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Commit 79443f28 authored by Antoine Cyril David Hoffmann's avatar Antoine Cyril David Hoffmann :seedling:
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update scripts for adiab ions

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wk/fast_analysis.m
+ 24
− 14
View file @ 79443f28
......@@ -5,8 +5,8 @@ addpath(genpath([gyacomodir,'matlab/compute'])) % ... add
addpath(genpath([gyacomodir,'matlab/load'])) % ... add
default_plots_options
% Partition of the computer where the data have to be searched
PARTITION = '/misc/gyacomo23_outputs/';
% PARTITION = '/home/ahoffman/gyacomo/';
% PARTITION = '/misc/gyacomo23_outputs/';
PARTITION = '/home/ahoffman/gyacomo/';
%% Tests
% resdir = 'test_stepon_AA/CBC_stepon_AA';
......@@ -56,11 +56,21 @@ PARTITION = '/misc/gyacomo23_outputs/';
% resdir = 'paper_2_GYAC23/collision_study/nuDGGK_scan_kT_5.3/9x5x192x96x24/nu_0.2';
% resdir = 'paper_2_GYAC23/collision_study/nuDGGK_scan_kT_5.3/17x9x192x96x24/nu_0.2';
% resdir = 'paper_2_GYAC23/collision_study/nuDGGK_scan_kT_5.3/9x5x192x96x24/nu_0.02';
resdir = 'paper_2_GYAC23/collision_study/nuDGGK_scan_kT_5.3/17x9x192x96x24/nu_0.02';
% resdir = 'paper_2_GYAC23/collision_study/nuDGGK_scan_kT_5.3/17x9x192x96x24/nu_0.02';
% resdir = 'paper_2_GYAC23/collision_study/nuSGGK_scan_kT_5.3/17x9x192x96x24/nu_0.02';
% resdir = 'paper_2_GYAC23/collision_study/nuSGGK_scan_kT_5.3/9x5x192x96x24/nu_0.2';
% resdir = 'paper_2_GYAC23/collision_study/nuDGGK_scan_kT_5.3/17x9x192x96x24/continue_SG_nu_0.02';
% resdir = 'paper_2_GYAC23/collision_study/nuSGGK_scan_kT_5.3/5x3x192x96x24/nu_0.02';
% resdir = 'paper_2_GYAC23/collision_study/nuSGGK_scan_kT_5.3/9x5x192x96x24/nu_0.02';
% resdir = 'paper_2_GYAC23/collision_study/nuSGGK_scan_kT_5.3/17x9x192x96x24/nu_0.02';
% resdir = 'paper_2_GYAC23/collision_study/nuSGGK_scan_kT_5.3/17x9x192x96x24/nu_0.005';
% resdir = 'paper_2_GYAC23/collision_study/nuLDGK_scan_kT_5.3/5x3x192x96x24/nu_0.005';
% resdir = 'paper_2_GYAC23/collision_study/nuLDGK_scan_kT_5.3/9x5x192x96x24/nu_0.005';
% resdir = 'paper_2_GYAC23/collision_study/nuLDGK_scan_kT_5.3/17x9x128x64x24/nu_0.005';
%% kT eff study
% resdir = 'paper_2_GYAC23/kT_eff_study/1x3x128x64x24_kT_3.0/Lx120';
% resdir = 'paper_2_GYAC23/kT_eff_study/1x3x128x64x24_kT_3.0/Lx240';
......@@ -71,9 +81,9 @@ resdir = 'paper_2_GYAC23/collision_study/nuDGGK_scan_kT_5.3/17x9x192x96x24/nu_0.
% resdir = 'paper_2_GYAC23/kT_eff_study/7x3x128x64x24_kT_3.6/dmax';
%% dev
% PARTITION='';
PARTITION='';
% resdir = '/home/ahoffman/gyacomo/testcases/zpinch_3D';
% resdir = '/home/ahoffman/gyacomo';
resdir = '/home/ahoffman/gyacomo/results/dev/3D_kine_zpinch_test';
%% CBC benchmark
% resdir = '/misc/gyacomo23_outputs/paper_2_GYAC23/kT_scan_nu_1e-3/3x2x128x64x24/kT_7.0';
% resdir = '/misc/gyacomo23_outputs/paper_2_GYAC23/kT_scan_nu_1e-3/5x3x128x64x24/kT_7.0';
......@@ -81,7 +91,7 @@ resdir = 'paper_2_GYAC23/collision_study/nuDGGK_scan_kT_5.3/17x9x192x96x24/nu_0.
