#!/bin/bash

export LESS=-R

export PATH=~/jorek/util/:$PATH

export PATH=~/scripts/bin/:$PATH

export PATH=~/scripts/screenFetch:$PATH

#ulimit -s unlimited

#ulimit -m unlimited

## Compile commands

# ./util/config.sh model=710 n_tor=1 n_period=1 n_plane=1 && make clean && make cleanall && make -j 8 && mv jorek_model710 jorek_model710_ntor1

# ./util/config.sh model=710 n_tor=5 n_period=1 n_plane=8 && make clean && make cleanall && make -j 8 && make -j 8 jorek2vtk jorek2_postproc jorek2_poincare q_fmhd

alias rm="rm -i"

alias lsr="ls -lrt"

alias gv="gv -antialias"

alias myrsync="rsync -aAXvP"

alias myquota="/usr/lpp/mmfs/bin/mmlsquota --block-size auto"

alias gitResetPushedCommit='git reset --soft HEAD~1'

alias sqcdjobid='source ~/scripts/slurm_dir.sh '

alias plot_live_data='plot_live_data.sh'

alias tmux_attach_t='tmux attach -t '

alias dsgetmykeys='cd ~/.ssh/ && ds get mykeys/my_key.pub mykeys/my_key mykeys/my_key-cert.pub && cd -'

# alias mysq="squeue -u $USER"

# alias sqnow='sacct --starttime 2023-08-09 --format=User,JobID,Jobname%30,state,start,end,elapsed,nnodes,WorkDir%180 | grep "$USER " | grep "RUNNING\|PENDING"'

alias sqdir='scontrol show job | grep "WorkDir=$WORKDIR"'

alias mysq="squeue -o '%.29j %.10i %.8q %.8M %.3D %.3L %.1T %.17r %.8u' -u $USER"

alias sqhist='sacct --starttime 2023-08-09 --format=User,JobID,Jobname%30,state,start,end,elapsed,nnodes,WorkDir%180 | grep "$USER "'

alias sqnow='sacct --starttime 2023-08-09 --format=User,JobID,Jobname%20,state,WorkDir%180 | grep "$USER " | grep "RUNNING\|PENDING"'

alias watchsq='watch -n 1 squeue -u $USER'

alias sqmemory='sacct -a --format=user%10,jobname%30,node%10,start%20,end%20,elapsed%10,MaxRSS -j'

alias jorekShowSteps="egrep -i 'info\(2|time iterat|time step :|min,max deltas' logfile"

#alias bpeek="egrep -i 'info\(2|time iterat|time step :|min,max deltas' logfile"

alias tailf='tail logfile -f | grep -e "time step :" -e "Elapsed time ITERATION" -e "min,max deltas =" -e "Elapsed time in construct " -e "Number of iterations" -e "After step " -e "Elapsed time updating preconditioner "'

alias llh='du -h --max-depth=1 | sort -h'

alias cpXfiles='find ./ -maxdepth 1 -type f -perm /a+x | xargs cp -t ' # followed by target path

alias renameH5_to_short='rename jorek0 jorek jorek0?????.h5'

alias renameH5_to_long='rename jorek jorek0 jorek?????.h5'

alias stopJorek='touch STOP_NOW'

alias luJorek='touch REDO_LU'

alias outputJorek='touch OUTPUT_NOW'

alias reg_cases_ls='reg_tests/run_test.sh -l'

alias reg_case_comp_and_run='reg_tests/run_test.sh -j 8 '

alias reg_case_compile='reg_tests/run_test.sh -p -j 8 '

alias reg_case_run='reg_tests/run_test.sh -k -n '

alias reg_clean_all='reg_tests/cleanup.sh'

alias live_data='time2si && plot_live_data -noplot'

#alias time2si="time2si=$(grep "@times_y2si:" macroscopic_vars.dat | awk '{print $2}')"

alias jorek_post='./jorek2_postproc < ~/scripts/postproc_script.txt && sed -i '1s/^#//' postproc/exprs_averaged_s*.dat && sed -i '/^#/d' postproc/qprofile_s*.dat'

alias jorek_post2='sed -i '1s/^#//' ' # remove first # in first line in postproc/exprs_averaged_s*.dat

alias jorek_post3='sed -i '/^#/d' ' # remove first line start with # in postproc/qprofile_s*.dat

alias touch_all_folder_file='find . -exec touch {} +'

alias touch_all_file='find . -type f -exec touch {} +'

alias touch_all_folder='find . -type d -exec touch {} +'

alias plot_multiple_files='plot_multiple_files.py'

# Function to set more_outfile_digits to false

set_more_outfile_digits_false() {

sed -i 's/^more_outfile_digits=true/more_outfile_digits=false/' ~/jorek/util/convert2vtk.sh

echo "Set more_outfile_digits to false."

}

# Function to revert more_outfile_digits back to true

set_more_outfile_digits_true() {

sed -i 's/^more_outfile_digits=false/more_outfile_digits=true/' ~/jorek/util/convert2vtk.sh

echo "Set more_outfile_digits to true."

