/usr/share/votca/scripts/inverse/potential_to_generic.sh is in votca-csg-scripts 1.3.0-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 | #!/bin/bash
#
# Copyright 2009-2014 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.
#
if [ "$1" = "--help" ]; then
cat <<EOF
${0##*/}, version %version%
This script is a high class wrapper to convert a potential to the generic
3 column tab format used by espresso and espressopp
Usage: ${0##*/}
EOF
exit 0
fi
[[ -z $1 || -z $2 ]] && die "${0##*/}: missing argument"
input="$1"
trunc="${1%%.*}"
[[ -f $input ]] || die "${0##*/}: Could not find input file '$input'"
output="$2"
echo "Convert $input to $output"
bondtype="$(csg_get_interaction_property bondtype)"
[[ $bondtype != non-bonded ]] && die "${0##*/}: conversion of bonded interaction to generic tables is not implemented yet!"
sim_prog="$(csg_get_property cg.inverse.program)"
r_cut=$(csg_get_interaction_property max)
step=$(csg_get_interaction_property step)
r_min=$(csg_get_interaction_property min)
bin_size="$(csg_get_interaction_property --allow-empty inverse.$sim_prog.table_bins)"
[[ -z ${bin_size} ]] && bin_size="${step}"
comment="$(get_table_comment)"
table_begin="$(csg_get_interaction_property --allow-empty inverse.$sim_prog.table_begin)"
if [[ -z ${table_begin} ]]; then
table_begin="$r_min"
else
#keep the grid for now, so that extrapolate can calculate the right mean
smooth2="$(critical mktemp ${trunc}.pot.extended.XXXXX)"
critical csg_resample --in ${input} --out "${smooth2}" --grid "${table_begin}:${step}:${r_cut}" --comment "$comment"
extrapolate="$(critical mktemp ${trunc}.pot.extrapolated.XXXXX)"
do_external potential extrapolate --type "$bondtype" "${smooth2}" "${extrapolate}"
input="${extrapolate}"
fi
#enable shift whenever bonded interaction are supported here
#do_external potential shift --type "$bondtype" "${extrapolate}" "${tshift}"
smooth="$(critical mktemp ${trunc}.pot.smooth.XXXXX)"
deriv="$(critical mktemp ${trunc}.pot.deriv.XXXXX)"
critical csg_resample --in ${input} --out "${smooth}" --der "${deriv}" --grid "${table_begin}:${bin_size}:${r_cut}" --comment "$comment"
do_external convert_potential tab --header "${sim_prog}" --type "${bondtype}" "${smooth}" "${deriv}" "${output}"
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