/usr/share/votca/scripts/inverse/potential_to_dlpoly.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 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 | #!/bin/bash
#
# Copyright 2009-2014 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 is a high class wrapper to convert a potential to the dlpoly format
Usage: ${0##*/}
EOF
exit 0
fi
[[ -z $1 || -z $2 ]] && die "${0##*/}: missing argument"
input="$1"
trunc="${1%%.*}"
[[ -f $input ]] || die "${0##*/}: Could not find input file '$input'"
output="$2"
echo "Convert $input to $output"
table_zero="0"
step="$(csg_get_interaction_property step)"
bondtype="$(csg_get_interaction_property bondtype)"
if [[ $bondtype = "non-bonded" ]]; then
OUT="TABLE"
table_end="$(csg_get_property cg.inverse.dlpoly.table_end)"
table_grid="$(csg_get_property cg.inverse.dlpoly.table_grid)"
bin_size="$(csg_calc "$table_end" "/" $table_grid)"
# make sure the TAB* file is removed externally
if [[ ! -f "${OUT}" ]]; then
echo "Table for dlpoly from VOTCA with love" > "${OUT}" #max 80 chars
# see dlpoly manual ngrid = int(cut/delta) + 4
table_grid="$(($table_grid+4))"
# nm -> Angs
bin_size1="$(csg_calc "$bin_size" "*" 10)"
table_end1="$(csg_calc "$table_end" "*" 10)"
echo "$bin_size1 $table_end1 $table_grid" >> "${OUT}"
fi
elif [[ $bondtype = "bond" ]]; then
OUT="TABBND"
table_end="$(csg_get_property cg.inverse.dlpoly.bonds.table_end)"
table_grid="$(csg_get_property cg.inverse.dlpoly.bonds.table_grid)"
bin_size="$(csg_calc "$table_end" "/" $table_grid)"
# make sure the TAB* file is removed externally
if [[ ! -f "${OUT}" ]]; then
echo "# Table for dlpoly from VOTCA with love" > "${OUT}" #max 80 chars
# nm -> Angs
table_end1="$(csg_calc "$table_end" "*" 10)"
echo "# $table_end1 $table_grid" >> "${OUT}"
fi
elif [[ $bondtype = "angle" ]]; then
OUT="TABANG"
table_end="3.14159265359"
table_grid="$(csg_get_property cg.inverse.dlpoly.angles.table_grid)"
bin_size="$(csg_calc "$table_end" "/" $table_grid)"
# make sure the TAB* file is removed externally
if [[ ! -f "${OUT}" ]]; then
echo "# Table for dlpoly from VOTCA with love" > "${OUT}" #max 80 chars
echo "# $table_grid" >> "${OUT}"
fi
elif [[ $bondtype = "dihedral" ]]; then
OUT="TABDIH"
table_zero="-3.14159265359"
table_end="3.14159265359"
table_grid="$(csg_get_property cg.inverse.dlpoly.dihedrals.table_grid)"
bin_size="$(csg_calc "$table_end" "-" $table_zero)"
bin_size="$(csg_calc "$bin_size" "/" $table_grid)"
# make sure the TAB* file is removed externally
if [[ ! -f "${OUT}" ]]; then
echo "# Table for dlpoly from VOTCA with love" > "${OUT}" #max 80 chars
echo "# $table_grid" >> "${OUT}"
fi
else
die "${0##*/}: conversion of ${bondtype} interaction to generic tables is not implemented yet!"
fi
# Yes, the dlpoly table starts at ${bin_size}
table_begin="$(csg_calc "$table_zero" "+" $bin_size)"
#keep the grid for now, so that extrapolate can calculate the right mean
comment="$(get_table_comment)"
smooth2="$(critical mktemp ${trunc}.pot.extended.XXXXX)"
critical csg_resample --in ${input} --out "${smooth2}" --grid "${table_zero}:${step}:${table_end}" --comment "$comment"
extrapolate="$(critical mktemp ${trunc}.pot.extrapolated.XXXXX)"
do_external potential extrapolate --type "$bondtype" "${smooth2}" "${extrapolate}"
smooth="$(critical mktemp ${trunc}.pot.smooth.XXXXX)"
deriv="$(critical mktemp ${trunc}.pot.deriv.XXXXX)"
critical csg_resample --in ${extrapolate} --out "${smooth}" --der "${deriv}" --grid "${table_begin}:${bin_size}:${table_end}" --comment "$comment"
#shift does not change derivative
tshift="$(critical mktemp ${trunc}.pot.shift.XXXXX)"
do_external potential shift --type "$bondtype" "${smooth}" "${tshift}"
do_external convert_potential tab --header dlpoly --type "${bondtype}" "${tshift}" "${deriv}" "${output}"
if [[ -f $OUT ]]; then
echo "Appending $output to $OUT"
if [[ $bondtype = "non-bonded" ]]; then
#votca non-bonded types might not correspond to dl_poly's internal types, only use a failback
header="$(csg_get_interaction_property --allow-empty dlpoly.header)"
[[ -z ${header} ]] && header="$(csg_get_interaction_property type1) $(csg_get_interaction_property type2)"
echo "${header}" >> "$OUT"
else
header="$(csg_get_interaction_property dlpoly.header)"
# an empty line must precede each data block (for another bond type), then the bond type (two atom types) follow
echo "" >> "$OUT"
echo "# ${header}" >> "$OUT"
fi
cat "${output}" >> "$OUT"
fi
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