%% QUICK RUN SCRIPT
% This script create a directory in /results and run a simulation directly
% from matlab framework. It is meant to run only small problems in linear
% for benchmark and debugging purpose since it makes matlab "busy"
%
% SIMID   = 'lin_ITG';  % Name of the simulation
SIMID   = 'dbg';  % Name of the simulation
RUN     = 1; % To run or just to load
addpath(genpath('../matlab')) % ... add
default_plots_options
gyacomodir = '/home/ahoffman/gyacomo/';
% EXECNAME = 'gyacomo_1.0';
% EXECNAME = 'gyacomo_dbg';
EXECNAME = 'gyacomo';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
CLUSTER.TIME  = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU      = 0.05;           % Collision frequency
TAU     = 1.0;            % e/i temperature ratio
K_Ne    = 0*2.22;            % ele Density '''
K_Te    = 6.96;            % ele Temperature '''
K_Ni    = 0*2.22;            % ion Density gradient drive
K_Ti    = 6.96;            % ion Temperature '''
SIGMA_E = 0.05196152422706632;   % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
% SIGMA_E = 0.0233380;   % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
KIN_E   = 0;         % 1: kinetic electrons, 2: adiabatic electrons
BETA    = 0.0;     % electron plasma beta
%% GRID PARAMETERS
P = 4;
J = P/2;
PMAXE   = P;     % Hermite basis size of electrons
JMAXE   = J;     % Laguerre "
PMAXI   = P;     % " ions
JMAXI   = J;     % "
NX      = 20;    % real space x-gridpoints
NY      = 2;     %     ''     y-gridpoints
LX      = 2*pi/0.8;   % Size of the squared frequency domain
LY      = 2*pi/0.3;     % Size of the squared frequency domain
NZ      = 32;    % number of perpendicular planes (parallel grid)
NPOL    = 1;
SG      = 0;     % Staggered z grids option
%% GEOMETRY
% GEOMETRY= 's-alpha';
GEOMETRY= 'miller';
Q0      = 1.4;    % safety factor
SHEAR   = 0.8;    % magnetic shear
KAPPA   = 1.0;    % elongation
DELTA   = 0.0;    % triangularity
ZETA    = 0.0;    % squareness
NEXC    = 1;      % To extend Lx if needed (Lx = Nexc/(kymin*shear))
EPS     = 0.18;   % inverse aspect ratio
%% TIME PARMETERS
TMAX    = 25;  % Maximal time unit
DT      = 3e-3;   % Time step
SPS0D   = 1;      % Sampling per time unit for 2D arrays
SPS2D   = 0;      % Sampling per time unit for 2D arrays
SPS3D   = 5;      % Sampling per time unit for 2D arrays
SPS5D   = 1/5;    % Sampling per time unit for 5D arrays
SPSCP   = 0;    % Sampling per time unit for checkpoints
JOB2LOAD= -1;
%% OPTIONS
LINEARITY = 'linear';   % activate non-linearity (is cancelled if KXEQ0 = 1)
% Collision operator
% (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
CO      = 'DG';
GKCO    = 0; % gyrokinetic operator
ABCO    = 1; % interspecies collisions
INIT_ZF = 0; ZF_AMP = 0.0;
CLOS    = 0;   % Closure model (0: =0 truncation, 1: v^Nmax closure (p+2j<=Pmax))s
NL_CLOS = 0;   % nonlinear closure model (-2:nmax=jmax; -1:nmax=jmax-j; >=0:nmax=NL_CLOS)
KERN    = 0;   % Kernel model (0 : GK)
INIT_OPT= 'mom00';   % Start simulation with a noisy mom00/phi/allmom
%% OUTPUTS
W_DOUBLE = 1;
W_GAMMA  = 1; W_HF     = 1;
W_PHI    = 1; W_NA00   = 1;
W_DENS   = 1; W_TEMP   = 1;
W_NAPJ   = 1; W_SAPJ   = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% unused
HD_CO   = 0.0;    % Hyper diffusivity cutoff ratio
MU      = 0.0; % Hyperdiffusivity coefficient
INIT_BLOB = 0; WIPE_TURB = 0; ACT_ON_MODES = 0;
MU_X    = MU;     %
MU_Y    = MU;     %
N_HD    = 4;
MU_Z    = 2.0;     %
MU_P    = 0.0;     %
MU_J    = 0.0;     %
LAMBDAD = 0.0;
NOISE0  = 0.0e-5; % Init noise amplitude
BCKGD0  = 1.0;    % Init background
GRADB   = 1.0;
CURVB   = 1.0;
%%-------------------------------------------------------------------------
%% RUN
setup
% system(['rm fort*.90']);
% Run linear simulation
if RUN
%     system(['cd ../results/',SIMID,'/',PARAMS,'/; time mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 4 1 0; cd ../../../wk'])
%     system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 4 1 0; cd ../../../wk'])
%     system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ',HELAZDIR,'bin/',EXECNAME,' 1 1 1 0; cd ../../../wk'])
    system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 1 2 3 0; cd ../../../wk'])
%     system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',HELAZDIR,'bin/',EXECNAME,' 1 6 1 0; cd ../../../wk'])
end

