Freq 2.s: Difference between revisions
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# Uso: freq_2.s OUTCAR | # Uso: freq_2.s OUTCAR | ||
# | # | ||
file=$1 | file=$1 | ||
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done | done | ||
echo [FR-NORM-COORD] >> MOLCAR | |||
for i in $(seq 1 $num_freq); do | |||
echo vibration $i >> MOLCAR | echo vibration $i >> MOLCAR | ||
cap=1 | cap=1 | ||
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done | done | ||
done | |||
molden MOLCAR | molden MOLCAR | ||
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done | done | ||
echo [FR-NORM-COORD] >> MOLCAR | |||
for i in $(seq 1 $num_freq); do | |||
echo vibration $i >> MOLCAR | echo vibration $i >> MOLCAR | ||
cap=1 | cap=1 | ||
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echo $dX $dY $dZ >> MOLCAR | echo $dX $dY $dZ >> MOLCAR | ||
done | |||
done | |||
molden MOLCAR | molden MOLCAR | ||
#rm MOLCAR | #rm MOLCAR | ||
Revision as of 14:22, 14 May 2010
go back to Main Page, Computational Resources, Scripts, Useful scripts
Execute this script (freq.s OUTCAR) will generate a file called MOLCAR. This file is legible for MOLDEN, and includes all the vibrations.
# # Gerard Novell Leruth # Conversion archivos OUTCAR de frecuencias VASP 4.6 a molden format con duplicación de celda en XY # Uso: freq_2.s OUTCAR #
file=$1
echo [MOLDEN FORMAT] > MOLCAR
echo [FREQ] >> MOLCAR
declare -a typ_freq declare -a list_freq declare -a num_ions_type
num_freq=$(grep cm-1 $file | awk '{print $1}' | tail -1) list_freq=($(grep cm-1 $file | cut -b 10- | awk '{print $5}' | tail -$num_freq)) typ_freq=($(grep cm-1 $file | awk '{print $2}' ))
let k=$num_freq-1 for i in $(seq 0 $k); do
if [[ ${typ_freq[$i]} = "f/i=" ]];then
list_freq[$i]=-${list_freq[$i]}
fi
echo ${list_freq[$i]} >> MOLCAR
done
num_ions_type=($(grep "ions per type" $file | cut -b 20- )) let j=$(grep -c POTCAR $file)/2 for i in $(seq 1 $j); do
let k=$i-1
ions_type[$k]=$(grep POTCAR $file | awk '{print $3}' | head -$i | tail -1 )
done num_ions=$(grep IONS $file | awk '{print $12}')
echo [FR-COORD] >> MOLCAR
let k=$num_ions
p=0
j=${num_ions_type[$p]}
cap=0
for i in $(seq 1 $k); do
atom=${ions_type[$p]}
if $j = $i && $j != $k ; then
let p=$p+1
let j=$j+${num_ions_type[$p]}
fi
let cap=$i+1
b=1.88973
X=$(echo "sacale=5; $(grep -$cap cm-1 $file | tail -1 | awk '{print $1}')*$b " | bc)
Y=$(echo "sacale=5; $(grep -$cap cm-1 $file | tail -1 | awk '{print $2}')*$b " | bc)
Z=$(echo "sacale=5; $(grep -$cap cm-1 $file | tail -1 | awk '{print $3}')*$b " | bc)
echo $atom $X $Y $Z >> MOLCAR
Vx=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -3 | head -1 |awk '{print $1}')*$b " | bc)
X1=$(echo "sacale=5; $X+$Vx " | bc)
Vy=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -3 | head -1 |awk '{print $2}')*$b " | bc)
Y1=$(echo "sacale=5; $Y+$Vy " | bc)
Vz=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -3 | head -1 |awk '{print $3}')*$b " | bc)
Z1=$(echo "sacale=5; $Z+$Vz " | bc)
echo $atom $X1 $Y1 $Z1 >> MOLCAR
Vxx=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -2 | head -1 |awk '{print $1}')*$b " | bc)
X1=$(echo "sacale=5; $X+$Vxx " | bc)
Vyy=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -2 | head -1 |awk '{print $2}')*$b " | bc)
Y1=$(echo "sacale=5; $Y+$Vyy " | bc)
Vzz=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -2 | head -1 |awk '{print $3}')*$b " | bc)
Z1=$(echo "sacale=5; $Z+$Vzz " | bc)
echo $atom $X1 $Y1 $Z1 >> MOLCAR
X1=$(echo "sacale=5; $X+$Vx+$Vxx " | bc)
