/usr/share/votca/scripts/inverse/postadd_convergence.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 | #! /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%
postadd convergence script, calcs norm of error (\${name}.DIST.BASE-\${name}.DIST.new)
and saves it to \${name}.conv.
DIST stands for 'dist', but can be changed by onvergence.what option
usage: ${0##*/}
EOF
exit 0
fi
if [[ $(csg_get_property cg.inverse.method) = "optimizer" ]]; then
msg "WARNING: postadd convergency make no sense for method optimizer as convergency is calculated anyway - skipping"
exit 0
fi
name=$(csg_get_interaction_property name)
max=$(csg_get_interaction_property max)
min=$(csg_get_interaction_property min)
step=$(csg_get_interaction_property step)
#these are arrays
weights=( $(csg_get_interaction_property inverse.post_add_options.convergence.weight) )
what_to_do_list=( $(csg_get_interaction_property inverse.post_add_options.convergence.what) )
#base stands for the extension(s) of file(s) of data against which convergence is checked
bases=( $(csg_get_interaction_property inverse.post_add_options.convergence.base) )
#what error norm to use 1st or 2nd,
norms=( $(csg_get_interaction_property inverse.post_add_options.convergence.norm) )
[[ ${#weights[@]} -ne ${#what_to_do_list[@]} ]] && die "${0##*/}: number of weights does not match number of 'what' to calc convergence from"
[[ ${#bases[@]} -ne ${#what_to_do_list[@]} ]] && die "${0##*/}: number of bases does not match number of 'what' to calc convergence from"
[[ ${#norms[@]} -ne ${#what_to_do_list[@]} ]] && die "${0##*/}: number of norms does not match number of 'what' to calc convergence from"
sum=0
#we allow multiple thing per interaction to be checked
for ((i=0;i<${#what_to_do_list[@]};i++)); do
dist=${what_to_do_list[$i]}
weight=${weights[$i]}
base=${bases[$i]}
norm=${norms[$i]}
if [[ ${base} = "cur" ]]; then
tmp1=${name}.${dist}.new
else
tmp1="$(critical mktemp ${name}.${dist}.new.resample.XXX)"
fi
if [[ ! -f "${name}.${dist}.${base}" ]]; then
#if we need $name.dist.tgt we know how to create it
if [[ ${dist} = "dist" ]]; then
do_external resample target "$(csg_get_interaction_property inverse.target)" "${name}.dist.${base}"
else
die "${0##*/}: file '${name}.${dist}.${base}' was not found. Add the script to create this file to the postadd routine of interaction $name or put it in the maindir and add it to cg.inverse.filelist."
fi
fi
if [[ ! -f ${name}.${dist}.new ]]; then
#pot.new won't there yet as postadd dummy is called after postadd task automatically in post_add_single.sh
if [[ ${dist} = pot ]]; then
do_external postadd dummy "$1" "$2"
else
die "${0##*/}: file '${name}.${dist}.new' was not found, add a postadd routine of interaction $name to calculate it."
fi
fi
#resample this, as density dist maybe has the wrong grid
if [[ ! ${base} = "cur" ]]; then
critical csg_resample --in ${name}.${dist}.new --out $tmp1 --grid "$min:$step:$max"
fi
#choose operation based on the selected error norm
case ${norm} in
1)
opr=d ;;
2)
opr=d2 ;;
*)
die "${0##*/}: convergence check norm '${norm}' specified for '${name}.${dist}.${base}' not yet implemented."
esac
# compute error only for 'i' flagged entries, neglect 'o' flagged entries
diff=$(do_external table combine --sum --withflag i --op ${opr} "$tmp1" "${name}.${dist}.${base}")
is_num "$diff" || die "${0##*/}: strange - result of do_external table difference '$tmp1' and '${name}.${dist}.${base}' was not a number"
#store error norm for current interactions current DIST
echo "$diff" > ${name}.${dist}.conv
wdiff=$(csg_calc "$weight" "*" "${diff}")
echo "Convergence of $dist for ${name} was ${diff} and has weight $weight, so difference is $wdiff"
sum=$(csg_calc $sum + $wdiff)
done
echo "$sum" > ${name}.conv
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