From 7a631a931c3d6941e01aa64969c72a9800a60357 Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Mon, 7 Dec 2020 16:08:10 +0100
Subject: [PATCH] minor changes
---
src/srcinfo.h | 4 +--
src/srcinfo/srcinfo.h | 4 +--
wk/analysis_2D.m | 25 ++++++++------
wk/flux_results.m | 2 +-
wk/fort.90 | 16 ++++-----
wk/linear_study.m | 76 +++++++++++++++++++++++++++++--------------
wk/parameters_ZP.m | 3 +-
wk/setup.m | 2 ++
wk/test_parallel.m | 11 ++++---
9 files changed, 89 insertions(+), 54 deletions(-)
diff --git a/src/srcinfo.h b/src/srcinfo.h
index be4f109c..036a616f 100644
--- a/src/srcinfo.h
+++ b/src/srcinfo.h
@@ -3,8 +3,8 @@ character(len=40) BRANCH
character(len=20) AUTHOR
character(len=40) EXECDATE
character(len=40) HOST
-parameter (VERSION='8dcebe0-dirty')
+parameter (VERSION='15a591a-dirty')
parameter (BRANCH='MPI')
parameter (AUTHOR='ahoffman')
-parameter (EXECDATE='Fri Nov 27 17:13:58 CET 2020')
+parameter (EXECDATE='Thu Dec 3 10:18:01 CET 2020')
parameter (HOST ='spcpc606')
diff --git a/src/srcinfo/srcinfo.h b/src/srcinfo/srcinfo.h
index be4f109c..036a616f 100644
--- a/src/srcinfo/srcinfo.h
+++ b/src/srcinfo/srcinfo.h
@@ -3,8 +3,8 @@ character(len=40) BRANCH
character(len=20) AUTHOR
character(len=40) EXECDATE
character(len=40) HOST
-parameter (VERSION='8dcebe0-dirty')
+parameter (VERSION='15a591a-dirty')
parameter (BRANCH='MPI')
parameter (AUTHOR='ahoffman')
-parameter (EXECDATE='Fri Nov 27 17:13:58 CET 2020')
+parameter (EXECDATE='Thu Dec 3 10:18:01 CET 2020')
parameter (HOST ='spcpc606')
diff --git a/wk/analysis_2D.m b/wk/analysis_2D.m
index a47bcc7a..080186af 100644
--- a/wk/analysis_2D.m
+++ b/wk/analysis_2D.m
@@ -1,4 +1,9 @@
%% Load results
+if LOAD_MARCONI
+ hostfolder = ['/marconi_scratch/userexternal/ahoffman/HeLaZ/results/',BASIC.SIMID,'/',BASIC.PARAMS];
+ localfolder= [BASIC.RESDIR,'..'];
+ system(['scp -r ahoffman@login.marconi.cineca.it:',hostfolder,' ',localfolder])
+end
% JOBNUM = 0; load_results;
% JOBNUM = 1; load_results;
compile_results
@@ -233,7 +238,7 @@ save_figure
end
%%
-t0 = 0;
+t0 = 50;
skip_ = 1;
DELAY = 0.01*skip_;
FRAMES = floor(t0/(Ts2D(2)-Ts2D(1)))+1:skip_:numel(Ts2D);
@@ -358,20 +363,20 @@ end
%%
if 0
%% Show frame in kspace
-tf = 20; [~,it] = min(abs(Ts5D-tf));
-fig = figure; FIGNAME = ['krkz_frame',sprintf('_%.2d',JOBNUM)];
+tf = 200; [~,it2] = min(abs(Ts2D-tf)); [~,it5] = min(abs(Ts5D-tf));
+fig = figure; FIGNAME = ['krkz_frame',sprintf('t=%.0f',Ts2D(it2))];set(gcf, 'Position', [100, 100, 700, 600])
subplot(221); plt = @(x) fftshift((abs(x)),2);
- pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(PHI(:,:,it))); set(pclr, 'edgecolor','none'); colorbar;
- xlabel('$k_r$'); ylabel('$k_z$'); title(sprintf('t=%.3d',Ts5D(it))); legend('$|\hat\phi|$');
+ pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(PHI(:,:,it2))); set(pclr, 'edgecolor','none'); colorbar;
+ xlabel('$k_r$'); ylabel('$k_z$'); title(sprintf('$t c_s/R=%.0f$',Ts2D(it2))); legend('$|\hat\phi|$');
subplot(222); plt = @(x) fftshift(abs(x),2);
- pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(Ni00(:,:,it))); set(pclr, 'edgecolor','none'); colorbar;
- xlabel('$k_r$'); ylabel('$k_z$'); title(sprintf('t=%.3d',Ts5D(it))); legend('$|\hat n_i^{00}|$');
+ pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(Ni00(:,:,it2))); set(pclr, 'edgecolor','none'); colorbar;
+ xlabel('$k_r$'); ylabel('$k_z$'); legend('$|\hat n_i^{00}|$');
subplot(223); plt = @(x) fftshift(abs(x),2);
- pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(Ne00(:,:,it))); set(pclr, 'edgecolor','none'); colorbar;
- xlabel('$k_r$'); ylabel('$k_z$'); title(sprintf('t=%.3d',Ts5D(it))); legend('$|\hat n_e^{00}|$');
+ pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(Ne00(:,:,it2))); set(pclr, 'edgecolor','none'); colorbar;
+ xlabel('$k_r$'); ylabel('$k_z$'); legend('$|\hat n_e^{00}|$');
if strcmp(OUTPUTS.write_non_lin,'.true.')