% resdir = '/misc/gyacomo23_outputs/paper_2_GYAC23/kT_scan_nu_1e-3/17x9x128x64x24/kT_7.0';
% resdir = '/misc/gyacomo23_outputs/paper_2_GYAC23/kT_scan_nu_1e-3/31x16x128x64x24/kT_7.0';
%%
J0 = 00; J1 = 10;
J0 = 00; J1 = 20;
% Load basic info (grids and time traces)
DATADIR = [PARTITION,resdir,'/'];
......@@ -111,16 +121,16 @@ if 0
% data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
options.INTERP = 1;
options.POLARPLOT = 0;
% options.NAME = '\phi';
options.NAME = '\phi';
% options.NAME = '\phi^{NZ}';
% options.NAME = '\omega_z';
options.NAME = 'N_i^{00}';
% options.NAME = 'N_i^{00}';
% options.NAME = 's_{Ey}';
% options.NAME = 'n_i^{NZ}';
% options.NAME = 'Q_x';
% options.NAME = 'n_i';
% options.NAME = 'n_i-n_e';
options.PLAN = 'xy';
options.PLAN = 'xz';
% options.NAME = 'f_i';
% options.PLAN = 'sx';
options.COMP = 'avg';
......@@ -144,8 +154,8 @@ options.INTERP = 0;
options.POLARPLOT = 0;
options.AXISEQUAL = 0;
options.NORMALIZE = 0;
options.NAME = 'N_i^{00}';
% options.NAME = '\phi';
% options.NAME = 'N_i^{00}';
options.NAME = '\phi';
options.PLAN = 'xy';
options.COMP = 'avg';
options.TIME = [100 200 300];
......@@ -166,8 +176,8 @@ options.ST = 1;
options.NORMALIZED = 0;
options.LOGSCALE = 1;
options.FILTER = 0; %filter the 50% time-average of the spectrum from
options.TAVG_2D = 1; %Show a 2D plot of the modes, 50% time averaged
options.TAVG_2D_CTR= 1; %make it contour plot
options.TAVG_2D = 0; %Show a 2D plot of the modes, 50% time averaged
options.TAVG_2D_CTR= 0; %make it contour plot
fig = show_moments_spectrum(data,options);
end
......
wk/lin_AUG.m 0 → 100644
+ 177
− 0
View file @ 79443f28
%% 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);
addpath(genpath([gyacomodir,'matlab'])) % Add matlab module
addpath(genpath([gyacomodir,'matlab/plot'])) % Add plot module
addpath(genpath([gyacomodir,'matlab/compute'])) % Add compute module
addpath(genpath([gyacomodir,'matlab/load'])) % Add load module
%% Set simulation parameters
SIMID = 'lin_KBM'; % Name of the simulation
RUN = 1; % To run or just to load
default_plots_options
% EXECNAME = 'gyacomo23_sp'; % single precision
EXECNAME = 'gyacomo23_dp'; % double precision
% EXECNAME = 'gyacomo23_debug'; % single precision
%% Set up physical parameters
CLUSTER.TIME = '99:00:00'; % Allocation time hh:mm:ss
NU = 0.1; % Collision frequency
TAU = 1.38; % e/i temperature ratio
K_Ne = 34; % ele Density '''
K_Te = 56; % ele Temperature '''
K_Ni = 34; % ion Density gradient drive
K_Ti = 21; % ion Temperature '''
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
NA = 2; % number of kinetic species
ADIAB_E = (NA==1); % adiabatic electron model
BETA = 1.52e-4; % electron plasma beta
MHD_PD = 0; % MHD pressure drift
%% Set up grid parameters
P = 2;
J = P/2;%P/2;
PMAX = P; % Hermite basis size
JMAX = J; % Laguerre basis size
NX = 4; % real space x-gridpoints
NY = 2; % real space y-gridpoints
LX = 2*pi/0.3; % Size of the squared frequency domain in x direction
LY = 2*pi/0.2; % Size of the squared frequency domain in y direction
NZ = 16; % number of perpendicular planes (parallel grid)
SG = 0; % Staggered z grids option
NEXC = 1; % To extend Lx if needed (Lx = Nexc/(kymin*shear))
%% GEOMETRY
% GEOMETRY= 's-alpha';
GEOMETRY= 'miller';
EPS = 0.3; % inverse aspect ratio
% EPS = 0.18; % inverse aspect ratio
Q0 = 5.7; % safety factor
% Q0 = 1.4; % safety factor
SHEAR = 4.6; % magnetic shear
% SHEAR = 0.8; % magnetic shear
KAPPA = 1.8; % elongation
% KAPPA = 1.0; % elongation
S_KAPPA = 0.0;
DELTA = 0.4; % triangularity
% DELTA = 0.0; % triangularity
S_DELTA = 0.0;
ZETA = 0.0; % squareness
S_ZETA = 0.0;
PARALLEL_BC = 'dirichlet'; % Boundary condition for parallel direction ('dirichlet','periodic','shearless','disconnected')
SHIFT_Y = 0.0; % Shift in the periodic BC in z
NPOL = 1; % Number of poloidal turns
