source: utils/Python/generate_bondtable.sh.in@ 802a9d

#!/usr/bin/env bash
#
# Generates a bond table file by using the python script compute_pair_bondlength.py
# on a given pair of elements

# get options
test ! -z "$3" || { echo "Usage: $0 -H <server address> -p <server port> -o <bond table file> [-b <basis set>]"; exit 255; }

POSITIONAL_ARGS=()

while [[ $# -gt 0 ]]; do
  case $1 in
    -H|--server-address)
      SERVER_ADDRESS="$2"
      shift # past argument
      shift # past value
      ;;
    -p|--server-port)
      SERVER_PORT="$2"
      shift # past argument
      shift # past value
      ;;
    -o|--output-file)
      BONDTABLEFILE="$2"
      shift # past argument
      shift # past value
      ;;
    -b|--basis-set)
      BASISSET_CMD="$2"
      shift # past argument
      shift # past value
      ;;
    --default)
      DEFAULT=YES
      shift # past argument
      ;;
    -*|--*)
      echo "Unknown option $1"
      exit 1
      ;;
    *)
      POSITIONAL_ARGS+=("$1") # save positional arg
      shift # past argument
      ;;
  esac
done

# default values for command-line options
BASISSET="${BASISSET_CMD:-6-31G}"

# constants
DIR=`dirname $0`
PREFIX="bondtable-$(date "+%Y-%m-%d_%H-%M-%S").csv"
JOBS="8"
FOLDER="computation"

# state options
echo "Using server at $SERVER_ADDRESS:$SERVER_PORT."
echo "Using $BASISSET as basis set."
echo "Output bond table to $BONDTABLEFILE."

# array of elements: without noble gases (and metals that take longer to compute)
elements=("H" "Li" "Be" "B" "C" "N" "O" "F" "Na" "Mg" "Al" "Si" "P" "S" "Cl" "K" "Ca")

### generate pairs and fill string
element_pairs=""
for ((i=0;i<${#elements[*]};i++)); do
    elem1="${elements[$i]}"
    for ((j=i;j<${#elements[*]};j++)); do
        elem2="${elements[$j]}"
        if test -z "$element_pairs"; then
            element_pairs="$elem1\n$elem2"
        else
            element_pairs="${element_pairs}\n$elem1\n$elem2"
        fi
    done
done

### go through all ordered pairs using gnu parallel
echo -e $element_pairs | \
parallel \
    -P $JOBS \
    --nice 10 \
    -N 2 \
    --silent \
    --results "$FOLDER" \
    ./"$DIR"/compute_pair_bondlength \
        --server-address "$SERVER_ADDRESS" \
        --server-port "$SERVER_PORT" \
        --output-prefix "$PREFIX" \
        --basis-set "$BASISSET" \
        --elements {} >/dev/null

### analyse distances from log files and create bond table file
rm -f "$BONDTABLEFILE"
for ((i=0;i<${#elements[*]};i++)); do
  echo -n -e "\t\"${elements[$i]}\"" >>"$BONDTABLEFILE"
done
echo -e -n "\n" >>"$BONDTABLEFILE"
for ((i=0;i<${#elements[*]};i++)); do
    elem1="${elements[$i]}"
    echo -n -e "\"$elem1\"" >>"$BONDTABLEFILE"
    for ((j=0;j<${#elements[*]};j++)); do
        elem2="${elements[$j]}"
        LOGFILENAME="$FOLDER/1/$elem1/1/$elem2/stdout"
        if test ! -f "$LOGFILENAME"; then
          LOGFILENAME="$FOLDER/1/$elem2/1/$elem1/stdout"
        fi
        distance=$(grep "DISTANCE:" "$LOGFILENAME" | sed -e "s#DISTANCE:\s*[A-Za-z]\+\s\+[A-Za-z]\+:\s*\(.*\)#\1#" | awk '{print int($1*100)/100}')
        if test $? != 0; then
          distance="-1"
        fi
        echo -e -n "\t$distance" >>"$BONDTABLEFILE"
    done
    echo -e -n "\n" >>"$BONDTABLEFILE"
done