subplot(224); plt = @(x) fftshift((abs(x)),2);
- pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(Si00(:,:,it))); set(pclr, 'edgecolor','none'); colorbar;
+ pclr = pcolor(fftshift(KR,2),fftshift(KZ,2),plt(Si00(:,:,it5))); set(pclr, 'edgecolor','none'); colorbar;
xlabel('$k_r$'); ylabel('$k_z$');legend('$\hat S_i^{00}$');
end
save_figure
diff --git a/wk/flux_results.m b/wk/flux_results.m
index 2ff3e223..566c6308 100644
--- a/wk/flux_results.m
+++ b/wk/flux_results.m
@@ -88,7 +88,7 @@ end
end
grid on; title('$\nu = 0.1$')
legend('Mix. Length, Ricci 2006','$P=2$, $J=1$','$P=3$, $J=2$','$P=4$, $J=2$')
-FIGNAME = [SIMDIR,'flux_study_nu_1e-2.png'];
+FIGNAME = [SIMDIR,'flux_study_nu_1e-1.png'];
saveas(fig,FIGNAME);
disp(['Figure saved @ : ',FIGNAME])
end
\ No newline at end of file
diff --git a/wk/fort.90 b/wk/fort.90
index b2f3f7a2..21d7c268 100644
--- a/wk/fort.90
+++ b/wk/fort.90
@@ -1,23 +1,23 @@
&BASIC
nrun = 100000000
dt = 0.005
- tmax = 200
- RESTART = .true.
+ tmax = 100
+ RESTART = .false.
/
&GRID
pmaxe =2
jmaxe = 1
pmaxi = 2
jmaxi = 1
- Nr = 400
+ Nr = 512
Lr = 100
- Nz = 400
+ Nz = 512
Lz = 100
kpar = 0
CANCEL_ODD_P = .false.
/
&OUTPUT_PAR
- nsave_0d = 200
+ nsave_0d = 4
nsave_1d = 0
nsave_2d = 200
nsave_5d = 2000
@@ -26,8 +26,8 @@
write_phi = .true.
write_non_lin = .true.
write_doubleprecision = .true.