PB_PHASE= 0;
%% TIME PARAMETERS
TMAX = 5; % Maximal time unit
DT = 2e-3; % Time step
DTSAVE0D = 1; % Sampling per time unit for 0D arrays
DTSAVE2D = -1; % Sampling per time unit for 2D arrays
DTSAVE3D = 3; % Sampling per time unit for 3D arrays
DTSAVE5D = 100; % Sampling per time unit for 5D arrays
JOB2LOAD = -1; % Start a new simulation serie
%% OPTIONS
LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
CO = 'DG'; % Collision operator (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
GKCO = 1; % Gyrokinetic operator
ABCO = 1; % INTERSPECIES collisions
INIT_ZF = 0; % Initialize zero-field quantities
HRCY_CLOS = 'truncation'; % Closure model for higher order moments
DMAX = -1;
NLIN_CLOS = 'truncation'; % Nonlinear closure model for higher order moments
NMAX = 0;
KERN = 0; % Kernel model (0 : GK)
INIT_OPT = 'phi'; % Start simulation with a noisy mom00/phi/allmom
NUMERICAL_SCHEME = 'RK4'; % Numerical integration scheme (RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5)
%% OUTPUTS
W_DOUBLE = 1; % Output flag for double moments
W_GAMMA = 1; % Output flag for gamma (Gyrokinetic Energy)
W_HF = 1; % Output flag for high-frequency potential energy
W_PHI = 1; % Output flag for potential
W_NA00 = 1; % Output flag for nalpha00 (density of species alpha)
W_DENS = 1; % Output flag for total density
W_TEMP = 1; % Output flag for temperature
W_NAPJ = 1; % Output flag for nalphaparallel (parallel momentum of species alpha)
W_SAPJ = 0; % Output flag for saparallel (parallel current of species alpha)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% UNUSED PARAMETERS
% These parameters are usually not to play with in linear runs
MU = 0.1; % Hyperdiffusivity coefficient
MU_X = MU; % Hyperdiffusivity coefficient in x direction
MU_Y = MU; % Hyperdiffusivity coefficient in y direction
N_HD = 4; % Degree of spatial-hyperdiffusivity
MU_Z = 10.0; % Hyperdiffusivity coefficient in z direction
HYP_V = 'hypcoll'; % Kinetic-hyperdiffusivity model
MU_P = 0.0; % Hyperdiffusivity coefficient for Hermite
MU_J = 0.0; % Hyperdiffusivity coefficient for Laguerre
LAMBDAD = 0.0; % Lambda Debye
NOISE0 = 0.0e-5; % Initial noise amplitude
BCKGD0 = 1.0e-5; % Initial background
k_gB = 1.0; % Magnetic gradient strength
k_cB = 1.0; % Magnetic curvature strength
COLL_KCUT = 1; % Cutoff for collision operator
%%-------------------------------------------------------------------------
%% RUN
setup
% 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 2 2 0;'];
% RUN =['time mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 1 6 1 0;'];
RUN =['time mpirun -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 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 = 0; J1 = 0;
data = {}; % Initialize data as an empty cell array
% load grids, inputs, and time traces
data = compile_results_low_mem(data,LOCALDIR,J0,J1);
if 0 % 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.KX_TW = [0.2 1]*data.Ts3D(end);
options.KY_TW = [0.2 1]*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.fftz.flag = 0; % Set fftz.flag option to 0
fig = mode_growth_meter(data,options); % Call the function mode_growth_meter with data and options as input arguments, and store the result in fig
end
if 1
%% 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 = [0.5];
options.normalized = 1;
% options.field = 'phi';
fig = plot_ballooning(data,options);
end
wk/lin_ITG_salpha.m
+ 7
− 7
View file @ 79443f28
......@@ -20,19 +20,19 @@ EXECNAME = 'gyacomo23_sp'; % single precision
%% Set up physical parameters
CLUSTER.TIME = '99:00:00'; % Allocation time hh:mm:ss
NU = 0.001; % Collision frequency
NU = 0.005; % Collision frequency
TAU = 1.0; % e/i temperature ratio
K_Ne = 0*2.22; % ele Density
K_Te = 0*6.96; % ele Temperature
K_Ni = 2.22; % ion Density gradient drive
