Abstract
Auto-CO-AFM is an open-source software package for scanning probe microscopes that enables the automatic functionalization of scanning probe tips with carbon monoxide molecules. This enables machine operators to specify the quality of the tip needed utilizing a pre-trained library with off-the-shelf software. From a single image, the software package can determine which molecules on a surface are carbon monoxide, perform the necessary tip functionalization procedures, interface with microscope software to control the tip position, and determines the centeredness of the tip after a successful functionalization. This is of particular interest for atomic force microscopy imaging of molecules on surfaces, where the tip functionalization is a necessary and time consuming step needed for sub-molecular resolution imaging. This package is freely available under the MIT License. Program summaryProgram Title: Auto-CO-AFMCPC Library link to program files:https://doi.org/10.17632/khfvjhx4vb.1Developer's repository link:https://github.com/SINGROUP/Auto-CO-AFMLicensing provisions: MITProgramming language: PythonSupplementary material: Supplementary Information as PDFNature of problem: Scanning probe microscopy experiments are limited by the lack of automated tools in tip preparation, particularly when functionalizing an adatom or molecule on the end of a tip. These tip functionalizations are commonly manually-driven processes that are time-consuming for the operator.Solution method: We have developed an automated solution for tip functionalization for carbon monoxide molecules, which combines machine learning descriptors with automated software control of the tip preparation process. The Python program interfaces with a major vendor's software to scan, functionalize, and verify the tip quality for the operator. The source code, documentation, and basic program are posted online.Additional comments including restrictions and unusual features: Current version of software in publication requires STMAFM software from CreaTec GmbH in physical connection with a CreaTec DSP.
Highlights
✩ The review of this paper was arranged by Prof
This is of particular interest for atomic force microscopy imaging of molecules on surfaces, where the tip functionalization is a necessary and time consuming step needed for submolecular resolution imaging
To identify tip quality we take advantage of the fact that a carbon monoxide (CO) molecule adsorbed on a Cu(111) surface can be utilized to image the tip apex, which is the basis of the widely used carbon-monoxide front atom identification (COFI) method [41,42,43]
Summary
✩ The review of this paper was arranged by Prof. Volker Blum. ✩✩ This paper and its associated computer program are available via the Computer Physics Communications homepage on ScienceDirect (http://www.sciencedirect. com/science/journal/00104655). There has been significant recent interest in automated methods for preparing and analyzing tip quality for the operator [21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39] These advances have helped move the field of SPM forward by reducing the time and resources spent on the preparation of metallic tips. We perform STM imaging with a CO-functionalized tip apex, which gives characteristic sombrero-shaped images of the surface adsorbed CO [13] (see Fig. 1) The symmetry of these images allows determination of the configuration of the tip-adsorbed CO molecule and distinguishes CO from other adsorbates on the substrate. Auto-CO-AFM provides a working model to identify CO molecules from a variety of other impurities, control the hardware to perform spectroscopy on a particular CO molecule, and confirm that the tip has been functionalized and the quality of the functionalization
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