Hex, Bugs and More Physics | Emre S. Tasci

Converts POSCAR files to CIF format. Uses Octave (latvec2par) to convert the unit cell vectors to lattice cell parameters. It is assumed (compulsory) that the atom coordinates in the POSCAR file are in fractional (direct) coordinates.

Parameters

f         : input file  (Default = POSCAR)
o         : output file (Default = <inputfilename>.cif)
t         : if set (t=1), then the output is written to the screen
speclist  : Define the name of the species, seperated by 'xx' or ',' to be used
            with neighbour listing (Default = AxxBxxCxx...)
            (Labels can also be seperated via [space] as long as speclist is given
            in quotation -- Example: ... speclist=\"Au Si\" )

Example

sururi@husniya OUTCARs_final_structures $ cat POSCAR_Pd3S
Pd3S
   1.00000000000000
     4.7454403619558345    0.0098182468538853    0.0000000000000000
    -1.4895902658503473    4.5055989020479856    0.0000000000000000
     0.0000000000000000    0.0000000000000000    7.2191545483192190
   6   2
Direct
  0.1330548697855782  0.5102695954022698  0.2500000000000000
  0.4897304045977232  0.8669451452144267  0.7500000000000000
  0.5128136657304309  0.1302873334247993  0.2500000000000000
  0.8697126665752007  0.4871863042695738  0.7500000000000000
  0.0013210250693640  0.9986789749306360  0.0000000000000000
  0.0013210250693640  0.9986789749306360  0.5000000000000000
  0.6856021298170862  0.6825558526447357  0.2500000000000000
  0.3174442073552622  0.3143978111829124  0.7500000000000000

sururi@husniya OUTCARs_final_structures $ php POSCAR2CIF.php f=POSCAR_Pd3S t=1 speclist=Pd,S
data_
loop_
_symmetry_equiv_pos_as_xyz
x,y,z
_cell_length_a  4.745451
_cell_length_b  4.745451
_cell_length_c  7.219155
_cell_angle_alpha       90.000000
_cell_angle_beta        90.000000
_cell_angle_gamma       108.175792
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Pd01    Pd        0.1330548697855782  0.5102695954022698  0.2500000000000000
Pd02    Pd        0.4897304045977232  0.8669451452144267  0.7500000000000000
Pd03    Pd        0.5128136657304309  0.1302873334247993  0.2500000000000000
Pd04    Pd        0.8697126665752007  0.4871863042695738  0.7500000000000000
Pd05    Pd        0.0013210250693640  0.9986789749306360  0.0000000000000000
Pd06    Pd        0.0013210250693640  0.9986789749306360  0.5000000000000000
S01     S         0.6856021298170862  0.6825558526447357  0.2500000000000000
S02     S         0.3174442073552622  0.3143978111829124  0.7500000000000000

Code

#!/usr/bin/php
<?PHP
/* Emre S. Tasci <e.tasci@tudelft.nl>                    *
 * Script name: POSCAR2CIF.php                           *
 * Converts the specified POSCAR file to CIF format      *
 * Uses octave to convert the unit cell vectors          *
 * to lattice parameters.                                *
 *                                              23/05/09 */
 
 
//require("/code/toolbox/commandline.inc.php"); # Equivalent handling of $_GET / $_POST
# ============/code/toolbox/commandline.inc.php========================================
// Enables the same treat for command line parameters
// as those of GET parameters.
// Also sets the $first, $last ranges including the gall parameter
 
//Support for command line variable passing:
for($i=1;$i<sizeof($_SERVER["argv"]);$i++)
{
  list($var0,$val0) = explode("=",$_SERVER["argv"][$i]);
  $_GET[$var0] = $val0;
}
 
$first = -2; //disabled by default
$last  = -3;
 
if($_GET["gfirst"]) $first = $_GET["gfirst"];
if($_GET["glast"] ) $last  = $_GET["glast"];
if($_GET["gall"] ) {$first = $_GET["gall"]; $last = $first;}
# ============/code/toolbox/commandline.inc.php========================================
 
 
if($_GET["h"]||$_GET["help"])
{
$help = <<<lol
 * Script name: POSCAR2CIF.php                           *
 * Converts the specified POSCAR file to CIF format      *
 * Uses octave to convert the unit cell vectors          *
 * to lattice parameters.                                *
 
