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lammps/tools/eff/structure_generators/Diamond.pl
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Diamond.pl
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#!/usr/bin/perl
# Usage: diamond <nx> <ny> <nz> > data.diamond
#
# Generates diamond A4 structure.
$nx = shift(@ARGV);
$ny = shift(@ARGV);
$nz = shift(@ARGV);
#$scale = shift(@ARGV);
$scale = 1.045;
$L = 7.33461; # eFF optimized (6.740 expt)
$re_core = 0.328; # core electron
$re_sigma = 1.559; # sigma electrons
#$r_threshold = $scale * 1.6 / 0.529; # threshold for sigma bond length
$r_threshold = $scale * 1.6 / 0.5 ; # threshold for sigma bond length
@xunit = (0, 0, 0.5, 0.5, 0.25, 0.75, 0.25, 0.75);
@yunit = (0, 0.5, 0, 0.5, 0.25, 0.75, 0.75, 0.25);
@zunit = (0, 0.5, 0.5, 0, 0.25, 0.25, 0.75, 0.75);
$idx = 0;
for ($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 * $L + $xunit[$i] * $L;
$ynuc[$idx] = $y * $L + $yunit[$i] * $L;
$znuc[$idx] = $z * $L + $zunit[$i] * $L;
$idx++;
}
}
}
}
$numnuc = $idx;
$xx = $L * $nx;
$yy = $L * $ny;
$zz = $L * $nz;
# Print length of supercell
printf("Created with Diamond.pl\n\n");
printf("%d atoms\n",$numnuc*7);
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 * $nz);
printf("Masses\n\n");
printf("1 12.01070\n");
printf("2 1.000000\n\n");
printf("Atoms\n\n");
# Print out the nuclei and the core electrons
for ($i = 0; $i < $numnuc; $i++)
{
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 1, 6.0, 0.0, 0.0, $xnuc[$i], $ynuc[$i], $znuc[$i]);
}
for ($i = 0; $i < $numnuc; $i++)
{
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0, 1, $re_core,$xnuc[$i], $ynuc[$i], $znuc[$i]);
printf("%i %i %f %i %f %f %f %f\n", $j+=1, 2, 0.0,-1, $re_core,$xnuc[$i], $ynuc[$i], $znuc[$i]);
}
# Print out sigma electrons
$LLx = $L * $nx;
$LLy = $L * $ny;
$LLz = $L * $nz;
$k=$j;
for ($i = 0; $i < $numnuc; $i++)
{
for ($j = 0; $j < $i; $j++)
{
$x = $xnuc[$j] - $xnuc[$i];
$y = $ynuc[$j] - $ynuc[$i];
$z = $znuc[$j] - $znuc[$i];
# Minimum image convention
if ($x > $LLx/2) {$x -= $LLx;}
if ($y > $LLy/2) {$y -= $LLy;}
if ($z > $LLz/2) {$z -= $LLz;}
if ($x < -$LLx/2) {$x += $LLx;}
if ($y < -$LLy/2) {$y += $LLy;}
if ($z < -$LLz/2) {$z += $LLz;}
$r = sqrt($x * $x + $y * $y + $z * $z);
if ($r < $r_threshold)
{
$bond_x = $xnuc[$i] + $x / 2;
$bond_y = $ynuc[$i] + $y / 2;
$bond_z = $znuc[$i] + $z / 2;
# Minimum image convention
if ($bond_x > $LLx) {$bond_x -= $LLx};
if ($bond_y > $LLy) {$bond_y -= $LLy};
if ($bond_z > $LLz) {$bond_z -= $LLz};
if ($bond_x < 0) {$bond_x += $LLx};
if ($bond_y < 0) {$bond_y += $LLy};
if ($bond_z < 0) {$bond_z += $LLz};
printf("%i %i %f %i %f %f %f %f\n", $k+=1, 2, 0.0, 1, $re_sigma,$bond_x, $bond_y, $bond_z);
printf("%i %i %f %i %f %f %f %f\n", $k+=1, 2, 0.0,-1, $re_sigma,$bond_x, $bond_y, $bond_z);
}
}
}
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