Chimie Théorique » scripts_chimie4psmn » DockOnSurf

h1. 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

h1. Installation:

Download the @dockonsurf@ directory and place it somewhere in your computer,
by typing in your terminal:
<pre>
git clone http://forge.cbp.ens-lyon.fr/git/dockonsurf
</pre>
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:
<pre>
PATH="$PATH:$HOME/dockonsurf/"
</pre>
If you downloaded it elsewhere, replace @$HOME@ for the actual path where your code is
(where you did the @git clone@ command).
If you want to permanently add the DockOnSurf directory in your path add
@PATH="$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/)

h1. Requirements:

* "Python":http://www.python.org/ >= 3.6
* "Matplotlib":https://matplotlib.org ~= 3.2.1
* "NumPy":http://docs.scipy.org/doc/numpy/reference/ >= 1.16.6
* "RDKit":https://rdkit.org/ ~= 2019.9.3
* "scikit-learn":https://scikit-learn.org/ ~= 0.23.1
* "HDBSCAN":https://hdbscan.readthedocs.io/en/latest/basic_hdbscan.html ~= 0.8.26
* "ASE":https://wiki.fysik.dtu.dk/ase/ ~= 3.19.1
* "NetworkX":https://networkx.org/ >= 2.4
* "python-daemon":https://pypi.org/project/python-daemon/ ~= 2.2.4
* "pymatgen":https://pymatgen.org/ ~= 2020.11.11
* "pycp2k":https://github.com/SINGROUP/pycp2k ~= 0.2.2

h1. Testing

(To be done)

h1. 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.

h1. Example

(To be done)