update matlab scripts

matlab/load/read_namelist.m

-
 function S = read_namelist(filename)
 %   S = READ_NAMELIST(FILENAME) returns the struct S containg namelists and
 %   variables in the file FILENAME organised in hierachical way:
@@ -80,11 +79,7 @@ while i < c;
             nmlst_bdy = [nmlst_bdy ' ' line];
         end
         % Parse current namelist (set of variables)
-        switch namelst
-            case 'info'
-            otherwise
-            S.(namelst) = parse_namelist(nmlst_bdy);        
-        end
+        S.(namelst) = parse_namelist(nmlst_bdy);        
     end
 end
 function S = parse_namelist(strng)
@@ -126,9 +121,7 @@ for k = 1:nvars,
     if k > 1, arg_end(k - 1) = i; end    
     vars{k} = ['S.' strng(i + 1: j)];
 end
-if numel(arg_end) > 0
 arg_end(end) = length(strng);
-end
 % This variables are used in the eval function to evaluate True/False, 
 % so don't remove it!
 T = '.true.';
@@ -137,6 +130,7 @@ F = '.false.';
 for k = 1:nvars,    
     arg = strng(arg_start(k):arg_end(k));
     arglit = islit(arg_start(k):arg_end(k))';
+    
     % Remove commas in non literal string...
     commas = ~arglit & arg == ',';
     if any(commas)

matlab/plot/imagesc_custom.m

 function [ fig ] = imagesc_custom( XX,YY,FF)
 % CUSTOM IMAGESC this custom function is meant to be used exaclty as pcolor
 % but plotting array values in pixels (like imagesc) and not in vertices (like pcolor).
-
-fig = imagesc( XX(1,:), YY(:,1), FF);
+x = reshape(XX(1,:),[numel(XX(1,:)), 1]);
+y = reshape(YY(:,1),[numel(YY(:,1)), 1]);
+fig = imagesc( x, y, FF);
 set(gca,'YDir','normal')        
-xticks(XX(1,:));
-xticklabels(num2str(XX(1,:)));
-yticks(YY(:,1));
-yticklabels(num2str(YY(:,1)));
+xticks(x);
+xticklabels(num2str(x));
+yticks(y);
+yticklabels(num2str(y));
 end
 

matlab/plot/photomaton.m

@@ -14,7 +14,7 @@ Nrows  = ceil(Nframes/4);
 Ncols  = ceil(Nframes/Nrows);
 %
 if OPTIONS.LOGSCALE
-    toplot.FIELD = max(abs(toplot.FIELD),1e-20);
+    toplot.FIELD = max(abs(toplot.FIELD),1e-40);
     toplot.FIELD = log(toplot.FIELD);
 end
 TNAME = [];

wk/lin_run_script.m

@@ -15,34 +15,33 @@ addpath(genpath([gyacomodir,'matlab/load']))    % Add load folder
 addpath(genpath([gyacomodir,'wk/parameters']))  % Add parameters folder
 
 %% Setup run or load an executable
-RUN = 0; % To run or just to load
+RUN = 1; % To run or just to load
 default_plots_options
 % EXECNAME = 'gyacomo23_sp_save'; % single precision
-EXECNAME = 'gyacomo23_sp'; % single precision
-% EXECNAME = 'gyacomo23_dp'; % double precision
+% EXECNAME = 'gyacomo23_sp'; % single precision
+EXECNAME = 'gyacomo23_dp'; % double precision
 % EXECNAME = 'gyacomo23_debug'; % double precision
 
