DOI: 10.5281/zenodo.6626953
title: On-Surface Synthesis of Disilabenzene-Bridged Covalent Organic Frameworks

description: Here you will find the list of folders and their contents used to generate the data and the figures published on "On-Surface Synthesis of Disilabenzene-Bridged Covalent Organic Frameworks" paper <strong>On SiCOF_data.zip you will find the following folders:</strong><br> <strong>2D_network_on_au:</strong><br> outcar_k3.fin: VASP output file. Contains the DFT parameters used to relax the Si-COF network geometry on gold<br> poscar_k3.fin: VASP geometry file. This is the relaxed geometry of the Si-COF network on gold obtained in the previous calculation<br> output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si-COF network on gold<br> <strong>C4Si2_ribb_on_au:</strong><br> outcar.fin: VASP output file. Contains the DFT parameters used to relax the Si ribbon 1 geometry on gold<br> poscar.fin: VASP geometry file. This is the relaxed geometry of the Si ribbon 1 on gold obtained in the previous calculation<br> output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si ribbon 1 network on gold<br> <strong>C4Si_ribb_on_au:</strong><br> outcar.fin: VASP output file. Contains the DFT parameters used to relax the Si ribbon 2 network geometry on gold<br> poscar.fin: VASP geometry file. This is the relaxed geometry of the Si ribbon 2 network on gold obtained in the previous calculation<br> output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si ribbon 2 network on gold<br> <strong>critic2</strong>:<br> - Example of input files to simulate constant current (cc) and constant height (ch) stm using the Tersoff-Hamann approximation through the critic2 code:<br> stm_cc.inp stm_ch.inp<br> <strong>NICs</strong>:<br> - ORCA output files. Contains the DFT parameters and geometries used to calculate the nucleus independent nuclear shift (NICs) of several molecules:<br> 2D-buckled.out<br> benzene.out<br> disilahexa.out<br> mol2Br.out<br> 2D-flat.out<br> Brsila.out<br> mol2Br+2Au.out<br> silaben.out<br> <strong>PPSTM</strong>:<br> params.ini: control file for the PPM (PP-AFM) code, that is used to calculate the position of oxygen for the relaxed STM scan calculated by PP-STM<br> <strong>PPSTM_simple.py</strong>: Script running PP-STM simulations with 13% of s and 87% of pxy orbitals (one possibility for simulating CO tip) <strong>On Source_data.zip you will find all the unprocessed images used in the paper. Additionally, it is included in CHGCAR_files.zip the charge densities used to generate the supplementary figure 5. </strong> <strong>Version of the softwares and workflow on the PP-STM:</strong><br> FHI-aims version ( https://aimsclub.fhi-berlin.mpg.de ) was aims.191119.mpi.scalapack.x .<br> cirtic2: https://aoterodelaroza.github.io/critic2/examples/example_14_01_stmqe/<br> PPM (PP-AFM) version was a master version from Nov 4, 2021: https://github.com/ProkopHapala/ProbeParticleModel/commit/327c61cdbd348307c5255c4618f12d28f4ababd5<br> PP-STM version was a master version from Nov 16, 2021: https://github.com/Probe-Particle/PPSTM/commit/4434739bd737e58a2fc556dff24e8e7d6eab084e The workflow for the PP-STM (CO-tip STM) images was as follows:<br> Using the poscar*.fin for creating the geometry.<br> Run a single point (no optimization) calculation with FHI-aims for creating the hartree potential ("cube_001_hartree_potential.cube") and <br> then with control.in and PPSTM_simple.py file in the folder and with properly set way to<br> PP-AFM folder and PP-STM path (in the top of the PPSTM_simple.py file) running following commands in command line: python3 PPAFM_PATH/generate_LJFF.py -i cube_001_hartree_potential.cube<br> python3 PPAFM_PATH/generate_ElFF.py -i cube_001_hartree_potential.cube # these will create force-field for PP-AFM calculations #<br> python3 PPAFM_PATH/relaxed_scan.py --pos # this will create position of Probe Particle (simulating oxygen postions ) for the STM scan #<br> python3 PPSTM_simple.py # will create the PPSTM images #