* wip
* user my fork for rdkit-js temporarily
* clean up obsolete files and refactor readme for it to make sense with new rdkit-js repository
* fix dockerfile
* fix URLs and cleanup documentation hierarchy
* further replacement of rdkit-js references where it makes sense
* add link to 2021 UGM in readme
Dear rdkit Developers,
We have implemented a high-throughput python algorithm that uses rdkit to automatically find the most stable geometry for molecules on surfaces. Among the different features it is able to:
- 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.
For further information you can read:
its corresponding paper (https://www.doi.org/10.26434/chemrxiv.14095699)
its source code (https://gitlab.com/lch_interfaces/dockonsurf)
its documentation (https://dockonsurf.readthedocs.io)
Thnaks for the consideration.
Yours sincerely
Carles Martí
