/usr/share/votca/scripts/inverse/postupd_pressure.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 66 67 | #! /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 implements the pressure update
Usage: ${0##*/} infile outfile
EOF
exit 0
fi
[[ -z $1 || -z $2 ]] && die "${0##*/}: Missing arguments"
[[ -f $2 ]] && die "${0##*/}: $2 is already there"
[[ $(csg_get_interaction_property bondtype) = "thermforce" ]] && die "${0##*/}: pressure correction for thermforce makes no sense!"
step_nr="$(get_current_step_nr)"
sim_prog="$(csg_get_property cg.inverse.program)"
[[ $sim_prog != gromacs ]] && die "${0##*/}: pressure correction for ${sim_prog} is not implemented yet!"
name=$(csg_get_interaction_property name)
min=$(csg_get_interaction_property min)
max=$(csg_get_interaction_property max)
step=$(csg_get_interaction_property step)
p_file="${name}.pressure"
do_external pressure "$sim_prog" "$p_file"
p_now="$(sed -n 's/^Pressure=\(.*\)/\1/p' "$p_file")" || die "${0##*/}: sed of Pressure failed"
[[ -z $p_now ]] && die "${0##*/}: Could not get pressure from simulation"
echo "New pressure $p_now"
ptype="$(csg_get_interaction_property inverse.post_update_options.pressure.type)"
pscheme=( $(csg_get_interaction_property inverse.post_update_options.pressure.do) )
pscheme_nr=$(( ( $step_nr - 1 ) % ${#pscheme[@]} ))
if [[ ${pscheme[$pscheme_nr]} = 1 ]]; then
echo "Apply ${ptype} pressure correction for interaction ${name}"
# wjk needs rdf
if [[ ! -f ${name}.dist.new && $ptype = wjk ]]; then
do_external rdf $(csg_get_property cg.inverse.program)
fi
do_external pressure_cor $ptype $p_now ${name}.pressure_correction
comment="$(get_table_comment ${name}.pressure_correction)"
tmpfile=$(critical mktemp ${name}.pressure_correction_cut.XXX)
critical csg_resample --in ${name}.pressure_correction --out ${tmpfile} --grid $min:$step:$max --comment "$comment"
do_external table add "$1" ${tmpfile} "$2"
else
echo "NO pressure correction for interaction ${name}"
do_external postupd dummy "$1" "$2"
fi
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