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Hands-on exercises part 1

Explore ADFjobs GUI for job bookkeeping, molecule building, spectroscopy calculations, and band structure analysis. Execute hands-on exercises for practical understanding and application in computational chemistry.

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Hands-on exercises part 1

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  1. Hands-on exercises part 1

  2. Getting started with the GUI Starting ADFjobs: job bookkeeping tool • Win: dbl-click desktop item • Mac: open Application • Linux: run $ADFBIN/adfjobs • Other GUI modules: (Input, View, Levels, Movie, Spectra, Band Structure, ADFTrain, COSMO-RS, …) • Can be opened by dbl-clicking ‘.exe’ (Win) or opening e.g. ‘$ADFBIN/adfinput’

  3. ADFjobs: job bookkeeping switch GUI functionality define & switch queues reports & templates change default e.g. cores / nodes job status see files for this job queue search all jobs / folder view

  4. Basic calculations & settings switch modules search job types & set up job type charge/spin functional & relativistic appr basis & numerical accuracy builder tools preoptimize > = more details symmetryze

  5. GUI input editor controls

  6. GUI input editor controls

  7. Building molecules www.scm.com/doc/Tutorials/GUI_overview/Building_Molecules.html • NB: tutorials also offline! • Import: SMILES, xyz, cif, pdb, … • Included library + building • Excercise: Build acetophenone • By searching for it in the GUI • By starting from the benzene template (press 2 for double bond, Ctrl+E to add Hs) • By importing smiles CC(=O)c1ccccc1 (e.g. from Wikipedia or Chemspider) • Exercise: Symmetrize, pre-opt (MOPAC, DFTB) • Optimize with ADF: SR-ZORA-PBE-D3(BJ)/DZP – differences? speed?

  8. Quick properties with COSMO-RS • From the SCM menu, choose COSMO-RS • Add the acetophenone smiles string • Properties => Pure compound properties • Other properties (vapor pressure, solubility (install database), logP, … ) • Results should be better with MOPAC or ADF calculations of compounds

  9. Spectra: IR www.scm.com/doc/Tutorials/ADF/ADF-GUI_tutorials.html#spectroscopy • Excercise: Calculate & visualize frequencies • First optimize geometry, or compound job ADF/AMS • Try ADF, DFTB3-D3BJ/3-ob, GFN-xTB, MOPAC • NB analytical frequencies for most GGAs, not for hybrids • Go to spectra, visualize the CO stretch at ~1690cm-1 • Increase the line width to ~20 & compare to NIST data • Add spectra of other calculations (File -> Add) 1.3 2. 1 2 or

  10. Spectra: UV/VIS • Exercise: • With ADF: calculate 10 allowed excitations • use SAOP model potential, DZP (or TZP), no core • See also UV/VIS FAQ for more tips • Go to spectra, change x-axis to nm • Increase the line width to ~10 • Visualize the pi-pi* NTOs at ~250 & 285nm • Compare to NIST data • Now rerun with method ‘sTDA’ and tick TDA • Also try TD-DFT+TB (ADF) • and TDDFTB (DFTB3-D3BJ/3-ob, QN2013, GFN-xTB) • Compare timings & spectra (File -> add spectra)

  11. Band structure, pDOS, fat bands, COOP • Exercise: ZnS bulk • New input, go to BAND • click on the ‘crystal’ builder tool in the bottom • select cubic -> Zincblende and accept the default • Settings: BP, SR-ZORA, and DZP • Select DOS and Bandstructure (default interpolation) • Run it!

  12. Band structure, pDOS, fat bands, COOP • Exercise: ZnS bulk • Visualize the band structure (SCM Menu). You will automatically see the pDOS and ‘fat bands’ • ZnS is a direct band gap semiconductor (p-s transition) • Check the logfile and output for band gap info and kmesh • Low band gap: try model potentials (TB-mBJ, GLLB-sc, GGA-1/2, HSE06? (benchmark study) • Should also be converged wrtkpoints, basis, etc. • Restart the calculation from SCF and in the DOS details tick ‘COOP’ • Visualize the crystal orbital overlap population between the Zn s and S p orbitals

  13. Band structure, pDOS with QE • Exercise: ZnS bulk with QE • Switch from BAND to Quantum ESPRESSO (may prompt download request) • Choose the same k-mesh (5x5x5), functional and Vanderbilt pseudopotentials • You will see a similar band structure, but they aren’t colored according to character • DOS can be projected by QE

  14. Surfaces, dielectric function • Exercise: ZnS monolayer: 2D-TDCDFT • Cut the 111 surface with the slicer tool, and choose 1 layer • From properties -> dielectric function choose NewResponse • Calculate 30 frequencies between 2-5 eV • Set the SCF convergence criterion to 0.01 and switch off the z-component • Run it (you will prompted Nosymm is used)

  15. Surfaces, dielectric function • Exercise: ZnS monolayer: 2D-TDCDFT • SCM -> Spectra will show the averaged dielectric function • Look at the susceptibility, polarizability and refractive index in Spectra->TDCDFT • You could use a ‘scissor’ shift to upshift the virtuals (from GLLB-sc, DFT-1/2, TB-mBJ?) • Converge with respect to k-points! • Geometry of the ions should be optimized, this will affect electronic properties • For free-standing ML, also optimize lattice ?!

  16. 2D PES scan on 2D system • Exercise: physisorption of H2 on graphene • Make graphene (start with graphite, create 001 1L surface, delete 1 layer), make a 3x3 supercell • Add H2 with the builder tools about 4A above the surface (move it) • Choose GFN-xTB, choose PES Scan as a task, and go to details (>) • Set up to scan the H-C distance 4-2.8A (7 points) and C-H-H angle 180-90 (6 points) • Reduce convergence criteria (Details) with a factor of 5 • Run and visualize with ADFmovie • Find the lowest point, load into ADFinput and minimize without constraints

  17. 1D PES scan on 2D system: find TS • Exercise: chemisorption of H2 on graphene • Bond the H atoms to adjacent C atoms • (Partially) Pre-optimize. NB: you can select atoms to pre-optimize interactively • PES scan, increasing both C-H distances simultaneously to 1.8 A, in 8 steps, low convergence • Try find a TS, followed by frequencies. How many imaginary modes do you have? • 2? => get rid of the 2nd one. Scan 2D? Manually break the symmetry?

  18. The molecule gun: H2 on graphene • Exercise: hitting graphene with H2 using DFTB • Use DFTB3-D3(BJ)/3ob-3-1 (you may have made a preset by now); Choose Molecular Dynamics • Make a 4x4 supercell of 1L graphene. Add H2 some 6A above surface • MD details: 2000 steps, sample every 10, T = 100K, Berendsen thermostat, 100 fs, T=100K • Keeping H2 selected, in Model -> Molecule gun, choose Add molecule; System -> New Region • Frequency 200, start at step 1 until 2000, coords sigma 3 3 0.2, rotate, energy 0.05 eV • Run & visualize move (View-> Loop)

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