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 python libraries listed under 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¶