AiiDAlab - Empa Surfaces app

The Empa Surfaces AiiDAlab app enables the user to prepare and run automatic AiiDA workflows for calculations relevant in on-surface chemistry. Features include:

generating various metal slab geometries;
geometry optimizations of adsorbed systems, bulk systems and isolated molecules;
chains of constrained geometry optimizations;
Nudged Elastic Band (NEB) calculations;
GW calculations for isolated systems;
...

AiiDAlab app for Scanning Probe Microscopy simulations

This repository contains AiiDA workflows and Jupyter GUI for running scanning probe microscopy simulations. The calculations are performed on top of a CP2K wave function optimization (ran with diagonalization) with the cp2k-spm-tools. The external tools need to be set up on the remote computer and can be conveniently done with setup_codes interface, which also installs the corresponding AiiDA plugins.

Features include:

Scanning tunnelling microscopy/spectroscopy (STM/STS) simulations.
Orbital analysis - calculates the STM/STS signatures of orbitals of isolated molecules.
Projected Density of States (PDOS) analysis - calculates the DOS projection on the adsorbed molecule together with gas-phase orbital content.
Atomic force microscopy (AFM) simulations - calls the ProbeParticle code.
High-resolution STM - simulates the STM/STS signatures performed with the CO tip.

For maintainers

To create a new release, clone the repository, install development dependencies with pip install '.[dev]', and then execute bumpver update --dry --major (--minor/--patch). This will display the changes that will be made to the repository - check them carefully.

Once you are happy with the changes, remove the --dry option and re-execute the command. This will:

Create a tagged release with bumped version and push it to the repository.
Trigger a GitHub actions workflow that creates a GitHub release.

Additional notes:

The release tag (e.g. a/b/rc) is determined from the last release. Use the --tag beta (alpha/gamma) option to switch the release tag.

Contact

For inquiries concerning Materials Cloud, please use the public issue tracker. For inquiries concerning the Empa Surfaces App, please contact carlo.pignedoli@empa.ch.

Acknowledgements

We acknowledge support from:

the NCCR MARVEL funded by the Swiss National Science Foundation;
the swissuniversities P-5 project "Materials Cloud".

Name		Name	Last commit message	Last commit date
Latest commit History 461 Commits
.github/workflows		.github/workflows
miscellaneous/logos		miscellaneous/logos
surfaces_tools		surfaces_tools
.gitignore		.gitignore
.pre-commit-config.yaml		.pre-commit-config.yaml
LICENSE.txt		LICENSE.txt
README.md		README.md
comments.ipynb		comments.ipynb
export_structure.ipynb		export_structure.ipynb
search.ipynb		search.ipynb
setup.cfg		setup.cfg
setup.py		setup.py
start.py		start.py
submit_adsorption_energy.ipynb		submit_adsorption_energy.ipynb
submit_geometry_optimization.ipynb		submit_geometry_optimization.ipynb
submit_gw.ipynb		submit_gw.ipynb
submit_gw_ic.ipynb		submit_gw_ic.ipynb
submit_pdos.ipynb		submit_pdos.ipynb
submit_phonons.ipynb		submit_phonons.ipynb
submit_reactions.ipynb		submit_reactions.ipynb
submit_spm.ipynb		submit_spm.ipynb
view_adsorption_energy.ipynb		view_adsorption_energy.ipynb
view_afm.ipynb		view_afm.ipynb
view_geometry_optimization.ipynb		view_geometry_optimization.ipynb
view_gw.ipynb		view_gw.ipynb
view_gw_ic.ipynb		view_gw_ic.ipynb
view_hrstm.ipynb		view_hrstm.ipynb
view_neb.ipynb		view_neb.ipynb
view_orbitals.ipynb		view_orbitals.ipynb
view_pdos.ipynb		view_pdos.ipynb
view_phonons.ipynb		view_phonons.ipynb
view_replica.ipynb		view_replica.ipynb
view_stm.ipynb		view_stm.ipynb

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nanotech-empa/aiidalab-empa-surfaces

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AiiDAlab - Empa Surfaces app

AiiDAlab app for Scanning Probe Microscopy simulations

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