Putontop: Difference between revisions
New page: = 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 ato... |
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= General information = | = General information = | ||
'''WARNING: This script is | '''WARNING: This script is an alpha version. CHECK THE OUTPUT BEFORE!''' | ||
Putontop is a Perl script that takes as | 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 == | == Installation == | ||
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[[Image:Putontop.tgz]] | [[Image:Putontop.tgz]] | ||
To untar in your /home/user/bin | To untar in your /home/user/bin directory: | ||
tar -xvzf putontop.tgz -C ~/bin | tar -xvzf putontop.tgz -C ~/bin | ||
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$3 For the distance between the lowest atom of the molecule and the higher atom 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 | For example, to generate a POSCAR file with a Fructose molecule over a Graphite surface with 2.0 Å distance: | ||
putontop ../MOLECULES/CONTCAR ../GRAPHITE/CONTCAR 2.0 > POSCAR | 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. | 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 == | == More information == | ||
Latest revision as of 16:42, 14 September 2018
go back to Main Page, Computational Resources, Scripts or VASP, Scripts for VASP
General information[edit]
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[edit]
Download the file:
File:Putontop.tgz
To untar in your /home/user/bin directory:
tar -xvzf putontop.tgz -C ~/bin
Usage[edit]
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[edit]
Title[edit]
The title of the generated file will be: "Title of the Molecule" over "Title of the Surface"
x/y displacement[edit]
The molecule is displaced to the x/y middle point of the surface. The lowest atom of the molecule is taken as a reference.
[edit]
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