diff --git a/scripts/submit_00.cmd b/bash scripts/submit_00.cmd
similarity index 100%
rename from scripts/submit_00.cmd
rename to bash scripts/submit_00.cmd
diff --git a/fort_example.90 b/fort_example.90
deleted file mode 100644
index 667ca822dc99fa1be56b21f9052bb6e26f5177dc..0000000000000000000000000000000000000000
--- a/fort_example.90
+++ /dev/null
@@ -1,91 +0,0 @@
-&BASIC
- nrun = 100000000 !number of maximal time steps
- dt = 0.01 !time step
- tmax = 500 !maximal physical time
- maxruntime = 60 ! 1h 14400 !4h !maximal wallclock run time (in seconds)
-/
-&GRID
- pmaxe = 6 !maximal degree of Hermite polynomials for e
- jmaxe = 3 !maximal degree of Laguerre polynomials for e
- pmaxi = 6 !maximal degree of Hermite polynomials for i
- jmaxi = 3 !maximal degree of Laguerre polynomials for i
- Nx = 200 !resolution in x (=Nkx)
- Lx = 120 !box size in x
- Ny = 64 !resolution in y (=2(Nky-1))
- Ly = 160 !box size in y
- Nz = 24 !resolution in z
- Npol = 1 !number of poloidal turns (Lz=2piNpol)
- Nexc = 1 !factor to increase Lx in sheared geometry
- SG = .f. !staggered grid option (not recommended)
-/
-&GEOMETRY
- geom = 's-alpha' !magnetic equilibrium geometry (Z-pinch,s-alpha,miller)
- q0 = 1.4 !safety factor (s-alpha,miller only)
- shear = 0.8 !shear (s-alpha,miller only)
- eps = 0.18 !inverse aspect ratio (s-alpha,miller only)
- kappa = 1 !elongation (miller only)
- delta = 0 !triangularity (miller only)
- zeta = 0 !squareness (miller only)
- parallel_bc = 'dirichlet' !boundary condition for modes that does not connect due to shear (dirichlet,periodic)
-/
-&OUTPUT_PAR
- nsave_0d = 50 !period in number of step for time traces
- nsave_1d = -1 !unused
- nsave_2d = -1 !unused
- nsave_3d = 100 !period in number of step for 3D fields (phi,psi,...)
- nsave_5d = 1000 !period in number of step for 5D fields (moments)
- write_doubleprecision = .t. !for HDF5 output (double precision faster on marconi)
- write_gamma = .t. !to write particle flux
- write_hf = .t. !to write heat flux
- write_phi = .t. !to write ES and EM potentials
- write_Na00 = .t. !to write gyrocenter densities
- write_Napj = .t. !to write moments
- write_Sapj = .f. !to write nonlinear terms
- write_dens = .t. !to write particle densities
- write_temp = .t. !to write particle temperatures
- job2load = -1 !ID of the job to load in a restart (-1 means no restart)
-/
-&MODEL_PAR
- ! Collisionality
- CLOS = 0 !closure model (0: zero-truncation)
- NL_CLOS = 0 !NL closure model (-1 is full FLR sum until n=J-j, n>-1 is up to nth term)
- LINEARITY = 'nonlinear' !to activate nonlinear term (linear,nonlinear)
- KIN_E = .f. !to have a kinetic electron model (adiabatic otherwise)
- mu_x = 1.0 !x numerical diffusion coefficient
- mu_y = 1.0 !y numerical diffusion coefficient
- N_HD = 4 !xy numerical diffusion order
- mu_z = 2.0 !z numerical diffusion coefficient (order 4)
- mu_p = 0 !p numerical diffusion coefficient (usually not used)
- mu_j = 0 !j numerical diffusion coefficient (usually not used)
- nu = 0.05 !collision frequency (=0.49*nu_GENE)
- tau_e = 1 !electron temperature ratio
- tau_i = 1 !ion temperature ratio
- sigma_e = 0.023338 !electron mass ratio
- sigma_i = 1 !ion mass ratio
- q_e = -1 !electron charge
- q_i = 1 !ion charge
- K_Ne = 2.22 !electron density gradient intensity
- K_Te = 6.96 !electron temperature gradient intensity
- K_Ni = 2.22 !ion density gradient intensity
- K_Ti = 6.96 !ion density temperature intensity
- k_gB = 1 !magnetic field gradient strength
- k_cB = 1 !magnetic curvature strength
- lambdaD = 0 !Debye length (not tested when non zero)
-/
-&COLLISION_PAR
- collision_model = 'DG' !collision model (DG,SG,LD,LR), all need a matrix except DG
- GK_CO = .f. !activate gyrokinetic terms in the CO
- INTERSPECIES = .t. !activate INTERSPECIES if CO has some
- mat_file = 'LDGK_P10_J5_dk_5e-2_km_5_NFLR_30.h5' !path to find the collision matrix
- collision_kcut = 1.8 !maximal wavelength of the CO matrix. For higher kperp, the matrix at collision_kcut will be applied.
