/usr/share/votca/scripts/inverse/calc_rdf_generic.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 51 52 | #! /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 implemtents statistical analysis for the iterative Boltzmann inversion
using generic csg tools (csg_stat)
Usage: ${0##*/}
EOF
exit 0
fi
sim_prog="$(csg_get_property cg.inverse.program)"
if [ "$sim_prog" = "gromacs" ]; then
topol=$(csg_get_property cg.inverse.gromacs.rdf.topol "topol.tpr")
[ -f "$topol" ] || die "${0##*/}: gromacs topol file '$topol' not found"
ext=$(csg_get_property cg.inverse.gromacs.traj_type "xtc")
traj="traj.${ext}"
[ -f "$traj" ] || die "${0##*/}: gromacs traj file '$traj' not found"
else
die "${0##*/}: Simulation program '$sim_prog' not supported yet"
fi
equi_time="$(csg_get_property cg.inverse.$sim_prog.equi_time 0)"
first_frame="$(csg_get_property cg.inverse.$sim_prog.first_frame 0)"
tasks=$(get_number_tasks)
if is_done "rdf_analysis"; then
echo "rdf analysis is already done"
else
msg "Calculating rdfs with csg_stat using $tasks tasks"
critical csg_stat --nt $tasks --options "$CSGXMLFILE" --top "$topol" --trj "$traj" --begin $equi_time --first-frame $first_frame
mark_done "rdf_analysis"
fi
|