DOI: 10.5281/zenodo.3926678
title: On-Surface Synthesis of a π-Extended Diaza[8]circulene

description: <strong>All the data necessary for reproducing Probe-Particle Simulations published in :</strong> On-Surface Synthesis of a π-Extended Diaza[8]circulene Kimihiro Nakamura, Qiang-Qiang Li, Ondřej Krejčí, Adam S. Foster<strong>*</strong>, Kewei Sun, Shigeki Kawai<strong>*</strong>, and Shingo Ito<strong>*</strong> <em>J. Am. Chem. Soc.</em> 2020, 142, 26, 11363–11369 Publication Date:May 15, 2020 https://doi.org/10.1021/jacs.0c02534 The protocol (and description of the files) is as follows: 1. <strong>POSCAR</strong>, which contains: DFT optimised geometry of DBCOT/Au(111) (w. 5 layers of Au) as calculated via VASP by Adam. S. Foster <strong>2. INCAR,</strong> Input file for DFT-VASP optimisation performed by Adam S. Foster containing physical and output settings of the DFT calculations <strong>3. geometry.in.</strong> FHI-AIMS input geometry w. 3 Au layers used for eigenvectors output (1st FHI-AIMS run) and PDOS (2nd FHI-AIMS run) <strong>4. control-eigenvectors.in,</strong> Input file containing physical and output settings of the DFT calculations performed with FHI-AIMS. To run the actual calculation renaming to "control.in" is necessary. This file was used for printing out the eigenvectors <strong>5. control-pdos.in, </strong> Input file containing physical and output settings of the DFT calculations performed with FHI-AIMS. To run the actual calculation renaming to "control.in" is necessary. The file used for printing out atom Projected Density Of States (PDOS). <strong>6. NO FILE</strong>: FHI-AIMS PBE calculation performed on Triton (Aalto Uni.) cluster w. developers version of FHI-AIMS from 19th November 2019 compiled with OpenMPI and Intel (2017) ifort & mkl:<br> 1) KS. eigenvectors with only mpi version aims.191119.mpi.x (personal note: not needed any more, one can use the scalapack version as well)<br> 2) PDOS w. mpi and scalapack version aims.191119.mpi.scalapack.x Except for the txt (ASCII) output files, all the other files not shown. (too much data, can be reproduced with given geometry.in & control.in files) <strong>7. output_mpi.txt</strong>, FHI-AIMS 1st run text output in ASCII format(used for eigenvectors production) <strong>8. output_scalapack.txt</strong>, FHI-AIMS 2nd run output in ASCII format (used for PDOS production) <strong>9. LOCPOT.xsf.tar.gz </strong>gunzip compressed LOCPOT.xsf file containing electrostatic potential from the original VASP calculation. LOCPOT -&gt; LOCPOT.xsf conversion were proceeded via v2xsf <strong>10. NO FILE</strong>, PP-AFM master github this version used for creation of relaxed Probe Particle (PP) positions above the sample. <strong>11. params-stright.ini</strong>, input file for the PP-AFM simulations with physical settings. Before the run necessary to rename to "params.ini". This file was used for the simulation with a straight tip. !!! Small mistake here - monopole instead of 4pole used for the calculations !!! <strong>12. params-tilt.ini</strong>, input file for the PP-AFM simulations with physical settings. Before the run necessary to rename to "params.ini". This file was used for the simulation with a straight tip. !!! Small mistake here - monopole instead of 4pole used for the calculations !!! <strong>13. NO FILE</strong>, the PP-AFM workflow goes as written on the wiki: <pre><code>python PP-AFM/generateElFF.py -i LOCPOT.xsf python PP-AFM/generateLJFF.py -i LOCPOT.xsf python PP-AFM/relaxed_scan.py --pos</code></pre> The inter-created files are not saved here, but can be recreated with given files and workflow. <strong>14. NO FILE</strong>, PP-STM, version used for CO-tip STM (close aka High Resolution; and far away) and for "reconstruction" of electronic densities within certain energy window: Master b66fa0d commited on 24 Oct 2019. The PP-AFM (used internally in PP-STM for xsf and npy reading, was the last version of python2 ) <strong>15. PPSTM_simple_e0.3.py</strong>, Script running PP-STM simulations for "s" orbital of CO-tip for straight scan <strong>16. PPSTM_simple_e0.3_pxy.py</strong>, Script running PP-STM simulations for "pxy" orbitals of CO-tip for straight scan <strong>17. SUM_no_atoms.py</strong>, Script for creating images using pre-calculated "s" and "pxy" orbitals. <strong>18. Straight_tip_height_002.jpg</strong>, a different visualisation of the image with height 002, which is used in the article. <strong>19. distance_measurements.png</strong>, Screenshot from measurements of distances - using Gwyddion and original PNG file as input - the black and white image was coloured by Gwyddion - written distances are 10x lower, than in reality, see measurement 9 for comparison with plotted ticks. <strong>20. PPSTM_simple_e0.3_pz_tilt.py, </strong>PP-STM script for calculation of tilting "pz" orbital on CO-tip, as the tip is relaxing. The tip has originally tilted equilibrium position. <strong>21. PPSTM_simple_e0.3_pxy_tilt.py, </strong>PP-STM script for calculation of tilting "<em>px</em>" and "<em>py</em>" orbitals on CO-tip, as the tip is relaxing. The tip has originally tilted equilibrium position. <strong>22. SUM_no_atoms_tilt.py</strong>, PP-STM script for summing contribution of tilting "pz" and "pxy" orbitals of CO-tip and production of images <strong>23. PPSTM_simple_f_e0.3.py</strong>, PP-STM script for creation of dI/dV images w. fixed CO-tip (25%s + 75%pxy) - 4Å above the molecule <strong>25. fixed_tip_dIdV_simulations.png</strong>, all far away -fixed- CO-tip (25%s,75%pxy) dIdV simulations 4Å above the molecule <strong>26. DOS_plot_and_view.nb</strong>, Density of states were plotted using slightly modified DOS_plot_and_view.nb Wolfram Mathematica notebook (fromMathemticaForDFTnSPM github repository); here is the original mathematica notebook. <strong>27. DOS_plot_and_view.pdf</strong>, printed out important part of the Mathematica notebook. <strong>28. PPSTM_xsf</strong>, PP-STM script for creation of XSF files for "reconstruction" of real space electron density within given energy windows. We used energy windows: {-0.95,-0,85} for HOMO-1, {-0.65,-0,55} for HOMO,{+1.35,+1.45} for LUMO and {+1.55,+1.65} for LUMO+1. All the energies are in eV. The XSF file, which was visually checked via VESTA software. The XSF files are not stored here, but can be recreated using this workflow. <strong>29. measurement_gwyddion.gwy</strong>, Gwyddion file w. saved distances measurements.
description: Small mistake here - monopole instead of 4pole used in for the Probe-Particle calculations; Not changing the physical reality in the paper, just some of the calculated line-lenghts could differ by a little bit