}

alias cvt2vtkno0='convert2vtk.sh -no0 -j 8 jorek2vtk '

alias cvt2vtk='convert2vtk.sh -j 8 jorek2vtk '

alias cvt2vtkno0si='convert2vtk.sh -no0 -si -j 8 jorek2vtk '

alias cvt2vtksi='convert2vtk.sh -si -j 8 jorek2vtk '

cvt2vtk_itor() {

local itor="$1"

local input="$2"

if [ -n "$3" ]; then

local only="$3"

echo "Only processing nsteps of: "$only

convert2vtk.sh -i_tor "$itor" -only "$only" -j 8 jorek2vtk "$input"

else

convert2vtk.sh -i_tor "$itor" -j 8 jorek2vtk "$input"

fi

}

cvt2vtk_iplane() {

local ip="$1"

local input="$2"

if [ -n "$3" ]; then

local only="$3"

echo "Only processing nsteps of: "$only

convert2vtk.sh -i_plane "$ip" -only "$only" -j 8 jorek2vtk "$input"

else

convert2vtk.sh -i_plane "$ip" -j 8 jorek2vtk "$input"

fi

}

cvt2vtksi_iplane() {

local ip="$1"

local input="$2"

if [ -n "$3" ]; then

local only="$3"

echo "Only processing nsteps of: "$only

convert2vtk.sh -si -i_plane "$ip" -only "$only" -j 8 jorek2vtk "$input"

else

convert2vtk.sh -si -i_plane "$ip" -j 8 jorek2vtk "$input"

fi

}

cvt2vtk_iplane_nsub() {

local ip="$1"

local nsub="$2"

local input="$3"

if [ -n "$4" ]; then

local only="$4"

echo "Only processing nsteps of: "$only

convert2vtk.sh -i_plane "$ip" -nsub "$nsub" -only "$only" -j 8 jorek2vtk "$input"

else

convert2vtk.sh -i_plane "$ip" -nsub "$nsub" -j 8 jorek2vtk "$input"

fi

}

cvt2vtkno0_iplane() {

local ip="$1"

local input="$2"

if [ -n "$3" ]; then

local only="$3"

echo "Only processing nsteps of: "$only

convert2vtk.sh -i_plane "$ip" -only "$only" -no0 -j 8 jorek2vtk "$input"

else

convert2vtk.sh -i_plane "$ip" -no0 -j 8 jorek2vtk "$input"

fi

}

cvt2vtk_itor_iplane() {

local itor="$1"

local ip="$2"

local input="$3"

if [ -n "$4" ]; then

local only="$4"

echo "Only processing nsteps of: "$only

convert2vtk.sh -i_tor "$itor" -i_plane "$ip" -only "$only" -j 8 jorek2vtk "$input"

else

convert2vtk.sh -i_tor "$itor" -i_plane "$ip" -j 8 jorek2vtk "$input"

fi

}

# Define a function to echo array elements

print_array() {

local array=("$@") # Receive the array as arguments

for element in "${array[@]}"; do

echo "$element"

done

}

jorek_post_time() {

./jorek2_postproc < ~/scripts/postproc_script_time_series.txt

sed -i '1s/^#//' postproc/exprs_at*.dat

}

jorek_post_count() {

local directory="$1"

# Check if directory is provided, otherwise use current directory

if [ -z "$directory" ]; then

directory="postproc/"

fi

# Count files with the specified prefix

local prefix="fluxsurfaces_s"

local count=$(find "$directory" -type f -name "${prefix}*" | wc -l)

echo "Find $count ${prefix}* files."

local prefix="qprofile_s"

local count=$(find "$directory" -type f -name "${prefix}*" | wc -l)

echo "Find $count ${prefix}* files."

local prefix="exprs_averaged_s"

local count=$(find "$directory" -type f -name "${prefix}*" | wc -l)

echo "Find $count ${prefix}* files."

local prefix="exprs_midplane_s"

local count=$(find "$directory" -type f -name "${prefix}*" | wc -l)

echo "Find $count ${prefix}* files."

local count=$(find ./ -maxdepth 1 -type f -name "jorek*.h5" | wc -l)

echo "Find $count jorek*.h5 files."

