List of Scripts (HPC and Research)

To get the output geometry of a *.out file (Q-Chem)

Using rev, column commands

grep "  B  " lda_bnr_2_n_ring_03_geo_restricted_singlet.out | tail -n6 | awk 'BEGIN {OFS=" ";} {print $1, $3, $5}' | rev | column -t | rev

Using AWK 

grep "  B  " lda_bnr_2_n_ring_03_geo_restricted_singlet.out | tail -n6 | awk 'BEGIN {OFS="
 ";} {print $1, $3, $5}'

To extract the geometry from a *.out file ($f) and paste in a ea/ip file (and insert $molecule at the beginning)

#!/usr/bin/env bash

for f in *.out; do

    for g in ea*.in; do

        n=$(((ls $f) | cut -d_ -f6))

        t=$((2 * $n ))

        grep "  B  " $f | tail -${t} | awk 'BEGIN {OFS=" ";} {print $1, $4, $5, $6}' | rev | column -t | rev > xyz.xyz

        sed -i '1i -1 2' xyz.xyz

        sed -i '1i $molecule' xyz.xyz

        echo '$end' >> xyz.xyz

        cat xyz.xyz ./input_ea.in > $g

     done

done

ClusterHOme$ ./script_ea_input.sh
./script_ea_input.sh: line 4: (ls lda_bnr_2_n_ring_05_geo_restricted_singlet.out) | cut -d_ -f6: syntax error: invalid arithmetic operator (error token is ".out) | cut -d_ -f6")

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Using two for loops:

for i in *.out; do 
    for j in *.in; do 
       what/you/want/to/do 
    done
done