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Antoine Cyril David Hoffmann
Gyacomo
Commits
b2925afb
Commit
b2925afb
authored
1 year ago
by
Antoine Cyril David Hoffmann
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generic scripts to run and scan parameter files
parent
0a0786eb
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wk/lin_run_script.m
+86
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86 additions, 0 deletions
wk/lin_run_script.m
wk/lin_scan_script.m
+134
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wk/lin_scan_script.m
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wk/lin_run_script.m
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+
86
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b2925afb
%% 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
);
mpirun
=
'mpirun'
;
% mpirun = '/opt/homebrew/bin/mpirun'; % for macos
addpath
(
genpath
([
gyacomodir
,
'matlab'
]))
% Add matlab folder
addpath
(
genpath
([
gyacomodir
,
'matlab/plot'
]))
% Add plot folder
addpath
(
genpath
([
gyacomodir
,
'matlab/compute'
]))
% Add compute folder
addpath
(
genpath
([
gyacomodir
,
'matlab/load'
]))
% Add load folder
addpath
(
genpath
([
gyacomodir
,
'wk/parameters'
]))
% Add parameters folder
%% Setup run or load an executable
RUN
=
1
;
% To run or just to load
default_plots_options
EXECNAME
=
'gyacomo23_sp'
;
% single precision
% EXECNAME = 'gyacomo23_dp'; % double precision
%% Setup parameters
% run lin_DTT_AB_rho85_PT
% run lin_Entropy
% run lin_ITG
%%-------------------------------------------------------------------------
%% 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 8 '
,
gyacomodir
,
'bin/'
,
EXECNAME
,
' 1 4 2 0;'
];
% RUN =['time ',mpirun,' -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0;'];
% RUN = ['./../../../bin/gyacomo23_sp 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
.
PLOT_KP
=
0
;
% options.field = 'phi';
fig
=
plot_ballooning
(
data
,
options
);
end
This diff is collapsed.
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wk/lin_scan_script.m
0 → 100644
+
134
−
0
View file @
b2925afb
%% 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
);
mpirun
=
'mpirun'
;
% mpirun = '/opt/homebrew/bin/mpirun'; % for macos
addpath
(
genpath
([
gyacomodir
,
'matlab'
]))
% Add matlab folder
addpath
(
genpath
([
gyacomodir
,
'matlab/plot'
]))
% Add plot folder
addpath
(
genpath
([
gyacomodir
,
'matlab/compute'
]))
% Add compute folder
addpath
(
genpath
([
gyacomodir
,
'matlab/load'
]))
% Add load folder
addpath
(
genpath
([
gyacomodir
,
'wk/parameters'
]))
% Add parameters folder
%% Setup run or load an executable
RUN
=
1
;
% To run or just to load
RERUN
=
0
;
% rerun if the data does not exist
default_plots_options
EXECNAME
=
'gyacomo23_sp'
;
% single precision
% EXECNAME = 'gyacomo23_dp'; % double precision
%% Setup basic parameters
run
lin_DTT_AB_rho85_PT
% run lin_Entropy
% run lin_ITG
%% Modify parameters
% NZ = 1;
NY
=
2
;
DT
=
2e-3
;
%% Scan parameters
SIMID
=
[
SIMID
,
'_scan'
];
P_a
=
[
2
4
8
];
ky_a
=
0.1
:
0.1
:
0.5
;
%% Scan loop
% arrays for the result
g_ky
=
zeros
(
numel
(
ky_a
),
numel
(
P_a
),
2
);
g_avg
=
g_ky
*
0
;
g_std
=
g_ky
*
0
;
j
=
1
;
for
PMAX
=
P_a
JMAX
=
P
/
2
;
i
=
1
;
for
ky
=
ky_a
LY
=
2
*
pi
/
ky
;
%% RUN
setup
% naming
filename
=
[
SIMID
,
'/'
,
PARAMS
,
'/'
];
LOCALDIR
=
[
gyacomodir
,
'results/'
,
filename
,
'/'
];
% check if data exist to run if no data
data_
=
{};
try
data_
=
compile_results_low_mem
(
data_
,
LOCALDIR
,
00
,
00
);
Ntime
=
numel
(
data_
.
Ts0D
);
catch
data_
.
outfilenames
=
[];
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
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
)
>
5
% 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
i
=
i
+
1
;
end
j
=
j
+
1
;
end
%% take max growth rate among z coordinate
y_
=
g_ky
(:,:,
2
);
e_
=
g_std
(:,:,
2
);
%% Save scan results (gamma)
if
(
numel
(
ky_a
)
>
1
&&
numel
(
P_a
)
>
1
)
pmin
=
num2str
(
min
(
P_a
));
pmax
=
num2str
(
max
(
P_a
));
kymin
=
num2str
(
min
(
ky_a
));
kymax
=
num2str
(
max
(
ky_a
));
filename
=
[
num2str
(
NX
),
'x'
,
num2str
(
NZ
),
'_ky_'
,
kymin
,
'_'
,
kymax
,
...
'_P_'
,
pmin
,
'_'
,
pmax
,
'_'
,
CONAME
,
'_'
,
num2str
(
NU
),
'_be_'
,
num2str
(
BETA
),
'.mat'
];
metadata
.
name
=
filename
;
metadata
.
kymin
=
ky
;
metadata
.
title
=
[
'$\nu_{'
,
CONAME
,
'}=$'
,
num2str
(
NU
),
'$\kappa_T=$'
,
num2str
(
K_Ti
),
', $\kappa_N=$'
,
num2str
(
K_Ni
)];
metadata
.
par
=
[
num2str
(
NX
),
'x1x'
,
num2str
(
NZ
)];
metadata
.
nscan
=
2
;
metadata
.
s2name
=
'$P$'
;
metadata
.
s2
=
P_a
;
metadata
.
s1name
=
'$ky$'
;
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
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