}

jorek_post_all() {

live_data

live_data -q ti

sed -i '1a 0 0' times.dat

unset id ids sorted_ids unique_ids ids_exist file_id

# Check if an ID was provided as a parameter

if [ -n "$1" ]; then

#id="$1" # Use the provided ID

# for id in "$@"; do

# echo "post_porcessing: $id"

# sed -i 's/\b[0-9]\{5\}\b/'"$id"'/g' ~/scripts/postproc_script.txt

# ./jorek2_postproc < ~/scripts/postproc_script.txt > postproc.log

# done

ids=("$@")

else

# Extract IDs and store them in an array

ids=($(find ./ -maxdepth 1 -type f -name 'jorek*.h5' | grep -oE 'jorek[0-9]+\.h5' | sed 's/jorek\([0-9]\+\)\.h5/\1/'))

# print_array "${ids[@]}"

# ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'exprs_averaged_s*.dat' | grep -oE 'exprs_averaged_s[0-9]+\.dat' | sed 's/exprs_averaged_s\([0-9]\+\)\.dat/\1/'))

ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'exprs_midplane_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

# ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'exprs_averaged_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

# ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'fluxsurfaces_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

# ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'qprofile_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

fi

sorted_ids=($(printf "%s\n" "${ids[@]}" | sort -n))

# Loop through the sorted IDs and exist IDs and add them to unique_ids if they are not already in it

for id in "${sorted_ids[@]}"; do

if [[ ! " ${unique_ids[@]} " =~ " $id " ]] && [[ ! " ${ids_exist[@]} " =~ " $id " ]]; then

unique_ids+=("$id")

fi

done

# Counter for active threads

active_threads=0

# Maximum number of threads in parallel

max_threads=10 # Adjust based on your preference

mkdir ~/scripts/tmp_postproc

# Loop through the IDs and replace them in postproc_script.txt

for id in "${unique_ids[@]}"; do

# Check if the maximum number of threads is reached

if [ "$active_threads" -ge "$max_threads" ]; then

# Wait for one background process to finish

wait

active_threads=0

fi

echo "post_porcessing: $id" && \

file_id=~/scripts/tmp_postproc/"postproc_script_$id.txt" && \

cp ~/scripts/postproc_script.txt $file_id && \

sed -i 's/\b[0-9]\{5\}\b/'"$id"'/g' $file_id && \

./jorek2_postproc < $file_id > postproc.log &

((active_threads++))

done

wait

for id in "${unique_ids[@]}"; do

echo "cleaning up: $id"

file_id=~/scripts/tmp_postproc/"postproc_script_$id.txt"

rm $file_id -f

done

sed -i '1s/^#//' postproc/exprs_averaged_s*.dat

sed -i '1s/^#//' postproc/exprs_midplane_s*.dat

sed -i '1s/^#//' postproc/int3Dprofile_s*.dat

sed -i '1s/^#//' postproc/exprs_surface_flux_s*.dat

sed -i '/^#/d' postproc/qprofile_s*.dat

cp ~/scripts/postproc_script.txt postproc/

unset id ids sorted_ids unique_ids ids_exist file_id

}

jorek_post_all_reduced() {

live_data

live_data -q ti

sed -i '1a 0 0' times.dat

unset id ids sorted_ids unique_ids ids_exist file_id

# Check if an ID was provided as a parameter

if [ -n "$1" ]; then

ids=("$@")

else

# Extract IDs and store them in an array

ids=($(find ./ -maxdepth 1 -type f -name 'jorek*.h5' | grep -oE 'jorek[0-9]+\.h5' | sed 's/jorek\([0-9]\+\)\.h5/\1/'))

# print_array "${ids[@]}"

ids_exist=($(find ./postproc_reduced/ -maxdepth 1 -type f -name 'exprs_midplane_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

fi

sorted_ids=($(printf "%s\n" "${ids[@]}" | sort -n))

# Loop through the sorted IDs and exist IDs and add them to unique_ids if they are not already in it

for id in "${sorted_ids[@]}"; do

if [[ ! " ${unique_ids[@]} " =~ " $id " ]] && [[ ! " ${ids_exist[@]} " =~ " $id " ]]; then

unique_ids+=("$id")

fi

done

# Counter for active threads

active_threads=0

# Maximum number of threads in parallel

max_threads=10 # Adjust based on your preference

mkdir ~/scripts/tmp_postproc_reduced

# Loop through the IDs and replace them in postproc_reduced_script.txt

for id in "${unique_ids[@]}"; do

# Check if the maximum number of threads is reached

if [ "$active_threads" -ge "$max_threads" ]; then

# Wait for one background process to finish

wait

active_threads=0

fi

echo "post_porcessing: $id" && \

file_id=~/scripts/tmp_postproc_reduced/"postproc_reduced_script_$id.txt" && \

cp ~/scripts/postproc_reduced_script.txt $file_id && \

sed -i 's/\b[0-9]\{5\}\b/'"$id"'/g' $file_id && \

./jorek2_postproc < $file_id > postproc_reduced.log &

((active_threads++))

done

wait

for id in "${unique_ids[@]}"; do

echo "cleaning up: $id"

file_id=~/scripts/tmp_postproc_reduced/"postproc_reduced_script_$id.txt"