-/
-&INITIAL_CON
- INIT_OPT = 'phi' !initialization option (phi,mom00,allmom,ppj)
- ACT_ON_MODES = 'donothing' !to perform numerical experiments (unused)
- init_background = 0 !background value for a noise initialization
- init_noiselvl = 0.0001 !fluctuation value ''
- iseed = 42 !seed of the noise
-/
-&TIME_INTEGRATION_PAR
- numerical_scheme = 'RK4' !numerical scheme for time-stepping (RK2,RK3,RK4,DOPRI5)
-/
diff --git a/scripts/job_pipeline.sh b/scripts/job_pipeline.sh
deleted file mode 100644
index 342eaa463b7f328324530386a48cb0ec3ada4e80..0000000000000000000000000000000000000000
--- a/scripts/job_pipeline.sh
+++ /dev/null
@@ -1,44 +0,0 @@
-#! /bin/bash
-#This script automatizes the launch of multiple job with chain dependency.
-nu_=0.01
-dnu=0.01
-
-Tm_=2000
-dTm=2000
-
-# First submit
-lastji=$(sbatch submit_00.cmd)
-lastjid=${lastji##* }
-echo $lastji
-#echo $lastjid
-
-for i in {1..1}; do
- # Setup indices of job id (current and previous one)
- im1=$(awk "BEGIN {print $i-1}")
- idm1=$(printf '%02d' $im1)
- id=$(printf '%02d' $i)
-
- # Create new submit file from older one
- awk -v "ID=$id" '{
- if (NR == 8) print "#SBATCH --error=err_"ID".txt";
- else if (NR == 9) print "#SBATCH --output=out_"ID".txt";
- else if (NR == 12) print "srun --cpu-bind=cores ./gyacomo 2 24 1 "ID;
- else print $0}' submit_$idm1.cmd > submit_$id.cmd
-
- # Create new input file from older one
- awk -v "NU=$nu_" -v "TM=$Tm_" -v "J2L=$im1" '{
- if (NR == 04) print " tmax = "TM;
- else if (NR == 40) print " job2load = "J2L;
- else if (NR == 54) print " nu = "NU;
- else print $0}' fort_$idm1.90 > fort_$id.90
-
- # Retrieve last jobid and launch next job with dep
- lastji=$(sbatch --dependency=afterok:$lastjid submit_0$i.cmd)
- lastjid=${lastji##* }
- echo $lastjid
-
- # Increment variables
- nu_=$(awk "BEGIN {print $nu_+$dnu}")
- Tm_=$(awk "BEGIN {print $Tm_+$dTm}")
-done
-
diff --git a/scripts/scan_kN_pipeline.sh b/scripts/scan_kN_pipeline.sh
deleted file mode 100644
index 8b9cef7e67996733bebf806abc7ad0e4f3987d8f..0000000000000000000000000000000000000000
--- a/scripts/scan_kN_pipeline.sh
+++ /dev/null
@@ -1,59 +0,0 @@
-#! /bin/bash
-# lastjid=$(sbatch submit_00.cmd)
-
-nu_=0.01
-dnu=0.0
-kn_=1.7
-dkn=0.2
-kt_=0.425
-dkt=0.05
-Lx_=150
-dLx=030
-
-Tm_=4000
-dTm=1000
-
-# First submit
-istart=0
-lastji=$(sbatch submit_0$istart.cmd)
-lastjid=${lastji##* }
-echo $lastji
-
-for i in {1..5}; do
- # Setup indices of job id (current and previous one)
- im1=$(awk "BEGIN {print $i-1}")
- idm1=$(printf '%02d' $im1)
- id=$(printf '%02d' $i)
-
- # Create new submit file from older one
- awk -v "ID=$id" '{