K_Ti = 6.96; % ion Temperature
K_Ti = 5.3; % ion Temperature
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
NA = 1; % number of kinetic species
ADIAB_E = (NA==1); % adiabatic electron model
BETA = 0.0; % electron plasma beta
%% Set up grid parameters
P = 2;
J = 1;%P/2;
P = 4;
J = 2;%P/2;
PMAX = P; % Hermite basis size
JMAX = J; % Laguerre basis size
NX = 8; % real space x-gridpoints
......@@ -58,7 +58,7 @@ NPOL = 1; % Number of poloidal turns
%% TIME PARAMETERS
TMAX = 50; % Maximal time unit
DT = 10e-3; % Time step
DT = 1e-2; % Time step
DTSAVE0D = 1; % Sampling per time unit for 0D arrays
DTSAVE2D = -1; % Sampling per time unit for 2D arrays
DTSAVE3D = 2; % Sampling per time unit for 3D arrays
......@@ -68,7 +68,7 @@ JOB2LOAD = -1; % Start a new simulation serie
%% OPTIONS
LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
CO = 'DG'; % Collision operator (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
GKCO = 0; % Gyrokinetic operator
GKCO = 1; % Gyrokinetic operator
ABCO = 1; % INTERSPECIES collisions
INIT_ZF = 0; % Initialize zero-field quantities
HRCY_CLOS = 'truncation'; % Closure model for higher order moments
......@@ -107,7 +107,7 @@ NOISE0 = 0.0e-5; % Initial noise amplitude
BCKGD0 = 1.0e-5; % Initial background
k_gB = 1.0; % Magnetic gradient strength
k_cB = 1.0; % Magnetic curvature strength
COLL_KCUT = 1000; % Cutoff for collision operator
COLL_KCUT = 1; % Cutoff for collision operator
%%-------------------------------------------------------------------------
%% RUN
......
wk/lin_KBM.m 0 → 100644
+ 168
− 0
View file @ 79443f28
%% 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);
addpath(genpath([gyacomodir,'matlab'])) % Add matlab module
addpath(genpath([gyacomodir,'matlab/plot'])) % Add plot module
addpath(genpath([gyacomodir,'matlab/compute'])) % Add compute module
addpath(genpath([gyacomodir,'matlab/load'])) % Add load module
%% Set simulation parameters
SIMID = 'lin_KBM'; % Name of the simulation
RUN = 1; % To run or just to load
default_plots_options
EXECNAME = 'gyacomo23_sp'; % single precision
% EXECNAME = 'gyacomo23_dp'; % double precision
%% Set up physical parameters
CLUSTER.TIME = '99:00:00'; % Allocation time hh:mm:ss
NU = 0.00; % Collision frequency
TAU = 1.0; % e/i temperature ratio
K_Ne = 3; % ele Density '''
K_Te = 4.5; % ele Temperature '''
K_Ni = 3; % ion Density gradient drive
K_Ti = 8; % ion Temperature '''
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
NA = 2; % number of kinetic species
ADIAB_E = (NA==1); % adiabatic electron model
BETA = 0.03; % electron plasma beta
%% Set up grid parameters
P = 2;
J = P/2;%P/2;
PMAX = P; % Hermite basis size
JMAX = J; % Laguerre basis size
NX = 12; % real space x-gridpoints
NY = 2; % real space y-gridpoints
LX = 2*pi/0.1; % Size of the squared frequency domain in x direction
LY = 2*pi/0.25; % Size of the squared frequency domain in y direction
NZ = 24; % number of perpendicular planes (parallel grid)
SG = 0; % Staggered z grids option
NEXC = 1; % To extend Lx if needed (Lx = Nexc/(kymin*shear))
%% GEOMETRY
% GEOMETRY= 's-alpha';
GEOMETRY= 'miller';
EPS = 0.18; % inverse aspect ratio
Q0 = 1.4; % safety factor
SHEAR = 0.8; % magnetic shear
KAPPA = 1.0; % elongation
DELTA = 0.0; % triangularity
ZETA = 0.0; % squareness
PARALLEL_BC = 'dirichlet'; % Boundary condition for parallel direction ('dirichlet','periodic','shearless','disconnected')
SHIFT_Y = 0.0; % Shift in the periodic BC in z
NPOL = 1; % Number of poloidal turns
%% TIME PARAMETERS
TMAX = 15; % Maximal time unit
DT = 5e-3; % Time step
DTSAVE0D = 1; % Sampling per time unit for 0D arrays
DTSAVE2D = -1; % Sampling per time unit for 2D arrays
DTSAVE3D = 2; % Sampling per time unit for 3D arrays
DTSAVE5D = 100; % Sampling per time unit for 5D arrays
JOB2LOAD = -1; % Start a new simulation serie
