Putontop

General information

WARNING: This script is in a alpha version. CHECK THE OUTPUT BEFORE!

Putontop is a Perl script that takes as an input a CONTCAR file from a molecule or atom and a CONTCAR file from a surface and then displaces the molecule over the surface.

Installation

Download the file:

File:Putontop.tgz

To untar in your /home/user/bin folder:

tar -xvzf putontop.tgz -C ~/bin

Usage

At the moment, the script does not run in Tekla2 due to Perl version problems, you need Perl 5.10 or newer to run this script.

The script takes three arguments:

$1 For the CONTCAR file of the molecule.
$2 For the CONTCAR file of the surface.
$3 For the distance between the lowest atom of the molecule and the higher atom of the surface

For example, to generate a POSCAR file with a Furctose molecule over a Graphite surface at a 2.0 Å distance:

putontop ../MOLECULES/CONTCAR ../GRAPHITE/CONTCAR 2.0 > POSCAR

The script uses the cell parameters of the surface and writes the output in cartesian coordinates. Both CONTCAR files must be in direct coordinates.

More information

Title

The title of the generated file will be: "Title of the Molecule" over "Title of the Surface"

x/y displacement

The molecule is displaced to the x/y middle point of the surface. The lowest atom of the molecule is taken as a reference.

Shared elements

If the surface and the molecule share some elements, then the script unifies the shared atoms and writes the atoms in order. For example, if you have a graphite surface and a methane molecule:

Methane:
C H
1 4

Graphite:
C
216

Methane over Graphite:
C   H
217 4