From dd62fee629cfff072ac40f4d6e5704afb0fff019 Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Mon, 15 Mar 2021 16:10:44 +0100
Subject: [PATCH] Added an option to start with only noise in phi for smoother
starts
---
matlab/setup.m | 4 ++--
matlab/write_fort90.m | 3 ++-
wk/daint_run.m | 12 ++++++------
wk/linear_study.m | 43 ++++++++++++++++++++++---------------------
wk/local_run.m | 23 ++++++++++++-----------
wk/marconi_run.m | 21 +++++++++++----------
6 files changed, 55 insertions(+), 51 deletions(-)
diff --git a/matlab/setup.m b/matlab/setup.m
index 6460fe51..6f42c2b2 100644
--- a/matlab/setup.m
+++ b/matlab/setup.m
@@ -34,10 +34,10 @@ MODEL.eta_n = ETAN; % source term kappa for HW
MODEL.eta_T = ETAT; % Temperature
MODEL.eta_B = ETAB; % Magnetic
MODEL.lambdaD = LAMBDAD;
-if A0KH ~= 0; SIMID = [SIMID,'_Nz_',num2str(L/2/pi*KR0KH),'_A_',num2str(A0KH)]; end;
+% if A0KH ~= 0; SIMID = [SIMID,'_Nz_',num2str(L/2/pi*KR0KH),'_A_',num2str(A0KH)]; end;
% Time integration and intialization parameters
TIME_INTEGRATION.numerical_scheme = '''RK4''';
-INITIAL.only_Na00 = '.false.';
+if INIT_PHI; INITIAL.init_noisy_phi = '.true.'; else; INITIAL.init_noisy_phi = '.false.';end;
INITIAL.initback_moments = 0.0e-5;
INITIAL.initnoise_moments = NOISE0;
INITIAL.iseed = 42;
diff --git a/matlab/write_fort90.m b/matlab/write_fort90.m
index bf34207b..1e2f98da 100644
--- a/matlab/write_fort90.m
+++ b/matlab/write_fort90.m
@@ -57,7 +57,8 @@ fprintf(fid,[' lambdaD = ', num2str(MODEL.lambdaD),'\n']);
fprintf(fid,'/\n');
fprintf(fid,'&INITIAL_CON\n');
-fprintf(fid,[' only_Na00 =', INITIAL.only_Na00,'\n']);
+fprintf(fid,[' INIT_NOISY_PHI =', INITIAL.init_noisy_phi,'\n']);
+% fprintf(fid,[' only_Na00 =', '.false.','\n']);
fprintf(fid,[' initback_moments =', num2str(INITIAL.initback_moments),'\n']);
fprintf(fid,[' initnoise_moments =', num2str(INITIAL.initnoise_moments),'\n']);
fprintf(fid,[' iseed =', num2str(INITIAL.iseed),'\n']);
diff --git a/wk/daint_run.m b/wk/daint_run.m
index 73efd98c..772458f0 100644
--- a/wk/daint_run.m
+++ b/wk/daint_run.m
@@ -6,7 +6,7 @@ addpath(genpath('../matlab')) % ... add
%% CLUSTER PARAMETERS
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.NTPN = '36'; % 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
@@ -15,8 +15,8 @@ CLUSTER.MEM = '12GB'; % Memory
CLUSTER.JNAME = 'gamma_inf';% Job name
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 1.0; % Collision frequency
-ETAB = 0.6; % Magnetic gradient
+NU = 0.1; % Collision frequency
+ETAB = 0.7; % Magnetic gradient
NU_HYP = 0.1; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
N = 200; % Frequency gridpoints (Nkr = N/2)
@@ -26,14 +26,14 @@ 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
-TMAX = 1000; % Maximal time unit
+TMAX = 2500; % 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 = 0; % Sampling per time unit for checkpoints
-RESTART = 0; % To restart from last checkpoint
-JOB2LOAD= 0;
+RESTART = 1; % To restart from last checkpoint
+JOB2LOAD= 1;
%% OPTIONS
% SIMID = ['debug']; % Name of the simulation
SIMID = ['Daint_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
diff --git a/wk/linear_study.m b/wk/linear_study.m
index 51d8c938..06f646f3 100644
--- a/wk/linear_study.m
+++ b/wk/linear_study.m
@@ -5,23 +5,23 @@ default_plots_options
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 1.0; % Collision frequency
+NU = 0.5; % Collision frequency
TAU = 1.0; % e/i temperature ratio