%% OPTIONS
LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
CO = 'DG'; % Collision operator (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
GKCO = 0; % Gyrokinetic operator
ABCO = 1; % INTERSPECIES collisions
INIT_ZF = 0; % Initialize zero-field quantities
HRCY_CLOS = 'truncation'; % Closure model for higher order moments
DMAX = -1;
NLIN_CLOS = 'truncation'; % Nonlinear closure model for higher order moments
NMAX = 0;
KERN = 0; % Kernel model (0 : GK)
INIT_OPT = 'mom00'; % Start simulation with a noisy mom00/phi/allmom
NUMERICAL_SCHEME = 'RK4'; % Numerical integration scheme (RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5)
%% OUTPUTS
W_DOUBLE = 1; % Output flag for double moments
W_GAMMA = 1; % Output flag for gamma (Gyrokinetic Energy)
W_HF = 1; % Output flag for high-frequency potential energy
W_PHI = 1; % Output flag for potential
W_NA00 = 1; % Output flag for nalpha00 (density of species alpha)
W_DENS = 1; % Output flag for total density
W_TEMP = 1; % Output flag for temperature
W_NAPJ = 1; % Output flag for nalphaparallel (parallel momentum of species alpha)
W_SAPJ = 0; % Output flag for saparallel (parallel current of species alpha)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% UNUSED PARAMETERS
% These parameters are usually not to play with in linear runs
MU = 0.0; % Hyperdiffusivity coefficient
MU_X = MU; % Hyperdiffusivity coefficient in x direction
MU_Y = MU; % Hyperdiffusivity coefficient in y direction
N_HD = 4; % Degree of spatial-hyperdiffusivity
MU_Z = 1.0; % Hyperdiffusivity coefficient in z direction
HYP_V = 'hypcoll'; % Kinetic-hyperdiffusivity model
MU_P = 0.0; % Hyperdiffusivity coefficient for Hermite
MU_J = 0.0; % Hyperdiffusivity coefficient for Laguerre
LAMBDAD = 0.0; % Lambda Debye
NOISE0 = 0.0e-5; % Initial noise amplitude
BCKGD0 = 1.0e-5; % Initial background
k_gB = 1.0; % Magnetic gradient strength
k_cB = 1.0; % Magnetic curvature strength
COLL_KCUT = 1; % Cutoff for collision operator
%%-------------------------------------------------------------------------
%% RUN
setup
% 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 2 2 0;'];
% RUN =['time mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 1 6 1 0;'];
% RUN =['time mpirun -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 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 = 0; J1 = 0;
data = {}; % Initialize data as an empty cell array
% load grids, inputs, and time traces
data = compile_results_low_mem(data,LOCALDIR,J0,J1);
if 0 % 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.KX_TW = [0.2 1]*data.Ts3D(end);
options.KY_TW = [0.2 1]*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.fftz.flag = 0; % Set fftz.flag option to 0
fig = mode_growth_meter(data,options); % Call the function mode_growth_meter with data and options as input arguments, and store the result in fig
end
if 1
%% 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 = [0.25];
options.normalized = 1;
% options.field = 'phi';
fig = plot_ballooning(data,options);
end
wk/CBC_P_J_scan.m → wk/paper_2_scripts_and_results/CBC_P_J_scan.m
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− 0
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File moved
wk/CBC_ky_PJ_scan.m → wk/paper_2_scripts_and_results/CBC_ky_PJ_scan.m
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− 3
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......@@ -11,14 +11,14 @@ CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%
SIMID = 'p2_linear_new'; % Name of the simulation
RERUN = 0; % rerun if the data does not exist
RUN = 1;
RUN = 0;
K_T = 5.3;
P_a = [2 4 8 10];
P_a = [2 4 8 16];
% P_a = 10;
ky_a= [0.05:0.05:1.0];
% ky_a = 0.05;
% collision setting
CO = 'LD';
CO = 'SG';
GKCO = 1; % gyrokinetic operator
COLL_KCUT = 1.75;
NU = 1e-2;
......