- resfile0 = '../results/test_parallel/400x200_L_100_Pe_2_Je_1_Pi_2_Ji_1_nB_0.6_nN_1_nu_1e-01_FC_mu_5e-04/outputs'
- rstfile0 = '../results/test_parallel/400x200_L_100_Pe_2_Je_1_Pi_2_Ji_1_nB_0.6_nN_1_nu_1e-01_FC_mu_5e-04/checkpoint'
+ resfile0 = '../results/Marconi/512x256_L_100_Pe_2_Je_1_Pi_2_Ji_1_nB_0.5_nN_1_nu_1e-01_FC_mu_5e-04/outputs'
+ rstfile0 = '../results/Marconi/512x256_L_100_Pe_2_Je_1_Pi_2_Ji_1_nB_0.5_nN_1_nu_1e-01_FC_mu_5e-04/checkpoint'
job2load = 0
/
&MODEL_PAR
@@ -45,7 +45,7 @@
q_i = 1
eta_n = 1
eta_T = 0
- eta_B = 0.6
+ eta_B = 0.5
lambdaD = 0
kr0KH = 0
A0KH = 0
diff --git a/wk/linear_study.m b/wk/linear_study.m
index 0e08540a..b84475b5 100644
--- a/wk/linear_study.m
+++ b/wk/linear_study.m
@@ -1,38 +1,37 @@
-clear all;
+%clear all;
addpath(genpath('../matlab')) % ... add
default_plots_options
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 1e-2; % Collision frequency
+NU = 1e0; % Collision frequency
TAU = 1.0; % e/i temperature ratio
-ETAB = 0.8;
+ETAB = 0.5;
ETAN = 1.0; % Density gradient
ETAT = 0.0; % Temperature gradient
-MU = 1e-4; % Hyper diffusivity coefficient
+MU = 0e-4; % Hyper diffusivity coefficient
LAMBDAD = 0.0;
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
-N = 40; % Frequency gridpoints (Nkr = N/2)
-L = 60; % Size of the squared frequency domain
+N = 50; % Frequency gridpoints (Nkr = N/2)
+L = 100; % Size of the squared frequency domain
PMAXE = 12;
JMAXE = 6;
PMAXI = 12;
JMAXI = 6;
KREQ0 = 1; % put kr = 0
-CANCEL_ODD_P = 1;% Cancels the odd polynomials degree
%% TIME PARAMETERS
TMAX = 300; % Maximal time unit
-DT = 3e-2; % Time step
+DT = 1e-3; % Time step
SPS0D = 0.5; % Sampling per time unit for 2D arrays
SPS2D = 1; % Sampling per time unit for 2D arrays
SPS5D = 0.1; % Sampling per time unit for 5D arrays
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 00;
%% OPTIONS
-SIMID = 'test_linear_study'; % Name of the simulation
-NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
+SIMID = 'linear_study'; % Name of the simulation
+NON_LIN = 0 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
CO = -1; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -41,29 +40,27 @@ KR0KH = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
NO_E = 0; % Remove electrons dynamic
% DK = 0; % Drift kinetic model (put every kernel_n to 0 except n=0 to 1)
JOBNUM = 00;
+CANCEL_ODD_P = 0;% Cancels the odd polynomials degree
KPAR = 0.0 * (1-CANCEL_ODD_P); % Parellel wave vector component
-setup
-
-
%% PARAMETER SCANS
-if 0
+if 1
%% Parameter scan over PJ
NU = 1e-2; % Collision frequency
-ETAB = 1.0;
+ETAB = 0.5;
ETAN = 1.0;
TMAX = 400;
-PA = [2,6,10,14,20,40,80];
-JA = [1,3,5,7,10,20,20];
-% PA = [4];
-% JA = [2];
+PA = [2, 8, 12, 20, 40];
+JA = [1, 4, 6, 10, 20];
+% PA = [40];
+% JA = [20];
Nparam = numel(PA);
param_name = 'PJ';
CO = -2; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
DT = 5e-3; % Time step
gamma_Ni = zeros(Nparam,N);
-
+Ni00_ST = zeros(Nparam,N,TMAX);
for i = 1:Nparam
% Change scan parameter
PMAXE = PA(i); PMAXI = PA(i);
@@ -73,15 +70,44 @@ for i = 1:Nparam
system('./../bin/helaz');
% Load and process results
load_results
- tend = Ts2D(end); tstart = 0.9*tend;
+ tend = Ts2D(end); tstart = 0.4*tend;
for ikz = 1:N
gamma_Ni(i,ikz) = LinearFit_s(Ts2D,squeeze(abs(Ni00(1,ikz,:))),tstart,tend);
+ Ni00_ST(i,ikz,1:numel(Ts2D)) = squeeze((Ni00(1,ikz,:)));
end
gamma_Ni(i,:) = real(gamma_Ni(i,:) .* (gamma_Ni(i,:)>=0.0));
% Clean output
-% system(['rm -r ',BASIC.RESDIR])
+ %system(['rm -r ',BASIC.RESDIR])
+end
+% if 0
+% %% Plot
+% fig = figure; FIGNAME = 'space_time_Ni00';
+% i = 1;
+%
+% [YY, XX] = meshgrid(Ts2D,kz);
+% plt = @(x) squeeze(log(abs(x)))
