sph

#!/usr/bin/bash

# Script for running XTB jobs with customizable options.
# Use with:
#   xtb_run [infile] [options]
#   Example: xtb_run molecule.inp -P 16 --solvent water -c 1 -u 2

usage() {
  echo "Usage: $0 [infile] [options]"
  echo
  echo "Arguments:"
  echo "  infile         The input file for the XTB job (e.g., molecule.inp)."
  echo
  echo "Options:"
  echo "  -T N           Number of processors to use (default: 6)."
  echo "  --solvent NAME Specify the solvent model (optional)."
  echo "  -c CHARGE      Specify the molecular charge (default: 0)."
  echo "  -u UNPAIRED    Specify the number of unpaired electrons (default: 0)."
  echo "  -h, --help     Show this help message."
  exit 1
}

# Default values
processors=6
solvent=""
charge=0
unpaired=0
infile=""

# Parse arguments
while [[ $# -gt 0 ]]; do
  case "$1" in
    -h|--help)
      usage
      ;;
    -T|--threads)
      processors="$2"
      shift 2
      ;;
    -s|--solvent)
      solvent="$2"
      shift 2
      ;;
    -c|--charge)
      charge="$2"
      shift 2
      ;;
    -u|--uhf)
      unpaired="$2"
      shift 2
      ;;
    *)
      if [[ -z "$infile" ]]; then
        infile="$1"
      else
        echo "ERROR: Unknown argument '$1'."
        usage
      fi
      shift
      ;;
  esac
done

# Ensure required arguments are provided
if [[ -z "$infile" ]]; then
  echo "ERROR: Missing required input file."
  usage
fi

# Set output file name
outfile="${infile%%.*}.sph"

# Construct the XTB command
xtb_cmd="xtb $infile --bhess -P $processors -c $charge -u $unpaired"

# Add the solvent option if provided
if [[ -n "$solvent" ]]; then
  xtb_cmd+=" --alpb $solvent"
fi

# echo $xtb_cmd

# Run the XTB command
$xtb_cmd > "$outfile"