DockOnSurf¶

DockOnSurf is a program to automatically find the most stable geometry for molecules
on surfaces.

webpage: https://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurf

Installation:¶

Download the dockonsurf directory and place it somewhere in your computer, by typing in your terminal:

git clone http://forge.cbp.ens-lyon.fr/git/dockonsurf

In order to be able to execute DockOnSurf by simply typing dockonsurf.py You need to add the DockOnSurf directory in your PATH. Assuming you download it in your $HOME directory, add $HOME/dockonsurf to your PATH variable by typing:

    PATH="$PATH:$HOME/dockonsurf/"

If you downloaded it elsewhere, replace $HOME for the actual path where your code is (where you did the git clone command).
If you want this to be permanent, add PATH="$PATH:$HOME/dockonsurf/" at the end of your $HOME/.bashrc file.

DockOnSurf needs the following requirements to be installed and available. The easiest way to do this is with conda package and environment management system (see https://docs.conda.io/en/latest/)

Requirements:¶

Python >= 3.6
Matplotlib ~= 3.2.1
NumPy >= 1.16.6
RDKit ~= 2019.9.3
scikit-learn ~= 0.23.1
HDBSCAN ~= 0.8.26
ASE ~= 3.19.1
NetworkX >= 2.4
python-daemon ~= 2.2.4
pymatgen ~= 2020.11.11
pycp2k ~= 0.2.2

Testing¶

(To be done)

Contact¶

Submit an issue in:
https://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurf/issues

Please send us bug-reports, patches, code, ideas and questions.

Example¶