D,GFLUX_RI,'--'); hold on
+ plot(Ts2D,GFLUX_RI,'-'); hold on
+ plot(Ts5D,PFLUX_RI,'.'); hold on
% plot(Ts2D,Bohm_transport*ones(size(Ts2D)),'--'); hold on
ylabel('$\Gamma_r$'); grid on
title(['$\eta=',num2str(ETAB),'\quad',...
@@ -354,13 +355,6 @@ FIELD = real(ni00); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
FIELDNAME = '$n_i$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
create_gif
end
-if 0
-%% Density electron
-GIFNAME = ['ne',sprintf('_%.2d',JOBNUM)]; INTERP = 1;
-FIELD = real(ne00); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
-FIELDNAME = '$n_e$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
-create_gif
-end
if 1
%% Phi real space
GIFNAME = ['phi',sprintf('_%.2d',JOBNUM)];INTERP = 1;
@@ -368,6 +362,13 @@ FIELD = real(phi); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
FIELDNAME = '$\phi$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
create_gif
end
+if 0
+%% radial particle transport
+GIFNAME = ['gamma_r',sprintf('_%.2d',JOBNUM)]; INTERP = 1;
+FIELD = real(ni00.*dzphi); X = RR; Y = ZZ; T = Ts2D; FRAMES = FRAMES_2D;
+FIELDNAME = '$\Gamma_r$'; XNAME = '$r/\rho_s$'; YNAME = '$z/\rho_s$';
+create_gif
+end
if 1
%% Phi fourier
GIFNAME = ['FFT_phi',sprintf('_%.2d',JOBNUM)];INTERP = 0;
@@ -391,14 +392,6 @@ FIELDNAME = '$N_i^{00}$'; XNAME = '$k_r\rho_s$'; YNAME = '$k_z\rho_s$';
create_gif
end
if 0
-%% Density ion frequency @ kr = 0
-GIFNAME = ['Ni00_kr0',sprintf('_%.2d',JOBNUM)]; INTERP = 0;
-FIELD =(squeeze(abs(Ni00(1,:,:)))); linestyle = 'o-.'; FRAMES = FRAMES_2D;
-X = (kz); T = Ts2D; YMIN = -.1; YMAX = 1.1; XMIN = min(kz); XMAX = max(kz);
-FIELDNAME = '$N_i^{00}(kr=0)$'; XNAME = '$k_r\rho_s$';
-create_gif_1D
-end
-if 0
%% kr vs P Si
GIFNAME = ['Sip0_kr',sprintf('_%.2d',JOBNUM)]; INTERP = 0;
plt = @(x) squeeze(max((abs(x)),[],4));
@@ -422,20 +415,4 @@ FIELD = plt(Nipj); X = sort(kz'); Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
FIELDNAME = 'N_i'; XNAME = '$k_z\rho_s$'; YNAME = '$P$, ${k_r}^{max}$';
create_gif_5D
end
-if 0
-%% maxkz, kr vs p, for all Nepj over time
-GIFNAME = ['Nepj_kr',sprintf('_%.2d',JOBNUM)]; INTERP = 0;
-plt = @(x) squeeze(max((abs(x)),[],4));
-FIELD = plt(Nepj); X = kr'; Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
-FIELDNAME = 'N_e'; XNAME = '$k_r\rho_s$'; YNAME = '$P$, ${k_z}^{max}$';
-create_gif_5D
-end
-if 0
-%% maxkz, kz vs p, for all Nepj over time
-GIFNAME = ['Nepj_kz',sprintf('_%.2d',JOBNUM)]; INTERP = 0;
-plt = @(x) fftshift(squeeze(max((abs(x)),[],3)),3);
-FIELD = plt(Nepj); X = sort(kz'); Y = Pi'; T = Ts5D; FRAMES = FRAMES_5D;
-FIELDNAME = 'N_e'; XNAME = '$k_z\rho_s$'; YNAME = '$P$, ${k_r}^{max}$';
-create_gif_5D
-end
%%
\ No newline at end of file
diff --git a/wk/daint_run.m b/wk/daint_run.m
index 6b343440..73efd98c 100644
--- a/wk/daint_run.m
+++ b/wk/daint_run.m
@@ -4,23 +4,25 @@ addpath(genpath('../matlab')) % ... add
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CLUSTER PARAMETERS
-CLUSTER.TIME = '06:00:00'; % allocation time hh:mm:ss
-CLUSTER.NODES = '1'; % MPI process
-CLUSTER.CPUPT = '1'; % CPU per task
-CLUSTER.NTPN = '24'; % N tasks per node
-CLUSTER.PART = 'normal'; % debug or normal
