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Be-solid.pl
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Sat, Aug 3, 17:44

Be-solid.pl
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#!/usr/bin/perl
# Usage: Be-solid.pl <nx> <ny> <nz> > data.Be
#
# Generates a beryllium solid LAMMPS data file.
$nx = shift(@ARGV);
$ny = shift(@ARGV);
$nz = shift(@ARGV);
$La = 4.592; # eFF optimized (4.33 expt)
$Lc = 7.025; # eFF optimized (6.78 expt)
# This part changes for different lattices
@xunit = (0, 0.5, 0, 0.5);
@yunit = (0, 0.5, 0.5 * (4/3), (1/3) * 0.5);
@zunit = (0, 0, 0.5, 0.5);
$Lx = $La;
$Ly = $La * sqrt(3);
$Lz = $Lc;
$idx = 0;
for ($x = 0; $x < $nx; $x++)
{
for ($y = 0; $y < $ny; $y++)
{
for ($z = 0; $z < $nz; $z++)
{
for ($i = 0; $i <= $#xunit; $i++)
{
$xnuc[$idx] = ($x + .25) * $Lx + $xunit[$i] * $Lx;
$ynuc[$idx] = ($y + .25) * $Ly + $yunit[$i] * $Ly;
$znuc[$idx] = ($z + .25) * $Lz + $zunit[$i] * $Lz;
$idx++;
}
}
}
}
$numnuc = $idx;
# Print length of supercell
printf("Created by Be-solid.pl\n\n");
printf("%d atoms\n",$numnuc+$numnuc*2+$numnuc*2);
printf("2 atom types\n\n");
printf("%f %f xlo xhi\n", 0, $Lx * $nx);
printf("%f %f ylo yhi\n", 0, $Ly * $ny);
printf("%f %f zlo zhi\n\n", 0, $Lz * $nz);
printf("Masses\n\n");
printf("1 9.012182\n");
printf("2 1.000000\n\n");
printf("Atoms\n\n");
$j=0;
# Print out the nuclei
for ($i = 0; $i < $numnuc; $i++)
{
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 1, 4.0, 0, 0.0, $xnuc[$i], $ynuc[$i], $znuc[$i]);
}
# Print out the core electrons
$r_core = 0.5;
for ($i = 0; $i < $numnuc; $i++)
{
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_core,$xnuc[$i], $ynuc[$i], $znuc[$i]);
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_core,$xnuc[$i], $ynuc[$i], $znuc[$i]);
}
# Print out the valence electrons
$r_valence = 2.5;
for ($i = 0; $i < $numnuc; $i += 4)
{
$x = &BoundX($xnuc[$i] + $Lx / 2.0);
$y = &BoundY($ynuc[$i] + $Lx / (2.0 * sqrt(3)));
$z = $znuc[$i];
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_valence,$x, $y, $z);
$x = &BoundX($xnuc[$i] + $Lx / 2.0);
$y = &BoundY($ynuc[$i] + $Lx / (2.0 * sqrt(3)));
$z = $znuc[$i];
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_valence,$x, $y, $z);
$x = &BoundX($xnuc[$i+1] + $Lx / 2.0);
$y = &BoundY($ynuc[$i+1] + $Lx / (2.0 * sqrt(3)));
$z = $znuc[$i+1];
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_valence, $x, $y, $z);
$x = &BoundX($xnuc[$i+1] + $Lx / 2.0);
$y = &BoundY($ynuc[$i+1] + $Lx / (2.0 * sqrt(3)));
$z = $znuc[$i+1];
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_valence,$x, $y, $z);
$x = &BoundX($xnuc[$i+2] - $Lx / 2.0);
$y = &BoundY($ynuc[$i+2] - $Lx / (2.0 * sqrt(3)));
$z = $znuc[$i+2];
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_valence,$x, $y, $z);
$x = &BoundX($xnuc[$i+2] - $Lx / 2.0);
$y = &BoundY($ynuc[$i+2] - $Lx / (2.0 * sqrt(3)));
$z = $znuc[$i+2];
printf("%i %i %f %f %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_valence,$x, $y, $z);
$x = &BoundX($xnuc[$i+3] - $Lx / 2.0);
$y = &BoundY($ynuc[$i+3] - $Lx / (2.0 * sqrt(3)));
$z = $znuc[$i+3];
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $r_valence, $x, $y, $z);
$x = &BoundX($xnuc[$i+3] - $Lx / 2.0);
$y = &BoundY($ynuc[$i+3] - $Lx / (2.0 * sqrt(3)));
$z = $znuc[$i+3];
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, -1, $r_valence,$x, $y, $z);
}
sub BoundX {
$x = $_[0];
if ($x > $Lx * $nx) {$x -= $Lx * $nx;}
if ($x < 0) {$x += $Lx * $nx;}
return $x;
}
sub BoundY {
$y = $_[0];
if ($y > $Ly * $ny) {$y -= $Ly * $ny;}
if ($y < 0) {$y += $Ly * $ny;}
return $y;
}
sub BoundZ {
$z = $_[0];
if ($z > $Lz * $nz) {$z -= $Lz * $nz;}
if ($z < 0) {$z += $Lz * $nz;}
return $z;
}

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