-ETAB = 0.6;
+ETAB = 0.5;
ETAN = 1.0; % Density gradient
ETAT = 0.0; % Temperature gradient
NU_HYP = 0.1; % Hyperdiffusivity coefficient
LAMBDAD = 0.0;
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
-N = 150; % Frequency gridpoints (Nkr = N/2)
-L = 70; % Size of the squared frequency domain
+N = 200; % Frequency gridpoints (Nkr = N/2)
+L = 120; % Size of the squared frequency domain
KREQ0 = 1; % put kr = 0
MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARMETERS
-TMAX = 100; % Maximal time unit
-DT = 1e-2; % Time step
+TMAX = 200; % Maximal time unit
+DT = 3e-2; % Time step
SPS0D = 0.5; % Sampling per time unit for 2D arrays
SPS2D = 1; % Sampling per time unit for 2D arrays
SPS5D = 1; % Sampling per time unit for 5D arrays
@@ -29,12 +29,12 @@ SPSCP = 0; % Sampling per time unit for checkpoints
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 00;
%% OPTIONS
-SIMID = 'linear_study_test_mu_kin'; % Name of the simulation
+SIMID = 'linear_study_test'; % Name of the simulation
NON_LIN = 0 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
CO = -3; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : 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)
-
+INIT_PHI= 0; % Start simulation with a noisy phi and moments
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% unused
@@ -48,13 +48,13 @@ MU = NU_HYP/(HD_CO*kmax)^4 % Hyperdiffusivity coefficient
%% PARAMETER SCANS
if 1
%% Parameter scan over PJ
-PA = [2, 3, 4, 6, 8, 10];
-JA = [1, 2, 2, 3, 4, 5];
-DTA= DT./sqrt(JA);
+% PA = [2, 3, 4, 6, 8, 10];
+% JA = [1, 2, 2, 3, 4, 5];
+% DTA= DT./sqrt(JA);
mup_ = MU_P;
muj_ = MU_J;
-% PA = [4];
-% JA = [2];
+PA = [8];
+JA = [4];
Nparam = numel(PA);
param_name = 'PJ';
gamma_Ni00 = zeros(Nparam,N/2+1);
@@ -65,13 +65,13 @@ for i = 1:Nparam
% Change scan parameter
PMAXE = PA(i); PMAXI = PA(i);
JMAXE = JA(i); JMAXI = JA(i);
- DT = DTA(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 4 ./../../../bin/helaz; cd ../../../wk']...
+ ['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ./../../../bin/helaz 1 6; cd ../../../wk']...
)
% Load and process results
load_results
@@ -86,40 +86,41 @@ for i = 1:Nparam
end
gamma_Ni00(i,:) = real(gamma_Ni00(i,:) .* (gamma_Ni00(i,:)>=0.0));
gamma_Ni21(i,:) = real(gamma_Ni21(i,:) .* (gamma_Ni21(i,:)>=0.0));
- kzmax = abs(kr(ikzmax));
- Bohm_transport(i) = ETAB/ETAN*gmax/kzmax^2;
+% kzmax = abs(kr(ikzmax));
+% Bohm_transport(i) = ETAB/ETAN*gmax/kzmax^2;
% Clean output
system(['rm -r ',BASIC.RESDIR])
end
if 1
%% Plot
+SCALE = sqrt(2);
fig = figure; FIGNAME = 'linear_study';
plt = @(x) x;
subplot(211)
for i = 1:Nparam
clr = line_colors(mod(i-1,numel(line_colors(:,1)))+1,:);
linestyle = line_styles(floor((i-1)/numel(line_colors(:,1)))+1);
- plot(plt(kr),plt(gamma_Ni00(i,:)),...
+ plot(plt(SCALE*kr),plt(gamma_Ni00(i,:)),...
'Color',clr,...
'LineStyle',linestyle{1},...
'DisplayName',['$P=$',num2str(PA(i)),', $J=$',num2str(JA(i))]);
hold on;
end
- grid on; xlabel('$k_z\rho_s$'); ylabel('$\gamma(N_i^{00})\rho_s/c_s$'); xlim([0.0,max(kr)]);
+ grid on; xlabel('$k_z\rho_s^{R}$'); ylabel('$\gamma(N_i^{00})\rho_s/c_s$'); xlim([0.0,max(kr)]);
title(['$\eta_B=',num2str(ETAB),'$, $\nu_{',CONAME,'}=',num2str(NU),'$, ', CLOSNAME])
legend('show')
subplot(212)
for i = 1:Nparam
clr = line_colors(mod(i-1,numel(line_colors(:,1)))+1,:);
linestyle = line_styles(floor((i-1)/numel(line_colors(:,1)))+1);
- plot(plt(kr),plt(gamma_Ni21(i,:)),...
