script to run Cyclone test case for GENE benchmark

wk/cyclone_test_case.m

+addpath(genpath('../matlab')) % ... add
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Set Up parameters
+CLUSTER.TIME  = '99:00:00'; % allocation time hh:mm:ss
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% PHYSICAL PARAMETERS
+NU      = 0.01;   % Collision frequency
+K_N     = 2.22;      % Density gradient drive
+K_T     = 6.9;       % Temperature '''
+K_E     = 0.00;    % Electrostat gradient
+SIGMA_E = 0.05196;   % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
+NU_HYP  = 0.01;
+KIN_E   = 0;         % Kinetic (1) or adiabatic (2) electron model
+%% GRID PARAMETERS
+NX      = 100;     % Spatial radial resolution ( = 2x radial modes)
+LX      = 200;    % Radial window size
+NY      = 100;     % Spatial azimuthal resolution (= azim modes)
+LY      = 100;    % Azimuthal window size
+NZ      = 30;     % number of perpendicular planes (parallel grid)
+P       = 4;
+J       = 2;
+%% GEOMETRY PARAMETERS
+Q0      = 1.4;       % safety factor
+SHEAR   = 0.0;       % magnetic shear
+EPS     = 0.18;      % inverse aspect ratio
+GRADB   = 1.0;       % Magnetic  gradient
+CURVB   = 1.0;       % Magnetic  curvature
+SG      = 1;         % Staggered z grids option
+%% TIME PARAMETERS
+TMAX    = 500;  % Maximal time unit
+DT      = 5e-2;   % Time step
+SPS0D   = 2;      % Sampling per time unit for profiler
+SPS2D   = 1;      % Sampling per time unit for 2D arrays
+SPS3D   = 1/2;      % Sampling per time unit for 3D arrays
+SPS5D   = 1/200;  % Sampling per time unit for 5D arrays
+SPSCP   = 0;    % Sampling per time unit for checkpoints/10
+JOB2LOAD= -1;
+%% OPTIONS AND NAMING
+% Collision operator
+% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle ; 4 : Coulomb; +/- for GK/DK)
+CO      = 1;
+CLOS    = 0;   % Closure model (0: =0 truncation)
+NL_CLOS = 0;   % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
+SIMID   = 'Cyclone';  % Name of the simulation
+% SIMID   = 'simulation_A';  % Name of the simulation
+% SIMID   = ['v3.0_P_',num2str(P),'_J_',num2str(J)];  % Name of the simulation
+NON_LIN  = 1;   % Non linear model (0: linear, 0.5: semi linear, 1: non linear)
+% INIT options
+INIT_PHI= 0;   % Start simulation with a noisy phi (0= noisy moments 00)
+INIT_ZF   = 0; ZF_AMP = 0.0;
+INIT_BLOB = 0; WIPE_TURB = 0; WIPE_ZF = 0;
+%% 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
+PMAXE   = P;    % Highest electron Hermite polynomial degree
+JMAXE   = J;     % Highest ''       Laguerre ''
+PMAXI   = P;     % Highest ion      Hermite polynomial degree
+JMAXI   = J;     % Highest ''       Laguerre ''
+KERN    = 0;   % Kernel model (0 : GK)
+KX0KH   = 0; A0KH = 0; % Background phi mode to drive Ray-Tay inst.
+KPAR    = 0.0;    % Parellel wave vector component
+LAMBDAD = 0.0;
+kmax    = NX*pi/LX;% Highest fourier mode
+HD_CO   = 0.5;    % Hyper diffusivity cutoff ratio
+MU      = NU_HYP/(HD_CO*kmax)^4; % Hyperdiffusivity coefficient
+NOISE0  = 1.0e-5;
+BCKGD0  = 0.0;    % Init background
+TAU     = 1.0;    % e/i temperature ratio
+MU_P    = 0.0;     % Hermite  hyperdiffusivity -mu_p*(d/dvpar)^4 f
+MU_J    = 0.0;     % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
+%% Setup and file management
+setup
+system('rm fort*.90');
+outfile = [BASIC.RESDIR,'out.txt'];
+disp(outfile);