/usr/share/votca/scripts/inverse/update_ibi_pot.pl 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 | #! /usr/bin/perl -w
#
# 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.
#
use strict;
( my $progname = $0 ) =~ s#^.*/##;
if (defined($ARGV[0])&&("$ARGV[0]" eq "--help")){
print <<EOF;
$progname, version %version%
This script calcs dU out of two rdfs with the rules of inverse boltzmann
In addition, it does some magic tricks:
- do not update if one of the two rdf is undefined
Usage: $progname target_rdf new_rdf cur_pot outfile
EOF
exit 0;
}
die "4 parameters are necessary\n" if ($#ARGV<3);
use CsgFunctions;
my $pref=csg_get_property("cg.inverse.kBT");
my $aim_rdf_file="$ARGV[0]";
my @r_aim;
my @rdf_aim;
my @flags_aim;
(readin_table($aim_rdf_file,@r_aim,@rdf_aim,@flags_aim)) || die "$progname: error at readin_table\n";
my $cur_rdf_file="$ARGV[1]";
my @r_cur;
my @rdf_cur;
my @flags_cur;
(readin_table($cur_rdf_file,@r_cur,@rdf_cur,@flags_cur)) || die "$progname: error at readin_table\n";
my $cur_pot_file="$ARGV[2]";
my @pot_r_cur;
my @pot_cur;
my @pot_flags_cur;
(readin_table($cur_pot_file,@pot_r_cur,@pot_cur,@pot_flags_cur)) || die "$progname: error at readin_table\n";
#should never happen due to resample, but better check
die "Different grids \n" if (($r_aim[1]-$r_aim[0]-$r_cur[1]+$r_cur[0])>0.0001);
die "Different start potential point \n" if (($r_aim[0]-$r_cur[0]) > 0.0001);
die "Different end potential point \n" if ( $#r_aim != $#r_cur );
my $outfile="$ARGV[3]";
my @dpot;
my @flag;
my $value=0.0;
#start from the end to make the begining have the last value
for (my $i=$#r_aim;$i>=0;$i--){
if (($rdf_aim[$i] > 1e-10) && ($rdf_cur[$i] > 1e-10)) {
$dpot[$i]=log($rdf_cur[$i]/$rdf_aim[$i])*$pref;
$flag[$i]="i";
} else {
$dpot[$i]=$value;
$flag[$i]="o";
}
if($pot_flags_cur[$i] =~ /[u]/) {
$dpot[$i]=$value;
$flag[$i]="o";
}
else {
$value=$dpot[$i];
}
}
my $comment="#progname: aim_rdf=$aim_rdf_file cur_rdf=$cur_rdf_file cur_pot=$cur_rdf_file\n";
saveto_table($outfile,@r_aim,@dpot,@flag,$comment) || die "$progname: error at save table\n";
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