Y1=$(echo "sacale=5; $Y+$Vy+$Vyy " | bc)
Z1=$(echo "sacale=5; $Z+$Vz+$Vzz " | bc)
echo $atom $X1 $Y1 $Z1 >> MOLCAR
done
echo [FR-NORM-COORD] >> MOLCAR
for i in $(seq 1 $num_freq); do
echo vibration $i >> MOLCAR
cap=1
txt=$i" f"
for t in $(seq 1 $num_ions); do
let cap=$cap+1
b=1
dX=$(echo "sacale=5; $(grep -$cap "$txt" $file | tail -1 | awk '{print $4}')*$b " | bc)
dY=$(echo "sacale=5; $(grep -$cap "$txt" $file | tail -1 | awk '{print $5}')*$b " | bc)
dZ=$(echo "sacale=5; $(grep -$cap "$txt" $file | tail -1 | awk '{print $6}')*$b " | bc)
echo $dX $dY $dZ >> MOLCAR
echo $dX $dY $dZ >> MOLCAR
echo $dX $dY $dZ >> MOLCAR
echo $dX $dY $dZ >> MOLCAR
done
done
molden MOLCAR
- rm MOLCARfile=$1
echo [MOLDEN FORMAT] > MOLCAR echo [FREQ] >> MOLCAR
declare -a typ_freq declare -a list_freq declare -a num_ions_type
num_freq=$(grep cm-1 $file | awk '{print $1}' | tail -1) list_freq=($(grep cm-1 $file | cut -b 10- | awk '{print $5}' | tail -$num_freq)) typ_freq=($(grep cm-1 $file | awk '{print $2}' ))
let k=$num_freq-1 for i in $(seq 0 $k); do
if [[ ${typ_freq[$i]} = "f/i=" ]];then
list_freq[$i]=-${list_freq[$i]}
fi
echo ${list_freq[$i]} >> MOLCAR
done
num_ions_type=($(grep "ions per type" $file | cut -b 20- )) let j=$(grep -c POTCAR $file)/2 for i in $(seq 1 $j); do
let k=$i-1
ions_type[$k]=$(grep POTCAR $file | awk '{print $3}' | head -$i | tail -1 )
done num_ions=$(grep IONS $file | awk '{print $12}')
echo [FR-COORD] >> MOLCAR
let k=$num_ions
p=0
j=${num_ions_type[$p]}
cap=0
for i in $(seq 1 $k); do
atom=${ions_type[$p]}
if $j = $i && $j != $k ; then
let p=$p+1
let j=$j+${num_ions_type[$p]}
fi
let cap=$i+1
b=1.88973
X=$(echo "sacale=5; $(grep -$cap cm-1 $file | tail -1 | awk '{print $1}')*$b " | bc)
Y=$(echo "sacale=5; $(grep -$cap cm-1 $file | tail -1 | awk '{print $2}')*$b " | bc)
Z=$(echo "sacale=5; $(grep -$cap cm-1 $file | tail -1 | awk '{print $3}')*$b " | bc)
echo $atom $X $Y $Z >> MOLCAR
Vx=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -3 | head -1 |awk '{print $1}')*$b " | bc)
X1=$(echo "sacale=5; $X+$Vx " | bc)
Vy=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -3 | head -1 |awk '{print $2}')*$b " | bc)
Y1=$(echo "sacale=5; $Y+$Vy " | bc)
Vz=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -3 | head -1 |awk '{print $3}')*$b " | bc)
Z1=$(echo "sacale=5; $Z+$Vz " | bc)
echo $atom $X1 $Y1 $Z1 >> MOLCAR
Vxx=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -2 | head -1 |awk '{print $1}')*$b " | bc)
X1=$(echo "sacale=5; $X+$Vxx " | bc)
Vyy=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -2 | head -1 |awk '{print $2}')*$b " | bc)
Y1=$(echo "sacale=5; $Y+$Vyy " | bc)
Vzz=$(echo "sacale=5; $(grep "direct lattice" $file -3 | tail -2 | head -1 |awk '{print $3}')*$b " | bc)
Z1=$(echo "sacale=5; $Z+$Vzz " | bc)
echo $atom $X1 $Y1 $Z1 >> MOLCAR
X1=$(echo "sacale=5; $X+$Vx+$Vxx " | bc)
Y1=$(echo "sacale=5; $Y+$Vy+$Vyy " | bc)
Z1=$(echo "sacale=5; $Z+$Vz+$Vzz " | bc)
echo $atom $X1 $Y1 $Z1 >> MOLCAR
done
echo [FR-NORM-COORD] >> MOLCAR
for i in $(seq 1 $num_freq); do
echo vibration $i >> MOLCAR
cap=1
txt=$i" f"
for t in $(seq 1 $num_ions); do
let cap=$cap+1
b=1
dX=$(echo "sacale=5; $(grep -$cap "$txt" $file | tail -1 | awk '{print $4}')*$b " | bc)
dY=$(echo "sacale=5; $(grep -$cap "$txt" $file | tail -1 | awk '{print $5}')*$b " | bc)
dZ=$(echo "sacale=5; $(grep -$cap "$txt" $file | tail -1 | awk '{print $6}')*$b " | bc)
echo $dX $dY $dZ >> MOLCAR
echo $dX $dY $dZ >> MOLCAR
echo $dX $dY $dZ >> MOLCAR
echo $dX $dY $dZ >> MOLCAR
done done
molden MOLCAR
- rm MOLCAR