 %% Setup parameters
 % run lin_DTT_HM_rho85
 % run lin_DTT_HM_rho98
-% run lin_DTT_LM_rho90
-% run lin_DTT_LM_rho95
+run lin_DIIID_LM_rho90
+% run lin_DIIID_LM_rho95
 % run lin_JET_rho97
 % run lin_Entropy
-run lin_ITG
+% run lin_ITG
 % run lin_KBM
 %% Change parameters
 EXBRATE = 0.0;              % Background ExB shear flow
-NY   = 40;
-NX   = 8;
-PMAX = 16;
-JMAX = PMAX/2;
-ky   = 0.05;
-LY   = 2*pi/ky;
-DT   = 5e-3;
-TMAX = 50;
-% % SIGMA_E = 0.04;
-% TMAX     = 10;
+NY   = 2;
+NX   = 4;
+% PMAX = 4;
+% JMAX = PMAX/2;
+ky   = 0.8; LY   = 2*pi/ky;
+DT   = 1e-4;
+TAU  = 2.1;
+% SIGMA_E = 0.02;
+% TMAX = 50;
 % DTSAVE0D = 200*DT;
 % DTSAVE3D = TMAX/50;
 %%-------------------------------------------------------------------------
@@ -53,8 +52,8 @@ setup
 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 8 ',gyacomodir,'bin/',EXECNAME,' 2 2 2 0;'];
+   RUN  =['time ',mpirun,' -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0;'];
+     % RUN  =['time ',mpirun,' -np 8 ',gyacomodir,'bin/',EXECNAME,' 2 2 2 0;'];
     % RUN  =['time ',mpirun,' -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0;'];
       % RUN = ['./../../../bin/gyacomo23_sp 0;'];
     MVOUT='cd ../../../wk;';
@@ -88,6 +87,7 @@ options.iz     = 'avg'; % Compressing z
 options.ik     = 1; %
 options.GOK2   = 0; % plot gamma/k^2
 options.fftz.flag = 0; % Set fftz.flag option to 0
+options.FIELD = 'phi';
 [fig, kykx, wkykx, ekykx] = 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
 
@@ -98,7 +98,7 @@ if data.inputs.BETA > 0
 [data.PSI, data.Ts3D] = compile_results_3D(LOCALDIR,J0,J1,'psi');
 end
 options.time_2_plot = [120];
-options.kymodes     = [0.25];
+options.kymodes     = [0.2 0.3 0.4];
 options.normalized  = 1;
 options.PLOT_KP     = 0;
 % options.field       = 'phi';

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_DTT_HM_rho90';  % Name of the simulation
+SIMID   = 'lin_DIID_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)
@@ -20,8 +20,8 @@ P = 2;
 J = P/2;%P/2;
 PMAX = P;                   % Hermite basis size
 JMAX = J;                   % Laguerre basis size
-NX = 8;                    % real space x-gridpoints
-NY = 2;                     % real space y-gridpoints
+NX = 2;                    % real space x-gridpoints
+NY = 4;                     % real space y-gridpoints
 LX = 2*pi/0.1;              % Size of the squared frequency domain in x direction
 LY = 2*pi/0.3;             % Size of the squared frequency domain in y direction
 NZ = 32;                    % number of perpendicular planes (parallel grid)
@@ -45,8 +45,8 @@ SHIFT_Y = 0.0;    % Shift in the periodic BC in z
 NPOL   = 1;       % Number of poloidal turns
 PB_PHASE = 0;
 %% TIME PARAMETERS
-TMAX     = 15;  % Maximal time unit
-DT       = 1e-3;   % Time step
+TMAX     = 10;  % Maximal time unit
+DT       = 5e-4;   % Time step
 DTSAVE0D = 0.5;      % Sampling time for 0D arrays
 DTSAVE2D = -1;     % Sampling time for 2D arrays
 DTSAVE3D = 0.5;      % Sampling time for 3D arrays

wk/test_ExB_shear.m

@@ -13,15 +13,15 @@ EXECDIR  = [curdir(1:end-2),'bin/'];
 % EXECNAME = 'gyacomo23_dp_O1';
 % EXECNAME = 'gyacomo23_dp';
 % EXECNAME = 'gyacomo23_sp';
-% EXECNAME = 'gyacomo23_test';
-EXECNAME = 'gyacomo23_debug';
+EXECNAME = 'gyacomo23_test';
+% EXECNAME = 'gyacomo23_debug';
 % ------
-NP = '1'; PARA = '1 1 1';
+% NP = '1'; PARA = '1 1 1';
 % NP = '2'; PARA = '1 2 1';
-% NP = '6'; PARA = '1 6 1';
+NP = '6'; PARA = '1 6 1';
 %------
 % Picture, const. zonal mode in phi in nonlin term
-% INNAME = '0';
+INNAME = '0';
 % Picture, bckg ExB shear
 % INNAME = '1';
 % NL with padrallel modes initialization no ExB shear
@@ -35,7 +35,7 @@ NP = '1'; PARA = '1 1 1';
 % Mcmillan et al. 2019 correction
 % INNAME = '6';
 % Single mode single step
-INNAME = '7';
+% INNAME = '7';
 %-------
 RUN   = [MPIRUN,' -np ',NP,' ',EXECDIR,EXECNAME,' ',PARA,' ',INNAME];
 system([MVIN,'; ',RUN,'; ',MVOUT]);