 * Emre S. Tasci <e.tasci@tudelft.nl>                    *
 *                                              23/05/09 *
 
 Usage:
 f         : input file  (Default = POSCAR)
 o         : output file (Default = <inputfilename>.cif)
 t         : if set (t=1), then the output is written to the screen
 speclist  : Define the name of the species, seperated by 'xx' or ',' to be used
             with neighbour listing (Default = AxxBxxCxx...)
             (Labels can also be seperated via [space] as long as speclist is given
             in quotation -- Example: ... speclist=\"Au Si\" )
 
 Example : php POSCAR2CIF.php f=POSCAR_RhBi4 speclist=Bi,Rh
lol;
 echo $help."\n";
 exit;
}
 
 
if($_GET["file"])$inputfile = $_GET["file"];
else if($_GET["f"])$inputfile = $_GET["f"];
else $inputfile="POSCAR";
 
$outfile = $inputfile.".cif";
if($_GET["o"]) $outfile=$_GET["o"];
if($_GET["t"]) $outfile = "php://stdout";
 
$species_type_template = Array("A","B","C","D","E","F","G","H","I","J","K","L","M","N","O","P","Q","R","S","T","U","V","W","X","Y","Z");
if($_GET["speclist"])$species_type_template = split("xx| |,",$_GET["speclist"]);
 
//echo sizeof($_GET["speclist"])."\n";
exec('sed -n "3,6p" '.$inputfile.'|awk \'{print $1"\t"$2"\t"$3}\'',$out);
$octfp = fopen("octrungetvolnpar.m","w");
 
fwrite($octfp,"kini=[\n");
for ($i=0;$i<3;$i++)
    fwrite($octfp,$out[$i]."\n");
fwrite($octfp,"];\n\n");
 
fwrite($octfp,"numatom = [".$out[3]."];\n\n");
$numatoms = split("[ \t]+",trim($out[3]));
 
// Write the octave operations
fwrite($octfp,"k1 = latvec2par (kini);totatom=sum(numatom );\n");
fwrite($octfp,"for i=1:6;printf(\"%f\\n\",k1(i));endfor;\nprintf(\"%d\\n\",totatom)\n");
 
fclose($octfp);
 
// Execute the octave file to find the lattice parameters and volume
exec('octave -q '.$thisdir.'octrungetvolnpar.m',$out3);
unlink("octrungetvolnpar.m");
//echo $out3[0]."\n";
 
/*
for ($i=0;$i<sizeof($out3);$i++)
    echo $i."\t".$out3[$i]."\n";
 */
 
exec('grep "Direct" '.$inputfile.' -n|sed "s:^\([0-9]\+\).*:\1:"',$start);# Line number of the Direct prompt
$start = $start[0];
$start++;
$finish = $start+$out3[sizeof($out3)-1]-1;
exec('sed -n "'.$start.','.$finish.'p" '.$inputfile,$outr);
$fpo = fopen($outfile, "w");
fwrite($fpo, "data_\nloop_\n_symmetry_equiv_pos_as_xyz\nx,y,z\n");
fwrite($fpo, "_cell_length_a\t".$out3[0]."\n");
//echo $out3[0];
fwrite($fpo, "_cell_length_b\t".$out3[1]."\n");
fwrite($fpo, "_cell_length_c\t".$out3[2]."\n");
fwrite($fpo, "_cell_angle_alpha\t".$out3[3]."\n");
fwrite($fpo, "_cell_angle_beta\t".$out3[4]."\n");
fwrite($fpo, "_cell_angle_gamma\t".$out3[5]."\n");
fwrite($fpo, "loop_\n_atom_site_label\n_atom_site_type_symbol\n_atom_site_fract_x\n_atom_site_fract_y\n_atom_site_fract_z\n");
$k = 0;
for($specie=0;$specie<sizeof($numatoms);$specie++)
    for($i=1;$i<=$numatoms[$specie];$i++)
    {
        fwrite($fpo, $species_type_template[$specie].sprintf("%02d",$i)."\t".$species_type_template[$specie]."\t".$outr[$k]."\n");
        $k++;
    }
 
 
fclose($fpo);
?>