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Antoine Cyril David Hoffmann
Gyacomo
Commits
a3ccca4f
Commit
a3ccca4f
authored
10 months ago
by
Antoine Cyril David Hoffmann
🌱
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add a basic matlab analysis script
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scripts/matlab_utilities/analysis.m
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a3ccca4f
%% This is a example of matlab analysis script
gyacomodir
=
'/Users/ahoffmann/gyacomo/'
;
% get code directory
addpath
(
genpath
([
gyacomodir
,
'matlab'
]))
% ... add
addpath
(
genpath
([
gyacomodir
,
'matlab/plot'
]))
% ... add
addpath
(
genpath
([
gyacomodir
,
'matlab/compute'
]))
% ... add
addpath
(
genpath
([
gyacomodir
,
'matlab/load'
]))
% ... add
default_plots_options
% Directory where the data sits -------------------------------
DATADIR
=
'/Users/ahoffmann/gyacomo/simulations/problem_01/'
;
% Jobs to load (from outputs_J0.h5 to outputs_J1.h5 if exists)
J0
=
00
;
J1
=
10
;
% main structure that will contain all the loaded data
data
=
{};
% Load basic info (grids and time traces)
data
=
compile_results_low_mem
(
data
,
DATADIR
,
J0
,
J1
);
% load EM fields -------------------------------
% Electrostatic potential
[
data
.
PHI
,
data
.
Ts3D
]
=
compile_results_3D
(
DATADIR
,
J0
,
J1
,
'phi'
);
% Electromagnetic potential (if beta non zero)
if
data
.
inputs
.
BETA
>
0
[
data
.
PSI
,
data
.
Ts3D
]
=
compile_results_3D
(
DATADIR
,
J0
,
J1
,
'psi'
);
end
% load moments -------------------------------
% temperature
[
TEMP
,
data
.
Ts3D
]
=
compile_results_3Da
(
data
.
folder
,
J0
,
J1
,
'temp'
);
% parallel velocity
[
UPAR
,
data
.
Ts3D
]
=
compile_results_3Da
(
data
.
folder
,
J0
,
J1
,
'upar'
);
% perpendicular velocity
[
UPER
,
data
.
Ts3D
]
=
compile_results_3Da
(
data
.
folder
,
J0
,
J1
,
'uper'
);
% density
[
DENS
,
data
.
Ts3D
]
=
compile_results_3Da
(
data
.
folder
,
J0
,
J1
,
'dens'
);
% gyrocenter density (first GM)
[
Na00
,
data
.
Ts3D
]
=
compile_results_3Da
(
DATADIR
,
J0
,
J1
,
'Na00'
);
% asign them to species
% first index is ions
data
.
TEMP_I
=
reshape
(
TEMP
(
1
,:,:,:,:),
data
.
grids
.
Nky
,
data
.
grids
.
Nkx
,
data
.
grids
.
Nz
,
numel
(
data
.
Ts3D
));
data
.
UPAR_I
=
reshape
(
UPAR
(
1
,:,:,:,:),
data
.
grids
.
Nky
,
data
.
grids
.
Nkx
,
data
.
grids
.
Nz
,
numel
(
data
.
Ts3D
));
data
.
UPER_I
=
reshape
(
UPER
(
1
,:,:,:,:),
data
.
grids
.
Nky
,
data
.
grids
.
Nkx
,
data
.
grids
.
Nz
,
numel
(
data
.
Ts3D
));
data
.
DENS_I
=
reshape
(
DENS
(
1
,:,:,:,:),
data
.
grids
.
Nky
,
data
.
grids
.
Nkx
,
data
.
grids
.
Nz
,
numel
(
data
.
Ts3D
));
data
.
Ni00
=
reshape
(
Na00
(
1
,:,:,:,:),
data
.
grids
.
Nky
,
data
.
grids
.
Nkx
,
data
.
grids
.
Nz
,
numel
(
data
.
Ts3D
));
% if we have a second species we store in electrons
if
data
.
inputs
.
Na
>
1
data
.
TEMP_E
=
reshape
(
data
.
TEMP
(
2
,:,:,:,:),
data
.
grids
.
Nky
,
data
.
grids
.
Nkx
,
data
.
grids
.
Nz
,
numel
(
data
.
Ts3D
));
data
.
DENS_E
=
reshape
(
data
.
DENS
(
2
,:,:,:,:),
data
.
grids
.
Nky
,
data
.
grids
.
Nkx
,
data
.
grids
.
Nz
,
numel
(
data
.