rm $file_id -f

done

mkdir postproc_reduced

mv postproc/* postproc_reduced/

sed -i '1s/^#//' postproc_reduced/exprs_averaged_s*.dat

sed -i '1s/^#//' postproc_reduced/exprs_midplane_s*.dat

sed -i '1s/^#//' postproc_reduced/int3Dprofile_s*.dat

sed -i '1s/^#//' postproc_reduced/exprs_surface_flux_s*.dat

sed -i '/^#/d' postproc_reduced/qprofile_s*.dat

cp ~/scripts/postproc_reduced_script.txt postproc_reduced/

unset id ids sorted_ids unique_ids ids_exist file_id

}

jorek_post_all_ompnum() {

plot_live_data.sh -noplot

plot_live_data.sh -noplot -q ti

unset id ids sorted_ids unique_ids ids_exist file_id

# Check if an ID was provided as a parameter

if [ -n "$1" ]; then

#id="$1" # Use the provided ID

# for id in "$@"; do

# echo "post_porcessing: $id"

# sed -i 's/\b[0-9]\{5\}\b/'"$id"'/g' ~/scripts/postproc_script.txt

# ./jorek2_postproc < ~/scripts/postproc_script.txt > postproc.log

# done

ids=("$@")

else

# Extract IDs and store them in an array

ids=($(find ./ -maxdepth 1 -type f -name 'jorek*.h5' | grep -oE 'jorek[0-9]+\.h5' | sed 's/jorek\([0-9]\+\)\.h5/\1/'))

# print_array "${ids[@]}"

# ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'exprs_averaged_s*.dat' | grep -oE 'exprs_averaged_s[0-9]+\.dat' | sed 's/exprs_averaged_s\([0-9]\+\)\.dat/\1/'))

ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'exprs_midplane_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

# ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'exprs_averaged_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

# ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'fluxsurfaces_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

# ids_exist=($(find ./postproc/ -maxdepth 1 -type f -name 'qprofile_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

fi

sorted_ids=($(printf "%s\n" "${ids[@]}" | sort -n))

# Loop through the sorted IDs and exist IDs and add them to unique_ids if they are not already in it

for id in "${sorted_ids[@]}"; do

if [[ ! " ${unique_ids[@]} " =~ " $id " ]] && [[ ! " ${ids_exist[@]} " =~ " $id " ]]; then

unique_ids+=("$id")

fi

done

# Counter for active threads

active_threads=0

# Maximum number of threads in parallel

max_threads=$OMP_NUM_THREADS # Adjust based on your preference

mkdir ~/scripts/tmp_postproc

# Loop through the IDs and replace them in postproc_script.txt

for id in "${unique_ids[@]}"; do

# Check if the maximum number of threads is reached

if [ "$active_threads" -ge "$max_threads" ]; then

# Wait for one background process to finish

wait

active_threads=0

fi

echo "post_porcessing: $id" && \

file_id=~/scripts/tmp_postproc/"postproc_script_$id.txt" && \

cp ~/scripts/postproc_script.txt $file_id && \

sed -i 's/\b[0-9]\{5\}\b/'"$id"'/g' $file_id && \

./jorek2_postproc < $file_id > postproc.log &

((active_threads++))

done

wait

for id in "${unique_ids[@]}"; do

echo "cleaning up: $id"

file_id=~/scripts/tmp_postproc/"postproc_script_$id.txt"

rm $file_id -f

done

sed -i '1s/^#//' postproc/exprs_averaged_s*.dat

sed -i '1s/^#//' postproc/exprs_midplane_s*.dat

sed -i '1s/^#//' postproc/int3Dprofile_s*.dat

sed -i '1s/^#//' postproc/exprs_surface_flux_s*.dat

sed -i '/^#/d' postproc/qprofile_s*.dat

unset id ids sorted_ids unique_ids ids_exist file_id

}

jorek_poincare_all() {

unset id ids sorted_ids unique_ids ids_exist input_file_name

mkdir poincares

while [[ $# -gt 0 ]]; do

case "$1" in

-fn)

if [ -n "$2" ]; then

input_file_name="$2"

shift 2

else

echo "Error: Missing argument for -fn flag (the input file)."

exit 1

fi

;;

*)

# Capture other parameters in the 'ids' array

ids+=("$1")

shift

;;

esac

done

# Check if an ID was provided as a parameter

# if [ -n "$1" ]; then

# ids=("$@")

# else

if [ ${#ids[@]} -gt 0 ]; then

echo "Ids is not empty: ${ids[@]}"

else

# Extract IDs and store them in an array

ids=($(find ./ -maxdepth 1 -type f -name 'jorek*.h5' | grep -oE 'jorek[0-9]+\.h5' | sed 's/jorek\([0-9]\+\)\.h5/\1/'))

ids_exist=($(find ./poincares/ -maxdepth 1 -type f -name 'poinc_R-Z_s*.dat' | grep -oE '_s[0-9]+\.dat' | sed 's/_s\([0-9]\+\)\.dat/\1/'))

fi

sorted_ids=($(printf "%s\n" "${ids[@]}" | sort -n))

