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"en": "The collection and preprocessing of this dataset has been reported in detail in Juola J., Hovi A., Rautiainen M., 2022. A spectral analysis of stem bark for boreal and temperate tree species. Ecology and Evolution. DOI:10.1002/ece3.8718\r\n\r\nThe dataset includes stem bark reflectance spectra of ten boreal and temperate tree species. We measured hemispherical-directional reflectance factors (HDRF) of stem bark samples. The data were measured using a Specim IQ imaging spectrometer attached to a tree mounting setup. The imaging spectrometer operates in the visible and near-infrared wavelength region (400–1000 nm). The measurements were made in the Greater Helsinki area in Finland, and in Järvselja in Estonia. We measured 20 trees per species, accounting to a total of 200 unique stem bark samples. One sample refers to a hyperspectral reflectance image taken of a single tree stem. The 200 mean spectral signatures (presented in this dataset) were calculated for each sample by averaging the HDRF values over all pixels per wavelength. The measurements were conducted from May to August 2020. All measurements were made under natural illumination conditions and the images were taken in perpendicular view-angle to the tree stem. The dataset includes two tabular files that contain: 1) the mean reflectance spectrum for each of the ten common boreal and temperate tree species (calculated from the 20 samples per species), and 2) all 200 reflectance spectra (20 per tree species). The sampled species were: Scots pine (Pinus sylvestris L.), Norway spruce (Picea abies (L.) Karst), silver birch (Betula pendula Roth), grey alder (Alnus incana (L.) Moench), black alder (Alnus glutinosa (L.) Gaertn.), English oak (Quercus robur L.), European aspen (Populus tremula L.), European ash (Fraxinus excelsior L.), Norway maple (Acer platanoides L.), and littleleaf linden (Tilia cordata Mill.).\r\n\r\nThe two spreadsheets are organized as follows: first three rows that start with hashtag (#) contain comments for citing, first column \"tree_species\" (Pinus_sylvestris, Picea_abies, Betula_pendula...) indicates the tree species, and the subsequent columns \"wl397.32\"-\"wl1003.58\" indicate the measured HDRF value at that wavelength. The encoding of the csv file is UTF-8. \r\n\r\nThe data in file \"mean_tree_species_stem_bark_reflectance_spectra_Juola_et_al_2021.csv\" is the same as what can be found in Version 1. We only changed the first row's naming to make it clearer.\r\n\r\nIf you use this dataset, please cite Juola et al. [1,2]:\r\n[1] Juola J., Hovi A., Rautiainen M., 2022. A spectral analysis of stem bark for boreal and temperate tree species. Ecology and Evolution. DOI:10.1002/ece3.8718\r\n[2] Juola J., Hovi A., Rautiainen M., 2022. A dataset of stem bark reflectance spectra for boreal and temperate tree species. Mendeley Data, V2, doi: 10.17632/pwfxgzz5fj.2"
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"en": "Thickness profile data measured for aluminium oxide thin film grown by atomic layer deposition (ALD) using trimethylaluminium and water as reactants at 300 degrees Celsius on an all-silicon lateral high-aspect-ratio (LHAR) test structure of type PillarHall(TM) LHAR3 (layout v1b), nominal gap height 500 nm. Part of this data has been used in the publication \"Saturation profile based conformality analysis for atomic layer deposition: aluminum oxide in lateral high-aspect-ratio channels\" https://doi.org/10.1039/D0CP03358H, where this sample was number 8 (unique manufacturing code V0001, see Table S3 of the supplementary info, which also contains details of the layouts: http://www.rsc.org/suppdata/d0/cp/d0cp03358h/d0cp03358h1.pdf) \r\n\r\nThickness profiles have been measured optically after removal of the top membrane by adhesive tape, by spectroscopic reflectometry in the visible wavelength range. In the optical thickness measurements, the refractive index is assumed constant (refractive index vs. wavelength this has been determined earlier for similar films also grown at 300 degrees Celsius) and thickness is allowed to vary. The optical model consists of smooth single-crystal silicon and ALD aluminium oxide films. Any silicon oxide below the ALD film is counted in the aluminium oxide thickness. Also roughness will impact the measurement result. For each measurement point, the location, the fitted thickness, and the goodness of fit is presented. For the 50x magnification, measurement spot diameter size is estimated as about 5-6 micrometers. The raw data have the centre of measurement as zero point of horizontal axis. The data needs to be shifted horizontally to have the zero point at the beginning of the LHAR cavity. Sometimes, the removal of the membrane has not worked in the beginning of the cavity (where the support pillars in the PillarHall LHAR3 design are more densely located) and the measurement has been made on a place that includes membrane remnants. In such cases, the fit of the optical model to the results has been poor and the data points should be rejected."