Ts3D
));
data
.
Ne00
=
reshape
(
data
.
Na00
(
2
,:,:,:,:),
data
.
grids
.
Nky
,
data
.
grids
.
Nkx
,
data
.
grids
.
Nz
,
numel
(
data
.
Ts3D
));
end
clear
TEMP
UPAR
UPER
DENS
Na00
;
%% Plot transport and phi radial profile
options
.
TAVG_0
=
25
;
% averaging start time for the flux
options
.
TAVG_1
=
50
;
% end time
options
.
NCUT
=
5
;
% Number of cuts for averaging and error estimation
options
.
NMVA
=
1
;
% Moving average for time traces
options
.
ST_FIELD
=
'\phi'
;
% chose your field to plot in spacetime diag (e.g \phi,v_x,G_x,upar,N_i^{00} etc.)
options
.
INTERP
=
0
;
% interp the pcolor plot or not
plot_radial_transport_and_spacetime
(
data
,
options
);
%% 2D field snapshots
% Options
options
.
INTERP
=
1
;
options
.
AXISEQUAL
=
1
;
options
.
NORMALIZE
=
0
;
options
.
LOGSCALE
=
0
;
% chose the name (available : n_i,upar_i,T_i,Q_{xi},v_{Ey},w_{Ez},\phi,\psi
options
.
NAME
=
'n_i'
;
options
.
PLAN
=
'xy'
;
options
.
COMP
=
floor
(
data
.
grids
.
Nz
/
2
)
+
1
;
% options.PLAN = 'xz'; options.COMP ='avg';
% options.PLAN = '3D';
options
.
XYZ
=
[
-
11
20
-
2
];
options
.
TIME
=
[
50
];
options
.
TAVG
=
0
;
% options.TIME = [50:500]; options.TAVG = 1;
options
.
RESOLUTION
=
256
;
fig
=
photomaton
(
data
,
options
);
colormap
(
bluewhitered
)
colorbar
% set(gca,'ColorScale','log')
% save_figure(data,fig)
if
0
%% Mode evolution
options
.
NORMALIZED
=
0
;
options
.
TIME
=
data
.
Ts3D
;
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
=
64
;
options
.
iz
=
'avg'
;
% avg or index
options
.
ik
=
1
;
% sum, max or index
options
.
fftz
.
flag
=
0
;
options
.
FIELD
=
'Ni00'
;
options
.
GOK2
=
0
;
options
.
SHOWFIG
=
1
;
[
fig
,
wkykx
,
ekykx
]
=
mode_growth_meter
(
data
,
options
);
end
if
0
%% Hermite-Laguerre spectrum
[
data
.
Napjz
,
data
.
Ts3D
]
=
compile_results_3Da
(
DATADIR
,
J0
,
J1
,
'Napjz'
);
options
.
ST
=
1
;
options
.
NORMALIZED
=
0
;
options
.
LOGSCALE
=
1
;
options
.
FILTER
=
0
;
%filter the 50% time-average of the spectrum from
options
.
TAVG_2D
=
0
;
%Show a 2D plot of the modes, 50% time averaged
options
.
TAVG_2D_CTR
=
0
;
%make it contour plot
options
.
TWINDOW
=
[
20
20
];
fig
=
show_moments_spectrum
(
data
,
options
);
end
if
0
%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
options
.
INTERP
=
1
;
options
.
POLARPLOT
=
0
;
options
.
BWR
=
0
;
% bluewhitered plot or gray
options
.
CLIMAUTO
=
1
;
% adjust the colormap auto
options
.
NAME
=
'\phi'
;
% options.NAME = 'w_{Ez}';
% options.NAME = '\psi';
% options.NAME = 'T_i';
% options.NAME = '\phi^{NZ}';
% options.NAME = ['N_i^{00}'];
% options.NAME = ['N_e^{00}'];
options
.
PLAN
=
'xy'
;
options
.
COMP
=
floor
(
data
.
grids
.
Nz
/
2
)
+
1
;
% options.PLAN = 'xz'; options.COMP ='avg';
% options.PLAN = '3D';
options
.
XYZ
=
[
-
21
20
0
];
options
.
TIME
=
data
.
Ts3D
(
1
:
1
:
end
);
data
.
EPS
=
0.1
;
data
.
a
=
data
.
EPS
*
2000
;
options
.
RESOLUTION
=
256
;
options
.
FPS
=
12
;
options
.
RMAXIS
=
0
;
create_film
(
data
,
options
,
'.gif'
);
end
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