Editing Putontop (section)

= General information =

 '''WARNING: This script is an alpha version. CHECK THE OUTPUT BEFORE!'''

Putontop is a Perl script that takes as a 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:
 [[Image:Putontop.tgz]]

To untar in your /home/user/bin directory:
 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 Fructose molecule over a Graphite surface with 2.0 Å distance:
 putontop ../MOLECULES/FRUCTOSE/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