plotoptics

#! /bin/bash

# Get system name
NAME=$(NAME= cat vasprun.xml | grep SYSTEM | tail -1 | sed -e 's,.*>\([^<]*\)</.*,\1,g')
mkdir $NAME
cp vasprun.xml $NAME/vasprun.xml
cd $NAME  

#exctract dielectric functions from vasprun.xml
#this portion of code taken from http://cms.mpi.univie.ac.at/wiki/index.php/Dielectric_properties_of_SiC

awk 'BEGIN{i=1} /imag/,\
                /\/imag/ \
                 {a[i]=$2 ; b[i]=$3 ; i=i+1} \
     END{for (j=12;j<i-3;j++) print a[j],b[j]}' vasprun.xml > imag.dat

awk 'BEGIN{i=1} /real/,\
                /\/real/ \
                 {a[i]=$2 ; b[i]=$3 ; i=i+1} \
     END{for (j=12;j<i-3;j++) print a[j],b[j]}' vasprun.xml > real.dat

cat >plotfile<<!
# set term postscript enhanced eps colour lw 2 "Helvetica" 20
# set output "optics.eps"
plot [0:25] "imag.dat" using (\$1):(\$2) w lp, "real.dat" using (\$1):(\$2) w lp
!

usage="$(basename "$0") [-h] [-a] [-t] [-l] [-e] [-r] [-x] -- program to calculate optical properties of solids

where:
    -h  show this help text
    -a	make all plots
    -t	tauc plot
    -l	absorption plotted versus lambda
    -e	absorption plotted versus energy[eV]
    -r  reflection versus energy and lambda
    -x  loss function v. energy and lambda

notes:
    all plots are saved to .png format
    all data are saved to .dat format"

while getopts hatlerx option; do
  case "$option" in
    h) echo "$usage"
       exit
       ;;
    a) Rscript ../plot.R
       Rscript ../plot_lambda.R
       Rscript ../plot_tauc.R
       Rscript ../plot_reflection.R
       Rscript ../plot_loss.R
       exit 1
       ;;
    t) Rscript ../plot_tauc.R
       exit 1
       ;;
    l) Rscript ../plot_lambda.R
       exit 1
       ;;
    e) Rscript ../plot.R 
       exit 1
       ;;
    r) Rscript ../plot_reflection.R
       exit 1
       ;;
    x) Rscript ../plot_loss.R
       exit 1
       ;;
   \?) printf "illegal option: -%s\n" "$OPTARG" >&2
       echo "$usage" >&2
       exit 1
       ;;
  esac
done
shift $((OPTIND - 1))