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h2.pl
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Created
Sat, Oct 12, 08:47
Size
1 KB
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text/x-perl
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Mon, Oct 14, 08:47 (2 d)
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blob
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21588022
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rLAMMPS lammps
h2.pl
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#!/usr/bin/perl
# Usage: h2.pl <nx> <ny> <nz> <rs> > data.h2
#
# Generates rectangular lattice of hydrogen atoms, # in each direction = nx,
# with Wigner radius rs.
# ...
# Shifts H atoms in alternating directions so they form H2 molecule
# starting structures.
$nx = shift(@ARGV);
$ny = shift(@ARGV);
$nz = shift(@ARGV);
$rs = shift(@ARGV);
$L = 1.6119919540164693 * $rs; # length of unit cell ((4/3 pi)^(1/3)
$re = 1.823572; # electron radius
$dshift = 0.5;
$idx = 0;
for ($x = 0; $x < $nx; $x++)
{
for ($y = 0; $y < $ny; $y++)
{
$dsign = 1;
for ($z = 0; $z < $nz; $z++)
{
$xnuc[$idx] = $x * $L + 0.5 * $L;
$ynuc[$idx] = $y * $L + 0.5 * $L;
$znuc[$idx] = $z * $L + 0.5 * $L + $dshift * $dsign;
$dsign = -$dsign;
$idx++;
}
}
}
$numnuc = $idx;
# Print length of supercell
printf("Created with h2.pl\n\n");
printf("%d atoms\n",$numnuc*2);
printf("2 atom types\n\n");
printf("%f %f xlo xhi\n", 0, $L * $nx);
printf("%f %f ylo yhi\n", 0, $L * $ny);
printf("%f %f zlo zhi\n\n", 0, $L * $nz);
printf("Masses\n\n");
printf("1 1.007940\n");
printf("2 1.000000\n\n");
printf("Atoms\n\n");
$j=0;
# Print out the nuclei and the core electrons
for ($i = 0; $i < $numnuc; $i++)
{
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 1, 1.0, 0, 0.0, $xnuc[$i], $ynuc[$i], $znuc[$i]);
}
$spin = 1;
for ($i = 0; $i < $numnuc; $i++)
{
if ($spin == 1) {$spin = -1;} else {$spin = 1;}
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, $spin, $re, $xnuc[$i], $ynuc[$i], $znuc[$i]);
}
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