wk/CBC_ky_PJ_scan_colless.m → wk/paper_2_scripts_and_results/CBC_ky_PJ_scan_colless.m
+ 11
− 10
View file @ 79443f28
......@@ -11,12 +11,12 @@ CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%
SIMID = 'p2_linear_new'; % Name of the simulation
RERUN = 0; % rerun if the data does not exist
RUN = 1;
K_T = 6.96;
% P_a = [2 4 8 16 32 48];
P_a = 64;
% ky_a= [0.05:0.05:1.0];
ky_a= [0.25:0.05:0.65];
RUN = 0;
K_T = 5.3;
P_a = [2 4 8 16 32 64];
% P_a = 32;
ky_a= [0.05:0.05:1.0];
% ky_a= [0.25:0.05:0.65];
% collision setting
CO = 'DG';
GKCO = 0; % gyrokinetic operator
......@@ -32,10 +32,10 @@ K_N = 2.22; % Density '''
GEOMETRY= 's-alpha';
SHEAR = 0.8; % magnetic shear
% time and numerical grid
DT0 = 2e-3;
DT0 = 1e-3;
TMAX = 30;
% arrays for the result
g_ky = zeros(numel(ky_a),numel(P_a),NY/2+1);
g_ky = zeros(numel(ky_a),numel(P_a),1);
g_avg= g_ky*0;
g_std= g_ky*0;
% Naming of the collision operator
......@@ -46,6 +46,7 @@ else
end
j = 1;
for P = P_a
J = P/2;
i = 1;
for ky = ky_a
%% PHYSICAL PARAMETERS
......@@ -139,8 +140,8 @@ for ky = ky_a
end
if RUN && (RERUN || isempty(data_.outfilenames) || Ntime < 10)
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',gyacomodir,'bin/',EXECNAME,' 2 2 1 0; cd ../../../wk'])
system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 3 2 1 0; cd ../../../wk'])
system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',gyacomodir,'bin/',EXECNAME,' 2 2 1 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 3 2 1 0; cd ../../../wk'])
end
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
[data_.PHI, data_.Ts3D] = compile_results_3D(LOCALDIR,00,00,'phi');
......
