/usr/share/votca/scripts/inverse/table_integrate.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 | #! /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;
$_=$0;
s#^.*/##;
my $progname=$_;
my $usage="Usage: $progname [OPTIONS] <in> <out>";
my $with_errors="no";
my $with_entropie="no";
my $kbT=undef;
# read program arguments
while ((defined ($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%
This script calculates the integral of a table. Please note the force is the NEGATIVE integral of the potential (use 'table linearop' and multiply the table with -1)
$usage
Allowed options:
--with-errors calculate error
--with-S Add entropic contribution to force ''\$2k_B T/r\$''
--kbT NUMBER use NUMBER as ''\$k_B*T\$'' for the entropic part
-h, --help Show this help message
Examples:
* $progname --with-S --kbT 2.49435 tmp.force tmp.dpot
END
exit;
}
elsif ($ARGV[0] eq "--with-errors"){
shift(@ARGV);
$with_errors="yes";
}
elsif ($ARGV[0] eq "--with-S"){
shift(@ARGV);
$with_entropie="yes";
}
elsif ($ARGV[0] eq "--kbT"){
shift(@ARGV);
$kbT=shift(@ARGV);
}
else
{
die "Unknow option '".$ARGV[0]."' !\n";
}
}
#Print usage
die "no files given\n$usage\n" unless $#ARGV > 0;
use CsgFunctions;
my $infile="$ARGV[0]";
my @r;
my @force;
my @flag;
my @force_errors;
if ("$with_errors" eq "yes") {
(readin_table_err($infile,@r,@force,@force_errors,@flag)) || die "$progname: error at readin_table\n";
} else {
(readin_table($infile,@r,@force,@flag)) || die "$progname: error at readin_table\n";
}
if ("$with_entropie" eq "yes"){
die "$progname: kbT not defined specify it with --kbT option\n" unless defined($kbT);
for (my $i=$#r;$i>=0;$i--){
if ($r[$i]>0) {
$force[$i] += 2*$kbT/$r[$i];
}
}
}
my $outfile="$ARGV[1]";
my @pot;
my @pot_errors;
my @ww;
#calc pot with trapez rule
#int_j= sum_i^j (r_i+1 - r_i)*(f_i+f_i+1)/2
#int_j+1= int_j + (r_i+1 - r_i)*(f_i+f_i+1)/2
#int_j= int_j+1 - (r_i+1 - r_i)*(f_i+f_i+1)/2
#begin from end to make pot(max)=0
$pot[$#r]=0;
$ww[$#r]=0;
for (my $i=$#r-1;$i>=0;$i--){
#hh = delta x /2
my $hh=0.5*($r[$i+1]-$r[$i]);
$pot[$i]=$pot[$i+1] - $hh*($force[$i+1]+$force[$i]);
$ww[$i]+= $hh;
$ww[$i+1]+= $hh;
}
#ww contains w_i=(r_i+1-r_i-1)/2
if ("$with_errors" eq "yes") {
#all error are independent(we assume that)
#resort sum (only one force per summand)
# U_j= sum_i ^j = sum_i^j f_i(r_i+1 - r_i-1)/2 + randterm
# o^2(U_j)=sum_i o^2(f_i)*(r_i+1 - r_i-1)/2 + o^2(randterm)
my $var_int = ($ww[$#r]*$force_errors[$#r])**2;
$pot_errors[$#r]=sqrt($var_int);
for(my $i=$#r-1; $i>=0;$i--) {
my $hh = 0.5*($r[$i+1] - $r[$i]);
$pot_errors[$i] = sqrt($var_int + ($hh*$force_errors[$i])**2);
$var_int += ($ww[$i]*$force_errors[$i])**2;
}
}
if ("$with_errors" eq "yes") {
saveto_table_err($outfile,@r,@pot,@pot_errors,@flag) || die "$progname: error at save table\n";
}else {
saveto_table($outfile,@r,@pot,@flag) || die "$progname: error at save table\n";
}
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