update scripts

matlab/compile_results.m

@@ -62,7 +62,7 @@ while(CONTINUE)
         % Loading from output file
         % CPUTIME   = h5readatt(filename,'/data/input','cpu_time');
         % DT_SIM    = h5readatt(filename,'/data/input','dt');
-        [Pe, Je, Pi, Ji, kx, ky, z] = load_grid_data(filename);
+        [P, J, kx, ky, z] = load_grid_data(filename);
         W_GAMMA   = strcmp(h5readatt(filename,'/data/input','write_gamma'),'y');
         W_HF      = strcmp(h5readatt(filename,'/data/input','write_hf'   ),'y');
         W_PHI     = strcmp(h5readatt(filename,'/data/input','write_phi'  ),'y');
@@ -78,8 +78,8 @@ while(CONTINUE)
             BETA = 0;
         end
         % Check polynomials degrees
-        Pe_new= numel(Pe); Je_new= numel(Je);
-        Pi_new= numel(Pi); Ji_new= numel(Ji);
+        Pe_new= numel(P); Je_new= numel(J);
+        Pi_new= numel(P); Ji_new= numel(J);
         if(Pe_max < Pe_new); Pe_max = Pe_new; end;
         if(Je_max < Je_new); Je_max = Je_new; end;
         if(Pi_max < Pi_new); Pi_max = Pi_new; end;
@@ -305,13 +305,13 @@ else
     DATA.PSI  = PSI_; 
     DATA.KIN_E=KIN_E;
     % grids
-    DATA.Pe = Pe; DATA.Pi = Pi; 
-    DATA.Je = Je; DATA.Ji = Ji; 
+    DATA.Pe = P; DATA.Pi = P; 
+    DATA.Je = J; DATA.Ji = J; 
     DATA.kx = kx; DATA.ky = ky; DATA.z = z; DATA.Npol = -z(1)/pi;
     DATA.x  = x;  DATA.y  = y;
     DATA.ikx0 = ikx0; DATA.iky0 = iky0;
     DATA.Nx = Nx; DATA.Ny = Ny; DATA.Nz = Nz; DATA.Nkx = Nkx; DATA.Nky = Nky; 
-    DATA.Pmaxe = numel(Pe); DATA.Pmaxi = numel(Pi); DATA.Jmaxe = numel(Je); DATA.Jmaxi = numel(Ji);
+    DATA.Pmaxe = numel(P); DATA.Pmaxi = numel(P); DATA.Jmaxe = numel(J); DATA.Jmaxi = numel(J);
     DATA.dir      = DIRECTORY;
     DATA.localdir = DIRECTORY;
     DATA.param_title=['$\nu_{',DATA.CONAME,'}=$', num2str(DATA.NU), ...

matlab/compute/mode_growth_meter.m

@@ -160,7 +160,7 @@ for i = 1:2
         lb_= '\gamma';
     end
         errorbar(x_,y_,e_,'-ok',...
-                'LineWidth',1.5,...
+                'LineWidth',1.5,'MarkerSize',10,...
                 'DisplayName',...
                 ['$\gamma$, (',num2str(DATA.inputs.PMAX),',',num2str(DATA.inputs.JMAX),')']); 
         hold on;
@@ -172,8 +172,8 @@ for i = 1:2
         end
         % ylabel('$\gamma$');
     % yyaxis("right")
-        errorbar(k(MODES),imag(omega(ik)),imag(err(ik)),'--ok',...
-                'LineWidth',1.5,...
+        errorbar(k(MODES),imag(omega(ik)),imag(err(ik)),'*k',...
+                'LineWidth',1.5,'MarkerSize',10,...
                 'DisplayName',...
                 ['$\omega$, (',num2str(DATA.inputs.PMAX),',',num2str(DATA.inputs.JMAX),')']); 
         hold on;

