Chimie Théorique » scripts_chimie4psmn » DockOnSurf

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

Features

--------

* Generate a handful of adsorbate-surface structures by 

  combining:

  * surface sites

  * adsorbate's anchoring points

  * conformers

  * orientations

  * probe dissociation of acidic H

* Guess the direction where to place the adsorbate. 

  Useful for nanoparticles or stepped/kinked surfaces.

* Sample different orientations efficiently by using internal angles.

* Detect and correct atomic clashes.

* Optimize the geometry of the generated structures using CP2K or VASP.

* Submit jobs to your computing center and check if they have finished normally.

* Track progress by logging all events on a log file.

* Customize the execution by changing chemically meaningful  the edition of a simple input file.

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 DockOnSurf 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 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.

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

Example

-------

Execute DockOnSurf by typing

    dockonsurf.py -i dockonsurf.inp

where `dockonsurf.inp` is the dockonsurf input file. See a sample [here](https://forge.cbp.ens-lyon.fr/redmine/projects/dockonsurf/repository/revisions/master/entry/examples/dockonsurf.inp).

Testing

-------

(To be done)

Contact/Contribute 

-------

Submit an issue in:

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

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

License

-

DockOnSurf is licensed under the MIT license.