source: util/CreateFromXYZ.sh@ a0bcf1

#!/bin/sh

if [ -z "$2" ]; then
        echo "Usage: $0 <xyzfile> <path-to-target>"
        exit 1
fi

mol="${1}.xyz"
#pfad="${2}/`basename ${1}`"
pfad="$2"
molecuilder="/home/heber/workspace/pcp_alternate/bin/"
pseudopot="/home/heber/workspace/pcp_alternate/defaults/pseudopot"

echo "Target dir is ${pfad}, using xyz file ${mol}."

# Create path
mkdir -p "${pfad}"

number=`wc $mol | awk -F' ' {'print $1-2'}`
MOL=( `tail $mol -n $number | awk -F" " {'print $1'}` )
X=( `tail $mol -n $number | awk -F" " {'print $2'}` )
Y=( `tail $mol -n $number | awk -F" " {'print $3'}` )
Z=( `tail $mol -n $number | awk -F" " {'print $4'}` )

cd $molecuilder
./molecuilder "${pfad}/main_pcp_linux" -p ${pfad}/${mol} 2>/dev/null

echo "Scaling by 1.8897261 ..."
./molecuilder "${pfad}/main_pcp_linux" -s 1.8897261

echo "Translating within boundary box (5.,5.,5.) ..."
./molecuilder "${pfad}/main_pcp_linux" -g 5. 5. 0.

echo "changing path"
sed -i -e "s#defaultpath.*\# \(.*\)#defaultpath\t${pfad}/\t\# \1#" -e "s#pseudopotpath.*\# \(.*\)#pseudopotpath\t${pseudopot}/\t\# \1#" "${pfad}/main_pcp_linux"

echo -n "Creating list of elements ... "
elements=( `more "${pfad}/main_pcp_linux" | grep -v ^# | grep -v 'Ion_Type.*_.*' | grep Ion_Type | awk -F"\t" {'print $3'}` )
factors=( `more "${pfad}/main_pcp_linux" | grep -v ^# | grep -v 'Ion_Type.*_.*' | grep Ion_Type | awk -F"\t" {'print $2'}` )
maxtypes=`more "${pfad}/main_pcp_linux" | grep MaxTypes | awk -F"\t" {'print $2'}`
echo "done."

echo -n "Calculating number of orbitals needed ..."
orbitals=0
i=0
while [ "$i" -lt "$maxtypes" ]; do      
        #echo "Checking on element ${elements[$i]}"
        if [ "${elements[$i]}" -lt "10" ]; then
                zahl=`head -n 1 $pseudopot/pseudo.0${elements[$i]} | awk -F" " {'print $1'}`
                zahl=`awk "BEGIN { print $zahl; }"`
        else
                zahl=`head -n 1 $pseudopot/pseudo.${elements[$i]} | awk -F" " {'print $1'}`
                zahl=`awk "BEGIN { print $zahl; }"`
        fi
        let zahl="$zahl*${factors[$i]}"
        let orbitals="$orbitals+$zahl"
        let i=$i+1
done 
orbitalrest=`awk "BEGIN { print $orbitals % 2; }"`
orbitals=`awk "BEGIN { print $orbitals / 2; }"`
echo "done."
echo "Suggested SpinType: $orbitalrest"

echo -n " changing ..."
if [ "$orbitalrest" == "0" ]; then
        # even number: calculate with doubly occupied
        sed -i -e "s#^PsiType\t\t.*#PsiType\t\t0#" "${pfad}/main_pcp_linux"
else
        # odd number: calculate with single occupation (at least two Psi processes needed)
        sed -i -e "s#^PsiType\t\t.*#PsiType\t\t1#" "${pfad}/main_pcp_linux"
        sed -i -e "s#^ProcPEPsi\t\t.*#ProcPEPsi\t\t2#" "${pfad}/main_pcp_linux"
fi
sed -i -e "s#^PsiMaxNoDown\t.*#PsiMaxNoDown\t$orbitals#" "${pfad}/main_pcp_linux"
sed -i -e "s#^MaxPsiDouble\t.*#MaxPsiDouble\t$orbitals#" "${pfad}/main_pcp_linux"
sed -i -e "s#^MaxMinStopStep\t.*#MaxMinStopStep\t$orbitals#" "${pfad}/main_pcp_linux"
sed -i -e "s#^InitMaxMinStopStep\t.*#InitMaxMinStopStep\t$orbitals#" "${pfad}/main_pcp_linux"
# add odd rest upon SpinUp state number
let orbitals=$orbitals+$orbitalrest
sed -i -e "s#^PsiMaxNoUp\t.*#PsiMaxNoUp\t$orbitals#" "${pfad}/main_pcp_linux"

echo "done."