- if (NR == 8) print "#SBATCH --error=err_"ID".txt";
- else if (NR == 9) print "#SBATCH --output=out_"ID".txt";
- else if (NR == 12) print "srun --cpu-bind=cores ./gyacomo 2 24 1 "ID;
- else print $0}' submit_$idm1.cmd > submit_$id.cmd
-
- # Create new fort file from older one
- awk -v "NU=$nu_" -v "TM=$Tm_" -v "J2L=$im1" -v "KN=$kn_" -v "KT=$kt_" -v "LX=$Lx_" '{
- if (NR == 04) print " tmax = "TM;
- else if (NR == 40) print " job2load = "J2L;
- else if (NR == 13) print " Lx = "LX;
- else if (NR == 54) print " nu = "NU;
- else if (NR == 61) print " K_Ne = "KN;
- else if (NR == 62) print " K_Ni = "KN;
- else if (NR == 63) print " K_Te = "KT;
- else if (NR == 64) print " K_Ti = "KT;
- else print $0}' fort_$idm1.90 > fort_$id.90
-
- # Retrieve last jobid and launch next job with dep
- lastji=$(sbatch --dependency=afterok:$lastjid submit_$id.cmd)
- lastjid=${lastji##* }
- echo $lastjid
-
- # Increment variables
- Lx_=$(awk "BEGIN {print $Lx_+$dLx}")
- nu_=$(awk "BEGIN {print $nu_+$dnu}")
- kn_=$(awk "BEGIN {print $kn_+$dkn}")
- kt_=$(awk "BEGIN {print $kt_+$dkt}")
- Tm_=$(awk "BEGIN {print $Tm_+$dTm}")
-done
-
diff --git a/wk/analysis_gyacomo.m b/wk/analysis_gyacomo.m
index cb18516afc17a82032d8d52fbd0e41a64b4d6a74..188b4796dada9d74cd97d309dc54617b178830bf 100644
--- a/wk/analysis_gyacomo.m
+++ b/wk/analysis_gyacomo.m
@@ -100,20 +100,20 @@ options.INTERP = 0;
options.POLARPLOT = 0;
options.AXISEQUAL = 0;
options.NORMALIZE = 0;
-% options.NAME = '\phi';
+options.NAME = '\phi';
% options.NAME = '\psi';
% options.NAME = '\omega_z';
% options.NAME = 'T_i';
% options.NAME = 'n_i';
-options.NAME = '\phi^{NZ}';
+% options.NAME = '\phi^{NZ}';
% options.NAME = 'N_i^{00}';
% options.NAME = 'N_i^{00}-N_e^{00}';
% options.NAME = 's_{Ex}';
% options.NAME = 'Q_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'xy';
+options.PLAN = 'kxz';
options.COMP = 'avg';
-options.TIME = [80 200];
+options.TIME = [20 30 60];
options.RESOLUTION = 256;
data.a = data.EPS * 2e3;
diff --git a/wk/benchmark scripts/Ajay_scan_CH4_lin_ITG.m b/wk/benchmark and scan scripts/Ajay_scan_CH4_lin_ITG.m
similarity index 100%
rename from wk/benchmark scripts/Ajay_scan_CH4_lin_ITG.m
rename to wk/benchmark and scan scripts/Ajay_scan_CH4_lin_ITG.m
diff --git a/wk/CBC_P_J_scan.m b/wk/benchmark and scan scripts/CBC_P_J_scan.m
similarity index 100%
rename from wk/CBC_P_J_scan.m
rename to wk/benchmark and scan scripts/CBC_P_J_scan.m
diff --git a/wk/CBC_hypcoll_PJ_scan.m b/wk/benchmark and scan scripts/CBC_hypcoll_PJ_scan.m
similarity index 100%
rename from wk/CBC_hypcoll_PJ_scan.m
