%% 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_save'; % single 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_DIIID_LM_rho90
% run lin_DIIID_LM_rho95
% run lin_DIIID_LM_rho95_HEL
% run lin_JET_rho97
% run lin_Entropy
% run lin_ITG
% run lin_KBM
run lin_MTM_Hamed
% run lin_RHT
% run lin_Ivanov
% rho  = 0.95; TRIANG = 'NT'; READPROF = 1; 
% prof_folder = ['parameters/profiles/DIIID_Austin_et_al_2019/',TRIANG,'/'];
% prof_folder = ['parameters/profiles/DIIID_Oak_Nelson/',TRIANG,'/'];
% prof_folder = ['parameters/profiles/DIIID_Oak_Nelson_high_density/',TRIANG,'/'];
% run lin_DIIID_data
% run lin_STEP_EC_HD_psi71
% run lin_STEP_EC_HD_psi49
% if 1
% Plot the profiles
%  plot_params_vs_rho(geom,prof_folder,rho,0.01,1.1,Lref,mref,Bref,READPROF);
% end
% SIMID = ['rho_scan_DIIID_AUSTIN_2019/3x2x192x96x32/rho',num2str(rho)];
%% Change parameters
% GEOMETRY = 's-alpha';
% PMAX  = 2; JMAX = 1;
% DELTA = 0.2; 
% K_tB = 0; K_mB = 0; K_ldB = 1;
% K_Ni = 0; 
% K_Ne = 0;
% K_Ti = 0; 
% K_Te = 0; 
% DELTA = 0.0; 
% DELTA = 0.2; 
% S_DELTA = DELTA/2;
LY   = 2*pi/0.7;
% TMAX = 40;
% NY   = 20;
DT   = 0.001;
% CO   = 'DG';
% TAU  = 1; NU = 0.05;
% NA  = 1; ADIAB_E = 1; DT = 1e-2; DTSAVE3D = 1e-2; TMAX = 60;
% TAU = 1e-3; K_Ti = K_Ti/2/TAU; K_Ni = 0; 
% NU = 3*NU/8/TAU; PMAX = 2; JMAX = 1;
% K_Ti = K_Ti/4;
% MU_X = 1; MU_Y = 1;
%% RUN
setup
system(['cp ../results/',SIMID,'/',PARAMS,'/fort_00.90 ../results/',SIMID,'/.']);
% 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 4 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 = 00; J1 = 00;
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.KY_TW  = [0.25 1.0]*data.Ts3D(end);
options.KX_TW  = [0.25 1.0]*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.GOK2   = 0; % plot gamma/k^2
options.fftz.flag = 0; % Set fftz.flag option to 0
options.FIELD = 'phi';
options.SHOWFIG = 1;
[fig, wkykx, ekykx] = mode_growth_meter(data,options);
% %%
% kx = (1:data.grids.Nx/2)'*2*pi/data.fort_00.GRID.Lx;
% ky = (1:data.grids.Ny/2)'*2*pi/data.fort_00.GRID.Ly;
% gkxky = real(wkykx(2:end,1:data.grids.Nx/2))';
% gkxky(isnan(gkxky)) =0;
% gkxky(isinf(gkxky)) =0;
% figure; plot(ky,gkxky(1,:));
end

if (0 && 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     = [100];
options.normalized  = 1;
options.PLOT_KP     = 0;
% options.field       = 'phi';
options.SHOWFIG  = 1;
[fig, chi, phib, psib, ~] = plot_ballooning(data,options);
end

if 0
%% RH TEST
[data.PHI, data.Ts3D] = compile_results_3D(LOCALDIR,J0,J1,'phi');
ikx = 2; iky = 1; t0 = 1; t1 = data.Ts3D(end);
[~, it0] = min(abs(t0-data.Ts3D));[~, it1] = min(abs(t1-data.Ts3D));
plt = @(x) squeeze(mean(real(x(iky,ikx,:,it0:it1)),3))./squeeze(mean(real(x(iky,ikx,:,it0)),3));
t_ = data.Ts3D(it0:it1);
TH = 1.635*EPS^1.5 + 0.5*EPS^2+0.36*EPS^2.5; theory = 1/(1+Q0^2*TH/EPS^2);
clr_ = lines(20);
figure
plot(t_, -plt(data.PHI)); hold on;
plot(t_,0.5* exp(-t_*NU)+theory,'--k');
plot([t_(1) t_(end)],theory*[1 1],'-k');
plot([t_(1) t_(end)],-mean(plt(data.PHI))*[1 1],'-g');
xlabel('$t$'); ylabel('$\phi_z(t)/\phi_z(0)$')
title(sprintf('$k_x=$%2.2f, $k_y=$%2.2f',data.grids.kx(ikx),data.grids.ky(iky)))
end

if 0
    %% Geometry
    plot_metric(data);
end

if (1 && NZ>4)
%% Ballooning plot
% [data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
if data.inputs.BETA > 0
[data.PSI, data.Ts3D] = compile_results_3D(LOCALDIR,J0,J1,'psi');
end
options.time_2_plot = [10];
options.kymodes     = 1.5;
options.normalized  = 1;
options.PLOT_KP     = 0;
% options.field       = 'phi';
options.SHOWFIG  = 1;
[fig, chi, phib, psib, ~] = plot_ballooning(data,options);
end

if 0
%% Hermite-Laguerre spectrum
[data.Napjz, data.Ts3D] = compile_results_3Da(LOCALDIR,J0,J1,'Napjz');
% data.Napjz(1,3,1,:,:) = data.Napjz(1,3,1,:,:)*data.inputs.tau;
% data.Napjz(1,1,2,:,:) = data.Napjz(1,1,2,:,:)*data.inputs.tau;
% [data.Napjz, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'Nipjz');
options.ST         = 1;
options.NORMALIZED = 1;
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
options.TWINDOW    = [20 20];
fig = show_moments_spectrum(data,options);
end
