correction of the parameters

wk/parameters/lin_JET_rho97.m

-% Parameters found in Parisi et al. 2020
-% Jet shot 92174
+%% Parameters found in Parisi et al. 2020
+% Jet shot 92174 parameters
+BT0     = 1.9;      %[T]        Toroidal field @ 2.96m
+Ip      = 1.4;      %[MA]       Plasma current @ 2.96m
+PNBI    = 17.4;     %[MW]       NBI power
+rhoi    = 0.27;     %[cm]       Ion gyroradius
+R0      = 2.86;     %[m]        Major radius
+a       = 0.91;     %[m]        F-T minor radius
+Rc      = 2.91;     %[m]        ??
+rc      = 0.89;     %[m]        ??
+m_e     = 5.49e-4;  %[amu]      electron mass
+m_i     = 2.014;    %[amu]      deuterium mass
+% Dimless flux-tube parameters
+nuee    = 0.83;     %[vti/a]    e-e collision frequ.
+wTe     = 42;       %[a/L]      e-temp. gradient length
+wTi     = 11;       %[a/L]      i-temp. gradient length
+wNe     = 10;       %[a/L]      dens. gradient length
+tau     = 1/0.56;   %Ti/Te      i-e temperature ratio
+gE      = 0.56;     %[vti/a]    ExB shearing rate
+roa     = 0.9743;   % r/a       Flux surface position
+beta    = 0.0031;   % [8pi*ptot/B^2] with B = 1.99T
+% Normalization       
+% v0   = vth_i = sqrt(2*Ti/mi)                    
+% rho0 = rho_i = vti/omegai
+% Conversion factors from GYAC to paper results
+freq_conv = a/R0 * sqrt(tau/2); % from R/c_s to a/vti
+wave_conv = sqrt(2/tau);        % from rho_i  to rho_s
+grad_conv = a/R0;               % from R/LT   to a/LT
+
 %% Set simulation parameters
 SIMID   = 'lin_JET_rho97';  % Name of the simulation
 %% Set up physical parameters
-CLUSTER.TIME = '99:00:00';  % Allocation time hh:mm:ss
 NU      = 0.1;   % Not the true value 
-TAU     = 1/0.56;               % e/i temperature ratio
-K_Ne    = 10;             % ele Density '''
-K_Te    = 42;             % ele Temperature '''
-K_Ni    = 10;             % ion Density gradient drive
-K_Ti    = 11;             % ion Temperature '''
-SIGMA_E = 0.0233380;        % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
+TAU     = tau;         % i/e temperature ratio
+K_Ne    = wNe/grad_conv;  % ele Density '''
+K_Te    = wTe/grad_conv;  % ele Temperature '''
+K_Ni    = wNe/grad_conv;  % ion Density gradient drive
+K_Ti    = wTi/grad_conv;  % ion Temperature '''
+SIGMA_E = sqrt(m_e/m_i);  % mass ratio sqrt(m_e/m_i) (e-H = 0.0233380)
 NA      = 2;          % number of kinetic species
-ADIAB_E = (NA==1);          % adiabatic electron model
-BETA    = 0.0031;           % electron plasma beta
-MHD_PD  = 0;
+BETA    = beta;           % electron plasma beta
+MHD_PD  = 1;
+CO      = 'DG';       % Collision operator (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
+GKCO    = 1;          % Gyrokinetic operator
+ABCO    = 1;          % INTERSPECIES collisions
+COLL_KCUT= 100; % Cutoff for collision operator
 
 %% GEOMETRY
 % GEOMETRY= 's-alpha';
 GEOMETRY= 'miller';
-EPS     = 0.9753*0.91/2.91;    % inverse aspect ratio
-Q0      = 5.10;    % safety factor
-SHEAR   = 3.36;    % magnetic shear
-KAPPA   = 1.55;    % elongation
-S_KAPPA = 0.95;
-DELTA   = 0.26;    % triangularity
-S_DELTA = 0.74;
-ZETA    = 0;    % squareness
-S_ZETA  = 0;
-PARALLEL_BC = 'dirichlet'; % Boundary condition for parallel direction ('dirichlet','periodic','shearless','disconnected')
-SHIFT_Y = 0.0;    % Shift in the periodic BC in z
-NPOL   = 1;       % Number of poloidal turns
-PB_PHASE = 0;
+EPS     = a/R0;    % inverse aspect ratio
+Q0      = 5.100;    % safety factor
+SHEAR   = 3.360;    % magnetic shear
+KAPPA   = 1.550;    % elongation
+S_KAPPA = 0.949;
+DELTA   = 0.263;    % triangularity
+S_DELTA = 0.737;
 
