/usr/share/votca/scripts/inverse/table_to_tab.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 | #! /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 converts csg potential files to the tab format (as read by espresso).
Potential is copied in the C12 column.
In addition, it does some magic tricks:
- shift the potential, so that it is zero at the cutoff
- set all values to zero after the cutoff
Usage: $progname in_pot in_deriv_pot outfile
EOF
exit 0;
}
die "3 parameters are nessary\n" if ($#ARGV<2);
use CsgFunctions;
my $in_pot="$ARGV[0]";
my $in_deriv_pot="$ARGV[1]";
my $outfile="$ARGV[2]";
my $table_end=csg_get_property("cg.inverse.espresso.table_end");
my $table_bins=csg_get_property("cg.inverse.espresso.table_bins");
my @r;
my @r_repeat;
my @pot;
my @d_pot;
my @flag;
my @flag_repeat;
(readin_table($in_pot,@r,@pot,@flag)) || die "$progname: error at readin_table\n";
(readin_table($in_deriv_pot,@r_repeat,@d_pot,@flag_repeat)) || die "$progname: error at readin_table\n";
#cutoff is last point
my $i_cut=$#r;
#shift potential so that it is zero at cutoff
for (my $i=0;$i<=$i_cut;$i++){
$pot[$i]-=$pot[$i_cut];
}
my @force=@d_pot;
# set end of the potential to zero
for (my $i=$i_cut;$i<=$table_end/$table_bins;$i++) {
$pot[$i]=0;
$force[$i]=0;
$r[$i]=$r[$i-1]+$table_bins;
}
# Smooth out force (9-point avg)
for (my $i=4;$i<$#r_repeat-3;$i++){
$force[$i]=($d_pot[$i-4]+$d_pot[$i-3]+$d_pot[$i-2]
+$d_pot[$i-1]+$d_pot[$i]+$d_pot[$i+1]+$d_pot[$i+2]
+$d_pot[$i+3]+$d_pot[$i+4])/(9.);
}
# add extra 1/r factor for ESPResSo
for (my $i=1;$i<$#r_repeat;$i++){
$force[$i]*=-1.0/$r_repeat[$i];
}
$force[0]=$force[1];
open(OUTFILE,"> $outfile") or die "saveto_table: could not open $outfile\n";
# espresso specific header - no other starting comments
my $num_bins = $table_end/$table_bins;
printf(OUTFILE "#%d 0 %f\n", $num_bins, $table_end);
for(my $i=0;$i<=$#r;$i++){
printf(OUTFILE "%15.10e %15.10e %15.10e\n",
$r[$i], $force[$i], $pot[$i]);
}
close(OUTFILE) or die "Error at closing $outfile\n";
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