Include a folder for saving useful scripts

.gitignore

@@ -41,4 +41,5 @@ Gallery/
 .vscode/settings.json
 *figure*
 *results*
-out*
+out*
+!scripts/*

scripts/fort_00.90

+&BASIC
+  nrun   = 100000000
+  dt     = 0.01
+  tmax   = 500
+  maxruntime = 60 ! 1h 14400 !4h
+/
+&GRID
+  pmaxe  = 6
+  jmaxe  = 3
+  pmaxi  = 6
+  jmaxi  = 3
+  Nx     = 200
+  Lx     = 120
+  Ny     = 32
+  Ly     = 60
+  Nz     = 1
+  SG     = .f.
+/
+&GEOMETRY
+  geom   = 'Z-pinch'
+  q0     = 0
+  shear  = 0
+  eps    = 0
+/
+&OUTPUT_PAR
+  nsave_0d = 10
+  nsave_1d = -1
+  nsave_2d = -1
+  nsave_3d = 100
+  nsave_5d = 10000
+  write_doubleprecision = .t.
+  write_gamma = .t.
+  write_hf    = .t.
+  write_phi   = .t.
+  write_Na00  = .t.
+  write_Napj  = .t.
+  write_Sapj  = .f.
+  write_dens  = .t.
+  write_temp  = .t.
+  job2load    = -1
+/
+&MODEL_PAR
+  ! Collisionality
+  CLOS    = 0
+  NL_CLOS = 0
+  LINEARITY = 'nonlinear'
+  KIN_E   = .t.
+  mu_x    = 1.0
+  mu_y    = 1.0
+  N_HD    = 4
+  mu_z    = 0.0
+  mu_p    = 0
+  mu_j    = 0
+  nu      = 0.01
+  tau_e   = 1
+  tau_i   = 1
+  sigma_e = 0.023338
+  sigma_i = 1
+  q_e     = -1
+  q_i     = 1
+  K_Ne    = 1.7
+  K_Ni    = 1.7
+  K_Te    = 0.425
+  K_Ti    = 0.425
+  GradB     = 1
+  CurvB     = 1
+  lambdaD = 0
+/
+&COLLISION_PAR
+  collision_model = 'LD'
+  gyrokin_CO      = .true.
+  interspecies    = .true.
+  mat_file        = 'LDGK_P10_J5_dk_5e-2_km_5_NFLR_30.h5'
+  collision_kcut  = 1.8
+/
+&INITIAL_CON
+  INIT_OPT    = 'phi'
+  ACT_ON_MODES       = 'donothing'
+  init_background  = 0
+  init_noiselvl = 0.001
+  iseed         = 42
+/
+&TIME_INTEGRATION_PAR
+  numerical_scheme = 'RK4'
+/

scripts/job_pipeline.sh

+#! /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_$id.cmd
+ 
+    # Create new fort file from older one
+    awk -v "NU=$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
+

scripts/submit_00.cmd

+#!/bin/bash
+#SBATCH --job-name=test_pipe
+#SBATCH --time=00:02:00
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --ntasks-per-node=48
+#SBATCH --mem=64GB
+#SBATCH --error=err_00.txt
+#SBATCH --output=out_00.txt
+#SBATCH --account=FUA36_TSVVT422
+#SBATCH --partition=skl_fua_dbg
+srun --cpu-bind=cores ./gyacomo 2 24 1 0
+