About¶
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/
Related scientific article: J. Chem. Inf. Model. 2021, 61, 7, 3386–3396: https://pubs.acs.org/doi/10.1021/acs.jcim.1c00256
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 a computing center and check if they have finished normally.
Track progress by logging all events on a log file.
Customize the execution through the edition of a simple input file.