How to convert gjf format to xyz format?

The gjf format is as follows:

%chk=test.chk
# hf/3-21g geom=connectivity
Title Card Required
0 1 C 0.53424883 1.46721985 -0.02620215 H 0.89090326 0.45840985 -0.02620215 H 0.89092167 1.97161804 0.84744935 H 0.89092167 1.97161804 -0.89985366 H -0.53575117 1.46723303 -0.02620215 1 2 1.0 3 1.0 4 1.0 5 1.0 2 3 4 5

and xyz format is as follows:

5 # this is the number of atoms C 0.53424883 1.46721985 -0.02620215 H 0.89090326 0.45840985 -0.02620215 H 0.89092167 1.97161804 0.84744935 H 0.89092167 1.97161804 -0.89985366 H -0.53575117 1.46723303 -0.02620215

3 Answers

Here's a quick and dirty Awk refactoring.

#!/bin/sh
for file_name in *.gjf; do awk '/[0-9]\.[0-9][0-9]/ { a[++n] = $0 } END { print n; print; for(i=1; i<=n; ++i) print a[i] }' "$file_name" > "${file_name%.gjf}.xyz"
done

In very brief, we collect the matching lines into the array a, then print their number, an empty line, and the lines themselves.

This obviously requires you to have enough RAM to keep all lines in memory. If not, a temporary file is probably better (but your attempt could still benefit from some light refactoring).

I wrote some thing like below and it works but it is almost stupid

#!/bin/bash for file_name in *.gjf; do grep '[0-9]\.[0-9][0-9]' $file_name | cat > tmp cp tmp tmp2 wc -l < tmp > ${file_name%.*}.xyz echo "" >> ${file_name%.*}.xyz cat tmp2 >> ${file_name%.*}.xyz rm tmp tmp2 done

It is also good but not always!

#!/bin/bash
for file_name in *.gjf; do
tail -1 $file_name > ${file_name%.*}.xyz
echo"" >> ${file_name%.*}.xyz
grep '[0-9]\.[0-9][0-9]' $file_name >> ${file_name%.*}.xyz
done