wk/paper_2_scripts_and_results/CBC_ky_nu_scan_colless.m 0 → 100644
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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';
EXECNAME = 'gyacomo23_sp';
% EXECNAME = 'gyacomo23_dp';
% EXECNAME = 'gyacomo23_debug';
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%
SIMID = 'p2_linear_new'; % Name of the simulation
RERUN = 0; % rerun if the data does not exist
RUN = 1;
K_T = 5.3;
P = 16;
nu_a = [0.005 0.01 0.02 0.05];
% nu_a = 0.05;
ky_a = [0.05:0.05:1.0];
% ky_a = 0.35:0.05:0.6;
% collision setting
CO = 'LD';
GKCO = 1; % gyrokinetic operator
COLL_KCUT = 1.00;
% model
KIN_E = 0; % 1: kinetic electrons, 2: adiabatic electrons
BETA = 1e-4; % electron plasma beta
% background gradients setting
K_N = 2.22; % Density '''
% Geometry
% GEOMETRY= 'miller';
GEOMETRY= 's-alpha';
SHEAR = 0.8; % magnetic shear
% time and numerical grid
DT = 1e-3;
TMAX = 40;
% arrays for the result
g_ky = zeros(numel(ky_a),numel(nu_a),1);
g_avg= g_ky*0;
g_std= g_ky*0;
% Naming of the collision operator
if GKCO
CONAME = [CO,'GK'];
else
CONAME = [CO,'DK'];
end
j = 1;
for NU = nu_a
J = P/2;
i = 1;
for ky = ky_a
%% PHYSICAL PARAMETERS
TAU = 1.0; % e/i temperature ratio
% 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)
K_Te = K_T; % ele Temperature '''
K_Ti = K_T; % ion Temperature '''
K_Ne = K_N; % ele Density '''
K_Ni = K_N; % ion Density gradient drive
%% GRID PARAMETERS
% DT = DT0/sqrt(J);
PMAX = P; % Hermite basis size
JMAX = P/2; % Laguerre "
NX = 8; % real space x-gridpoints
NY = 2;
LX = 2*pi/0.8; % Size of the squared frequency domain
LY = 2*pi/ky; % 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';
EPS = 0.18; % inverse aspect ratio
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 = 'periodic'; %'dirichlet','periodic','shearless','disconnected'
SHIFT_Y = 0.0;
%% TIME PARMETERS
DTSAVE0D = 1; % Sampling per time unit for 0D arrays
DTSAVE2D = -1; % Sampling per time unit for 2D arrays
DTSAVE3D = 2; % Sampling per time unit for 3D arrays
DTSAVE5D = 100; % Sampling per time unit for 5D arrays
JOB2LOAD = -1; % Start a new simulation serie
%% OPTIONS
LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
% Collision 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 = 0;
W_GAMMA = 1; W_HF = 1;
W_PHI = 1; W_NA00 = 1;
W_DENS = 0; W_TEMP = 1;
W_NAPJ = 0; W_SAPJ = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% unused
NA = 1;
ADIAB_E = (NA==1);
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;
HYP_V = 'none';
HRCY_CLOS = 'truncation'; % Closure model for higher order moments
DMAX = -1;
NLIN_CLOS = 'truncation'; % Nonlinear closure model for higher order moments
NMAX = 0;
MU_Z = 1.0; %
MU_P = 0.0; %
MU_J = 0.0; %
LAMBDAD = 0.0;
NOISE0 = 1.0e-5; % Init noise amplitude
BCKGD0 = 0.0; % Init background
k_gB = 1.0;
k_cB = 1.0;
%% RUN
setup
% naming
filename = [SIMID,'/',PARAMS,'/'];
LOCALDIR = [gyacomodir,'results/',filename,'/'];
EXIST= 0;
% check if data exist to run if no data
data_ = {};
try
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
Ntime = numel(data_.Ts0D);
EXIST = 1;
catch
data_.outfilenames = [];
EXIST = 0;
end
if RUN && (RERUN || isempty(data_.outfilenames) || Ntime < 10)
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0; cd ../../../wk'])
system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 3 2 1 0; cd ../../../wk'])
end
try
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
[data_.PHI, data_.Ts3D] = compile_results_3D(LOCALDIR,00,00,'phi');
if numel(data_.Ts3D)>10
if numel(data_.Ts3D)>10
% Load results after trying to run
filename = [SIMID,'/',PARAMS,'/'];
LOCALDIR = [gyacomodir,'results/',filename,'/'];
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
[data_.PHI, data_.Ts3D] = compile_results_3D(LOCALDIR,00,00,'phi');
% linear growth rate (adapted for 2D zpinch and fluxtube)
options.TRANGE = [0.5 1]*data_.Ts3D(end);
options.NPLOTS = 0; % 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
[~,it1] = min(abs(data_.Ts3D-0.5*data_.Ts3D(end))); % start of the measurement time window
[~,it2] = min(abs(data_.Ts3D-1.0*data_.Ts3D(end))); % end of ...
