Korea_handsonof terding jfjkkkjfijej.pptx

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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 a ll jobs / folder view j ob status reports & templates switch GUI functionality define & switch queues queue change default e.g . cores / nodes see files for this job search

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

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 wrt kpoints , 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 H 2 on graphene Make graphene (start with graphite, create 001 1L surface, delete 1 layer), make a 3x3 supercell Add H 2 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 H 2 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 2 nd one. Scan 2D? Manually break the symmetry?

18. The molecule gun: H 2 on graphene Exercise : hitting graphene with H 2 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 H 2 some 6A above surface MD details: 2000 steps, sample every 10, T = 100K, Berendsen thermostat, 100 fs, T=100K Keeping H 2 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)