On-Surface Synthesis of a π-Extended Diaza[8]circulene

All the data necessary for reproducing Probe-Particle Simulations published in :

On-Surface Synthesis of a π-Extended Diaza[8]circulene

Kimihiro Nakamura, Qiang-Qiang Li, Ondřej Krejčí, Adam S. Foster*, Kewei Sun, Shigeki Kawai*, and Shingo Ito*

J. Am. Chem. Soc. 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. POSCAR, which contains: DFT optimised geometry of DBCOT/Au(111) (w. 5 layers of Au) as calculated via VASP  by Adam. S. Foster

2. INCAR, Input file for DFT-VASP optimisation performed by Adam S. Foster containing physical and output settings of the DFT calculations

3. geometry.in. FHI-AIMS input geometry w. 3 Au layers used for eigenvectors output (1st FHI-AIMS run) and PDOS (2nd FHI-AIMS run)

4. control-eigenvectors.in, 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 

5. control-pdos.in,  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).

6. NO FILE:  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:
          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)
          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)

7. output_mpi.txt, FHI-AIMS 1st run text output in ASCII  format(used for eigenvectors production)

8. output_scalapack.txt,  FHI-AIMS 2nd run output in ASCII  format (used for PDOS production)

9. LOCPOT.xsf.tar.gz gunzip compressed LOCPOT.xsf file containing electrostatic potential from the original VASP calculation. LOCPOT -> LOCPOT.xsf conversion were proceeded via v2xsf

10. NO FILE, PP-AFM master github this version  used for creation of relaxed Probe Particle (PP) positions above the sample. 

11. params-stright.ini, 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 !!!

12. params-tilt.ini, 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 !!!

13. NO FILE, the PP-AFM workflow goes as written on the wiki:

python PP-AFM/generateElFF.py -i LOCPOT.xsf
python PP-AFM/generateLJFF.py -i LOCPOT.xsf
python PP-AFM/relaxed_scan.py --pos

The inter-created files are not saved here, but can be recreated with given files and workflow.

14. NO FILE, 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 ) 

15. PPSTM_simple_e0.3.py, Script running PP-STM simulations for "s" orbital of CO-tip for straight scan

16. PPSTM_simple_e0.3_pxy.py, Script running PP-STM simulations for "pxy" orbitals of CO-tip for straight scan

17. SUM_no_atoms.py, Script for creating images using pre-calculated "s" and "pxy" orbitals.

18. Straight_tip_height_002.jpg, a different visualisation of the image with height 002, which is used in the article.

19. distance_measurements.png, 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.

20. PPSTM_simple_e0.3_pz_tilt.py, PP-STM script for calculation of tilting "pz" orbital on CO-tip, as the tip is relaxing. The tip has originally tilted equilibrium position.

21. PPSTM_simple_e0.3_pxy_tilt.py, PP-STM script for calculation of tilting "px" and "py" orbitals on CO-tip, as the tip is relaxing. The tip has originally tilted equilibrium position.

22. SUM_no_atoms_tilt.py, PP-STM script for summing contribution of tilting "pz" and "pxy" orbitals of CO-tip and production of images

23. PPSTM_simple_f_e0.3.py, PP-STM script for creation of dI/dV images w. fixed CO-tip (25%s + 75%pxy) - 4Å above the molecule

25. fixed_tip_dIdV_simulations.png,  all far away -fixed- CO-tip (25%s,75%pxy) dIdV simulations 4Å above the molecule

26. DOS_plot_and_view.nb, 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.

27. DOS_plot_and_view.pdf, printed out important part of the Mathematica notebook.

28. PPSTM_xsf, 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.

29. measurement_gwyddion.gwy, Gwyddion file w. saved distances measurements.