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I want to cut all numbers in a file to the fifth decimal only. For example, I have this file:

1.0
 12.2348604202 0.0000000000 0.0000000000
 0.0000000000 3.0320000648 0.0000000000
 -1.3752052829 0.0000000000 5.6183021388
 Ga O
 8 12
Direct
 0.590021042 0.500000000 0.794251030
 0.409978979 0.500000000 0.205748985
 0.909978943 0.000000000 0.205749006
 0.090021023 -0.000000000 0.794251030
 0.658887031 0.000000000 0.314083014

So, I want to have the same file but with numbers with 5 decimal places only.

You can use sed:

sed -E 's/([0-9]+.[0-9]5)[0-9]*/1/g' file

Add -i option to add file in place.

With GNU awk:

awk 'print gensub(/([0-9]+.[0-9]5)[0-9]*/, "\1", "g")' input_file > output_file

This uses the awk function gensub to select a decimal number (/([0-9]+.[0-9]5)[0-9]*/) from a given file (input_file) and split it into two parts. The first part has 5 decimal places (([0-9]+.[0-9]5)) and the second part is the rest of the decimal number (([0-9]*)). gensub then replaces the selected number with its first part ("\1") and does that for all the decimal numbers it can find ("g") in input_file.

The command then saves the result to an output file (> output_file).

With GNU sed:

sed -E 's/.([0-9]5)[0-9]*/.1/g' file

Output:

1.0
 12.23486 0.00000 0.00000
 0.00000 3.03200 0.00000
 -1.37520 0.00000 5.61830
 Ga O
 8 12
Direct
 0.59002 0.50000 0.79425
 0.40997 0.50000 0.20574
 0.90997 0.00000 0.20574
 0.09002 -0.00000 0.79425
 0.65888 0.00000 0.31408

Use extended regular expressions with -E:

sed -E

Match the pattern .<five digits><n digits> with .([0-9]5)[0-9]*. Capture the 5 digits following the dot . with ([0-9]5)

s/.([0-9]5)[0-9]*/

Replace the match with the dot . and the captured pattern:

/.1/

If you don't mind the integers also being converted to floating point, you could use numfmt:

$ numfmt --field=1- --format=%.5f --invalid=ignore < file
1.00000
 12.23487 0.00000 0.00000
 0.00000 3.03201 0.00000
 -1.37521 0.00000 5.61831
 Ga O
8.00000 12.00000
Direct
 0.59003 0.50000 0.79426
 0.40998 0.50000 0.20575
 0.90998 0.00000 0.20575
 0.09003 0.00000 0.79426
 0.65889 0.00000 0.31409