#script written by JMB 2014
#This script calls Kirkland’s atompot and stemslic programs after first generating the input files.
#Please refer to the book “Advanced Computing in Electron Microscopy” by Earl J. Kirkland for line by line description.
#The script generates a frozen phonon using atom positions described by posgenu.rand and posgend.rand, which are an array of numbers to describe the beta to omega collapse.
#The script needs to renamed as *.sh and run in a shell environment


	touch Readfile.temp
	echo $1'(abcdefghijklmnopqrstuvwxyz)' >> Readfile.temp     


        for i in `seq 1 13`; 
        do
Num1=$(shuf -i 0-1000 -n 1)
Num2=$(shuf -i 0-1000 -n 1)
Num3=$(shuf -i 0-1000 -n 1)
Num4=$(shuf -i 0-1000 -n 1)

	touch $i'A'.dat 
        echo '7.985  2.82  2.305' >> $i'A'.dat
	echo '0' >> $i'A'.dat
	echo '22' >> $i'A'.dat
  	echo '1.0000  0.0000  0.0000' >> $i'A'.dat
	echo '1.0000  0.3333  0.'$(sed -n ''$Num1'p' posgenu.rand) >> $i'A'.dat
	echo '1.0000  0.6667  0.'$(sed -n ''$Num2'p' posgend.rand) >> $i'A'.dat
	echo ''>> $i'A'.dat
	echo ''>> $i'A'.dat
	echo 'space'>> $i'A'.dat
	touch $i'A'.txt
	echo $i'A'.dat >> $i'A'.txt 
	echo $i'A_pot.tif' >> $i'A'.txt
	echo $i'A_pot.tif' >> Readfile.temp
	echo '512 512' >> $i'A'.txt
	echo '4 12 1' >> $i'A'.txt
	echo 'n' >> $i'A'.txt


	touch $i'B'.dat 
        echo '7.985  2.82  2.305' >> $i'B'.dat
	echo '0' >> $i'B'.dat
	echo '22' >> $i'B'.dat
  	echo '1.0000  0.1667  0.'$(sed -n ''$Num3'p' posgend.rand) >> $i'B'.dat
	echo '1.0000  0.5000  0.0000' >> $i'B'.dat
	echo '1.0000  0.8333  0.'$(sed -n ''$Num4'p' posgenu.rand) >> $i'B'.dat	
	echo ''>> $i'B'.dat
	echo ''>> $i'B'.dat
	echo 'space'>> $i'B'.dat
	touch $i'B'.txt
	echo $i'B'.dat >> $i'B'.txt 
	echo $i'B_pot'.tif >> $i'B'.txt
	echo $i'B_pot.tif' >> Readfile.temp
	echo '512 512' >> $i'B'.txt
	echo '4 12 1' >> $i'B'.txt
	echo 'n' >> $i'B'.txt

        done  

#Read file continue

	echo '300 0 10 0 0 19.5' >> Readfile.temp
	echo '0 0' >> Readfile.temp
	echo '0 0' >> Readfile.temp
	echo '512 542' >> Readfile.temp
	echo '0 0' >> Readfile.temp
	echo 'n' >> Readfile.temp
	echo '1' >> Readfile.temp
	echo '53 318' >> Readfile.temp
	echo 'Out.tif' >> Readfile.temp
	echo '0 30 0 32 512 512' >> Readfile.temp

#Run atompot

for f in $(ls *.txt)
do
cat $f | ./../atompot while read line
echo "$line"
done



#Run stemslic

cat Readfile.temp | ./../stemslic while read line; do
echo "$line";

#Finish
echo 'End'
eog Out.tif