field = 0;
field_t = 0;
for ik = 2:NY/2+1
field = squeeze(sum(abs(data_.PHI),3)); % take the sum over z
field_t = squeeze(field(ik,1,:)); % take the kx =0, ky = ky mode only
to_measure = log(field_t(it1:it2));
tw = double(data_.Ts3D(it1:it2));
% gr = polyfit(tw,to_measure,1);
gr = fit(tw,to_measure,'poly1');
err= confint(gr);
g_ky(i,j,ik) = gr.p1;
g_std(i,j,ik) = abs(err(2,1)-err(1,1))/2;
end
[gmax, ikmax] = max(g_ky(i,j,:));
msg = sprintf('gmax = %2.2f, kmax = %2.2f',gmax,data_.grids.ky(ikmax)); disp(msg);
end
end
catch
g_ky(i,j,:) = gr.p1;
g_std(i,j,:) = abs(err(2,1)-err(1,1))/2;
end
i = i + 1;
end
j = j + 1;
end
if 0
%% Check time evolution
figure;
to_measure = log(field_t);
plot(data_.Ts3D,to_measure); hold on
plot(data_.Ts3D(it1:it2),to_measure(it1:it2),'--');
end
%% take max growth rate among z coordinate
y_ = g_ky(:,:,2);
e_ = g_std(:,:,2);
%%
if(numel(ky_a)>1 && numel(nu_a)>1)
%% Save metadata
numin = num2str(min(nu_a)); numax = num2str(max(nu_a));
kymin = num2str(min(ky_a)); kymax= num2str(max(ky_a));
filename = [num2str(NX),'x',num2str(NZ),'_P_',num2str(P),'_ky_',kymin,'_',kymax,...
'_',CONAME,'_nu_',numin,'_',numax,'_kT_',num2str(K_T),'.mat'];
metadata.name = filename;
metadata.kymin = ky;
metadata.title = ['$P=$',num2str(P),'$\kappa_T=$',num2str(K_T),', $\kappa_N=$',num2str(K_N)];
metadata.par = [num2str(NX),'x1x',num2str(NZ)];
metadata.nscan = 2;
metadata.s2name = ['$\nu_{',CONAME,'}=$'];
metadata.s2 = nu_a;
metadata.s1name = '$k_y$';
metadata.s1 = ky_a;
metadata.dname = '$\gamma c_s/R$';
metadata.data = y_;
metadata.err = e_;
save([SIMDIR,filename],'-struct','metadata');
disp(['saved in ',SIMDIR,filename]);
clear metadata tosave
end
wk/Dimits_fig3.m → wk/paper_2_scripts_and_results/Dimits_fig3.m
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File moved
wk/paper_2_scripts_and_results/fort_00.90 0 → 100644
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&BASIC
nrun = 100000000
dt = 0.0017678
tmax = 50
maxruntime = 356400
job2load = -1
/
&GRID
pmax = 16
jmax = 8
Nx = 8
Lx = 7.854
Ny = 2
Ly = 6.2832
Nz = 24
SG = .false.
Nexc = 1
/
&GEOMETRY
geom = 's-alpha'
q0 = 1.4
shear = 0.8
eps = 0.18
kappa = 1
delta = 0
zeta = 0
parallel_bc = 'dirichlet'
shift_y = 0
Npol = 1
/
&OUTPUT_PAR
dtsave_0d = 1
dtsave_1d = -1
dtsave_2d = -1
dtsave_3d = 2
dtsave_5d = 100
write_doubleprecision = .false.
write_gamma = .true.
write_hf = .true.
write_phi = .true.
write_Na00 = .true.
write_Napj = .false.
write_dens = .false.
write_temp = .true.
/
&MODEL_PAR
LINEARITY = 'linear'
RM_LD_T_EQ= .false.
Na = 1
mu_x = 0
mu_y = 0
N_HD = 4
mu_z = 1
HYP_V = 'none'
mu_p = 0
mu_j = 0
nu = 0.01
k_gB = 1
k_cB = 1
lambdaD = 0
beta = 0.0001
ADIAB_E = .true.
/
&CLOSURE_PAR
hierarchy_closure='truncation'
dmax =-1
nonlinear_closure='truncation'
nmax =0
/
&SPECIES
name_ = ions
tau_ = 1
sigma_ = 1
q_ = 1
K_N_ = 2.22
K_T_ = 5.3
/
&COLLISION_PAR
collision_model = 'SG'
GK_CO = .true.
INTERSPECIES = .true.
mat_file = '/home/ahoffman/gyacomo/wk/paper_2_scripts_and_resuliCa/gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
collision_kcut = 1.75
/
&INITIAL_CON
INIT_OPT = 'phi'
init_background = 0
init_noiselvl = 1e-05
iseed = 42
/
&TIME_INTEGRATION_PAR
numerical_scheme = 'RK4'
/
\ No newline at end of file
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