DOI: 10.5281/zenodo.4710346
title: CO-tip fm-nc-AFM simulations of 1S-camphor/Cu(111) stable configurations

description: Here are four *.zip files containing all the necessary data for recalculation of the PPM (PP-AFM) [see ref.] images for all the four theoretical structures ( A1 , A2 , A3 and A4 ) as they are published in the manuscriptr: J. Järvi, .B Alldritt, O. Krejcí, .M Todorovic, P. Liljeroth and P. Rinke Integrating Bayesian Inference with Scanning Probe Experiments for Robust Identification of Surface Adsorbate Configurations arXiv preprint arXiv:2104.05302 <em>Adv. Funct. Mater.</em> 2021, 2100519. https://doi.org/10.1002/adfm.202100519 In all these zip files you can find the exact pathway for reconstruction of the data as welll as the published results as saved in the separated README.txt files: ****************************************************************************************************************************************************************** Atomic geometry of the system is saved in a FHI-AIMS format in geometry.in file. The Hartree potential was calculated through the FHI-AIMS using the options and settings saved in control.in file The Hartree potential is stored in cube_001_hartree_potential.cube file. PPM (PP-AFM) simulations done with PP-AFM code: https://github.com/ProkopHapala/ProbeParticleModel &gt;&gt;&gt; &gt;&gt;&gt; commit 76f6104d52b9ce44b6bbf76ed96846bcc5433c96 (HEAD -&gt; master, origin/master, origin/HEAD) &gt;&gt;&gt; Author: Krejci Ondrej &lt;krejcio1@t30400-la055.org.aalto.fi&gt; &gt;&gt;&gt; Date: Wed Mar 25 15:31:14 2020 +020 The options and setting from the PPM (PP-AFM) run are saved in params.ini file. The PPM (PP-AFM) run was done through `./run_ppafm.sh` ; the run_ppafm bash file contains all 4 necessary steps for producing the simulated CO-AFM images. The PP-AFM code uses the geometry saved in the cube_001_hartree_potential.cube file as it shifts the coordinates according to the origin of the cube file. The images used for this publication are in the *.png files. The height stated in the *.png images is agains 0.0; The height against the heighest atom of the structure was calculated through coordinates stored in geometry.in (the error caused by the non 0. 0. 0. of the cube file is lower than 0.05 Angstroms) file. The final manuscript images were obtained via gwyddion ( http://gwyddion.net ) from the WSxM format of the data obtained through running the following command: `python PPM_Master/plot_results.py --WSxM --npy` in the same directory. The WSxM data are stored in *.xyz files. ****************************************************************************************************************************************************************** The input data and results (together with the procedure) of the statistical analysis of all the measured angles and lengths for all the experimental and simulation data can be found in: Stat_analysis_final.pdf
description: Controlling the properties of organic/inorganic materials requires detailed knowledge of their molecular adsorption geometries. This is often unattainable, even with current state-of-the-art tools. Visualizing the structure of complex non-planar adsorbates with atomic force microscopy (AFM) is challenging, and identifying it computationally is intractable with conventional structure search. In this fresh approach, cross-disciplinary tools are integrated for a robust and automated identification of 3D adsorbate configurations. Bayesian optimization is employed with first-principles simulations for accurate and unbiased structure inference of multiple adsorbates. The corresponding AFM simulations then allow fingerprinting adsorbate structures that appear in AFM experimental images. In the in-stance of bulky (1S)-camphor adsorbed on the Cu(111) surface, three matching AFM image contrasts are found, which allow correlating experimental image features to distinct cases of molecular adsorption.
description: {"references": ["P. Hapala, G. Kichin, C. Wagner, F. S. Tautz, R. Temirov, P. Jel\u00ednek, Phys. Rev. B 2014, 90, 085421.", "P. Hapala, R. Temirov, F. S. Tautz, P. Jel\u00ednek, Phys. Rev. Lett. 2014, 113, 226101.", "Probe Particle Model code repository, https://github.com/ProkopHapala/ProbeParticleModel."]}