/usr/share/votca/scripts/inverse/dist_boltzmann_invert.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 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 | #! /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#^.*/##;
my $usage="Usage: $progname [OPTIONS] <in> <out>";
my $kbT=undef;
my $dist_min=1e-10;
my $type="non-bonded";
while ((defined ($ARGV[0])) and ($ARGV[0] =~ /^-./))
{
if (($ARGV[0] !~ /^--/) and (length($ARGV[0])>2)){
$_=shift(@ARGV);
#short opt having agruments examples fo
if ( $_ =~ /^-[fo]/ ) {
unshift(@ARGV,substr($_,0,2),substr($_,2));
}
else{
unshift(@ARGV,substr($_,0,2),"-".substr($_,2));
}
}
if (($ARGV[0] eq "-h") or ($ARGV[0] eq "--help"))
{
print <<END;
$progname, version %version%
Boltzmann inverts a distribution (''\$F(x)=-k_B T\\\\ln g(x)\$'')
In addtion, it does some magic tricks:
- do not crash when calc log(0)
- choose the right normalization depending on the type of interaction
- input dist should be unnormalized (like csg_stat calcs it)
$usage
Allowed options:
--kbT NUMBER use NUMBER as ''\$k_B*T\$'' for the entropic part
--type XXX change the type of interaction
Default: $type
--min XXX minimum value to consider
Default: $dist_min
-h, --help Show this help message
Possible types: non-bonded, bond, angle, dihedral
Examples:
* $progname --kbT 2.49435 --min 0.001 tmp.dist tmp.pot
END
exit;
}
elsif ($ARGV[0] eq "--kbT"){
shift(@ARGV);
$kbT=shift(@ARGV);
}
elsif ($ARGV[0] eq "--type"){
shift(@ARGV);
$type = shift(@ARGV);
die "$progname: Unsupported type of interatction: $type -> go and implement it\n" unless (( "$type" eq "bond" ) or ("$type" eq "dihedral") or ("$type" eq "angle") or ("$type" eq "non-bonded"));
}
elsif ($ARGV[0] eq "--min"){
shift(@ARGV);
$dist_min = shift(@ARGV);
}
else {
die "Unknown option '".$ARGV[0]."' !\n";
}
}
die "2 parameters are necessary\n" if ($#ARGV<1);
die "$progname: kbT not defined specify it with --kbT option\n" unless defined($kbT);
use CsgFunctions;
my $infile="$ARGV[0]";
my $outfile="$ARGV[1]";
my @x;
my @dist;
my @flag;
(readin_table($infile,@x,@dist,@flag)) || die "$progname: error at readin_table\n";
my @pot;
for (my $i=0;$i<=$#x;$i++){
if ($dist[$i]>$dist_min) {
my $norm=1;
if ( "$type" eq "bond" ) {
$norm=$x[$i]*$x[$i];
} elsif ( "$type" eq "angle" ) {
$norm=sin($x[$i]);
}
$pot[$i]=-$kbT*log($dist[$i]/$norm);
}
else {
$pot[$i]="nan";
$flag[$i]="u";
}
}
#find a valid point
my $valid_i=-1;
for (my $i=0;$i<=$#pot;$i++){
if ($flag[$i] eq "i") {
$valid_i=$i;
last;
}
}
die "All data points from file '$infile' are invalid after Boltzmann inversion, please check if your distribution is a valid dist.\n" if ($valid_i==-1);
#set point at beginning to invalid
my $first=undef;
for (my $i=$valid_i;$i>=0;$i--){
if ($flag[$i] eq "u") {
$pot[$i]=$pot[$i+1];
$flag[$i]="o";
$first=$i unless defined $first;
}
}
$first=0 unless defined $first;
#set point at end to invalid
my $last=undef;
for (my $i=$valid_i;$i<=$#pot;$i++){
if ($flag[$i] eq "u") {
$pot[$i]=$pot[$i-1];
$flag[$i]="o";
$last=$i unless defined $last;
}
}
$last=$#pot unless defined $last;
my $n=10;
my $valid=$last-$first+1;
die "Only $valid points are valid after Boltzmann inversion from file '$infile', please check if your distribution is a valid dist.\n" if ($valid < $n);
saveto_table($outfile,@x,@pot,@flag) || die "$progname: error at save table\n";
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