+CLUSTER.TIME = '24:00:00'; % allocation time hh:mm:ss
+CLUSTER.NODES = '1'; % number of nodes
+CLUSTER.NTPN = '32'; % N tasks per node (mpi processes)
+CLUSTER.NTPC = '1'; % N tasks per core (openmp threads)
+CLUSTER.CPUPT = '1'; % CPU per task (number of CPU per mpi proc)
+CLUSTER.PART = 'normal'; % debug or normal
+if(strcmp(CLUSTER.PART,'debug')); CLUSTER.TIME = '00:30:00'; end;
CLUSTER.MEM = '12GB'; % Memory
CLUSTER.JNAME = 'gamma_inf';% Job name
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 0.1; % Collision frequency
+NU = 1.0; % Collision frequency
ETAB = 0.6; % Magnetic gradient
-NU_HYP = 0.2; % Hyperdiffusivity coefficient
+NU_HYP = 0.1; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
-N = 150; % Frequency gridpoints (Nkr = N/2)
-L = 70; % Size of the squared frequency domain
-P = 12; % Electron and Ion highest Hermite polynomial degree
-J = 06; % Electron and Ion highest Laguerre polynomial degree
+N = 200; % Frequency gridpoints (Nkr = N/2)
+L = 120; % Size of the squared frequency domain
+P = 10; % Electron and Ion highest Hermite polynomial degree
+J = 05; % Electron and Ion highest Laguerre polynomial degree
MU_P = 0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARAMETERS
diff --git a/wk/local_run.m b/wk/local_run.m
index bce436f3..856d8c64 100644
--- a/wk/local_run.m
+++ b/wk/local_run.m
@@ -5,36 +5,30 @@ CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 1.0; % Collision frequency
-TAU = 1.0; % e/i temperature ratio
-ETAB = 0.6; % Magnetic gradient
+ETAB = 0.5; % Magnetic gradient
ETAN = 1.0; % Density gradient
-ETAT = 0.0; % Temperature gradient
-HD_CO = 0.5; % Hyper diffusivity cutoff ratio
NU_HYP = 0.1;
%% GRID PARAMETERS
-N = 150; % Frequency gridpoints (Nkr = N/2)
-L = 70; % Size of the squared frequency domain
-PMAXE = 4; % Highest electron Hermite polynomial degree
-JMAXE = 4; % Highest '' Laguerre ''
-PMAXI = 4; % Highest ion Hermite polynomial degree
-JMAXI = 4; % Highest '' Laguerre ''
-MU_P = 0.1/PMAXI^2; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
-MU_J = 0.1/JMAXI^3; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
+N = 200; % Frequency gridpoints (Nkr = N/2)
+L = 125; % Size of the squared frequency domain
+PMAXE = 2; % Highest electron Hermite polynomial degree
+JMAXE = 1; % Highest '' Laguerre ''
+PMAXI = 2; % Highest ion Hermite polynomial degree
+JMAXI = 1; % Highest '' Laguerre ''
+
%% TIME PARAMETERS
-TMAX = 600; % Maximal time unit
-DT = 2e-2; % Time step
+TMAX = 50; % Maximal time unit
+DT = 1e-2; % Time step
SPS0D = 1/DT; % Sampling per time unit for profiler
-SPS2D = 1; % Sampling per time unit for 2D arrays
-SPS5D = 1; % Sampling per time unit for 5D arrays
+SPS2D = 1/2; % Sampling per time unit for 2D arrays
+SPS5D = 1/10; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints/10
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 0;
%% OPTIONS
-% SIMID = 'local_nu_%0.0e'; % Name of the simulation
+% SIMID = ['local_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
% SIMID = sprintf(SIMID,NU);
-% SIMID = 'Marconi_DGGK_nu_1e+00'; % Name of the simulation
-% SIMID = 'test_sapj_cut'; % Name of the simulation
-SIMID = 'test_moments_damping'; % Name of the simulation
