/usr/share/votca/scripts/inverse/calc_pressure_gromacs.sh is in votca-csg-scripts 1.2.4-1.
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 | #! /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 calcs the pressure for gromacs and writes it to outfile
Usage: ${0##*/} outfile
Used external packages: gromacs
EOF
exit 0
fi
[[ -z $1 ]] && die "${0##*/}: Missing argument"
tpr="$(csg_get_property cg.inverse.gromacs.g_energy.topol "topol.tpr")"
[[ -f $tpr ]] || die "${0##*/}: Gromacs tpr file '$tpr' not found"
g_energy="$(csg_get_property cg.inverse.gromacs.g_energy.bin "g_energy")"
[[ -n "$(type -p ${g_energy})" ]] || die "${0##*/}: g_energy binary '$g_energy' not found"
opts="$(csg_get_property --allow-empty cg.inverse.gromacs.g_energy.opts)"
begin="$(calc_begin_time)"
echo "Running ${g_energy}"
output=$(echo Pressure | critical ${g_energy} -b "${begin}" -s "${tpr}" ${opts})
echo "$output"
#the number pattern '-\?[0-9][^[:space:]]*[0-9]' is ugly, but it supports X X.X X.Xe+X Xe-X and so on
p_now=$(echo "$output" | sed -n 's/^Pressure[^-0-9]*\(-\?[0-9][^[:space:]]*[0-9]\)[[:space:]].*$/\1/p' ) || \
die "${0##*/}: awk failed"
[[ -z $p_now ]] && die "${0##*/}: Could not get pressure from simulation"
echo "Pressure=${p_now}" > "$1"
|