 %% Set up grid parameters
 P = 4;
 J = P/2;%P/2;
 PMAX = P;                   % Hermite basis size
 JMAX = J;                   % Laguerre basis size
-NX = 8;                    % real space x-gridpoints
-NY = 8;                     % real space y-gridpoints
+NX = 16;                    % real space x-gridpoints
+NY = 2;                     % real space y-gridpoints
 LX = 2*pi/0.1;              % Size of the squared frequency domain in x direction
 LY = 2*pi/0.2;             % Size of the squared frequency domain in y direction
 NZ = 32;                    % number of perpendicular planes (parallel grid)
@@ -55,11 +78,15 @@ DTSAVE3D = 0.5;      % Sampling time for 3D arrays
 DTSAVE5D = 100;     % Sampling time for 5D arrays
 JOB2LOAD = -1;     % Start a new simulation serie
 
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% UNUSED PARAMETERS
+% These parameters are usually not to play with in linear runs
+
 %% OPTIONS
+CLUSTER.TIME = '99:00:00';  % Allocation time hh:mm:ss
 LINEARITY = 'linear';   % activate non-linearity (is cancelled if KXEQ0 = 1)
-CO        = 'DG';       % Collision operator (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
-GKCO      = 1;          % Gyrokinetic operator
-ABCO      = 1;          % INTERSPECIES collisions
 INIT_ZF   = 0;          % Initialize zero-field quantities
 HRCY_CLOS = 'truncation';   % Closure model for higher order moments
 DMAX      = -1;
@@ -67,6 +94,8 @@ NLIN_CLOS = 'truncation';   % Nonlinear closure model for higher order moments
 NMAX      = 0;
 KERN      = 0;   % Kernel model (0 : GK)
 INIT_OPT  = 'phi';   % Start simulation with a noisy mom00/phi/allmom
+NOISE0    = 1.0e-5; % Initial noise amplitude
+BCKGD0    = 0.0e-5;    % Initial background
 NUMERICAL_SCHEME = 'RK4'; % Numerical integration scheme (RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5)
 
 %% OUTPUTS
@@ -80,22 +109,25 @@ W_TEMP   = 1;     % Output flag for temperature
 W_NAPJ   = 1;     % Output flag for nalphaparallel (parallel momentum of species alpha)
 W_SAPJ   = 0;     % Output flag for saparallel (parallel current of species alpha)
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% UNUSED PARAMETERS
-% These parameters are usually not to play with in linear runs
+%% Unused geometry
+ZETA    = 0;    % squareness
+S_ZETA  = 0;
+PARALLEL_BC = 'dirichlet'; % Boundary condition for parallel direction ('dirichlet','periodic','shearless','disconnected')
+SHIFT_Y  = 0.0;    % Shift in the periodic BC in z
+NPOL     = 1;       % Number of poloidal turns
+PB_PHASE = 0;
+
+%% Diffusions
 MU      = 0.0;    % Hyperdiffusivity coefficient
 MU_X    = MU;     % Hyperdiffusivity coefficient in x direction
 MU_Y    = MU;     % Hyperdiffusivity coefficient in y direction
 N_HD    = 4;      % Degree of spatial-hyperdiffusivity
-MU_Z    = 2.0;    % Hyperdiffusivity coefficient in z direction
+MU_Z    = 5.0;    % Hyperdiffusivity coefficient in z direction
 HYP_V   = 'hypcoll'; % Kinetic-hyperdiffusivity model
 MU_P    = 0.0;    % Hyperdiffusivity coefficient for Hermite
 MU_J    = 0.0;    % Hyperdiffusivity coefficient for Laguerre
 LAMBDAD = 0.0;    % Lambda Debye
-NOISE0  = 1.0e-5; % Initial noise amplitude
-BCKGD0  = 0.0e-5;    % Initial background
 k_gB   = 1.0;     % Magnetic gradient strength
 k_cB   = 1.0;     % Magnetic curvature strength
-COLL_KCUT = 1; % Cutoff for collision operator
-ADIAB_I = 0;          % adiabatic ion model
+ADIAB_I = 0;          % adiabatic ion model
+ADIAB_E = (NA==1);          % adiabatic electron model
\ No newline at end of file