diff --git a/matlab/load/read_namelist.m b/matlab/load/read_namelist.m
index 74f64c696c5c828d92d9046c5bcf61c62bd0f848..5dbbda9337ba82b2ff2674d9d30573dc51ba30e5 100644
--- a/matlab/load/read_namelist.m
+++ b/matlab/load/read_namelist.m
@@ -1,4 +1,3 @@
-
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)
diff --git a/matlab/plot/imagesc_custom.m b/matlab/plot/imagesc_custom.m
index 8183267986feee4dc1851770cf80954a72124e71..186a496450a0f61ea6961a6485bcbcd1b507efe8 100644
--- a/matlab/plot/imagesc_custom.m
+++ b/matlab/plot/imagesc_custom.m
@@ -1,12 +1,13 @@
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
diff --git a/matlab/plot/photomaton.m b/matlab/plot/photomaton.m
index a7af7038c227e5bb11c9a3618ef8482397ebf7f6..67b02747b9ca4d0f12ce50d12ff2a476018ecc3e 100644
--- a/matlab/plot/photomaton.m
+++ b/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 = [];
diff --git a/wk/lin_run_script.m b/wk/lin_run_script.m
index b4832e7da8a2dc06bf8c925f311142352b0c82c2..eddd7273611d1ccf7f977f4915f18d6420c6d9fd 100644
--- a/wk/lin_run_script.m
+++ b/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';
diff --git a/wk/parameters/lin_DIIID_LM_rho90.m b/wk/parameters/lin_DIIID_LM_rho90.m
index 43d9ea4fd87134e422c4d92411865dafe49d545c..c8ff82e27f3ceebee4d0ddb69aea3da9f0e873ad 100644
--- a/wk/parameters/lin_DIIID_LM_rho90.m
+++ b/wk/parameters/lin_DIIID_LM_rho90.m
@@ -1,7 +1,7 @@
%% 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
diff --git a/wk/test_ExB_shear.m b/wk/test_ExB_shear.m
index 8da0614ba155e5fe31a2afbadef0d5f927b1cdd8..d04abbcd83468bba1cf647a1c731cb2300069491 100644
--- a/wk/test_ExB_shear.m
+++ b/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]);