rename to wk/benchmark and scan scripts/CBC_hypcoll_PJ_scan.m
diff --git a/wk/CBC_kT_PJ_scan.m b/wk/benchmark and scan scripts/CBC_kT_PJ_scan.m
similarity index 100%
rename from wk/CBC_kT_PJ_scan.m
rename to wk/benchmark and scan scripts/CBC_kT_PJ_scan.m
diff --git a/wk/CBC_kT_nu_scan.m b/wk/benchmark and scan scripts/CBC_kT_nu_scan.m
similarity index 100%
rename from wk/CBC_kT_nu_scan.m
rename to wk/benchmark and scan scripts/CBC_kT_nu_scan.m
diff --git a/wk/CBC_nu_PJ_scan.m b/wk/benchmark and scan scripts/CBC_nu_PJ_scan.m
similarity index 100%
rename from wk/CBC_nu_PJ_scan.m
rename to wk/benchmark and scan scripts/CBC_nu_PJ_scan.m
diff --git a/wk/lin_3D_Zpinch.m b/wk/benchmark and scan scripts/lin_3D_Zpinch.m
similarity index 100%
rename from wk/lin_3D_Zpinch.m
rename to wk/benchmark and scan scripts/lin_3D_Zpinch.m
diff --git a/wk/lin_ETPY.m b/wk/benchmark and scan scripts/lin_ETPY.m
similarity index 100%
rename from wk/lin_ETPY.m
rename to wk/benchmark and scan scripts/lin_ETPY.m
diff --git a/wk/lin_ITG.m b/wk/benchmark and scan scripts/lin_ITG.m
similarity index 100%
rename from wk/lin_ITG.m
rename to wk/benchmark and scan scripts/lin_ITG.m
diff --git a/wk/lin_KBM.m b/wk/benchmark and scan scripts/lin_KBM.m
similarity index 100%
rename from wk/lin_KBM.m
rename to wk/benchmark and scan scripts/lin_KBM.m
diff --git a/wk/lin_MTM.m b/wk/benchmark and scan scripts/lin_MTM.m
similarity index 100%
rename from wk/lin_MTM.m
rename to wk/benchmark and scan scripts/lin_MTM.m
diff --git a/wk/lin_RHT.m b/wk/benchmark and scan scripts/lin_RHT.m
similarity index 100%
rename from wk/lin_RHT.m
rename to wk/benchmark and scan scripts/lin_RHT.m
diff --git a/wk/lin_TEM.m b/wk/benchmark and scan scripts/lin_TEM.m
similarity index 100%
rename from wk/lin_TEM.m
rename to wk/benchmark and scan scripts/lin_TEM.m
diff --git a/wk/fast_analysis.m b/wk/fast_analysis.m
index 10b931f35726afbf755b5aff570276f43148f36f..546abd56b3554df4f27ccf6653b4725756bda540 100644
--- a/wk/fast_analysis.m
+++ b/wk/fast_analysis.m
@@ -10,10 +10,11 @@ PARTITION = '/misc/gyacomo23_outputs/';
% resdir = 'paper_2_GYAC23/CBC/Full_NL_7x4x192x96x32_nu_0.05_muxy_1.0_muz_2.0';
%% tests
-% resdir = 'paper_2_GYAC23/precision_study/5x3x128x64x24_xp';
-resdir = 'paper_2_GYAC23/precision_study/5x3x128x64x24_sp';
+% resdir = 'paper_2_GYAC23/precision_study/5x3x128x64x24';
+resdir = 'paper_2_GYAC23/precision_study/5x3x128x64x24_xp';
+% resdir = 'paper_2_GYAC23/precision_study/5x3x128x64x24_sp';
% resdir = 'paper_2_GYAC23/precision_study/5x3x128x64x24_Lx_180';
-%%
+ %%
J0 = 00; J1 = 10;
% Load basic info (grids and time traces)
