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I am trying to run a script using sed i runing like this

for et in   1 # 2 3
    do

      if [ -d ET$et ]; then rm -rf ET$et; fi

        mkdir ET$et
        cd ET$et
        cp  $home/step_$i/FDE/diabatA/run.adf .
        cp  $home/step_$i/FDE/diabatA/mas$i.xyz .

        awk1=`awk '/type=fde/{print NR }' run.adf | head -1`
        awk2=`$(echo "$a+379" | bc -l )`
       sed -n "$awk1,"$awk2"p" run.adf > first

        awk3=`awk '/ATOMS/{print NR +1}' first`
        awk4=`cat mas$i.xyz | wc -l`
        awk4=$( echo "$awk4-1" | bc -l )
        awk5=`awk "/ATOMS/{print NR +"${awk4}" }" run.adf`
        sed -n "$awk3,"$awk4"p" first > atoms

        par=$( echo "$awk4-99" | bc -l )
        rho1=$(cat atoms | head -34 )
        rho2=$(cat atoms | head -64 | tail -31)
        rho3=$(cat atoms | head -97 | tail -33)
        rhoall=$(cat atoms | tail -${par} )

        echo -e "$rho1\n$rho2\n$rhoall" > eje
done

but is telling me this:

(standard_in) 1: syntax error
sed: -e expression #1, char 6: unexpected `,'
sed: -e expression #1, char 1: unknown command: `,'

Please, I appreciate any help with this issue...

Thanks Pablo

1

Both your sed expressions look malformed... here's the first:

sed -n "$awk1,"$awk2"p" run.adf > first

I would suggest you're actually looking for:

sed -n "s/$awk1/$awk2/p" run.adf > first

And alter the second one similarly.

sed -n "s/$awk3/$awk4/p" first > atoms
  • Thanks, However is telling me : (standard_in) 1: syntax error sed: -e expression #1, char 7: unknown command: /' sed: -e expression #1, char 3: unknown command: 2' Do you have any suggestion? Thanks again – Pablor Nov 5 '13 at 15:51
  • Yeah, that's my bad. See the updated version. – Oli Nov 5 '13 at 15:56
1

The unknown command ',' means that either $awk1 or $awk3 is empty. Instead of a line number, the first thing sed sees is a comma.

You need to do something if "run.adf" does not contain /type=fde/ or /ATOMS/

I highly recommend using better variable names: "awk1" does not convey to the reader that it contains a line number.

Your quoting could be more readable: sed -n "${awk1},${awk2}p"

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