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gyacomo/wk/quick_run.m
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quick_run.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"
%
RUN = 1; % To run or just to load
addpath(genpath('../matlab')) % ... add
default_plots_options
HELAZDIR = '/home/ahoffman/HeLaZ/';
EXECNAME = 'helaz3.12';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
NU = 0.0; % Collision frequency
TAU = 1.0; % e/i temperature ratio
K_N = 2.22; % Density gradient drive
K_T = 6.96; % Temperature '''
K_E = 0.0; % Electrostat '''
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 = 8; % Hermite basis size of electrons
JMAXE = 4; % Laguerre "
PMAXI = 8; % " ions
JMAXI = 4; % "
NX = 1; % real space x-gridpoints
NY = 20; % '' y-gridpoints
LX = 120; % Size of the squared frequency domain
LY = 120; % Size of the squared frequency domain
NZ = 16; % number of perpendicular planes (parallel grid)
NPOL = 1;
SG = 0; % Staggered z grids option
%% GEOMETRY
GEOMETRY= 'Z-pinch'; % Z-pinch overwrites q0, shear and eps
% GEOMETRY= 's-alpha';
Q0 = 1.4; % safety factor
SHEAR = 0.0; % magnetic shear (Not implemented yet)
EPS = 0.18; % inverse aspect ratio
%% TIME PARMETERS
TMAX = 50; % Maximal time unit
DT = 2e-2; % Time step
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = 0; % Sampling per time unit for 2D arrays
SPS3D = 1; % Sampling per time unit for 2D arrays
SPS5D = 1; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints
JOB2LOAD= -1;
%% OPTIONS
SIMID = 'quick_run'; % Name of the simulation
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 = 1; % Closure model (0: =0 truncation, 1: gyrofluid 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
%% 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
kmax = NX*pi/LX;% Highest fourier mode
MU = 0.0; % Hyperdiffusivity coefficient
INIT_BLOB = 0; WIPE_TURB = 0; ACT_ON_MODES = 0;
MU_X = MU; %
MU_Y = MU; %
MU_Z = 0.2; %
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;
%%-------------------------------------------------------------------------
%% 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 2 ',HELAZDIR,'bin/',EXECNAME,' 2 1 1 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 2 2 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',HELAZDIR,'bin/',EXECNAME,' 1 3 2 0; cd ../../../wk'])
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)
trange = [0.5 1]*data.Ts3D(end);
nplots = 1;
lg = compute_fluxtube_growth_rate(data,trange,nplots);
end
if 0
%% Ballooning plot
options.time_2_plot = data.Ts3D(end);
options.kymodes = [0.2 0.5 0.7];
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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