# Loop through the sorted IDs and exist IDs and add them to unique_ids if they are not already in it

for id in "${sorted_ids[@]}"; do

if [[ ! " ${unique_ids[@]} " =~ " $id " ]] && [[ ! " ${ids_exist[@]} " =~ " $id " ]]; then

unique_ids+=("$id")

fi

done

# Loop through the IDs

for id in "${unique_ids[@]}"; do

echo "poincare_porcessing file: jorek$id.h5"

cp "jorek$id.h5" jorek_poincare.h5

time ./jorek2_poincare < $input_file_name > poincare.log

echo "Finished, moving poinc_*.dat to poincares/"

mv poinc_R-Z.dat "poincares/poinc_R-Z_s$id.dat"

mv poinc_rho-theta.dat "poincares/poinc_rho-theta_s$id.dat"

mv poincare.ps "poincares/poincare$id.ps"

done

unset id ids sorted_ids unique_ids ids_exist input_file_name

}

make_jorek_kinetic() {

unset pfix underscore ext origin_file new_file

local usage="Usage: make_jorek_kinetic [model(=7xx) ntor(=2*n_max+1) nperiod(=1, usually) nplane(>=4*n_max)]"

local description="This function compiles executable files for specified model and parameters."

local help_text="$usage\n$description"

if [ $# -eq 0 ]; then

echo -e "$help_text"

echo "Example: make_jorek 710 5 1 8"

return

fi

local para_model="$1"

local para_ntor="$2"

local para_nperiod="$3"

local para_nplane="$4"

pfix="jorek_model"

underscore="_"

numone="1"

ext="$underscore$para_ntor$underscore$para_nperiod$underscore$para_nplane"

origin_file="$pfix$para_model"

new_file="$pfix$para_model$ext"

./util/config.sh model="$para_model" n_tor="$numone" n_period="$para_nperiod" n_plane="$numone" && make cleanall && make -j 8

make -j 8

mv "$origin_file" "$pfix$para_model$underscore$numone$underscore$para_nperiod$underscore$numone"

./util/config.sh model="$para_model" n_tor="$para_ntor" n_period="$para_nperiod" n_plane="$para_nplane" && make cleanall && make -j 8

make -j 8 jorek2vtk jorek2_postproc jorek2_poincare jorek2_four jorek2_target2vtk jorek2vtk_3d q_fmhd jorek2_fieldlines_vtk_newdiag kinetic_main #q_fmhd_3D

mv "$origin_file" "$new_file" && make install

cp models/model$para_model/mod_elt_matrix_fft.f90 bin/

unset pfix underscore ext origin_file new_file

}

make_jorek() {

unset pfix underscore ext origin_file new_file

local usage="Usage: make_jorek [model(=7xx) ntor(=2*n_max+1) nperiod(=1, usually) nplane(>=4*n_max)]"

local description="This function compiles executable files for specified model and parameters."

local help_text="$usage\n$description"

if [ $# -eq 0 ]; then

echo -e "$help_text"

echo "Example: make_jorek 710 5 1 8"

return

fi

local para_model="$1"

local para_ntor="$2"

local para_nperiod="$3"

local para_nplane="$4"

pfix="jorek_model"

underscore="_"

numone="1"

ext="$underscore$para_ntor$underscore$para_nperiod$underscore$para_nplane"

origin_file="$pfix$para_model"

new_file="$pfix$para_model$ext"

./util/config.sh model="$para_model" n_tor="$numone" n_period="$para_nperiod" n_plane="$numone" && make cleanall && make -j 8

make -j 8

mv "$origin_file" "$pfix$para_model$underscore$numone$underscore$para_nperiod$underscore$numone"

./util/config.sh model="$para_model" n_tor="$para_ntor" n_period="$para_nperiod" n_plane="$para_nplane" && make cleanall && make -j 8

make -j 8 jorek2vtk jorek2_postproc jorek2_poincare jorek2_four jorek2_target2vtk jorek2vtk_3d q_fmhd jorek2_fieldlines_vtk_newdiag #q_fmhd_3D

mv "$origin_file" "$new_file" && make install

cp models/model$para_model/mod_elt_matrix_fft.f90 bin/

unset pfix underscore ext origin_file new_file

}

make_jorek_gnu() {

unset pfix underscore ext origin_file new_file

local usage="Usage: make_jorek_gnu [model(=7xx) ntor(=2*n_max+1) nperiod(=1, usually) nplane(>=4*n_max)]"

local description="This function compiles executable files for specified model and parameters."

local help_text="$usage\n$description"

if [ $# -eq 0 ]; then

echo -e "$help_text"

echo "Example: make_jorek_gnu 710 5 1 8"

return

fi

cp Makefile.inc Makefile_backup_temp.inc

cp Makefile_gnu.inc Makefile.inc

source ~/source_gnu_env.sh

local para_model="$1"

local para_ntor="$2"

local para_nperiod="$3"

local para_nplane="$4"

pfix="jorek_model"

underscore="_"

numone="1"

ext="$underscore$para_ntor$underscore$para_nperiod$underscore$para_nplane"

origin_file="$pfix$para_model"

new_file="$pfix$para_model$ext"

