Gaussian

com_to_xyz.sh

#!/bin/bash

for i in $(ls *com)

do

base=$(basename $i .com)

cat ${base}.com | sed '/Tv/d' | sed "/^\$/d" | sed '1,3d' > temp.xyz # Remove translational vectors and Remove empty lines

nlines=$(wc -l < temp.xyz)

echo $nlines > ${base}.xyz

echo >> ${base}.xyz

cat temp.xyz >> ${base}.xyz

done

rm temp.xyz

Generating NTOs for all transitions

Generating NTOs for all transitions

#!/bin/bash

#=======================================================================

for j in $(seq 1 12) # change the number 12 to the highest trans number

do

cp ../*.chk . # keep the original check point file in previous folder

chkfile1=$(ls *.chk)

chkfile=$(echo ${chkfile1} | sed 's/.chk//g')

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

# replace minimal with NTO for versions above G09.B

rm trans_${j}.com

cat > trans_${j}.com <<END

%chk=${chkfile}.chk

%mem=4GB

%nproc=4

# Geom=AllCheck ChkBas Guess=(Read,Only) Density=(Check,Transition=${j}) Pop=(SaveNTO,Minimal)

--link1--

%chk=${chkfile}.chk

%mem=4GB

%nproc=4

# Geom=AllCheck ChkBas Guess=(Read,Only)

END

#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

g09 trans_${j}.com

formchk ${chkfile}.chk

cubegen 0 mo=homo ${chkfile}.fchk trans_${j}_homo.cub &

cubegen 0 mo=lumo ${chkfile}.fchk trans_${j}_lumo.cub

rm ${chkfile}.fchk

done

#=======================================================================

rm *.chk