/usr/share/votca/scripts/inverse/update_tf_single.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 68 69 70 | #! /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 the function update of a single interaction
for the thermodynamics force iteration
Usage: ${0##*/}
EOF
exit 0
fi
step_nr=$(get_current_step_nr)
scheme=( $(csg_get_interaction_property inverse.do_potential) )
scheme_nr=$(( ($step_nr - 1 ) % ${#scheme[@]} ))
name=$(csg_get_interaction_property name)
sim_prog="$(csg_get_property cg.inverse.program)"
mol="$(csg_get_interaction_property inverse.tf.molname)"
if [[ $sim_prog = gromacs ]]; then
adress_type=$(get_simulation_setting adress_type)
else
adress_type=$(csg_get_property cg.inverse.tf.adress_type)
fi
step=$(csg_get_interaction_property step)
opts=()
if [[ $adress_type = "sphere" ]]; then
echo "Adress type: $adress_type"
max=$(csg_get_interaction_property inverse.tf.spline_end)
if [[ $sim_prog = gromacs ]]; then
adressc="$(get_simulation_setting adress_reference_coords "0 0 0")"
else
adressc=$(csg_get_property cg.inverse.tf.adress_reference_coords)
fi
ref="$(echo "$adressc" | awk '{if (NF<3) exit 1; printf "[%s,%s,%s]",$1,$2,$3;}')" || die "${0##*/}: we need three numbers in adress_reference_coords, but got '$adressc'"
axis="r"
opts=( "--rmax" "$max" "--ref" "$ref" )
else
echo "Adress type: $adress_type"
axis="x"
fi
opts=( "${opts[@]}" "--molname" "$mol" "--axis" "$axis" "--step" "$step" )
do_external density $sim_prog "$name.dist.new" "${opts[@]}"
if [ "${scheme[$scheme_nr]}" = 1 ]; then
echo "Update tf ${name} : yes"
do_external calc thermforce ${name}.dist.new ${name}.dpot.new
else
echo "Update tf ${name} : no"
min=$(csg_get_interaction_property min)
step=$(csg_get_interaction_property step)
max=$(csg_get_interaction_property max)
do_external table dummy ${min}:${step}:${max} ${name}.dpot.new
fi
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