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gyacomo/wk/lin_3D_Zpinch.m
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lin_3D_Zpinch.m
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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"
%
% SIMID = 'lin_3D_Zpinch'; % Name of the simulation
SIMID = 'NL_3D_zpinch'; % 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
PROGDIR = '/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 = 2.0; % ele Density '''
K_Te = K_Ne/4; % ele Temperature '''
K_Ni = K_Ne; % ion Density gradient drive
K_Ti = K_Ni/4; % 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 = 1; % 1: kinetic electrons, 2: adiabatic electrons
BETA = 0.005; % electron plasma beta
%% GRID PARAMETERS
P = 2;
J = P/2;
PMAXE = P; % Hermite basis size of electrons
JMAXE = J; % Laguerre "
PMAXI = P; % " ions
JMAXI = J; % "
NX = 128; % real space x-gridpoints
NY = 32; % '' y-gridpoints
LX = 2*pi/0.1; % Size of the squared frequency domain
LY = 2*pi/0.1; % Size of the squared frequency domain
NZ = 20; % number of perpendicular planes (parallel grid)
NPOL = 1;
SG = 0; % Staggered z grids option
%% GEOMETRY
% GEOMETRY= 's-alpha';
% GEOMETRY= 'miller';
GEOMETRY= 'Z-pinch';
Q0 = 1.4; % safety factor
SHEAR = 0.8; % magnetic shear
KAPPA = 0.0; % 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 = 20; % Maximal time unit
DT = 1e-2; % 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 = 1; % 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 = 1.0e-5; % Init noise amplitude
BCKGD0 = 0.0; % Init background
GRADB = 1.0;
CURVB = 1.0;
COLL_KCUT = 1000;
%%-------------------------------------------------------------------------
%% RUN
setup
% system(['rm fort*.90']);
% Run linear simulation
if RUN
if NZ > 1
system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',HELAZDIR,'bin/',EXECNAME,' 1 2 3 0; cd ../../../wk'])
else
system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',HELAZDIR,'bin/',EXECNAME,' 1 6 1 0; cd ../../../wk'])
end
end
%% Load results
%%
filename = [SIMID,'/',PARAMS,'/'];
LOCALDIR = [HELAZDIR,'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 = 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
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
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