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#!/usr/bin/env bash
#
# Copyright 2009-2020 The VOTCA Development Team (http://www.votca.org)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
show_help () {
cat <<EOF
${0##*/}, version %version%
This script extrapolates a potential in the correct way depending on its type.
Usage: ${0##*/} [options] input output
Allowed options:
--help show this help
--clean remove all intermediate temp files
--type TYPE type of the potential
possible: ${pot_types}
--lfct FCT type of the left extrapolation function
possible: ${fct_type}
default: exponential(non-bonded), linear (bonded)
--rfct FCT type of the right extrapolation function
possible: ${fct_types}
default: constant(non-bonded), periodic(dihedral), linear (bonded)
--avg-points INT number of average points
default: $avg_points
EOF
}
clean="no"
lfct=
rfct=
fct_types="constant linear quadratic exponential sasha"
pot_type=
pot_types="non-bonded bond angle dihedral"
avg_points=3
### begin parsing options
shopt -s extglob
while [[ ${1} = --* ]]; do
case $1 in
--clean)
clean="yes"
shift ;;
--type)
pot_type="$2"
shift 2;;
--[rl]fct)
is_part "${2}" "${fct_types}" || die "${0##*/}: given function type ($2) is not in the list of functions (${fct_types})"
eval "${1#--}"="$2"
shift 2;;
--avg-points)
avg_points="$2";
is_int "$2" || die "${0##*/}: argument of --avg-point should be int"
shift 2;;
--help)
show_help
exit 0;;
*)
die "Unknown option '$1'";;
esac
done
### end parsing options
[[ -z $pot_type ]] && die "${0##*/}: please specify add potential type (--type options) from: ${pot_types}"
is_part "${pot_type}" "${pot_types}" || die "${0##*/}: given potential type($pot_type) is not in the list of types (${pot_types})"
[[ -z $1 || -z $2 ]] && die "${0##*/}: Missing arguments"
input="$1"
[[ -f $input ]] || die "${0##*/}: Could not find input file '$input'"
output="$2"
echo "Extrapolate $input to $output"
intermediate="$(critical mktemp "${input}.onlyleft.XXXXX")"
if [[ $pot_type = "non-bonded" ]]; then
do_external table extrapolate --function "${lfct:-exponential}" --avgpoints "$avg_points" --region left "${input}" "${intermediate}"
do_external table extrapolate --function "${rfct:-constant}" --avgpoints 1 --region right "${intermediate}" "${output}"
elif [[ $pot_type = "bond" || $pot_type = "angle" ]]; then
do_external table extrapolate --function "${lfct:-linear}" --avgpoints "$avg_points" --region left "${input}" "${intermediate}"
do_external table extrapolate --function "${rfct:-linear}" --avgpoints "$avg_points" --region right "${intermediate}" "${output}"
elif [[ $pot_type = "dihedral" ]]; then
do_external table extrapolate --function "${lfct:-linear}" --avgpoints "$avg_points" --region left "${input}" "${intermediate}"
do_external table extrapolate --function "${rfct:-periodic}" --avgpoints "$avg_points" --region right "${intermediate}" "${output}"
else
die "${0##*/}: I don't know how to extraploate potential type '$pot_type', go and implement it!"
fi
if [[ $clean = "yes" ]]; then
rm -f "${intermediate}"
fi
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