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"en": "This database contains all the necessary data (and metadata) for DFT calculations, PP-AFM and PP-STM simulations presented in:\r\n\r\nQitang Fan, Linghao Yan, Matthias W. Tripp, Ondřej Krejčí, Stavrina Dimosthenous, Stefan R. Kachel, Mengyi Chen, Adam S. Foster, Ulrich Koert, Peter Liljeroth and J. Michael Gottfried :\r\n\r\nBiphenylene network: A nonbenzenoid carbon allotrope ,\r\n\r\nScience 372, pp. 852-856 (2021); DOI: 10.1126/science.abg4509\r\n\r\n \r\n\r\nAltogether 12 different geometries of Biphenylene ribbons - 6 different widths and types of 2 edges (H and HF) - were calculated.\r\n\r\n \r\n\r\nAll the DFT calculations, were obtained with FHI-AIMS[1], HSE06[2] & TS-vdW[3] and light basis set (see `control.in` for more details)\r\n\r\n \r\n\r\nThe optimisations were done via FHI-AIMS (v. aims.191119.mpi.scalapack.x ). The inputs (and optimised geometries) can be found in zipped folder `opt` with separated folder for each type of ribbon. The parameters for the calculations can be found in `control.in` file. Input geometry in `geometry.in` and the optimized geometry in `geometry-opt.in`. The `run_aims_scalapack.slrm` was used for starting the calculations.\r\n\r\n \r\n\r\nThe calculations of bands (and plotted pDOS). The inputs, scripts and outputs can be found in zipped foled `bands` The FHI-aims version for these calculations was: aims.200229.mpi.scalapack.x, except for Biphenyl ribbon 6 ( aims.191119.mpi.scalapack.x ) and Biphenyl ribbon 21 ( aims.200422.mpi.scalapack.x ). The FHI-aims calculations were performed using standard inputs — `control.in` with physical settings and geometry.in with the geometries. For plotting the band structure the same way as it was done in the publication, the edges of the valence bands and conduction bands were extracted by means of the `grep_from_output.sh` scripts (except for 21H and 21HF, which are metallic) that produced `for_shift.txt` file. The important data in each directory — `atom_proj_dos_*****_raw.dat` and `band1001.out` together with the energy shifts — were then processed and plotted with Wolfram Mathematica (11.3.0.0) notebook `GNR_DOS_plot_and_view.nb` (optionally see the pdf). The plots for each width of the ribbons are in`bandsNdos_thor***.png`. \r\n\r\n \r\n\r\nThe PP-AFM[4] and PP-STM[5] calculations simulating CO-tip AFM and STM image are described in zipped folder `PP_simulations`; The calculations started with creation of 9x1x1 cell, because the PP-STM simulations can be done only at the Gamma k-point at the time. At the same time. the z-vector of the cell is lowered to 30 Å in order to save the memory space on the PP-AFM calculations. All of this was done via ASE[6] (by hand, not shown here). The (processed) geometries are written in `geometry.in`. The FHI-aims computations performed with aims.200422.scalapack.mpi.x. (with options saved in `control.in`) produced `cube_001_hartree_potential.cube`, containing the Hartree potential, and `KS_eigenvectors.band_1.kpt_1.out`, with the Eigen-energies and Eigen-vectors for the STM simulations. Both of these files are not saved (due to space reasons).\r\n\r\n \r\n\r\nThe PP-AFM simulations continued using the standard CO settings stored in `params.ini` using the `run_PPAFM.sh` script. The PP-AFM version was the Master branch:\r\n\r\n \r\n\r\n>>> Krejci Ondrej committed on 25 Mar 2020 \r\n\r\n>>> 1 parent 805f0bd\r\n\r\n>>> commit 76f6104d52b9ce44b6bbf76ed96846bcc5433c96\r\n\r\n \r\n\r\nThe resulting images are `df_atoms_002.png`. For plotting the overlaid atoms, it is important to have `input_plot.xyz` file with geometry (in the same directory), that will be plotted. This file was done from the 1x1x1 cell geometry through ASE.