/usr/share/votca/scripts/inverse/optimizer_prepare_state.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 | #! /bin/bash
#
# Copyright 2009-2011 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 generates the initial state file and puts all in-file together
Usage: ${0##*/} outputfile
EOF
exit 0
fi
[[ -z $1 ]] && die "${0##*/}: Missing argument"
names="$(csg_get_interaction_property --all name)"
parameters="$(csg_get_interaction_property --all inverse.optimizer.parameters)"
what=$(has_duplicate "${parameters[@]}") && die "${0##*/}: the parameter $what appears twice"
otype="$(csg_get_property cg.inverse.optimizer.type)"
liste=()
for name in $names; do
input="$name.${otype}.in"
[[ -f $input ]] || die "${0##*/}: Could not find $input"
[[ -n $(sed -n '/^[#@]/p' "$input") ]] && die "${0##*/}: $input has commentlines"
liste[${#liste[@]}]="$input"
done
get_table_comment | sed 's/^/#/' > "$1"
echo "#Interactions: ${names}" >> "$1"
echo "#Method: ${otype}" >> "$1"
echo "#State = Initialization" >> $1
echo "#Format $parameters conv flag" >> "$1"
#added conv=0 and flag=pending to all lines
critical paste "${liste[@]}" | critical sed -e 's/$/ 0 pending/' >> "$1"
#cma converts initial values to first population
if [[ $otype = cma ]]; then
tmpfile="$(critical mktemp "$1.XXX")"
eps="$(csg_get_property cg.inverse.optimizer.cma.eps)"
critical mv "$1" "$tmpfile"
do_external cma precede_state --eps "$eps" "$tmpfile" "$1"
fi
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