dockonsurf 0.0.1

Code to systematically find the most stable geometry for molecules on surfaces

DockOnSurf

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

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

current repository: https://gitlab.com/lch_interfaces/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.

Documentation

https://dockonsurf.readthedocs.io/

Installation:

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

git clone https://gitlab.com/lch_interfaces/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 >= 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

Example

Execute DockOnSurf by typing

dockonsurf.py -i dockonsurf.inp

where dockonsurf.inp is the dockonsurf input file. See a sample here.

Testing

(To be done)

Contact/Contribute

Submit an issue on: https://gitlab.com/lch_interfaces/dockonsurf

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

License

DockOnSurf is licensed under the MIT license.