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gyacomo/testcases/linear_damping.m
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linear_damping.m
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RUN = 1; % To run or just to load
addpath(genpath('../matlab')) % ... add
default_plots_options
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 0.1; % Collision frequency
TAU = 1.0; % e/i temperature ratio
K_N = 0.0; % Density gradient drive
K_T = 0.0; % Temperature '''
K_E = 0.0; % Electrostat '''
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
%% GRID PARAMETERS
NX = 64; % real space x-gridpoints
NY = 1; % '' y-gridpoints
LX = 100; % Size of the squared frequency domain
LY = 1; % Size of the squared frequency domain
NZ = 1; % number of perpendicular planes (parallel grid)
Q0 = 1.0; % safety factor
SHEAR = 0.0; % magnetic shear
EPS = 0.0; % inverse aspect ratio
SG = 1; % Staggered z grids option
%% TIME PARMETERS
TMAX = 500; % Maximal time unit
DT = 2e-2; % Time step
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = 0; % Sampling per time unit for 2D arrays
SPS3D = 1; % Sampling per time unit for 2D arrays
SPS5D = 1; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints
JOB2LOAD= -1;
%% OPTIONS
SIMID = 'damping_analysis'; % Name of the simulation
LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
KIN_E = 1;
% Collision operator
% (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
CO = 'DG';
GKCO = 1; % gyrokinetic operator
ABCO = 1; % interspecies collisions
INIT_ZF = 0; ZF_AMP = 0.0;
CLOS = 0; % Closure model (0: =0 truncation, 1: gyrofluid closure (p+2j<=Pmax))
NL_CLOS = 0; % nonlinear closure model (-2:nmax=jmax; -1:nmax=jmax-j; >=0:nmax=NL_CLOS)
KERN = 0; % Kernel model (0 : GK)
INIT_OPT= 'mom00'; % Start simulation with a noisy mom00/phi/allmom
%% OUTPUTS
W_DOUBLE = 1;
W_GAMMA = 1; W_HF = 1;
W_PHI = 1; W_NA00 = 1;
W_DENS = 1; W_TEMP = 1;
W_NAPJ = 1; W_SAPJ = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% unused
HD_CO = 0.5; % Hyper diffusivity cutoff ratio
kmax = NX*pi/LX;% Highest fourier mode
NU_HYP = 0.0; % Hyperdiffusivity coefficient
MU = NU_HYP/(HD_CO*kmax)^4; % Hyperdiffusivity coefficient
INIT_BLOB = 0; WIPE_TURB = 0; ACT_ON_MODES = 0;
MU_X = 0.0; %
MU_Y = 0.0; %
MU_Z = 0.0; %
MU_P = 0.0; %
MU_J = 0.0; %
LAMBDAD = 0.0;
NOISE0 = 0*1.0e-5; % Init noise amplitude
BCKGD0 = 1.0; % Init background
GRADB = 0.0;
CURVB = 0.0;
%% PARAMETER SCANS
if 1
%% Parameter scan over PJ
PA = [4];
JA = [2];
% PA = [2 4 8];
% JA = [1 2 4];
DTA= DT*ones(size(JA));%./sqrt(JA);
% DTA= DT;
mup_ = MU_P;
muj_ = MU_J;
Nparam = numel(PA);
param_name = 'PJ';
gamma_Ni00 = zeros(Nparam,floor(NX/2)+1);
gamma_Nipj = zeros(Nparam,floor(NX/2)+1);
gamma_phi = zeros(Nparam,floor(NX/2)+1);
for i = 1:Nparam
% Change scan parameter
PMAXE = PA(i); PMAXI = PA(i);
JMAXE = JA(i); JMAXI = JA(i);
DT = DTA(i);
setup
system(['rm fort*.90']);
% Run linear simulation
if RUN
system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ./../../../bin/helaz3 1 6 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 2 ./../../../bin/helaz 1 2 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; ./../../../bin/helaz 0; cd ../../../wk'])
end
% Load and process results
%%
filename = ['../results/',SIMID,'/',PARAMS,'/outputs_00.h5'];
load_results
tfit = []; gfit = [];
for ikx = 1:NX/2+1
tend = max(Ts3D);
tstart = 0.5*tend;
[~,itstart] = min(abs(Ts3D-tstart));
[~,itend] = min(abs(Ts3D-tend));
trange = itstart:itend;
% exp fit on moment 00
X_ = Ts3D(trange); Y_ = squeeze(abs(Ni00(ikx,1,1,trange)));
[gamma_Ni00(i,ikx),tfit(ikx,:),gfit(ikx,:)] = LinearFit_s(X_,Y_);
% exp fit on phi
X_ = Ts3D(trange); Y_ = squeeze(abs(PHI(ikx,1,1,trange)));
gamma_phi (i,ikx) = LinearFit_s(X_,Y_);
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));
if 1
%% Fit verification
figure;
for i = 1:5:NX/2+1
% X_ = Ts3D(:); Y_ = squeeze(abs(Ni00(i,1,1,:)));
% semilogy(X_,Y_,'DisplayName',['k=',num2str(kx(i))]); hold on;
plot(tfit(ikx,:),gfit(i,:),'DisplayName',['k=',num2str(kx(i))]); hold on;
end
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);
plot(plt(SCALE*kx),plt(gamma_Ni00(i,1:end)),...
'Color',clr,...
'LineStyle',linestyle{1},'Marker','^',...
...% 'DisplayName',['$\kappa_N=',num2str(K_N),'$, $\nu_{',CONAME,'}=',num2str(NU),'$, $P=',num2str(PA(i)),'$, $J=',num2str(JA(i)),'$']);
'DisplayName',[CONAME,', $P,J=',num2str(PA(i)),',',num2str(JA(i)),'$']);
hold on;
end
grid on; xlabel('$k_y\rho_s^{R}$'); ylabel('$\gamma(\phi)L_\perp/c_s$'); xlim([0.0,max(kx)]);
title(['$\kappa_N=',num2str(K_N),'$, $\nu_{',CONAME,'}=',num2str(NU),'$'])
legend('show'); %xlim([0.01,10])
saveas(fig,[SIMDIR,'/',PARAMS,'/gamma_vs_',param_name,'_',PARAMS,'.fig']);
saveas(fig,[SIMDIR,'/',PARAMS,'/gamma_vs_',param_name,'_',PARAMS,'.png']);
end
end
if 0
%% Space time
[YT,XT] = meshgrid(Ts3D,kx);
figure;
% pclr = surf(XT,YT,squeeze(abs(PHI_ST(1,:,:)))); set(pclr, 'edgecolor','none'); colorbar;
% pclr = pcolor(XT,YT,squeeze(abs(Ni00_ST(1,:,:)))); set(pclr, 'edgecolor','none'); colorbar;
semilogy(Ts3D(1:TMAX/SPS3D),squeeze(abs(PHI_ST(1,50:5:100,:))));
end
end
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