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gyacomo/wk/linear_study.m
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linear_study.m
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for NU = [0.14]
for ETAB = [1/1.4]
for CO = [3]
%clear all;
addpath(genpath('../matlab')) % ... add
default_plots_options
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
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 = 0.5;
ETAN = 1.0; % Density gradient
ETAT = 0.0; % Temperature gradient
NU_HYP = 0.0; % Hyperdiffusivity coefficient
LAMBDAD = 0.0;
NOISE0 = 1.0e-5;
%% GRID PARAMETERS
N = 50; % Frequency gridpoints (Nkr = N/2)
L = 100; % 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
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = 1; % Sampling per time unit for 2D arrays
SPS5D = 1/200; % Sampling per time unit for 5D arrays
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
NON_LIN = 0 *(1-KREQ0); % activate non-linearity (is cancelled if KREQ0 = 1)
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : 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)
NL_CLOS = 0; % nonlinear closure model (0: =0 nmax = jmax, 1: nmax = jmax-j, >1 : nmax = NL_CLOS)
KERN = 0; % Kernel model (0 : GK)
INIT_PHI= 0; % Start simulation with a noisy phi
INIT_ZF = 0; % Start simulation with a noisy phi
%% OUTPUTS
W_DOUBLE = 0;
W_GAMMA = 0;
W_PHI = 0;
W_NA00 = 1;
W_NAPJ = 1;
W_SAPJ = 0;
W_DENS = 0;
W_TEMP = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% unused
% DK = 0; % Drift kinetic model (put every kernel_n to 0 except n=0 to 1)
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
%% PARAMETER SCANS
if 1
%% Parameter scan over PJ
PA = [2, 6, 10];
JA = [1, 3, 5];
% PA = [2 4];
% JA = [1 2];
DTA= DT./sqrt(JA)/4;
% DTA= DT;
mup_ = MU_P;
muj_ = MU_J;
Nparam = numel(PA);
param_name = 'PJ';
gamma_Ni00 = zeros(Nparam,floor(N/2)+1);
gamma_Nipj = zeros(Nparam,floor(N/2)+1);
Bohm_transport = zeros(Nparam,1);
Ni00_ST = zeros(Nparam,floor(N/2)+1,floor(SPS2D*TMAX));
for i = 1:Nparam
% Change scan parameter
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'])
% 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));
for ikr = 1:N/2+1
gamma_Ni00(i,ikr) = (LinearFit_s(Ts2D(itstart:itend)',(squeeze(abs(Ni00(ikr,1,itstart:itend))))));
Ni00_ST(i,ikr,1:numel(Ts2D)) = squeeze((Ni00(ikr,1,:)));
end
tend = Ts5D(end); tstart = 0.4*tend;
[~,itstart] = min(abs(Ts5D-tstart));
[~,itend] = min(abs(Ts5D-tend));
for ikr = 1:N/2+1
gamma_Nipj(i,ikr) = LinearFit_s(Ts5D(itstart:itend)',squeeze(max(max(abs(Nipj(:,:,ikr,1,itstart:itend)),[],1),[],2)));
end
gamma_Ni00(i,:) = real(gamma_Ni00(i,:) .* (gamma_Ni00(i,:)>=0.0));
gamma_Nipj(i,:) = real(gamma_Nipj(i,:) .* (gamma_Nipj(i,:)>=0.0));
% kzmax = abs(kr(ikzmax));
% Bohm_transport(i) = ETAB/ETAN*gmax/kzmax^2;
% Clean output
system(['rm -r ',BASIC.RESDIR]);
end
if 1
%% Plot
SCALE = 1;%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);
semilogx(plt(SCALE*kr(2:numel(kr))),plt(gamma_Ni00(i,2:end)),...
'Color',clr,...
'LineStyle',linestyle{1},'Marker','^',...
'DisplayName',['$\eta_B=',num2str(ETAB),'$, $\nu_{',CONAME,'}=',num2str(NU),'$, $P=',num2str(PA(i)),'$, $J=',num2str(JA(i)),'$']);
hold on;
end
grid on; xlabel('$k_z\rho_s^{R}$'); ylabel('$\gamma(N_i^{00})L_\perp/c_s$'); xlim([0.0,max(kr)]);
title(['$\eta_B=',num2str(ETAB),'$, $\nu_{',CONAME,'}=',num2str(NU),'$'])
legend('show'); xlim([0.01,10])
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.png']);
end
end
if 0
%% Parameter scan over eta_B
PMAXE = 6; PMAXI = 6;
JMAXE = 3; JMAXI = 3;
TMAX = 400;
DT = 0.001;
eta_B = [0.45, 0.5, 0.55, 0.6, 0.65];
Nparam = numel(eta_B);
param_name = 'etaB';
CO = -2; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
NU = 1e-2; % Collision frequency
Bohm_transport = zeros(Nparam,1);
gamma_Ni = zeros(Nparam,N);
for i = 1:Nparam
% Change scan parameter
ETAB = eta_B(i);
setup
% Run linear simulation
system(...
['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ./../../../bin/helaz; cd ../../../wk']...
)
% Load and process results
load_results
tend = Ts2D(end); tstart = 0.4*tend;
for ikr = 1:N/2+1
gamma_Ni(i,ikr) = LinearFit_s(Ts2D,squeeze(abs(Ni00(ikr,1,:))),tstart,tend);
Ni00_ST(i,ikr,1:numel(Ts2D)) = squeeze((Ni00(ikr,1,:)));
end
gamma_Ni(i,:) = real(gamma_Ni(i,:) .* (gamma_Ni(i,:)>=0.0));
[gmax,ikzmax] = max(gamma_Ni(i,:));
kzmax = abs(kr(ikzmax));
Bohm_transport(i) = ETAB/ETAN*gmax/kzmax^2;
% Clean output
system(['rm -r ',BASIC.RESDIR])
end
if 0
%% Plot
fig = figure; FIGNAME = 'linear_study';
plt = @(x) circshift(x,N/2-1);
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(kz),plt(gamma_Ni(i,:)),...
'Color',clr,...
'LineStyle',linestyle{1},...
'DisplayName',['$\eta_B=$',num2str(eta_B(i))]);
hold on;
end
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')
saveas(fig,[SIMDIR,'gamma_Ni_vs_',param_name,'_',PARAMS,'.fig']);
end
if 1
%% Plot
fig = figure; FIGNAME = 'mixing_length';
plot(eta_B, Bohm_transport)
grid on; xlabel('$L_n/L_B$'); ylabel('$\eta\gamma_{max}/k_{max}^2$');
title(['$P_e=',num2str(PMAXE),'$',', $J_e=',num2str(JMAXE),'$',...
', $P_i=',num2str(PMAXE),'$',', $J_i=',num2str(JMAXI),'$'])
saveas(fig,[SIMDIR,FIGNAME,'_vs_',param_name,'_',PARAMS,'.fig']);
end
%%
end
end
end
end
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