extract_to_csv.sh

#!/bin/bash
#Run this script from root directory (/ontepconv/) as "./extract_to_csv.sh"

relative_dat_path=`echo ./input/*.dat | sed -r "s/\.dat\$//"`
rootname=$(basename "$relative_dat_path" .dat)


#This function enters all subdirectories and extracts forces and total energies from the .onetep files present
write_forc_energ_to_csv(){

for directory in */;
do
  echo $directory
  cd $directory
  rt_dir=$(basename "$directory")
  ###Extract Total DFT Energy from .onetep output file

  energy=`grep '<-- CG' *.onetep | awk {'print $3'}`
  echo "$rt_dir,$energy" >> ../energies.csv #write energies to root directory

  ###Extract Average Forces

  forcesString=`awk -v length=$(wc -l $rootname.onetep | awk '{print $1}')  -v start=$(grep -n "************************* Forces *************************" *.onetep | awk -F':' '{print $1}') -v end=$(grep -n "* TOTAL:" *.onetep | awk -F':' '{print $1}') '{if(NR>(start+5) && NR<(end-2)) print $4,$5,$6}' *.onetep # print the forces for each atom `
  numElements=`echo "${forcesString}" | wc -l`

  total_abs_force=0
  max=0.0
  for line in $forcesString;
  do
        abs=`echo ${line#-}`
        if (( $(echo "$abs $max" | awk '{print ($1 > $2)}') )); then max=$abs; fi
        #total_abs_force=`echo "${total_abs_force} + $abs" | bc`
  done

  #total_avg_force=`echo "${total_abs_force}/${numElements}" | bc -l`
 
  species_array+=("$species_line")

  echo "$rt_dir,${max}" >> ../forces.csv #write forces to root directory
  cd ..

done
}



read -p "Write CSV containing summary of results for cutoff energies? (in /cutoff/)? [y/n] " -n 1 -r
echo    # new line
if [[ $REPLY =~ ^[Yy]$ ]]
then
    > ./cutoff/forces.csv #empty file
    > ./cutoff/forces_sorted.csv #empty file
    > ./cutoff/energies.csv
    > ./cutoff/energies_sorted.csv
    cd ./cutoff
    write_forc_energ_to_csv
    ###########
    #Sort the CSV files from low energy/force to high 
    ########## 

    #-k1 tags the first field, the '1' means take the first field from the comma seperated field, the n means numerical result
    #the -k2 tag means a secondary sorting function. Here the ,2 means take the second comma seperated value and sort it via default means (alphanumeric) 
    sort --field-separator=',' -k1,1n ./energies.csv > ./energies_sorted.csv 
    sort --field-separator=',' -k1,1n ./forces.csv > ./forces_sorted.csv 
    cd ..
else
    echo "Skipping"
fi

read -p "Write CSV containing summary of results for number of NGWFs? (in /num_ngwf/)? [y/n] " -n 1 -r
echo    # new line
if [[ $REPLY =~ ^[Yy]$ ]]
then
    > ./num_ngwf/forces.csv #empty file
    > ./num_ngwf/forces_sorted.csv #empty file
    > ./num_ngwf/energies.csv
    > ./num_ngwf/energies_sorted.csv
    cd ./num_ngwf/
    write_forc_energ_to_csv
    # Sort the CSV files form low energy/force to high
    sort --field-separator='_' -k1,1 -k2,2n ./energies.csv > ./energies_sorted.csv 
    sort --field-separator='_' -k1,1 -k2,2n ./forces.csv > ./forces_sorted.csv 
    cd ..
else
    echo "Exiting"
    exit 101
fi

read -p "Write CSV containing summary of results for NGWFs Radii? (in /ngwf_radius/)? [y/n] " -n 1 -r
echo    # new line
if [[ $REPLY =~ ^[Yy]$ ]]
then
    > ./ngwf_radius/forces.csv #empty file
    > ./ngwf_radius/forces_sorted.csv #empty file
    > ./ngwf_radius/energies.csv
    > ./ngwf_radius/energies_sorted.csv
    cd ./ngwf_radius/
    write_forc_energ_to_csv
    # Sort the CSV files form low energy/force to high
    sort --field-separator='_' -k1,1 -k2,2n ./energies.csv > ./energies_sorted.csv 
    sort --field-separator='_' -k1,1 -k2,2n ./forces.csv > ./forces_sorted.csv 
    cd ..
else
    echo "Exiting"
    exit 101
fi
###########
#Plot Output.

#Remove exit 101 to plot cutoff energy/forces
exit 101

cat << __EOF | gnuplot -persist
set xtic auto                          # set xtics automatically
set ytic auto                          # set ytics automatically
set title "Forces versus Energy Cutoff"
set xlabel "Energy Cutoff (eV)"
set ylabel "Force (Ha/bohr)"
set datafile separator ","
set style line 1 lt 2 lc rgb "red" lw 1 pt 2 ps 3 
# use line style "ls" 1
plot './cutoff/forces_sorted.csv' using 1:2 with linespoints ls 1
__EOF

cat << __EOF | gnuplot -persist
set xtic auto                          # set xtics automatically
set ytic auto                          # set ytics automatically
set title "Total System Energy versus Energy Cutoff"
set xlabel "Energy Cutoff (eV)"
set ylabel "Total System Energy (Ha)"
set datafile separator ","
set style line 2 lt 2 lc rgb "blue" lw 1 pt 2 ps 3
plot './cutoff/energies_sorted.csv' using 1:2 with linespoints ls 2
__EOF