/usr/share/votca/scripts/inverse/RDF_to_POT.pl is in votca-csg-scripts 1.2.4-1.
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 | #! /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%
This script converts rdf to pot of mean force (''\$F(r)=-k_B T\\\\ln g(r)\$'')
In addtion, it does some magic tricks:
- do not crash when calc log(0)
- extrapolate the beginning of pot
- the maximum to interpolate is pot_max (see xml)
- bigger value will be set to that max
- shift the potential, so that it is zero at the cutoff
- set all values to zero after the cutoff
Usage: $progname infile outfile
EOF
exit 0;
}
die "2 parameters are nessary\n" if ($#ARGV<1);
use CsgFunctions;
my $infile="$ARGV[0]";
my $outfile="$ARGV[1]";
my $pref=csg_get_property("cg.inverse.kBT");
my $r_cut=csg_get_interaction_property("max");
my @r;
my @rdf;
my @flag;
(readin_table($infile,@r,@rdf,@flag)) || die "$progname: error at readin_table\n";
my @pot;
for (my $i=0;$i<=$#r;$i++){
# if ($flag[$i] eq "i"){
#rdf = 0 will give undefined pot
if ($rdf[$i]>1e-10) {
$pot[$i]=-$pref*log($rdf[$i]);
}
else {
$pot[$i]="nan";
$flag[$i]="u";
}
# }
}
#find first defined value (begining for r=0)
#but it is more stable to search first undefined value begin
#beginning form large r
my $first_undef_bin=-1;
for (my $i=$#pot;$i>=0;$i--){
if ($flag[$i] eq "u") {
$first_undef_bin=$i;
last;
}
}
die "All data points from file '$infile' are invalid after Boltzmann inversion, please check if your distribution is a valid rdf.\n" if ($first_undef_bin==$#pot);
#find i which is the cutoff
my $i_cut=$#r;
for (my $nr=0;$nr<=$#r;$nr++){
if ($r[$nr]>=$r_cut) {
$i_cut=$nr;
last;
}
}
#shift potential so that it is zero at cutoff
#first do the shift, then extrapolation
for (my $i=0;$i<=$i_cut;$i++){
$pot[$i]-=$pot[$i_cut] unless ($flag[$i] =~ /[u]/);
}
#quadratic extrapolation at the begining
my $slope=$pot[$first_undef_bin+1]-$pot[$first_undef_bin+2];
for (my $i=$first_undef_bin;$i>=0;$i--){
$slope+=$slope;
$pot[$i]=$pot[$i+1]+$slope;
$flag[$i]="o";
}
# set end of the potential to zero
for (my $i=$i_cut;$i<$#flag;$i++) {
$pot[$i]=0;
$flag[$i]="o";
}
saveto_table($outfile,@r,@pot,@flag) || die "$progname: error at save table\n";
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