%% 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);
% mpirun     = 'mpirun';
mpirun     = '/opt/homebrew/bin/mpirun'; % for macos
addpath(genpath([gyacomodir,'matlab']))         % Add matlab folder
addpath(genpath([gyacomodir,'matlab/plot']))    % Add plot folder
addpath(genpath([gyacomodir,'matlab/compute'])) % Add compute folder
addpath(genpath([gyacomodir,'matlab/load']))    % Add load folder
addpath(genpath([gyacomodir,'wk/parameters']))  % Add parameters folder

%% Setup run or load an executable
RUN = 1; % To run or just to load
default_plots_options
EXECNAME = 'gyacomo23_sp'; % single precision
% EXECNAME = 'gyacomo23_dp'; % 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_JET_rho97
% run lin_Entropy
% run lin_ITG
%% Change parameters
NY   = 2;
PMAX = 4;
JMAX = PMAX/2;
ky   = 1.0;
LY   = 2*pi/ky;
DT   = 1e-5;
% SIGMA_E = 0.04;
TMAX     = 10;
DTSAVE0D = 200*DT;
DTSAVE3D = TMAX/50;
%%-------------------------------------------------------------------------
%% 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 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;';
    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 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  = [0.2 1]*data.Ts3D(end);
options.KY_TW  = [0.2 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

if (1 && NZ>4)
%% Ballooning plot
[data.PHI, data.Ts3D] = compile_results_3D(LOCALDIR,J0,J1,'phi');
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.normalized  = 1;
options.PLOT_KP     = 0;
% options.field       = 'phi';
fig = plot_ballooning(data,options);
end