On-Surface Synthesis of Disilabenzene-Bridged Covalent Organic Frameworks

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

On SiCOF_data.zip you will find the following folders:
2D_network_on_au:
    outcar_k3.fin: VASP output file. Contains the DFT parameters used to relax the Si-COF network geometry on gold
    poscar_k3.fin: VASP geometry file. This is the relaxed geometry of the Si-COF network on gold obtained in the previous calculation
    output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si-COF network on gold
C4Si2_ribb_on_au:
    outcar.fin: VASP output file. Contains the DFT parameters used to relax the Si ribbon 1 geometry on gold
    poscar.fin: VASP geometry file. This is the relaxed geometry of the Si ribbon 1 on gold obtained in the previous calculation
    output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si ribbon 1 network on gold
C4Si_ribb_on_au:
    outcar.fin: VASP output file. Contains the DFT parameters used to relax the Si ribbon 2 network geometry on gold
    poscar.fin: VASP geometry file. This is the relaxed geometry of the Si ribbon 2 network on gold obtained in the previous calculation
    output_aims.txt: FHI-aims output file. Contains the DFT parameters used to print the eigenvectors of the Si ribbon 2 network on gold
critic2:
    - Example of input files to simulate constant current (cc) and constant height (ch) stm using the Tersoff-Hamann approximation     through the critic2 code:
    stm_cc.inp  stm_ch.inp
NICs:
    - ORCA output files. Contains the DFT parameters and geometries used to calculate the nucleus independent nuclear shift (NICs) of several molecules:
    2D-buckled.out
    benzene.out
    disilahexa.out
    mol2Br.out
    2D-flat.out
    Brsila.out
    mol2Br+2Au.out
    silaben.out
PPSTM:
    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
PPSTM_simple.py: Script running PP-STM simulations with 13% of s and 87% of pxy orbitals (one possibility for simulating CO tip)

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. 

Version of the softwares and workflow on the PP-STM:
FHI-aims version ( https://aimsclub.fhi-berlin.mpg.de ) was aims.191119.mpi.scalapack.x .
cirtic2: https://aoterodelaroza.github.io/critic2/examples/example_14_01_stmqe/
PPM (PP-AFM) version was a master version from Nov 4, 2021: https://github.com/ProkopHapala/ProbeParticleModel/commit/327c61cdbd348307c5255c4618f12d28f4ababd5
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:
Using the poscar*.fin for creating the geometry.
Run a single point (no optimization) calculation with FHI-aims for creating the hartree potential ("cube_001_hartree_potential.cube") and 
then with control.in and PPSTM_simple.py file in the folder and with properly set way to
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
python3 PPAFM_PATH/generate_ElFF.py -i cube_001_hartree_potential.cube # these will create force-field for PP-AFM calculations #
python3 PPAFM_PATH/relaxed_scan.py --pos # this will create position of Probe Particle (simulating oxygen postions ) for the STM scan #
python3 PPSTM_simple.py # will create the PPSTM images #