ProbeParticle workflow for water and CO adsorption on Calcite

Reusable workflow to generate ProbeParticle images, as used in::

Heggemann, Jonas, Yashasvi S. Ranawat, Ondřej Krejčí, Adam S. Foster, and Philipp Rahe. "Differences in Molecular Adsorption Emanating from the (2× 1) Reconstruction of Calcite (104)." The Journal of Physical Chemistry Letters 14, no. 7 (2023): 1983-1989.

Heggemann, Jonas, Simon Aeschlimann, Tobias Dickbreder, Yashasvi S. Ranawat, Ralf Bechstein, Angelika Kühnle, Adam S. Foster, and Philipp Rahe. "Water adsorption lifts the (2× 1) reconstruction of calcite (104)." Physical Chemistry Chemical Physics (2023).

Install

Clone the required git repositories::

git clone --recurse-submodules [email protected]:huangchieh/ProbeParticle_workflow.git

Install python dependencies, using pipenv:

pip install --user pipenv
pipenv sync
pipenv shell

Usage

Step 0: Enter pipenv as describe above Step 1:

./BatchRun.sh <structure1> <structure2> ...

The workflow requires POSCAR, LOCPOT and CHGCAR files from VASP simulation of the system. These files should be added to the data folder with the same prefix, as shown by "example" files. The workflow.ipynb has the cells to add the workflow to an ASE database.

NOTE: Add a vacuum of atleast 20Å over the system for better visualisation.

Runner is used to run the workflow. There are two ways to run the workflow once added to the database::

• with a slurm workflow manager
• with terminal.

Use the correct runner definition from the workflow.ipynb for your environment. Once added to the workflow, runner can be started by::

# for slurm runner
python run.py

# for terminal runner
python run_terminal.py

After the run finishes, the database is updated with the relevant data. This data can be retrieved by running the "data retrieval" cell in workflow.ipynb. This adds the relevant cells in the Images folder.

The Images.ipynb (in the Images folder) can be used to visualise the images generated from the ProbeParticle workflow.

Citation

The workflow::

@article{heggemann2023differences,
  title={Differences in Molecular Adsorption Emanating from the (2$\times$ 1) Reconstruction of Calcite (104)},
  author={Heggemann, Jonas and Ranawat, Yashasvi S and Krejčí, Ondřej and Foster, Adam S and Rahe, Philipp},
  journal={The Journal of Physical Chemistry Letters},
  volume={14},
  number={7},
  pages={1983--1989},
  year={2023},
  publisher={ACS Publications}
}

ProbeParticle model::

@article{hapala2014mechanism,
  title={Mechanism of high-resolution STM/AFM imaging with functionalized tips},
  author={Hapala, Prokop and Kichin, Georgy and Wagner, Christian and Tautz, F Stefan and Temirov, Ruslan and Jel{\'\i}nek, Pavel},
  journal={Physical Review B},
  volume={90},
  number={8},
  pages={085421},
  year={2014},
  publisher={APS}
}

@article{hapala2014origin,
  title={Origin of high-resolution IETS-STM images of organic molecules with functionalized tips},
  author={Hapala, Prokop and Temirov, Ruslan and Tautz, F Stefan and Jel{\'\i}nek, Pavel},
  journal={Physical review letters},
  volume={113},
  number={22},
  pages={226101},
  year={2014},
  publisher={APS}
}