./util/config.sh model="$para_model" n_tor="$numone" n_period="$para_nperiod" n_plane="$numone" && make cleanall && make -j 8

make -j 8

mv "$origin_file" "$pfix$para_model$underscore$numone$underscore$para_nperiod$underscore$numone"

./util/config.sh model="$para_model" n_tor="$para_ntor" n_period="$para_nperiod" n_plane="$para_nplane" && make cleanall && make -j 8

make -j 8 jorek2vtk jorek2_postproc jorek2_poincare jorek2_four jorek2_target2vtk jorek2vtk_3d q_fmhd jorek2_fieldlines_vtk_newdiag #q_fmhd_3D

mv "$origin_file" "$new_file" && make install

cp models/model$para_model/mod_elt_matrix_fft.f90 bin/

mv Makefile_backup_temp.inc Makefile.inc

source ~/.bashrc

unset pfix underscore ext origin_file new_file

}

# alias sbatch_dep='sbatch --dependency=afterok:' # e.g., sbatch --dependency=afterok:<first_job_id> my_second_job.sh # rok means run ok (succes)

sbatch_dep_job() {

local first_job_id="$1"

local script_name="$2"

sbatch --dependency=afterok:"$first_job_id" "$script_name"

}

sbatch_dep_job_any() {

local first_job_id="$1"

local script_name="$2"

sbatch --dependency=afternotok:"$first_job_id" "$script_name"

}

function sbatch_chain() {

if [ $# -lt 2 ]; then

echo "Usage: qsubchain jobscript1 jobscript2 [...]"

return

fi

thejobids=""

depend=""

while [ $# -gt 0 ]; do

thejobid=`sbatch $depend $1 | sed -e 's/Submitted batch job *//'`

thejobids="$thejobids $thejobid"

depend="--dependency=afterok:$thejobid"

shift

done

echo "JobIDs: $thejobids"

unset depend thejobid thejobids

}

function sbatch_chain_from() {

if [ $# -lt 2 ]; then

echo "Usage: sbatch_chain_from <job_ID> jobscript1 [jobscript2 ...]"

return 1

fi

start_jobid="$1"

shift

thejobids=""

depend="--dependency=afterok:${start_jobid}"

while [ $# -gt 0 ]; do

thejobid=$(sbatch $depend "$1" | sed -e 's/Submitted batch job *//')

thejobids="$thejobids $thejobid"

depend="--dependency=afterok:${thejobid}"

shift

done

echo "JobIDs:$thejobids"

unset depend thejobid thejobids start_jobid

}

function sbatch_chain_any() {

if [ $# -lt 2 ]; then

echo "Usage: qsubchain jobscript1 jobscript2 [...]"

return

fi

thejobids=""

depend=""

while [ $# -gt 0 ]; do

thejobid=`sbatch $depend $1 | sed -e 's/Submitted batch job *//'`

thejobids="$thejobids $thejobid"

depend="--dependency=afternotok:$thejobid"

shift

done

echo "JobIDs: $thejobids"

unset depend thejobid thejobids

}

# Submit a job that depends on a previous job completing successfully (afterok)

qsub_dep_job() {

local first_job_id="$1"

local script_name="$2"

# PBS uses -W depend=condition:jobid

qsub -W depend=afterok:"$first_job_id" "$script_name"

}

# Submit a job that depends on a previous job failing (afternotok)

# Note: Based on your provided code which used 'afternotok'.

# If you meant "run regardless of success/fail", change to 'afterany'.

qsub_dep_job_any() {

local first_job_id="$1"

local script_name="$2"

qsub -W depend=afternotok:"$first_job_id" "$script_name"

}

# Chain a list of scripts so they run one after another (on success)

function qsub_chain() {

if [ $# -lt 2 ]; then

echo "Usage: qsub_chain jobscript1 jobscript2 [...]"

return

fi

thejobids=""

depend=""

while [ $# -gt 0 ]; do

# qsub usually outputs only the Job ID (e.g., 12345.server), so no sed needed.

# We use -W depend=... only if $depend is set.

if [ -z "$depend" ]; then

thejobid=$(qsub "$1")

else

thejobid=$(qsub -W "$depend" "$1")

fi

thejobids="$thejobids $thejobid"

depend="depend=afterok:$thejobid"

shift

done

echo "JobIDs: $thejobids"

unset depend thejobid thejobids

}

# Chain a list of scripts starting after an existing Job ID

function qsub_chain_from() {

if [ $# -lt 2 ]; then

echo "Usage: qsub_chain_from <job_ID> jobscript1 [jobscript2 ...]"

return 1

fi

start_jobid="$1"

shift

thejobids=""

depend="depend=afterok:${start_jobid}"

while [ $# -gt 0 ]; do

thejobid=$(qsub -W "$depend" "$1")

thejobids="$thejobids $thejobid"

depend="depend=afterok:${thejobid}"

shift

done

echo "JobIDs:$thejobids"

unset depend thejobid thejobids start_jobid

}

# Chain a list of scripts where dependency is 'afternotok' (Run next only if previous failed)

function qsub_chain_any() {

if [ $# -lt 2 ]; then

echo "Usage: qsub_chain_any jobscript1 jobscript2 [...]"