+% pclr = pcolor(XX,YY,plt(Ni00_ST(i,:,:)));set(pclr, 'edgecolor','none');
+% grid on; xlabel('$k_z$'); ylabel('$t$');
+% title(['$\eta_B=',num2str(ETAB),'$,$P,J=',num2str(PA(i)),',',JA(i),'$'])
+% legend('show')
+% saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
+% saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.png']);
+% end
+if 0
+%% Plot
+fig = figure; FIGNAME = 'space_time_Ni00';
+i = 3;
+plt = @(x) squeeze((abs(x)));
+for ikz=1:4:numel(kz)/2+1
+ NAME = ['$k_z=',num2str(kz(ikz)),'$'];
+ semilogy(1:TMAX,plt(Ni00_ST(i,ikz,1:TMAX)), 'DisplayName', NAME); hold on;
+end
+grid on; xlabel('$t c_s/\rho_s$'); ylabel('$|Ni^{00}|$');
+title(['$\eta_B=',num2str(ETAB),'$; $P,J=',num2str(PA(i)),',',num2str(JA(i)),'$, $\nu=',num2str(NU),'$'])
+legend('show');
+saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
+saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.png']);
end
-
if 1
%% Plot
fig = figure; FIGNAME = 'linear_study';
@@ -96,7 +122,7 @@ for i = 1:Nparam
hold on;
end
grid on; xlabel('$k_z$'); ylabel('$\gamma(N_i^{00})$'); xlim([0.0,max(kz)]);
-title(['$\eta_B=',num2str(ETAB),'$'])
+title(['$\eta_B=',num2str(ETAB),'$, $\nu=',num2str(NU),'$'])
legend('show')
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.png']);
@@ -145,7 +171,7 @@ for i = 1:Nparam
'DisplayName',['$\eta_B=$',num2str(eta_B(i))]);
hold on;
end
-grid on; xlabel('$k_z$'); ylabel('$\gamma(N_i^{00})$'); xlim([0.0,max(kz)]);
+grid on; xlabel('$k_z\rho_s$'); ylabel('$\gamma(N_i^{00})\rho_2/c_s$'); xlim([0.0,max(kz)]);
title(['$P_e=',num2str(PMAXE),'$',', $J_e=',num2str(JMAXE),'$',...
', $P_i=',num2str(PMAXE),'$',', $J_i=',num2str(JMAXI),'$'])
legend('show')
diff --git a/wk/parameters_ZP.m b/wk/parameters_ZP.m
index e41c7578..7991aa72 100644
--- a/wk/parameters_ZP.m
+++ b/wk/parameters_ZP.m
@@ -1,4 +1,4 @@
-clear all;
+%clear all;
addpath(genpath('../matlab')) % ... add
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
@@ -39,6 +39,7 @@ KREQ0 = 0; % put kr = 0
KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
+LOAD_MARCONI = 0;
CANCEL_ODD_P = 0;% Cancels the odd polynomials degree
setup
diff --git a/wk/setup.m b/wk/setup.m
index 5c48f1a9..588e5354 100644
--- a/wk/setup.m
+++ b/wk/setup.m
@@ -73,6 +73,8 @@ resolution = [num2str(GRID.Nr),'x',num2str(GRID.Nz/2),'_'];
gridname = ['L_',num2str(L),'_'];
PARAMS = [resolution,gridname,degngrad];
BASIC.RESDIR = [SIMDIR,PARAMS,'/'];
+BASIC.PARAMS = PARAMS;
+BASIC.SIMID = SIMID;
BASIC.nrun = 1e8;
BASIC.dt = DT;
BASIC.tmax = TMAX; %time normalized to 1/omega_pe
diff --git a/wk/test_parallel.m b/wk/test_parallel.m
index 12a28d4b..2eb69bbc 100644
--- a/wk/test_parallel.m
+++ b/wk/test_parallel.m
@@ -6,26 +6,26 @@ addpath(genpath('../matlab')) % ... add
%% PHYSICAL PARAMETERS
NU = 1e-1; % 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
MU = 5e-4; % Hyper diffusivity coefficient
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
-N = 400; % Frequency gridpoints (Nkr = N/2)
+N = 512; % Frequency gridpoints (Nkr = N/2)
L = 100; % 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 = 200; % Maximal time unit
-DT = 5e-3; % Time step
+TMAX = 100; % 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
SPS5D = 0.1; % Sampling per time unit for 5D arrays
RESTART = 1; % To restart from last checkpoint
-JOB2LOAD= 0;
+JOB2LOAD= 1;
%% OPTIONS
SIMID = 'test_parallel'; % Name of the simulation
CO = -1; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
@@ -40,5 +40,6 @@ KPAR = 0.0; % Parellel wave vector component
LAMBDAD = 0.0;
NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
CANCEL_ODD_P = 0;% Cancels the odd polynomials degree
+MARCONI = 0;
setup
--
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