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gyacomo/testcases/linear_1D_entropy_mode.m
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linear_1D_entropy_mode.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 = 0.01; % Collision frequency
TAU = 1.0; % e/i temperature ratio
K_N = 2.0; % Density gradient drive
K_T = 0.25*K_N; % Temperature '''
K_E = 0.0; % Electrostat '''
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
%% GRID PARAMETERS
NX = 40; % real space x-gridpoints
NY = 1; % '' y-gridpoints
LX = 120; % Size of the squared frequency domain
LY = 1; % Size of the squared frequency domain
NZ = 1; % number of perpendicular planes (parallel grid)
SG = 1; % Staggered z grids option
%% GEOMETRY
GEOMETRY= 'Z-pinch';
Q0 = 1.0; % safety factor
SHEAR = 0.0; % magnetic shear
EPS = 0.0; % inverse aspect ratio
%% TIME PARMETERS
TMAX = 100; % Maximal time unit
DT = 1e-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 = 'Linear_scan'; % 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 = 0; % 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))s
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 = 0.0; % Hyper diffusivity cutoff ratio
kmax = NX*pi/LX;% Highest fourier mode
MU = 0.0; % Hyperdiffusivity coefficient
INIT_BLOB = 0; WIPE_TURB = 0; ACT_ON_MODES = 0;
MU_X = MU; %
MU_Y = MU; %
MU_Z = 0.0; %
MU_P = 0.0; %
MU_J = 0.0; %
LAMBDAD = 0.0;
NOISE0 = 1.0e-5; % Init noise amplitude
BCKGD0 = 0.0; % Init background
GRADB = 1.0;
CURVB = 1.0;
%% PARAMETER SCANS
if 1
% Parameter scan over PJ
PA = [4];
JA = [2];
Nparam = numel(PA);
% Parameter scan over KN
% PA = [4]; JA = [2];
% PMAXE = PA(1); PMAXI = PA(1);
% JMAXE = JA(1); JMAXI = JA(1);
% KNA = 1.5:0.05:2.5;
% ETA = 0.25;
% Nparam = numel(KNA);
%
DTA= DT*ones(1,Nparam)./sqrt(JA);
% DTA= DT;
param_name = 'KN';
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);
% K_N = KNA(i); K_T = ETA*K_N;
DT = DTA(i);
setup
system(['rm fort*.90']);
% Run linear simulation
if RUN
system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ./../../../bin/helaz3 1 1 1 0; cd ../../../wk'])
% disp([param_name,'=',num2str(K_N)]);
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ./../../../bin/helaz3 1 6 0 > out.txt; 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
for ikx = 1:NX/2+1
tend = max(Ts3D(abs(Ni00(ikx,1,1,:))~=0));
tstart = 0.6*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) = 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 0
%% Fit verification
figure;
for i = 1:1:NX/2+1
X_ = Ts3D(:); Y_ = squeeze(abs(Ni00(i,1,1,:)));
semilogy(X_,Y_,'DisplayName',['k=',num2str(kx(i))]); hold on;
end
end
if 1
%% Plot for PJ scan
SCALE = 1;%sqrt(2);
fig = figure; FIGNAME = 'linear_study';
plt = @(x) x;
% subplot(211)
for i = 1:Nparam
% colors = line_colors;
colors = jet(Nparam);
clr = 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_phi(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
%% Plot for KN scan
fig = figure; FIGNAME = 'linear_study';
[Y,X] = meshgrid(kx,KNA);
pclr = pcolor(Y,X,gamma_phi);set(pclr, 'edgecolor','none'); colorbar;
shading interp
% imagesc(kx,KNA,gamma_phi);
set(gca,'YDir','normal')
colormap(bluewhitered); xlim([kx(2) kx(end)]);
title(['$\gamma^p$, $\nu_{',CONAME,'}=',num2str(NU),'$'])
xlabel('$k_x$'); ylabel('$\kappa_N$');
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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