Advancing Scanning Probe Microscopy Simulations: A Decade of Development in Probe-Particle Models
arxiv(2024)
摘要
The probe-particle model is an open-source package designed for simulation of
scanning probe microscopy experiments, employing non-reactive, flexible tip
apices (e.g., carbon monoxide, xenon, or hydrogen molecules) to achieve
sub-molecular resolution. This abstract introduces the latest version of the
probe-particle model, highlighting substantial advancements in accuracy,
computational performance, and user-friendliness over previous versions. To
demonstrate this we provide a comprehensive review of theories for simulating
non-contact Atomic Force Microscopy (nc-AFM), spanning from the simple
Lennard-Jones potential to the latest full density-based model. Implementation
of these theories are systematically compared against ab initio calculated
reference, showcasing their respective merits. All parts of the probe-particle
model have undergone acceleration by 1-2 orders of magnitude through
parallelization by OpenMP on CPU and OpenCL on GPU. The updated package
includes an interactive graphical user interface (GUI) and seamless integration
into the Python ecosystem via pip, facilitating advanced scripting and
interoperability with other software. This adaptability positions the
probe-particle model as an ideal tool for high-throughput applications,
including the training of machine learning models for the automatic recovery of
atomic structures from nc-AFM measurements. We envision significant potential
for this application in future single-molecule analysis, synthesis, and
advancements of surface science in general. Additionally, we discuss
simulations of other sub-molecular scanning-probe imaging techniques, such as
bond-resolved scanning tunneling microscopy and kelvin probe force microscopy,
all built on the robust foundation of the probe-particle model. Altogether this
demonstrates the broad impact of the model across diverse domains of surface
science and molecular chemistry.
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