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%% 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"
%
gyacomodir = pwd;
gyacomodir = gyacomodir(1:end-2);
addpath(genpath([gyacomodir,'matlab'])) % ... add
addpath(genpath([gyacomodir,'matlab/plot'])) % ... add
addpath(genpath([gyacomodir,'matlab/compute'])) % ... add
addpath(genpath([gyacomodir,'matlab/load'])) % ... add% EXECNAME = 'gyacomo_1.0';
% SIMID = 'linear_CBC_benchmark_GX'; % Name of the simulation
default_plots_options
EXECNAME = 'gyacomo';
% EXECNAME = 'gyacomo_alpha';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
TAU = 1.0; % e/i temperature ratio
K_Ne = 0*2.22; % ele Density '''
K_Te = 0*6.96; % ele Temperature '''
K_Ni = 1*2.22; % ion Density gradient drive
K_Ti = 6.96; % ion Temperature '''
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% 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
%% GRID PARAMETERS
PMAXE = P; % Hermite basis size of electrons
JMAXE = J; % Laguerre "
PMAXI = P; % " ions
JMAXI = J; % "
LX = 2*pi/0.1; % Size of the squared frequency domain
LY = 2*pi/0.1; % Size of the squared frequency domain
NZ = 24; % number of perpendicular planes (parallel grid)
NPOL = 1;
SG = 0; % Staggered z grids option
NEXC = 1; % To extend Lx if needed (Lx = Nexc/(kymin*shear))
%% GEOMETRY
GEOMETRY= 's-alpha';
% GEOMETRY= 'miller';
Q0 = 1.4; % safety factor
KAPPA = 1.0; % elongation
DELTA = 0.0; % triangularity
ZETA = 0.0; % squareness
% PARALLEL_BC = 'dirichlet'; %'dirichlet','periodic','shearless','disconnected'
PARALLEL_BC = 'cyclic'; %'dirichlet','periodic','shearless','disconnected'
%% TIME PARMETERS
TMAX = 25; % Maximal time unit
% DT = 1e-2; % Time step
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = -1; % Sampling per time unit for 2D arrays
SPS3D = 1; % Sampling per time unit for 2D arrays
SPS5D = 1/20; % 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= 'phi'; % Start simulation with a noisy mom00/phi/allmom
NUMERICAL_SCHEME = 'RK4'; % RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5
%% 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 = 1.0; %
HYP_V = 'dvpar4';
MU_P = 0.5; %
MU_J = 0.0; %
LAMBDAD = 0.0;
NOISE0 = 1.0e-5; % Init noise amplitude
BCKGD0 = 0.0; % Init background
COLL_KCUT = 1000;
%%-------------------------------------------------------------------------
%% RUN
setup
% system(['rm fort*.90']);
% Run linear simulation
if RUN
system(['cd ../results/',SIMID,'/',PARAMS,'/; time mpirun -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 4 1 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0; cd ../../../wk'])
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% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 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 ',gyacomodir,'bin/',EXECNAME,' 1 6 1 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0; cd ../../../wk'])
end
%% Load results
%%
filename = [SIMID,'/',PARAMS,'/'];
LOCALDIR = [gyacomodir,'results/',filename,'/'];
FIGDIR = LOCALDIR;
% Load outputs from jobnummin up to jobnummax
data = compile_results(LOCALDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
data.FIGDIR = ['../results/',SIMID,'/',PARAMS,'/'];
%% Short analysis
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if 0
%% linear growth rate (adapted for 2D zpinch and fluxtube)
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options.NPLOTS = 3; % 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
%% Ballooning plot
options.time_2_plot = [10 50];
options.kymodes = [0.1 0.2 0.4];
options.normalized = 1;
% options.field = 'phi';
fig = plot_ballooning(data,options);
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
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if 1
%% Mode evolution
options.NORMALIZED = 1;
options.TIME = [000:9000];
options.KX_TW = [0.5 1]*data.Ts3D(end); %kx Growth rate time window
options.KY_TW = [0.5 1]*data.Ts3D(end); %ky Growth rate time window
options.NMA = 1;
options.NMODES = 800;
options.iz = 'avg'; % avg or index
options.ik = 1; % sum, max or index
options.fftz.flag = 0;
fig = mode_growth_meter(data,options);
end
%% 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