cleaning

wk/local_run.m

-%% QUICK RUN SCRIPT
-% This script creates a directory in /results and runs a simulation directly
-% from the Matlab framework. It is meant to run only small problems in linear
-% for benchmarking and debugging purposes since it makes Matlab "busy".
-
-%% Set up the paths for the necessary Matlab modules
-gyacomodir = pwd;
-gyacomodir = gyacomodir(1:end-2);
-addpath(genpath([gyacomodir,'matlab'])) % Add matlab module
-addpath(genpath([gyacomodir,'matlab/plot'])) % Add plot module
-addpath(genpath([gyacomodir,'matlab/compute'])) % Add compute module
-addpath(genpath([gyacomodir,'matlab/load'])) % Add load module
-
-%% Set simulation parameters
-SIMID = 'dbg'; % Name of the simulation
-RUN = 0; % To run or just to load
-default_plots_options
-EXECNAME = 'gyacomo23_sp'; % single precision
-% EXECNAME = 'gyacomo23_dp'; % double precision
-
-%% Set up physical parameters
-CLUSTER.TIME = '99:00:00';  % Allocation time hh:mm:ss
-NU = 0.001;                 % Collision frequency
-TAU = 1.0;                  % e/i temperature ratio
-K_Ne = 0*2.22;              % ele Density
-K_Te = 0*6.96;              % ele Temperature
-K_Ni = 1*2.22;              % ion Density gradient drive
-K_Ti = 6.96;              % ion Temperature
-SIGMA_E = 0.0233380;        % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
-NA = 1;                     % number of kinetic species
-ADIAB_E = (NA==1);          % adiabatic electron model
-BETA = 0.0;                 % electron plasma beta
-%% Set up grid parameters
-P = 60;
-J = P/2;
-DT   = 1e-2;   % Time step
-PMAX = P;                   % Hermite basis size
-JMAX = J;                   % Laguerre basis size
-NX = 8;                     % 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/0.1;              % Size of the squared frequency domain in y direction
-NZ = 24;                    % number of perpendicular planes (parallel grid)
-SG = 0;                     % Staggered z grids option
-NEXC = 1;                   % To extend Lx if needed (Lx = Nexc/(kymin*shear))
-
-%% GEOMETRY
-GEOMETRY= 's-alpha';
-% GEOMETRY= 'miller';
-EPS     = 0.18;   % inverse aspect ratio
-Q0      = 1.4;    % safety factor
-SHEAR   = 0.8;    % magnetic shear
-KAPPA   = 1.0;    % elongation
-DELTA   = 0.0;    % triangularity
-ZETA    = 0.0;    % squareness
-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
-
-%% TIME PARAMETERS
-TMAX     = 50;  % Maximal time unit
-DTSAVE0D = 1;      % Sampling per time unit for 0D arrays
-DTSAVE2D = -1;     % Sampling per time unit for 2D arrays
-DTSAVE3D = 1;      % Sampling per time unit for 3D arrays
-DTSAVE5D = 100;     % Sampling per time unit for 5D arrays
-JOB2LOAD = -1;     % Start a new simulation serie
-
-%% OPTIONS
-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
-HRCY_CLOS = 'monomial';   % Closure model for higher order moments
-DMAX      = -1;
-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
-NUMERICAL_SCHEME = 'RK4'; % Numerical integration scheme (RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5)
-% NUMERICAL_SCHEME = 'DOPRI5'; % Numerical integration scheme (RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5)
-
-%% OUTPUTS
-W_DOUBLE = 1;     % Output flag for double moments
-W_GAMMA  = 1;     % Output flag for gamma (Gyrokinetic Energy)
-W_HF     = 1;     % Output flag for high-frequency potential energy
-W_PHI    = 1;     % Output flag for potential
-W_NA00   = 1;     % Output flag for nalpha00 (density of species alpha)
-W_DENS   = 1;     % Output flag for total density
-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
-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
-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  = 0.0e-5; % Initial noise amplitude
-BCKGD0  = 1.0e-5;    % Initial background
-k_gB   = 1.0;     % Magnetic gradient strength
-k_cB   = 1.0;     % Magnetic curvature strength
-COLL_KCUT = 1000; % Cutoff for collision operator
-
-%%-------------------------------------------------------------------------
-%% RUN
-setup
-% system(['rm fort*.90']);
-% Run linear simulation
-if RUN
-    MVIN =['cd ../results/',SIMID,'/',PARAMS,'/;'];
-%     RUN  =['time mpirun -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0;'];
-    RUN  =['time mpirun -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0;'];
-%     RUN  =['time mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 1 6 1 0;'];
-%     RUN  =['time mpirun -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0;'];
-    MVOUT='cd ../../../wk;';
-    system([MVIN,RUN,MVOUT]);
-end
-
-%% Analysis
-% load
-filename = [SIMID,'/',PARAMS,'/']; % Create the filename based on SIMID and PARAMS
-LOCALDIR = [gyacomodir,'results/',filename,'/']; % Create the local directory path based on gyacomodir, results directory, and filename
-FIGDIR   = LOCALDIR; % Set FIGDIR to the same path as LOCALDIR
-% Load outputs from jobnummin up to jobnummax
-J0 = 0; J1 = 0;
-data = {}; % Initialize data as an empty cell array
-% load grids, inputs, and time traces
-data = compile_results_low_mem(data,LOCALDIR,J0,J1); 
-
-if 0
-%% Plot heat flux evolution
-figure
-semilogy(data.Ts0D,data.HFLUX_X);
-xlabel('$tc_s/R$'); ylabel('$Q_x$');
-end
-if 1 % Activate or not
-%% plot mode evolution and growth rates
-% Load phi
-[data.PHI, data.Ts3D] = compile_results_3D(LOCALDIR,J0,J1,'phi');
-options.NORMALIZED = 0; 
-options.TIME   = data.Ts3D;
- % Time window to measure the growth of kx/ky modes
-options.KX_TW  = [0.5 1]*data.Ts3D(end);
-options.KY_TW  = [0.5 1]*data.Ts3D(end);
-options.NMA    = 1; % Set NMA option to 1
-options.NMODES = 999; % Set how much modes we study
-options.iz     = 'avg'; % Compressing z
-options.ik     = 1; %
-options.fftz.flag = 0; % Set fftz.flag option to 0
-fig = mode_growth_meter(data,options); % Call the function mode_growth_meter with data and options as input arguments, and store the result in fig
-end
-
-
-