Probe-Particle Model

Simple and efficient simulation software for high-resolution atomic force microscopy (HR-AFM) and other scanning probe microscopy (SPM) techniques with sub-molecular resolution (STM, IETS, TERS). It simulates the deflection of the probe particle attached to the tip, where the probe particle represents a flexible tip apex (typically CO molecule, but also e.g. Xe, Cl-, H2O and others). The Python package is named as ppafm.

Documentation

• Wiki
• readthedocs
• Auto-generated:
  • DeepWiki
  • Context7

Installation

The standard way of installing ppafm is:

pip install ppafm

This should install the package and all its dependencies including CPU version and fully working CLI:

The most up-to-date installation guide can be found on the dedicated wiki page.

Command line interface (CLI)

Once ppafm is installed, a collection of command-line tools will become available to the user. Their names start with the ppafm- prefix. To get more information about a given tool, run it with the -h option, e.g.:

ppafm-generate-ljff -h

For more information, please consult the dedicated page on the command line interface of ppafm.

GPU version and Graphical User Interface (GUI)

The package comes with a GPU speedup version and convenient graphical user interface. Unlike CLI, these needs to be explicitly enabled during the installation. To enable it, check the dedicated section on the Install ppafm wiki page. To know more about the GUI interface, please consult the ppafm GUI wiki page. Additional information about the GPU version can be found on readthedocs tutorial, at models and models differences wiki pages.

Usage examples

We provide a set of examples in the examples directory. To run them, navigate to the directory and run the run.sh script. For example:

cd examples/PTCDA_single
./run.sh

You can study the script to see how to run the simulation. Also, have a look at the params.ini file and the wiki to see how to set up the simulation parameters.

Once the simulation is finished, several files and folders will be created.

See also the tutorial for using the Python API for running GPU-accelerated simulations.

For contributors

If you miss some functionality or have discovered issues with the latest release - let us know by creating an issue. If you would like to contribute to the development of the ppafm code, please read the Developer's Guide wiki page. Small improvements in the documentation or minor bug fixes are always welcome.

Publications describing the Probe-Particle Model

If you have used ppafm in your research, please cite the following articles:

• Niko Oinonen, Aliaksandr V. Yakutovich, Aurelio Gallardo, Martin Ondracek, Prokop Hapala, Ondrej Krejci, Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models, Comput. Phys. Commun. 305, 109341 - Available online 10 August 2024
• Prokop Hapala, Georgy Kichin, Christian Wagner, F. Stefan Tautz, Ruslan Temirov, and Pavel Jelínek, Mechanism of high-resolution STM/AFM imaging with functionalized tips, Phys. Rev. B 90, 085421 – Published 19 August 2014
• Prokop Hapala, Ruslan Temirov, F. Stefan Tautz, and Pavel Jelínek, Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips, Phys. Rev. Lett. 113, 226101 – Published 25 November 2014

License

MIT