+ plot(plt(SCALE*kr),plt(gamma_Ni21(i,:)),...
'Color',clr,...
'LineStyle',linestyle{1},...
'DisplayName',['$P=$',num2str(PA(i)),', $J=$',num2str(JA(i))]);
hold on;
end
- grid on; xlabel('$k_z\rho_s$'); ylabel('$\gamma(N_i^{21})\rho_s/c_s$'); xlim([0.0,max(kr)]);
+ grid on; xlabel('$k_z\rho_s^{R}$'); ylabel('$\gamma(N_i^{21})\rho_s/c_s$'); xlim([0.0,max(kr)]);
title(['$\eta_B=',num2str(ETAB),'$, $\nu_{',CONAME,'}=',num2str(NU),'$, ', CLOSNAME])
legend('show')
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
diff --git a/wk/local_run.m b/wk/local_run.m
index 856d8c64..142d0b92 100644
--- a/wk/local_run.m
+++ b/wk/local_run.m
@@ -4,34 +4,35 @@ addpath(genpath('../matlab')) % ... add
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 1.0; % Collision frequency
-ETAB = 0.5; % Magnetic gradient
+NU = 0.5; % Collision frequency
+ETAB = 0.6; % Magnetic gradient
ETAN = 1.0; % Density gradient
NU_HYP = 0.1;
%% GRID PARAMETERS
-N = 200; % Frequency gridpoints (Nkr = N/2)
-L = 125; % Size of the squared frequency domain
-PMAXE = 2; % Highest electron Hermite polynomial degree
+N = 50; % Frequency gridpoints (Nkr = N/2)
+L = 100; % Size of the squared frequency domain
+PMAXE = 10; % Highest electron Hermite polynomial degree
JMAXE = 1; % Highest '' Laguerre ''
-PMAXI = 2; % Highest ion Hermite polynomial degree
+PMAXI = 10; % Highest ion Hermite polynomial degree
JMAXI = 1; % Highest '' Laguerre ''
-
%% TIME PARAMETERS
-TMAX = 50; % Maximal time unit
-DT = 1e-2; % Time step
+TMAX = 10; % Maximal time unit
+DT = 2e-2; % Time step
SPS0D = 1/DT; % 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
+SPS5D = 1/4; % 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_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
% SIMID = sprintf(SIMID,NU);
+% SIMID = 'test_init_phi'; % 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)
+INIT_PHI= 1; % Start simulation with a noisy phi and moments
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% unused
@@ -43,7 +44,7 @@ NON_LIN = 1 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
kmax = N*pi/L;% Highest fourier mode
HD_CO = 0.5; % Hyper diffusivity cutoff ratio
% kmaxcut = 2.5;
-MU = NU_HYP/(kmax)^4 % Hyperdiffusivity coefficient
+MU = NU_HYP/(HD_CO*kmax)^4 % Hyperdiffusivity coefficient
NOISE0 = 1.0e-5;
TAU = 1.0; % e/i temperature ratio
ETAT = 0.0; % Temperature gradient
diff --git a/wk/marconi_run.m b/wk/marconi_run.m
index d53f5473..0b8a24c3 100644
--- a/wk/marconi_run.m
+++ b/wk/marconi_run.m
@@ -4,7 +4,7 @@ addpath(genpath('../matlab')) % ... add
%% Set Up parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% CLUSTER PARAMETERS
-CLUSTER.TIME = '12:00:00'; % allocation time hh:mm:ss
+CLUSTER.TIME = '24:00:00'; % allocation time hh:mm:ss
CLUSTER.NODES = '1'; % MPI process
CLUSTER.CPUPT = '1'; % CPU per task
CLUSTER.NTPN = '24'; % N tasks per node
@@ -13,14 +13,14 @@ CLUSTER.MEM = '16GB'; % Memory
CLUSTER.JNAME = 'gamma_inf';% Job name
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 1.0; % Collision frequency
+NU = 0.1; % Collision frequency
ETAB = 0.6; % Magnetic gradient
-NU_HYP = 0.2; % Hyperdiffusivity coefficient
+NU_HYP = 0.1; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
-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
+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
@@ -28,17 +28,18 @@ 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 = 1/4; % Sampling per time unit for 5D arrays
+SPS5D = 1/10; % 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_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
-% SIMID = 'Marconi_restart'; % Name of the simulation
+SIMID = ['Marconi_new_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
+% SIMID = 'Marconi_test'; % Name of the simulation
SIMID = sprintf(SIMID,NU);
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)
+INIT_PHI= 0; % Start simulation with a noisy phi and moments
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% fixed parameters (for current study)
--
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