At a Glance:
- New Paper on Arxiv: "Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models"
- Project: Probe Particle for Atomic Force Microscopy (PPAFM)
- Simulation Focus: High-Resolution Atomic Force Microscopy (HR-AFM) experiments
- Key Advancements: Enhanced computational performance, user-friendly interface, and model comparisons
- Applications: Suitable for HR-AFM, Kelvin Probe Force Microscopy (KPFM), and Bond-Resolved Scanning Tunneling Microscopy (BR-STM) simulations
- At Espeem, we are ready to adapt the code to your project
A Reliable Model - Now Faster and Easier to Use
At Espeem, we noticed a recent paper that landed on arxiv.org recently. It is titled "Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models" by Niko Oinonen et al. The Probe Particle for Atomic Force Microscopy (PPAFM) project is an open-source simulation tool indispensable for certain types of AFM experiments. The project benefits from active academic developers who have refined the code over a decade.
The Experiment that the PPAFM Code Simulates?
The PPAFM code is a sophisticated simulation tool designed to emulate Scanning Probe Microscopy (SPM) experiments, mainly High-Resolution Atomic Force Microscopy (HR-AFM). The model deals with the specialized case when the tip picks up an inert and flexible molecule from the surface. Picking up an inert and flexible molecule -- such as Xenon or carbon monoxide is done purposefully to achieve three effects:
Reproducibility: Having atomic control of the tip means eliminating a significant source of variability.
Prevent damage: Using an inert molecule will reduce the chance of a time-consuming tip crash or jump-to-contact.
Increase Resolution: Lateral forces will deflect a flexible tip. This effect creates distinctive abrupt jumps in the signal, which an experimentalist can use to identify a molecule or cluster.
How the Probe-Particle Code Works
The PPAFM code simulates the interaction between the tip and the sample by representing the flexible tip apex as a spherical particle attached to the AFM tip by a spring. The forces acting on this probe particle are calculated using various potential models, such as the Lennard-Jones potential, point charge electrostatics, and density functional theory (DFT) based electrostatics. This approach enables the precise simulation of the complex behaviors observed in high-resolution AFM images.
Key Advancements
Enhanced Computational Performance. The probe-particle model runs 1-2 orders of magnitude faster than previous versions through parallelization using OpenMP on CPUs and OpenCL on GPUs. This acceleration allows for rapid simulations, enabling high-throughput applications crucial for today's demanding R&D environments.
User-Friendly Interface. The updated package includes an interactive graphical user interface (GUI), making it easier for users to explore simulation results. Seamless integration into the Python ecosystem via pip facilitates advanced scripting and interoperability with other software.
Model Comparisons. The PPM project offers various approaches to simulate tip-sample interactions, ranging from the simple Lennard-Jones potential to sophisticated full-density-based models. The article's example calculations demonstrate the trade-offs incurred using different approximations. These comparisons make it much easier for a user to choose an appropriate approximation level.
The Expertise You Need to Run It
PPAFM is relatively easy to operate but relies on input from other atomistic codes. The inputs for the PPAFM code are charges, forces, relaxed coordinates, and electrostatic potential, so these inputs need to be generated from, for instance, VASP, QuantumEspresso, or SIESTA. Knowing how to transform outputs from these codes to other formats will also be necessary. Figuring out how to correctly use GPUs can be a challenge, but knowledge of GPUs is starting to be required to use many other atomic-scale codes anyway.
A Quick Example
Since PPAFM is based on Python scripts, installing and integrating the package into our workflow was quite simple. At Espeem, we like to use our in-house simulation workflow management, CalcTroll, to ensure all our tools work together and that we can quickly create a simple wrapper.
We used the Lennard-Jones plus point charges models (LJ + PC) on two molecules, water, and napthalene, at different heights.
The code was easy to use, well-documented, and fast as advertised.
More Than AFM
The software project can model other types of scanning probe microscopy (SPM) using the same tips, in addition to AFM with flexible tip apexes.
Kelvin Probe Force Microscopy (KPFM)
With the ability to simulate KPFM, researchers can study sub-molecular variations in charge distribution and polarizability within individual organic molecules, enhancing their understanding of material properties.
Bond-Resolved Scanning Tunneling Microscopy (BR-STM)
The model also supports Bond-Resolved Scanning Tunneling Microscopy (BR-STM) simulations. While the code can model the rigid tips, the main point is to use it for the flexible tips that this project specializes in.
How You Can Use the PPAFM Project
It is worth using this project if you regularly perform HR-AFM, KPFM, or BR-STM. If you or someone on your team has the time to set up the calculations, head to the PPAFM Project Site. However, if you need more time to set this up or have special requirements, we at Espeem would happily adapt the code to your needs or integrate it into your R&D workflows for atomistic simulations.
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