%% Load results
%%
filename = [SIMID,'/',PARAMS,'/'];
LOCALDIR  = [gyacomodir,'results/',filename,'/'];
% Load outputs from jobnummin up to jobnummax
JOBNUMMIN = 00; JOBNUMMAX = 00;
data = compile_results(LOCALDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing

%% Short analysis
if 1
%% linear growth rate (adapted for 2D zpinch and fluxtube)
options.TRANGE = [0.5 1]*data.Ts3D(end);
options.NPLOTS = 2; % 1 for only growth rate and error, 2 for omega local evolution, 3 for plot according to z
options.GOK    = 0; %plot 0: gamma 1: gamma/k 2: gamma^2/k^3
lg = compute_fluxtube_growth_rate(data,options);
[gmax,     kmax] = max(lg.g_ky(:,end));
[gmaxok, kmaxok] = max(lg.g_ky(:,end)./lg.ky);
msg = sprintf('gmax = %2.2f, kmax = %2.2f',gmax,lg.ky(kmax)); disp(msg);
msg = sprintf('gmax/k = %2.2f, kmax/k = %2.2f',gmaxok,lg.ky(kmaxok)); disp(msg);
end

if 1
%% Ballooning plot
options.time_2_plot = [120];
options.kymodes     = [0.3];
options.normalized  = 1;
% options.field       = 'phi';
fig = plot_ballooning(data,options);
end

if 0
%% Hermite-Laguerre spectrum
% options.TIME = 'avg';
options.P2J        = 1;
options.ST         = 1;
options.PLOT_TYPE  = 'space-time';
% options.PLOT_TYPE  =   'Tavg-1D';
% options.PLOT_TYPE  = 'Tavg-2D';
options.NORMALIZED = 0;
options.JOBNUM     = 0;
options.TIME       = [0 50];
options.specie     = 'i';
options.compz      = 'avg';
fig = show_moments_spectrum(data,options);
% fig = show_napjz(data,options);
save_figure(data,fig)
end

if 0
%% linear growth rate for 3D Zpinch (kz fourier transform)
trange = [0.5 1]*data.Ts3D(end);
options.keq0 = 1; % chose to plot planes at k=0 or max
options.kxky = 1;
options.kzkx = 0;
options.kzky = 0;
[lg, fig] = compute_3D_zpinch_growth_rate(data,trange,options);
save_figure(data,fig)
end
if 0
%% Mode evolution
options.NORMALIZED = 0;
options.K2PLOT = 1;
options.TIME   = [0:1000];
options.NMA    = 1;
options.NMODES = 1;
options.iz     = 'avg';
fig = mode_growth_meter(data,options);
save_figure(data,fig,'.png')
end


if 1
%% RH TEST
ikx = 2; iky = 2; t0 = 0; 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));
figure
plot(data.Ts3D(it0:it1), plt(data.PHI));
xlabel('$t$'); ylabel('$\phi_z(t)/\phi_z(0)$')
title(sprintf('$k_x=$%2.2f, $k_y=$%2.2f',data.kx(ikx),data.ky(iky)))
end