Hands-on exercises part 1

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’

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

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

GUI input editor controls

GUI input editor controls

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?

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

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

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)

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!

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

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

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)

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 ?!

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

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?

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)