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
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
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 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 (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 , rotate, energy 0.05 eV
Run & visualize move (View-> Loop)