xs2rates

#!/bin/sh

PROGRAM="$(basename "$0")"
JPROGRAM="${JULIABIN}/${PROGRAM}.jl"

usage() {

    cat <<help

$PROGRAM

    Wrapper for my julia script $PROGRAM (\${JULIABIN}), which converts scattering data between
    cross sections and rate coefficients. The rate coefficient (no kinetic averaging or convolution)
    is essentially just the cross section multiplied by the collider's velocity, (2*E/m)^1/2

    usage: ${PROGRAM} [operation] [operand]

    operations:               operand:   function:

        -h                    none       show this message.
        -i,--input            file       specify input  file
        -o,--output           file       specify output file
        --input-type          string     the input data type. Should be "XS" for cross sections or "RATE" for
                                         rate coefficients
        --xs-units            string     the unit type of the cross section data   (e.g., "cm" for cm^2).
        --rate-units-l        string     the length unit of the rate coefficient data   (e.g., "cm" for cm^3/s).
        --rate-units-t        string     the time unit of the rate coefficient data   (e.g., "s" for cm^3/s).
        --nrg-units           string     the unit type of the input energy (e.g., "eV" for electron volts).
        --no-ignore-comments  none       if supplied, do not ignore lines with comment characters. This will
                                         probably break the script. If omitted, ignore comments.
        -comment_char         string     the comment character (default '#'). This must be a single character.

    The following would be a valid implementation of ${PROGRAM} :

        ${PROGRAM} -i cross_sections.dat -o rates.dat \\
                  --input-type "XS" \\
                  --xs-units cm \\
                  --rate-units-l cm \\
                  --rate-units-t s \\
                  --nrg-units eV \\
                  -comment_char "#" \\

    Input file: a file of electron energies (Eel) and cross sections (σ) or rate coefficients (α)
    in any units of energy and length^2 (σ) or length^3/s (α), formatted as

      Eel  σ/α
       .   .
       .   .
       .   .

    Output file: a conversion between σ and α in the same format

      Eel  α/σ
      .    .
      .    .
      .    .

    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    !! Needed : my units script !!
    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

      https://github.com/banana-bred/units

help
}

die() {

  exit_code=1
  error_message="$1"

  echo  1>&2
	echo "${PROGRAM}: ${error_message}" 1>&2
  echo  1>&2

  usage

  exit "${exit_code}"

}

main() {

  ignore_comments="true"
  comment_char="#"

	while :; do
		case $1 in

			-h|-\?|--help)
				usage
				exit 0
				;;

			-i | --input)
				[ "$2" ] && input="${2}" && shift || die 'ERROR: "--input" requires a non-empty option argument.'
				;;
			-i= | --input=)
				die 'ERROR: "--input" requires a non-empty argument.'
				;;
			-i=?* | --input=?*)
				input="${1#*=}"
				;;

			-o | --output)
				[ "$2" ] && output="${2}" && shift || die 'ERROR: "--output" requires a non-empty option argument.'
				;;
			-o= | --output=)
				die 'ERROR: "--output" requires a non-empty argument.'
				;;
			-o=?* | --output=?*)
				output="${1#*=}"
				;;

			--input-type)
				[ "$2" ] && input_type="${2}" && shift || die 'ERROR: "--input-type" requires a non-empty option argument.'
				;;
			--input-type=)
				die 'ERROR: "--input-type" requires a non-empty argument.'
				;;
			--input-type=?*)
				input_type="${1#*=}"
				;;

			--xs-units )
				[ "$2" ] && XS_units="${2}" && shift || die 'ERROR: "--xs-units" requires a non-empty option argument.'
				;;
			--xs-units=)
				die 'ERROR: "--xs-units" requires a non-empty argument.'
				;;
			--xs-units=?*)
				XS_units="${1#*=}"
				;;

			--rate-units-l )
				[ "$2" ] && RATE_units_l="${2}" && shift || die 'ERROR: "--rate-units-l" requires a non-empty option argument.'
				;;
			--rate-units=)
				die 'ERROR: "--rate-units-l" requires a non-empty argument.'
				;;
			--rate-units=?*)
				RATE_units_l="${1#*=}"
				;;

			--rate-units-t )
				[ "$2" ] && RATE_units_t="${2}" && shift || die 'ERROR: "--rate-units-t" requires a non-empty option argument.'
				;;
			--rate-units=)
				die 'ERROR: "--rate-units-t" requires a non-empty argument.'
				;;
			--rate-units=?*)
				RATE_units_t="${1#*=}"
				;;

			--nrg-units )
				[ "$2" ] && nrg_units="${2}" && shift || die 'ERROR: "--nrg-units" requires a non-empty option argument.'
				;;
			--nrg-units=)
				die 'ERROR: "--nrg-units" requires a non-empty argument.'
				;;
			--nrg-units=?*)
				nrg_units="${1#*=}"
				;;

      --no-ignore-comments)
        ignore_comments="false"
        ;;

			-comment_char)
				[ "$2" ] && comment_char="${2}" && shift || die 'ERROR: "-comment_char" requires a non-empty option argument.'
				;;
			-comment_char=)
				die 'ERROR: "-comment_char" requires a non-empty argument.'
				;;
			-comment_char=?*)
				comment_char="${1#*=}"
				;;

			--)
				shift
				break
				;;

			-?*)
				printf 'WARN: Unknown option (ignored): %s\n' "${1}"
				;;

      *)
        break
        ;;

			esac
			shift

	done

  flag=false
  [ -z "${input}" ] && echo "Need an input file with -i" 1>&2 && flag=true
  [ -e "${input}" ] || (echo "Input file""'""$input""'"" does not exist" 1>&2 && flag=true)
  [ -z "${output}" ] && echo "Need an output file with -o" 1>&2 && flag=true
  [ -z "${XS_units}" ] && echo "Need to define input cross section units with --xs-units" 1>&2 && flag=true
  [ -z "${RATE_units_l}" ] && echo "Need to define rate coefficient length units with --rate-units-l" 1>&2 && flag=true
  [ -z "${RATE_units_t}" ] && echo "Need to define rate coefficient time units with --rate-units-t" 1>&2 && flag=true
  [ -z "${nrg_units}" ] && echo "Need to define input electron energy units with --nrg-units" 1>&2 && flag=true
  $flag && die "Variable(s) not defined. See above ^^^"

  # -- get mulitiplicative constants to convert data to the expected units
  xsConversion="$(units 1 "$XS_units" bohr)"
  rateLengthConversion="$(units 1 "$RATE_units_l" bohr)"
  rateTimeConversion="$(units 1 "$RATE_units_t" s)"
  nrgConversion="$(units 1 "$nrg_units" hartree)"

  julia "$JPROGRAM" "$input" "$output" "$xsConversion" "$rateLengthConversion" "$rateTimeConversion" "$nrgConversion" "$comment_char" "$ignore_comments" "$input_type"

}

main "$@"