+SIMID = 'test_parallel_p'; % Name of the simulation
CO = -3; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty, -3 : GK Dougherty)
CLOS = 0; % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
KERN = 0; % Kernel model (0 : GK)
@@ -47,9 +41,14 @@ KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
kmax = N*pi/L;% Highest fourier mode
-MU = NU_HYP/(HD_CO*kmax)^4 % Hyperdiffusivity coefficient
+HD_CO = 0.5; % Hyper diffusivity cutoff ratio
+% kmaxcut = 2.5;
+MU = NU_HYP/(kmax)^4 % Hyperdiffusivity coefficient
NOISE0 = 1.0e-5;
-
+TAU = 1.0; % e/i temperature ratio
+ETAT = 0.0; % Temperature gradient
+MU_P = 0.0/PMAXI^2; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
+MU_J = 0.0/JMAXI^3; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% Setup and file management
setup
system('rm fort.90');
\ No newline at end of file
diff --git a/wk/marconi_run.m b/wk/marconi_run.m
index 646ea136..d53f5473 100644
--- a/wk/marconi_run.m
+++ b/wk/marconi_run.m
@@ -15,25 +15,24 @@ CLUSTER.JNAME = 'gamma_inf';% Job name
%% PHYSICAL PARAMETERS
NU = 1.0; % Collision frequency
ETAB = 0.6; % Magnetic gradient
-NU_HYP = 0.1; % Hyperdiffusivity coefficient
+NU_HYP = 0.2; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
-N = 150; % Frequency gridpoints (Nkr = N/2)
+N = 200; % Frequency gridpoints (Nkr = N/2)
L = 70; % Size of the squared frequency domain
P = 10; % Electron and Ion highest Hermite polynomial degree
J = 5; % Electron and Ion highest Laguerre polynomial degree
MU_P = 0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARAMETERS
-TMAX = 500; % Maximal time unit
+TMAX = 1000; % Maximal time unit
DT = 1e-2; % Time step
SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1/2; % Sampling per time unit for 2D arrays
-SPS5D = 1/10; % Sampling per time unit for 5D arrays
-SPSCP = 1/10; % Sampling per time unit for checkpoints
-RESTART = 1; % To restart from last checkpoint
+SPS5D = 1/4; % Sampling per time unit for 5D arrays
+SPSCP = 0; % Sampling per time unit for checkpoints
+RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 0;
%% OPTIONS
-% SIMID = 'Marconi_DGGK_nu_%0.0e'; % Name of the simulation
SIMID = ['Marconi_DGGK_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
% SIMID = 'Marconi_restart'; % Name of the simulation
SIMID = sprintf(SIMID,NU);
@@ -61,6 +60,6 @@ ETAN = 1.0; % Density gradient
TAU = 1.0; % e/i temperature ratio
%% Run file management scripts
setup
-write_sbash
+write_sbash_marconi
system('rm fort.90 setup_and_run.sh batch_script.sh');
disp('done');
diff --git a/wk/untitled.m b/wk/untitled.m
new file mode 100644
index 00000000..73a43949
--- /dev/null
+++ b/wk/untitled.m
@@ -0,0 +1,32 @@
+N = 100;
+L = 20;
+
+A0 = 2;
+N0 = 4;
+K0 = 2*pi/L*N0;
+
+f = @(x_) A0 * sin(K0*x_);
+
+
+x = linspace(0,L, N);
+
+dk= 2*pi/L;
+k = dk*(-N/2:N/2-1);
+
+F = zeros(1,N);
+
+[~,ik0p] = min(abs(k-K0));
+[~,ik0m] = min(abs(k+K0));
+
+F(ik0p) = -A0/2 * 1i/dk;
+F(ik0m) = A0/2 * 1i/dk;
+
+
+f_ = ifft(fftshift(F));
+figure
+plot(x,f(x)); hold on;
+plot(x,N*dk*f_)
+
+%%
+figure
+plot(k,imag(F))
\ No newline at end of file
--
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