\r\n\r\n \r\n\r\nThe PP-STM simulations (dI/dV simulations) were done with the (last) python2 master version:\r\n\r\n \r\n\r\n>>> ondrejkrejci committed on 25 May 2020\r\n\r\n>>> 1 parent b66fa0d\r\n\r\n>>> commit 2b088e274240fd756bc8c2f53f870fe7a2e833ac\r\n\r\n \r\n\r\nThe original PPSTM_simple.py script was changed to the 2 new scripts used for the STM simulations: `PPSTM_cb.py` (conduction band) and `PPSTM_vb.py` (valence band). The Fermi Level was changed to the centre of the gap, with energies obtained of from the `for_shift.txt` created by the `grep_from_output.sh` script. The exceptions are 21H and 21HF, where the valence band was computed (just because of a history reason) through two separate runs with `PPSTM_e0.2_s.py` and `PPSTM_e0.2_pxy.py` and the final image was then created with `SUM_e0.2.py`. In these two cases, the Fermi Level was not changed, since these ribbons are metallic. \r\n\r\nThe 2 outputs (shown in fig. S18 in the Supplementary Information) are always in `didv_******.png` files\r\n\r\nReferences:\r\n\r\n[1] V. Blum et al., Ab initio molecular simulations with numeric atom-centered orbitals. Comput. Phys. Commun. 180, 2175-2196 (2009).\r\n\r\n[2] J. Heyd, G. E. Scuseria, M. Ernzerhof, Hybrid functionals based on a screened Coulomb potential. J. Chem. Phys. 118, 8207-8215 (2003).\r\n\r\n[3] A. Tkatchenko, R. A. DiStasio Jr., R. Car, M. Scheffler, Accurate and Efficient Method for Many-Body van der Waals Interactions. Phys. Rev. Lett. 8 108, 236402 (2012).\r\n\r\n[4] P. Hapala et al., Mechanism of high-resolution STM/AFM imaging with functionalized tips. Phys. Rev. B 90, 085421 (2014); P. Hapala, R. Temirov, F. S. Tautz, P. Jelínek, Origin of high-resolution IETS-STM images of organic molecules with functionalized tips. Phys. Rev. Lett. 113, 226101 (2014); https://github.com/ProkopHapala/ProbeParticleModel .\r\n\r\n[5] O. Krejčí, P. Hapala, M. Ondráček, P. Jelínek, Principles and simulations of high-resolution STM imaging with a flexible tip apex. Phys. Rev. B 95, 045407 (2017); https://github.com/ondrejkrejci/PPSTM ."
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"en": "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: \r\n\r\nJ. Järvi, .B Alldritt, O. Krejcí, .M Todorovic, P. Liljeroth and P. Rinke\r\n\r\nIntegrating Bayesian Inference with Scanning Probe Experiments for Robust Identification of Surface Adsorbate Configurations\r\n\r\narXiv preprint arXiv:2104.05302\r\n\r\n \r\n\r\nIn 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:\r\n\r\n******************************************************************************************************************************************************************\r\n\r\nAtomic geometry of the system is saved in a FHI-AIMS format in geometry.in file.\r\n\r\nThe Hartree potential was calculated through the FHI-AIMS using the options and settings saved in control.in file \r\n\r\nThe Hartree potential is stored in cube_001_hartree_potential.cube file.\r\n\r\n \r\n\r\nPPM (PP-AFM) simulations done with PP-AFM code: https://github.com/ProkopHapala/ProbeParticleModel \r\n\r\n>>>\r\n\r\n>>> commit 76f6104d52b9ce44b6bbf76ed96846bcc5433c96 (HEAD -> master, origin/master, origin/HEAD)\r\n\r\n>>> Author: Krejci Ondrej <krejcio1@t30400-la055.org.aalto.fi>\r\n\r\n>>> Date: Wed Mar 25 15:31:14 2020 +020\r\n\r\n \r\n\r\nThe options and setting from the PPM (PP-AFM) run are saved in params.ini file.\r\n\r\nThe 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.\r\n\r\nThe 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.\r\n\r\n \r\n\r\nThe 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\r\n\r\nstructure 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.\r\n\r\nThe final manuscript images were obtained via gwyddion ( http://gwyddion.net ) from the WSxM format of the data obtained through running the following command:\r\n\r\n`python PPM_Master/plot_results.py --WSxM --npy` in the same directory. The WSxM data are stored in *.xyz files.\r\n\r\n******************************************************************************************************************************************************************\r\n\r\n \r\n\r\nThe 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:\r\n\r\nStat_analysis_final.pdf"
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