Theoretial simulations for - Biphenylene network: A nonbenzenoid carbon allotrope

This database contains all the necessary data (and metadata) for DFT calculations, PP-AFM and PP-STM simulations presented in: Qitang 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 : Biphenylene network: A nonbenzenoid carbon allotrope , Science 372, pp. 852-856 (2021); DOI: 10.1126/science.abg4509 Altogether 12 different geometries of Biphenylene ribbons - 6 different widths and types of 2 edges (H and HF) - were calculated. All the DFT calculations, were obtained with FHI-AIMS[1], HSE06[2] & TS-vdW[3] and light basis set (see `control.in` for more details) The 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. The 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`. The 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). The 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: >>> Krejci Ondrej committed on 25 Mar 2020 >>> 1 parent 805f0bd >>> commit 76f6104d52b9ce44b6bbf76ed96846bcc5433c96 The 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. The PP-STM simulations (dI/dV simulations) were done with the (last) python2 master version: >>> ondrejkrejci committed on 25 May 2020 >>> 1 parent b66fa0d >>> commit 2b088e274240fd756bc8c2f53f870fe7a2e833ac The 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. The 2 outputs (shown in fig. S18 in the Supplementary Information) are always in `didv_******.png` files References: [1] V. Blum et al., Ab initio molecular simulations with numeric atom-centered orbitals. Comput. Phys. Commun. 180, 2175-2196 (2009). [2] J. Heyd, G. E. Scuseria, M. Ernzerhof, Hybrid functionals based on a screened Coulomb potential. J. Chem. Phys. 118, 8207-8215 (2003). [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). [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 . [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 .本数据库包含了发表于论文《Biphenylene network: A nonbenzenoid carbon allotrope》（联苯烯网络：一种非苯型碳同素异形体）、作者为Qitang Fan、Linghao Yan、Matthias W. Tripp、Ondřej Krejčí、Stavrina Dimosthenous、Stefan R. Kachel、Mengyi Chen、Adam S. Foster、Ulrich Koert、Peter Liljeroth与J. Michael Gottfried，刊载于《Science》372卷，第852-856页（2021年），DOI: 10.1126/science.abg4509）中所涉及的密度泛函理论（DFT, Density Functional Theory）计算、探针粒子原子力显微镜（PP-AFM, Probe Particle Atomic Force Microscopy）与探针粒子扫描隧道显微镜（PP-STM, Probe Particle Scanning Tunneling Microscopy）模拟所需的全部数据及元数据（metadata）。 本数据集中共包含12种不同构型的联苯烯纳米带（Biphenylene ribbon）——对应6种宽度与2种边缘类型（氢端H与氟氢端HF）的构型。所有DFT计算均通过FHI-AIMS[1]软件完成，泛函采用HSE06[2]与TS-vdW[3]，并使用轻量基组（详细设置详见`"control.in"`文件）。结构优化计算使用FHI-AIMS版本为aims.191119.mpi.scalapack.x。计算输入文件与优化后构型均可在压缩文件夹`"opt"`中获取，该文件夹下为每种纳米带类型单独设立了独立子目录。计算参数可在`"control.in"`文件中查看，初始构型存储于`"geometry.in"`，优化后构型存储于`"geometry-opt.in"`，计算启动脚本为`"run_aims_scalapack.slrm"`。 能带（bands）与投影态密度（pDOS, projected Density of States）计算相关的输入文件、脚本与输出文件可在压缩文件夹`"bands"`中获取。本次能带计算使用的FHI-aims版本为aims.200229.mpi.scalapack.x，仅联苯烯纳米带6（使用aims.191119.mpi.scalapack.x版本）与联苯烯纳米带21（使用aims.200422.mpi.scalapack.x版本）除外。本次FHI-aims计算均采用标准输入文件：包含物理设置的`"control.in"`与包含构型的`"geometry.in"`。 如需复刻论文中的能带结构绘图，需通过`"grep_from_output.sh"`脚本提取价带与导带的边界，该脚本会生成`"for_shift.txt"`文件（21H与21HF为金属体系除外）。各目录下的关键数据：`"atom_proj_dos_*****_raw.dat"`与`"band1001.out"`文件结合能量偏移量，将通过Wolfram Mathematica (11.3.0.0)笔记本`"GNR_DOS_plot_and_view.nb"`（亦可查看配套PDF文件）进行处理与绘图。各宽度纳米带的绘图结果存储于`"bandsNdos_thor***.png"`。 模拟一氧化碳修饰针尖的AFM与STM图像的相关内容存储于压缩文件夹`"PP_simulations"`。模拟初始会先创建9×1×1晶胞，因PP-STM模拟仅支持在Γ点（Gamma k-point）单次计算；同时将晶胞的z轴长度调整至30 Å以节省PP-AFM计算所需的内存空间。上述操作均通过原子模拟环境（ASE, Atomic Simulation Environment）[6]完成（手动操作，未展示具体流程）。处理后的构型存储于`"geometry.in"`。本次FHI-aims计算使用aims.200422.scalapack.mpi.x版本（参数存储于`"control.in"`），计算生成了包含哈特里势（Hartree potential）的`"cube_001_hartree_potential.cube"`，以及包含STM模拟所需本征能量（Eigen-energy）与本征矢量（Eigen-vector）的`"KS_eigenvectors.band_1.kpt_1.out"`，但因存储空间限制未保存这两个文件。 PP-AFM模拟部分：使用`"run_PPAFM.sh"`脚本，调用存储于`"params.ini"`中的标准CO针尖设置。本次PP-AFM版本为Master分支：>>>Krejčí Ondrej于2020年3月25日提交的提交记录：1个父提交805f0bd，提交哈希76f6104d52b9ce44b6bbf76ed96846bcc5433c96。最终生成的图像为`"df_atoms_002.png"`。如需绘制叠加原子的图像，需在对应目录下提供包含待绘图构型的`"input_plot.xyz"`文件，该文件通过ASE从1×1×1晶胞构型转换而来。 PP-STM模拟（微分电导（dI/dV）模拟）部分：使用Python 2的最新Master版本：>>>ondrejkrejci于2020年5月25日提交的提交记录：1个父提交b66fa0d，提交哈希2b088e274240fd756bc8c2f53f870fe7a2e833ac。原`"PPSTM_simple.py"`脚本被替换为两个用于STM模拟的新脚本：`"PPSTM_cb.py"`（导带）与`"PPSTM_vb.py"`（价带）。费米能级（Fermi Level）调整至带隙中心，能量偏移量通过`"grep_from_output.sh"`脚本生成的`"for_shift.txt"`文件获取。仅21H与21HF为例外：因历史原因，其价带通过分别运行`"PPSTM_e0.2_s.py"`与`"PPSTM_e0.2_pxy.py"`计算得到，最终图像通过`"SUM_e0.2.py"`生成，且因该两种纳米带为金属体系，未调整费米能级。这两种体系的输出结果（对应补充信息中的图S18）均存储于`"didv_******.png"`文件。 参考文献： [1] V. Blum et al., Ab initio molecular simulations with numeric atom-centered orbitals. Comput. Phys. Commun. 180, 2175-2196 (2009). [2] J. Heyd, G. E. Scuseria, M. Ernzerhof, Hybrid functionals based on a screened Coulomb potential. J. Chem. Phys. 118, 8207-8215 (2003). [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). [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 . [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 . [6] 原子模拟环境（ASE, Atomic Simulation Environment）