return

fi

thejobids=""

depend=""

while [ $# -gt 0 ]; do

if [ -z "$depend" ]; then

thejobid=$(qsub "$1")

else

thejobid=$(qsub -W "$depend" "$1")

fi

thejobids="$thejobids $thejobid"

depend="depend=afternotok:$thejobid"

shift

done

echo "JobIDs: $thejobids"

unset depend thejobid thejobids

}

time2si() {

time2si=$(grep "@times_y2si:" macroscopic_vars.dat | awk '{print $2}')

echo $time2si

}

bpeek() {

if [ -n "$1" ]; then

filename="$1"

else

filename=logfile

fi

egrep --text -i 'info\(2|time iterat|time step :|min,max deltas' $filename

}

#stopJorekAfterHours() {

# time="$1"

# echo "touch STOP_NOW" | at now + $time hours

#}

stopJorekAfterHoursMins() {

time1="$1" # hours

time2="$2" # minutes

# Calculate the total time in minutes

total_minutes=$((time1 * 60 + time2))

# Schedule the task using 'at' with the calculated time

echo "touch STOP_NOW" | at now + $total_minutes minutes

}

#stopJorekAfterMins() {

# time="$1"

# echo "touch STOP_NOW" | at now + $time minutes

#}

stopJorekAfterHoursMinsCron() {

time1="$1" # hours

time2="$2" # minutes

# Calculate the execution time

target_time=$(date -d "$time1 hours $time2 minutes" "+%M %H %d %m *")

# Add the task to crontab

(crontab -l 2>/dev/null; echo "$target_time touch $PWD/STOP_NOW") | crontab -

echo "Task scheduled: 'STOP_NOW' will be created in $time1 hours and $time2 minutes."

}

n_MPI_from_n_tor() {

local n_tor=$1

# Iterate over k from 1 to 10

for ((k = 1; k <= 10; k++)); do

# Perform the calculation

local n_MPI=$((k * (n_tor + 1) / 2))

# Print the result

echo "For k=$k, n_MPI = $n_MPI"

done

}

n_plane_from_n_tor() {

local n_tor=$1

# Iterate over k from 2 to 10

# At least 2*(n_tor-1)

for ((k = 2; k <= 10; k++)); do

# Perform the calculation

local n_plane=$((k * (n_tor - 1)))

# Print the result

echo "For k=$k, n_plane = $n_plane"

done

}

alias live_data_time="live_data -q ti && sed -i '1a 0 0' times.dat"

jorek_four_all() {

live_data

live_data -q ti

sed -i '1a 0 0' times.dat

unset id ids sorted_ids unique_ids ids_exist file_id input_file_name

while [[ $# -gt 0 ]]; do

case "$1" in

-fn)

if [ -n "$2" ]; then

input_file_name="$2"

shift 2

else

echo "Error: Missing argument for -fn flag (the input file)."

exit 1

fi

;;

*)

# Capture other parameters in the 'ids' array

ids+=("$1")

shift

;;

esac

done

# Check if an ID was provided as a parameter

if [ ${#ids[@]} -gt 0 ]; then

echo "Ids is not empty: ${ids[@]}"

else

# Extract IDs and store them in an array

ids=($(find ./ -maxdepth 1 -type f -name 'jorek*.h5' | grep -oE 'jorek[0-9]+\.h5' | sed 's/jorek\([0-9]\+\)\.h5/\1/'))

# print_array "${ids[@]}"

ids_exist=($(find ./four_results/ -maxdepth 1 -type f -name 'Uphi_n000_m000_step*' | grep -oE 'step[0-9]+' | sed 's/step//'))

fi

sorted_ids=($(printf "%s\n" "${ids[@]}" | sort -n))

# Loop through the sorted IDs and exist IDs and add them to unique_ids if they are not already in it

for id in "${sorted_ids[@]}"; do

if [[ ! " ${unique_ids[@]} " =~ " $id " ]] && [[ ! " ${ids_exist[@]} " =~ " $id " ]]; then

unique_ids+=("$id")

fi

done

# Counter for active threads

active_threads=0

# Maximum number of threads in parallel

max_threads=1 # Adjust based on your preference

# Loop through the IDs and replace them in postproc_script.txt

for id in "${unique_ids[@]}"; do

# Check if the maximum number of threads is reached

if [ "$active_threads" -ge "$max_threads" ]; then

# Wait for one background process to finish

wait

active_threads=0

fi

echo "four_porcessing: $id" && \

cp "jorek$id.h5" jorek_four.h5

./jorek2_four < ./${input_file_name} > four_logfile

((active_threads++))

done

wait

unset id ids sorted_ids unique_ids ids_exist file_id

}

# Function to update the time limit of a SLURM job

update_slurm_time() {

# Check if correct number of arguments is provided

if [ "$#" -ne 2 ]; then

echo "Usage: update_slurm_time <jobid> <new_time_limit>"

echo "Example: update_slurm_time 12345 03:00:00"

return 1

fi

# Assign variables

local jobid="$1"

local new_time_limit="$2"

