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.

本数据集包含复现发表于以下研究中的探针粒子模拟（Probe-Particle Simulations）所需全部数据：
《π扩展二氮杂[8]环烯的表面合成》（On-Surface Synthesis of a π-Extended Diaza[8]circulene）
作者：中村公博，李强强，翁德雷·克雷奇，亚当·S·福斯特*，孙克威，川合茂树*，伊藤真吾*
发表期刊：《美国化学会志》（J. Am. Chem. Soc.），2020年，第142卷，第26期，页码11363–11369
发表日期：2020年5月15日
DOI：https://doi.org/10.1021/jacs.0c02534

本数据集的文件说明与操作流程如下：
1. POSCAR：包含亚当·S·福斯特通过VASP（维也纳从头算模拟软件包）计算得到的DBCOT/Au(111)体系的密度泛函理论（Density Functional Theory，DFT）优化几何结构，该体系包含5层金原子层。
2. INCAR：亚当·S·福斯特用于DFT-VASP结构优化的输入文件，包含DFT计算的物理参数与输出设置。
3. geometry.in：FHI-AIMS（弗里茨·哈伯研究所从头算软件）的输入几何文件，包含3层金原子层，用于第一阶段FHI-AIMS计算输出本征矢，以及第二阶段FHI-AIMS计算输出投影态密度（Projected Density of States，PDOS）。
4. control-eigenvectors.in：基于FHI-AIMS完成的DFT计算的输入文件，包含物理参数与输出设置。实际运行计算前需将其重命名为"control.in"，该文件用于导出本征矢。
5. control-pdos.in：基于FHI-AIMS完成的DFT计算的输入文件，包含物理参数与输出设置。实际运行计算前需将其重命名为"control.in"，该文件用于导出原子投影态密度（PDOS）。
6. 无对应文件：在阿尔托大学Triton计算集群上完成的FHI-AIMS PBE泛函计算，所用FHI-AIMS开发版本发布于2019年11月19日，编译环境为OpenMPI以及英特尔（2017）ifort与MKL数学库：
1) 仅支持MPI版本的aims.191119.mpi.x用于导出科恩-沈（KS）本征矢（个人备注：现已无需使用该版本，亦可使用ScaLAPACK版本）
2) 支持MPI与ScaLAPACK的aims.191119.mpi.scalapack.x用于计算PDOS
除TXT（ASCII）格式的输出文件外，其余文件均未在此处提供（数据量过大，可通过已给出的geometry.in与control.in文件复现）。
7. output_mpi.txt：FHI-AIMS第一阶段计算的ASCII格式文本输出文件，用于本征矢生成。
8. output_scalapack.txt：FHI-AIMS第二阶段计算的ASCII格式输出文件，用于PDOS生成。
9. LOCPOT.xsf.tar.gz：经gunzip压缩的LOCPOT.xsf文件，包含原始VASP计算得到的静电势。LOCPOT文件到LOCPOT.xsf的转换通过v2xsf工具完成。
10. 无对应文件：本次所用PP-AFM（探针粒子原子力显微镜，Probe-Particle Atomic Force Microscopy）GitHub主分支版本，用于生成样品上方的弛豫探针粒子位置。
11. params-straight.ini：PP-AFM模拟的物理参数输入文件，实际运行前需将其重命名为"params.ini"。该文件用于直探针模拟。**注：此处存在一处小失误——计算中实际使用的是单极子而非四极子**。
12. params-tilt.ini：PP-AFM模拟的物理参数输入文件，实际运行前需将其重命名为"params.ini"。该文件用于倾斜探针模拟。**注：此处存在一处小失误——计算中实际使用的是单极子而非四极子**。
13. 无对应文件：PP-AFM的工作流程如下（详见项目Wiki）：
python PP-AFM/generateElFF.py -i LOCPOT.xsf
python PP-AFM/generateLJFF.py -i LOCPOT.xsf
python PP-AFM/relaxed_scan.py --pos
中间生成的文件未在此处存储，但可通过已提供的文件与上述工作流程复现。
14. 无对应文件：本次所用PP-STM（探针粒子扫描隧道显微镜，Probe-Particle Scanning Tunneling Microscopy）版本为2019年10月24日提交的Master分支b66fa0d，可用于CO修饰探针的STM成像（包括近场高分辨模式与远场模式），以及特定能量窗口内电子密度的“重构”。PP-AFM模块（用于PP-STM内部读取xsf与npy文件）为Python 2的最终版本。
15. PPSTM_simple_e0.3.py：用于直扫描模式下CO探针s轨道的PP-STM模拟脚本。
16. PPSTM_simple_e0.3_pxy.py：用于直扫描模式下CO探针pxy轨道的PP-STM模拟脚本。
17. SUM_no_atoms.py：基于预计算的s与pxy轨道生成成像结果的脚本。
18. Straight_tip_height_002.jpg：论文中使用的高度为002的成像结果可视化图的另一种展示形式。
19. distance_measurements.png：使用Gwyddion软件对原始PNG文件进行距离测量的截图。该黑白图像经Gwyddion着色后，标注的距离数值仅为实际值的1/10，可参考测量项9与绘图刻度进行对比校正。
20. PPSTM_simple_e0.3_pz_tilt.py：PP-STM模拟脚本，用于计算弛豫过程中CO探针pz轨道的倾斜效应，该探针初始处于倾斜平衡位置。
21. PPSTM_simple_e0.3_pxy_tilt.py：PP-STM模拟脚本，用于计算弛豫过程中CO探针px与py轨道的倾斜效应，该探针初始处于倾斜平衡位置。
22. SUM_no_atoms_tilt.py：PP-STM脚本，用于叠加CO探针倾斜时pz与pxy轨道的贡献并生成成像结果。
23. PPSTM_simple_f_e0.3.py：PP-STM模拟脚本，用于生成固定CO探针（25%s轨道+75%pxy轨道）在分子上方4埃处的dI/dV成像结果。
25. fixed_tip_dIdV_simulations.png：固定CO探针（25%s轨道+75%pxy轨道）在分子上方4埃处的dI/dV模拟成像结果。
26. DOS_plot_and_view.nb：用于绘制态密度的Wolfram Mathematica笔记本文件，该文件源自MathematicaForDFTnSPM GitHub仓库并经过小幅修改，此处提供原始版本的Mathematica笔记本。
27. DOS_plot_and_view.pdf：该Mathematica笔记本核心内容的打印输出文件。
28. PPSTM_xsf：PP-STM脚本，用于生成特定能量窗口内实空间电子密度“重构”所需的XSF文件。本次所用能量窗口如下：HOMO-1对应{-0.95,-0.85} eV，HOMO对应{-0.65,-0.55} eV，LUMO对应{+1.35,+1.45} eV，LUMO+1对应{+1.55,+1.65} eV，所有能量单位均为电子伏特（eV）。生成的XSF文件已通过VESTA软件进行可视化检查，此处未存储XSF文件，但可通过该工作流程复现。
29. measurement_gwyddion.gwy：保存了距离测量参数的Gwyddion项目文件。