/usr/share/votca/scripts/inverse/postupd_kbibi_correction.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 71 72 73 74 75 76 77 78 79 80 81 | #! /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 post update routine for
the various Kirkwood-Buff corrections
Usage: ${0##*/}
EOF
exit 0
fi
step_nr=$(get_current_step_nr)
name=$(csg_get_interaction_property name)
min=$(csg_get_interaction_property min)
max=$(csg_get_interaction_property max)
step=$(csg_get_interaction_property step)
[[ $(csg_get_interaction_property bondtype) = "non-bonded" ]] || die "${0##*/}: kbibi correction only makes sense for non-bonded interactions!"
# always calculate the kbint as there could be cross interaction changes
# needs current rdf and target rdf
if [[ ! -f ${name}.dist.new ]]; then
do_external rdf $(csg_get_property cg.inverse.program)
fi
if [[ ! -f ${name}.dist.tgt ]]; then
do_external resample target "$(csg_get_interaction_property inverse.target)" "${name}.dist.tgt"
fi
do_external calc kbint ${name}.dist.tgt ${name}.kbint.tgt
if [[ $(csg_get_interaction_property inverse.post_update_options.kbibi.kbint_with_errors) = "yes" ]]; then
sim_prog="$(csg_get_property cg.inverse.program)"
rdf_with_errors=$(csg_get_property cg.inverse.$sim_prog.rdf.with_errors)
[[ ${rdf_with_errors} != "yes" ]] && die "${0##*/}: kb integrals with errors need cg.inverse.${sim_prog}.rdf.with_errors to be yes"
for f in ${name}_*.dist.block; do
[[ -f $f ]] || die "${0##*/}: rdf block (${name}_*.dist.block) files not found"
do_external calc kbint ${f} ${f%.dist.block}.kbint.block
done
do_external table average --output ${name}.kbint.new ${name}_*.kbint.block
else
do_external calc kbint ${name}.dist.new ${name}.kbint.new
fi
kbibi=( $(csg_get_interaction_property inverse.post_update_options.kbibi.do) )
kbibi_nr=$(( ($step_nr - 1 ) % ${#kbibi[@]} ))
if [[ ${kbibi[$kbibi_nr]} = 1 ]]; then
echo "Apply kbibi correction for interaction ${name}"
kbibi_type="$(csg_get_interaction_property inverse.post_update_options.kbibi.type)"
tmpfile=$(critical mktemp ${name}.kbibi.XXX)
if [[ ${kbibi_type} = "ramp" ]]; then
do_external kbibi ramp_correction "${name}.kbint.tgt" "${name}.kbint.new" "${tmpfile}"
elif [[ ${kbibi_type} = "integral" ]]; then
do_external table integrate --sphere --from left "${name}.dist.tgt" "${name}.dist.tgt.int"
do_external table integrate --sphere --from left "${name}.dist.new" "${name}.dist.new.int"
do_external update ibi_pot "${name}.dist.tgt.int" "${name}.dist.new.int" "${name}.pot.cur" "${tmpfile}"
else
die "${0##*/}: kbibi type $kbibi_type not implemented yet"
fi
comment="$(get_table_comment ${tmpfile})"
tmpfile2=$(critical mktemp ${name}.kbibi.resample.XXX)
critical csg_resample --in "${tmpfile}" --out "${tmpfile2}" --grid $min:$step:$max --comment "$comment"
do_external table add "$1" "${tmpfile2}" "$2"
else
echo "NO kbibi correction for interaction ${name}"
do_external postupd dummy "$1" "$2"
fi
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