# Update the time limit using scontrol

scontrol update jobid=$jobid TimeLimit=$new_time_limit

# Check if the command was successful

if [ $? -eq 0 ]; then

echo "Time limit for job $jobid updated to $new_time_limit."

else

echo "Failed to update time limit for job $jobid."

return 1

fi

}

open_paraview() {

if [ -z "$1" ]; then

echo "Usage: open_paraview <directory_name>"

return 1

fi

paraview --data="$1/jorek...vtk"

}

make_install() {

# 1. Create the bin directory if it doesn't exist

if [[ ! -d "bin" ]]; then

mkdir -p bin

echo "Created bin/ directory."

fi

# 2. Loop through all files in the current directory

# -maxdepth 1 ensures we don't look into subdirectories

# -type f ensures we only look at files

for file in *; do

# Check if it's a regular file and if it's executable

if [[ -f "$file" && -x "$file" ]]; then

# Avoid moving the script itself if it's in the same folder

mv "$file" bin/

echo "Moved: $file -> bin/"

fi

done

}

get_step_from_time() {

local si_mode=0

local args=()

for arg in "$@"; do

if [[ "$arg" == "-si" ]]; then

si_mode=1

else

args+=("$arg")

fi

done

local target_time="${args[0]}"

local times_file="${args[1]:-times.dat}"

if [[ "$si_mode" == 1 ]]; then

local time2si

time2si=$(grep "@times_y2si:" macroscopic_vars.dat | awk '{print $2}')

echo time2si = $time2si [ms]

echo target_time = $target_time [ms]

target_time=$(awk -v t="$target_time" -v s="$time2si" 'BEGIN { print t / 1 / s }')

fi

echo target_time = $target_time [JOREK U.]

echo best_step:

awk -v t="$target_time" '

NR == 1 { next }

{

diff = $2 - t; if (diff < 0) diff = -diff

if (NR == 2 || diff < best_diff) { best_diff = diff; best_step = $1 }

}

END { print best_step }

' "$times_file"

}

export u0=1.2566370614359173e-06 # u0 vacuum magnetic permeability

export one_over_u0=795774.7154594767 # 1/u0

# Usage example:

# update_slurm_time 12345 03:00:00

# useful commands

# plot_q_versus_time.py -xm $time2si -xl "time [ms]" -ylim 0.0707 0.5 -cs 1.0 1.01 #-clim 0.928 1.300 -cs 0.99 1.0

# plot_f_versus_time.py -xm $time2si -fn exprs_midplane -yc 7 -xl "time [ms]" -clim -0.0000001 0.0000001 # -ylim 0.0707 0.5 -cs 1.0 1.01 #-clim 0.928 1.300 -cs 0.99 1.0

# plot_f_versus_time.py -xm $time2si -fn exprs_averaged -yc 7 -xl "time [ms]" -clim -0.0000001 0.0000001

# plot_f_versus_time.py -xm $time2si -fn exprs_averaged -yl '$\sqrt{\psi_n}$' -yc 35 -rp 1.0 -xl "time [ms]" -ylim 0.03 0.5 -cm 2170378.6432790086 -ti 'radial distribution of dynamo emf versus time' -fz 18

# plot_VxB_tor.py -np 32 -ns 43200 vtk_no0_iplane # -xylim 1.20 2.00 -0.20 0.30

# plot_multiple_files.py energies.dat -sk 1 -ys log -xm $time2si -xl "time[ms]" -yl "normalized energies" -ti "normalized energies vs time"

# plot_mn_mode_structures.py four_results -va rho T_e -nl 1 2 -ml 1 2 3 23 -st 02000 04000 -tm $time2si #-me al -ex True -er 0.3

# plot_multiple_files.py four_results/U_radial_n001_m001_step000400 -sk 1 -xp 0.5 -yc 1 2 3 -le 'abs' 're' 'im'

# plot_fft_1D_time_series.py four_results/1D_U_radial_n001_m002_vs_time_at_rhop_eq_0.30.dat -sk 1 -yc 2

# plot_midplane_vtk.py vtk_iplane -np 16 -va n_charge_SI -ns 200000 -clim ' -2.1e+10' 2.1e+10 -tm $time2si -ef True

# for i in {1..32}; do cvt2vtkno0_iplane $i input 40000; done

# for i in {1..16}; do cvt2vtk_iplane $i input; done

# rsync -aAXv 20230825_fix_axis_bug_get_all_commits --exclude={"*.vtk"} toki02jump:/u/hazh/WORKSPACE/MarconiSync/ #Ref: https://tecadmin.net/backup-linux-system/

# git checkout -b bugfix/ffprime_integration

# git push -u origin bugfix/ffprime_integration

# jorek_four_all -fn input