@@ -21,6 +22,7 @@ DATADIR = [PARTITION,resdir,'/'];
data = {};
data = compile_results_low_mem(data,DATADIR,J0,J1);
+if 0
%% Plot transport and phi radial profile
[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
@@ -33,6 +35,7 @@ options.ST_FIELD = '\phi'; % chose your field to plot in spacetime diag
options.INTERP = 0;
options.RESOLUTION = 256;
fig = plot_radial_transport_and_spacetime(data,options);
+end
if 0
%% MOVIES %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -59,3 +62,34 @@ data.a = data.EPS * 2000;
options.RESOLUTION = 256;
create_film(data,options,'.gif')
end
+
+if 0
+%% Hermite-Laguerre spectrum
+[data.Nipjz, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'Nipjz');
+data.Nipjz = log(data.Nipjz);
+% options.TIME = 'avg';
+options.P2J = 0;
+options.ST = 1;
+options.NORMALIZED = 0;
+options.TIME = [500:800];
+fig = show_moments_spectrum(data,options);
+% fig = show_napjz(data,options);
+% save_figure(data,fig,'.png');
+end
+
+if 0
+%% Mode evolution
+[data.PHI, data.Ts3D] = compile_results_3D(DATADIR,J0,J1,'phi');
+
+options.NORMALIZED = 0;
+options.TIME = [000:9000];
+options.KX_TW = [1 20]; %kx Growth rate time window
+options.KY_TW = [0 20]; %ky Growth rate time window
+options.NMA = 1;
+options.NMODES = 800;
+options.iz = 'avg'; % avg or index
+options.ik = 1; % sum, max or index
+options.fftz.flag = 0;
+fig = mode_growth_meter(data,options);
+% save_figure(data,fig,'.png')
+end
\ No newline at end of file
diff --git a/wk/Zpinch_coll_scan_kN_1.7.m b/wk/old scripts/Zpinch_coll_scan_kN_1.7.m
similarity index 100%
rename from wk/Zpinch_coll_scan_kN_1.7.m
rename to wk/old scripts/Zpinch_coll_scan_kN_1.7.m
diff --git a/wk/continue_multiple_runs_marconi.m b/wk/old scripts/continue_multiple_runs_marconi.m
similarity index 100%
rename from wk/continue_multiple_runs_marconi.m
rename to wk/old scripts/continue_multiple_runs_marconi.m
diff --git a/wk/debug_script.m b/wk/old scripts/debug_script.m
similarity index 100%
rename from wk/debug_script.m
rename to wk/old scripts/debug_script.m
diff --git a/wk/local_run.m b/wk/old scripts/local_run.m
similarity index 100%
rename from wk/local_run.m
rename to wk/old scripts/local_run.m
diff --git a/wk/marconi_run.m b/wk/old scripts/marconi_run.m
similarity index 100%
rename from wk/marconi_run.m
rename to wk/old scripts/marconi_run.m
diff --git a/wk/quick_run.m b/wk/old scripts/quick_run.m
similarity index 100%
rename from wk/quick_run.m
rename to wk/old scripts/quick_run.m
diff --git a/wk/save_iFFT.m b/wk/old scripts/save_iFFT.m
similarity index 100%
rename from wk/save_iFFT.m
rename to wk/old scripts/save_iFFT.m