Extract data from OUTCAR to series XYZ files as GAP training set (**Bash**)
===========

requires ASE installed (**recommended**)
::

    #!/home/lipai/anaconda3/bin/python
    #!lipai@mail.ustc.edu.cn
    from ase.io import read, write
    b=read("OUTCAR",index=":")
    for i in b:
        i.info['virial']=-i.calc.results['stress']*i.get_volume()
        del i.calc.results['stress']
        i.pbc=True      # ASE parse OUTCAR, incorrectly missed the pbc=True set
        write("out.xyz",b)


or use bash
::

    #!/bin/sh
    # lipai@mail.ustc.edu.cn
    # creat xyz files using OUTCAR only
    if [ $# = 0 ]; then
            out="OUTCAR"
            name=""
    else
            out=$1
            name=$1"-"
    fi
    echo "Input filename:"  $out
    rm *.temp
    
    # total number of ions in the system
    num_atom=`grep -m 1 "NIONS =" $out|awk '{print $12}'`
    echo "Total number of ions: $num_atom"
    
    # create temp files for writing xyz files
    typenum=`grep -m 1 'ions per type' $out |head -1 |awk '{print NF}' ` 
    typenum=$(($typenum-4)) # how many types of ions
    for i in `seq $typenum`
    do
            elename=`grep -m $i POTCAR $out |tail -1 |awk '{print $3}'`
            j=$(($i+4))
            elenum=`grep -m 1 "ions per type" $out |awk -v j=$j '{print $j}'`
            echo $elename $elenum
            for j in `seq $elenum`
            do
                echo $elename  >> type.temp
            done
    done
    grep -A 3 -m 1 "direct lattice vectors" $out \
    |tail -3 |awk '{printf("%f %f %f ",$1,$2,$3)}' >primvec.temp
    grep "energy  without " $out |awk '{print $4}' >energy.temp
    awk '/POSITION/,/drift/{ if(NF==6) print $0 }' $out  > pos.temp
    
    lines=`wc pos.temp|awk '{print $1}'`
    num_str=`echo "$lines/$num_atom" |bc` # how many structures
    echo "Number of structures: $num_str"
    if [  -f all.xyz ]; then
        rm all.xyz
    fi
 
    for i in `seq $num_str`
    do
            energy=`head -n $i energy.temp|tail -1`
            echo "$num_atom" >> str_$i.xyz
            echo -n "Lattice=\"" >> str_$i.xyz
            cat primvec.temp >> str_$i.xyz
            echo -n "\" Properties=species:S:1:pos:R:3:forces:R:3 " >> str_$i.xyz
            echo  "energy=$energy pbc=\"T T T\"" >> str_$i.xyz
            end=`echo "$i*$num_atom" |bc `
            head -n $end pos.temp|tail -n $num_atom >pos_i.temp
            paste type.temp pos_i.temp >> str_$i.xyz
            mv str_$i.xyz $name$i.xyz
            cat $name$i.xyz >>all.xyz
    done
    
    #rm *.temp
    if [ ! -d "struc" ]; then
            mkdir struc
    fi
    mv *xyz struc
    mv struc/all.xyz .
    rm *.temp