wk/analysis_demo.m

+gyacomodir = pwd; gyacomodir = gyacomodir(1:end-2); % get code directory
+addpath(genpath([gyacomodir,'matlab'])) % ... add
+addpath(genpath([gyacomodir,'matlab/plot'])) % ... add
+addpath(genpath([gyacomodir,'matlab/compute'])) % ... add
+addpath(genpath([gyacomodir,'matlab/load'])) % ... add
+default_plots_options
+options.RESOLUTION = 256;
+% Partition of the computer where the data have to be searched
+
+J0 = 00; J1 = 10;
+
+% DATADIR = '/Users/ahoffmann/gyacomo/testcases/DIII-D_triangularity_fast_nonlinear/';
+% DATADIR = '/Users/ahoffmann/gyacomo/testcases/HEL_DIII-D_triangularity/';
+DATADIR = '/Users/ahoffmann/gyacomo/testcases/cyclone_example/';
+data    = {};
+data    = compile_results_low_mem(data,DATADIR,J0,J1);
+
+if 1
+%% Plot transport and phi radial profile
+[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
+options.TAVG_0   = 100;
+options.TAVG_1   = 1000;
+options.NCUT     = 5;              % Number of cuts for averaging and error estimation
+options.NMVA     = 1;              % Moving average for time traces
+options.ST_FIELD = '\phi';          % chose your field to plot in spacetime diag (e.g \phi,v_x,G_x)
+options.INTERP   = 1;
+plot_radial_transport_and_spacetime(data,options);
+end
+
+if 0
+%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Options
+[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
+[data.Na00, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Na00');
+data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+options.INTERP    = 1;
+options.POLARPLOT = 0;
+options.BWR       = 1; % bluewhitered plot or gray
+options.CLIMAUTO  = 0; % adjust the colormap auto
+options.NAME      = '\phi';
+% options.NAME     = 'N_i^{00}';
+options.PLAN      = 'xy';
+options.COMP      = 9;
+options.TIME      =  data.Ts3D(1:2:end);
+data.EPS          = 0.1;
+data.a = data.EPS * 2000;
+create_film(data,options,'.gif')
+end
+
+if 0
+%% field snapshots
+% Options
+[data.Na00, data.Ts3D] = compile_results_3Da(data.folder,J0,J1,'Na00');
+[data.PHI, data.Ts3D] = compile_results_3D(data.folder,J0,J1,'phi');
+data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
+
+options.INTERP    = 0;
+options.POLARPLOT = 0;
+options.AXISEQUAL = 0;
+options.NORMALIZE = 0;
+options.LOGSCALE  = 0;
+options.CLIMAUTO  = 1;
+options.NAME      = 'N_i^{00}';
+% options.NAME      = 's_{Ey}';
+% options.NAME      = '\phi';
+options.PLAN      = 'yz';
+options.COMP      = 'avg';
+options.TIME      = [10 30];
+fig = photomaton(data,options);
+colormap(gray)
+clim('auto')
+% save_figure(data,fig)
+end
+if 0
+%% Performance profiler
+profiler(data)
+end
+
+if 0
+%% Hermite-Laguerre spectrum
+[data.Napjz, data.Ts3D] = compile_results_3Da(DATADIR,J0,J1,'Napjz');
+% [data.Napjz, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'Nipjz');
+options.ST         = 0;
+options.NORMALIZED = 0;
+options.LOGSCALE   = 1;
+options.FILTER     = 0; %filter the 50% time-average of the spectrum from
+options.TAVG_2D    = 0; %Show a 2D plot of the modes, 50% time averaged
+options.TAVG_2D_CTR= 0; %make it contour plot
+fig = show_moments_spectrum(data,options);
+end

wk/parameters/lin_DIIID_LM_rho90.m

 %% Reference values
 % See Neiser et al. 2019 Gyrokinetic GENE simulations of DIII-D near-edge L-mode plasmas
 %% Set simulation parameters
-SIMID   = 'lin_DIID_LM_rho90';  % Name of the simulation
+SIMID   = 'lin_DIIID_LM_rho90';  % Name of the simulation
 %% Set up physical parameters
 CLUSTER.TIME = '99:00:00';  % Allocation time hh:mm:ss
 NU = 1.0; %(0.00235 in GENE)
@@ -47,9 +47,9 @@ PB_PHASE = 0;
 %% TIME PARAMETERS
 TMAX     = 10;  % Maximal time unit
 DT       = 5e-4;   % Time step
-DTSAVE0D = 0.5;      % Sampling time for 0D arrays
+DTSAVE0D = 0.1;      % Sampling time for 0D arrays
 DTSAVE2D = -1;     % Sampling time for 2D arrays
-DTSAVE3D = 0.5;      % Sampling time for 3D arrays
+DTSAVE3D = 0.1;      % Sampling time for 3D arrays
 DTSAVE5D = 100;     % Sampling time for 5D arrays
 JOB2LOAD = -1;     % Start a new simulation serie
 

wk/parameters/lin_GASTD.m

+%% Reference values
+% See Staebler et al. 2023
+%% Set simulation parameters
+SIMID   = 'lin_GASTD';  % Name of the simulation
+%% Set up physical parameters
+CLUSTER.TIME = '99:00:00';  % Allocation time hh:mm:ss
+NU = 0.05; %(0.00235 in GENE)
+TAU = 1;               % i/e temperature ratio
+K_Ne    = 1;             % ele Density '''
+K_Te    = 3;             % ele Temperature '''
+K_Ni    = 1;             % ion Density gradient drive
+K_Ti    = 3;             % ion Temperature '''
+SIGMA_E = 0.0233380;%/sqrt(2);        % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
+NA      = 2;          % number of kinetic species
+ADIAB_E = (NA==1);          % adiabatic electron model
+BETA    = 0;           % electron plasma beta in prct
+MHD_PD  = 1;
+%% Set up grid parameters
+P = 2;
+J = P/2;%P/2;
+PMAX = P;                   % Hermite basis size
+JMAX = J;                   % Laguerre basis size
+NX = 4;                    % 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/0.5;             % Size of the squared frequency domain in y direction
+NZ = 16;                    % 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';
+Q0      = 2;    % safety factor
+SHEAR   = 1;    % magnetic shear
+EPS     = 1/3;    % inverse aspect ratio
+KAPPA   = 1.0;    % elongation
+S_KAPPA = 0;
+DELTA   = 0;    % triangularity
+S_DELTA = 0;
+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;
+%% TIME PARAMETERS
+TMAX     = 20;  % Maximal time unit
+DT       = 1e-2;   % Time step
+DTSAVE0D = 1.0;      % Sampling time for 0D arrays
+DTSAVE2D = -1;     % Sampling time for 2D arrays
+DTSAVE3D = 1.0;      % Sampling time for 3D arrays
+DTSAVE5D = 100;     % Sampling time 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
+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)
+
+%% 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    = 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
\ No newline at end of file