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

DockOnSurf needs the python libraries listed under *Requirements* to be installed 

and available. The easiest way to do this is with the @conda@ package and environment 

manager (see https://docs.conda.io/en/latest/). You can alternatively install 

them using @pip@ except from RDKit, which is not available as its core routines are 

written in C.

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)