upload scripts

wk/marconi_run.m

 clear all;
 addpath(genpath('../matlab')) % ... add
-SUBMIT = 0; % To submit the job automatically
+SUBMIT = 1; % To submit the job automatically
 % EXECNAME = 'helaz_dbg';
   EXECNAME = 'helaz_2.8';
-for ETAB = [0.6]
+for ETAN = [1.4]
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% Set Up parameters
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% CLUSTER PARAMETERS
-% CLUSTER.PART  = 'prod';     % dbg or prod
-CLUSTER.PART  = 'dbg';
+CLUSTER.PART  = 'prod';     % dbg or prod
+% CLUSTER.PART  = 'dbg';
 CLUSTER.TIME  = '24:00:00'; % allocation time hh:mm:ss
 if(strcmp(CLUSTER.PART,'dbg')); CLUSTER.TIME  = '00:30:00'; end;
 CLUSTER.MEM   = '128GB';     % Memory
 CLUSTER.JNAME = 'HeLaZ';% Job name
 NP_P          = 2;          % MPI processes along p  
-NP_KX         = 24;         % MPI processes along kr
+NP_KX         = 24;         % MPI processes along kx
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% PHYSICAL PARAMETERS
-NU      = 1e-3;   % Collision frequency
-% ETAB    = 0.7;   % Magnetic gradient
-NU_HYP  = 0.1;   % Hyperdiffusivity coefficient
+NU      = 1e-2;   % Collision frequency
+NU_HYP  = 0.0;   % Hyperdiffusivity coefficient
+% ETAN    = 1.0;    % Density gradient
 % (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle ; +/- for GK/DK)
-CO      = 2;
+CO      = 3;
 INIT_ZF = 0; ZF_AMP = 0.0;
 %% GRID PARAMETERS
-N       = 200;    % Frequency gridpoints (Nkr = N/2)
-L       = 60;    % Size of the squared frequency domain
-P       = 6;     % Electron and Ion highest Hermite polynomial degree
-J       = 3;     % Electron and Ion highest Laguerre polynomial degree
+N       = 300;    % Frequency gridpoints (Nkx = N/2)
+L       = 100;    % Size of the squared frequency domain
+P       = 10;     % Electron and Ion highest Hermite polynomial degree
+J       = 5;     % Electron and Ion highest Laguerre polynomial degree
 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 PARAMETERS
 TMAX    = 10000;  % Maximal time unit
-DT      = 1e-2;  % Time step
+DT      = 5e-3;  % Time step
 SPS0D   = 1;     % Sampling per time unit for profiler
 SPS2D   = 1/4;     % Sampling per time unit for 2D arrays
 SPS5D   = 1/300;  % Sampling per time unit for 5D arrays
@@ -43,12 +43,12 @@ JOB2LOAD= 0;
 %% Naming
 SIMID   = 'kobayashi';  % Name of the simulation
 % SIMID   = 'test';  % Name of the simulation
-% SIMID   = ['v2.7_P_',num2str(P),'_J_',num2str(J)];  % Name of the simulation
+% SIMID   = ['v2.8_P_',num2str(P),'_J_',num2str(J)];  % Name of the simulation
 PREFIX  =[];
-% PREFIX  = sprintf('%d_%d_',NP_P, NP_KR);
+% PREFIX  = sprintf('%d_%d_',NP_P, NP_KX);
 %% Options
 CLOS    = 0;   % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
-NL_CLOS = -1;  % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
+NL_CLOS = 0;  % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
 KERN    = 0;   % Kernel model (0 : GK)
 INIT_PHI= 1;   % Start simulation with a noisy phi and moments
 %% OUTPUTS
@@ -63,11 +63,11 @@ W_TEMP   = 1;
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 %% fixed parameters (for current study)
-KR0KH   = 0; A0KH = 0; % Background phi mode
-KREQ0   = 0;      % put kr = 0
+KX0KH   = 0; A0KH = 0; % Background phi mode
+KXEQ0   = 0;      % put kx = 0
 KPAR    = 0.0;    % Parellel wave vector component
 LAMBDAD = 0.0;
-NON_LIN = 1 *(1-KREQ0);   % activate non-linearity (is cancelled if KREQ0 = 1)
+NON_LIN = 1 *(1-KXEQ0);   % activate non-linearity (is cancelled if KXEQ0 = 1)
 PMAXE   = P;    % Highest electron Hermite polynomial degree
 JMAXE   = J;     % Highest ''       Laguerre ''
 PMAXI   = P;     % Highest ion      Hermite polynomial degree
@@ -78,14 +78,14 @@ HD_CO   = 0.5;    % Hyper diffusivity cutoff ratio
 MU      = NU_HYP/(HD_CO*kmax)^4; % Hyperdiffusivity coefficient
 NOISE0  = 1.0e-5;
 ETAT    = 0.0;    % Temperature gradient
-ETAN    = 1.0;    % Density gradient
+ETAB    = 1.0;   % Magnetic gradient
 TAU     = 1.0;    % e/i temperature ratio
 % Compute processes distribution
 Ntot = NP_P * NP_KX;
 Nnodes = ceil(Ntot/48);
 Nppn   = Ntot/Nnodes; 
 CLUSTER.NODES =  num2str(Nnodes);  % MPI process along p
-CLUSTER.NTPN  =  num2str(Nppn); % MPI process along kr
+CLUSTER.NTPN  =  num2str(Nppn); % MPI process along kx
 CLUSTER.CPUPT = '1';        % CPU per task
 %% Run file management scripts
 setup