Table of Contents
GUI Tutorials
Table of Contents
Introduction
Starting the GUI: start ADFjobs
UNIX (such as Linux) users
Windows users
Macintosh users
GUI modules (for the ADF-GUI, BAND-GUI, COSMO-RS GUI, ReaxFF-GUI, and so on)
Keyboard shortcuts
ADF-GUI overview tutorials
Tutorial 1: Geometry optimization of ethanol
Step 1: Preparations
Start ADFjobs
Make a directory for the tutorial
Start ADFinput
Undo
Step 2: Create your molecule
Create a molecule
Create the first carbon atom
Create the second carbon atom
Create the oxygen atom
Add the hydrogens
Pre-optimize the geometry
Viewing the molecule
Rotate, translate, or zoom
Atom colors
Save picture
Molecular conformation
Rotate such that you look along the C-C axis
Select the top CH3 group
Rotate the selection
Back to Staggered Geometry
Getting and setting geometry parameters
Bond length
Bond angle
Dihedral angle
Coordinates
Extending and changing your molecule
Delete an atom
Change the type of an atom
Change the bond type of an existing bond
Add new (bonded) atoms
Step 3: Select calculation options
Preset
Title
XC functional
Basis set
Integration
Other input options
Step 4: Run your calculation
Save your input and create a job script
Run your calculation
Step 5: Results of your calculation
Logfile: ADFtail
Files
Geometry changes: ADFmovie
Orbital energy levels: ADFlevels
Electron density, potential and orbitals: ADFview
Browsing the Output: ADFoutput
Tutorial 2: Building Molecules
Step 1: Start ADFinput
Step 2: Search for ethanol
Step 3: Import XYZ for ethanol
Step 4: Import SMILES string
Step 5: Build ethanol using the structure tool
Step 6: Building a peptide chain using the structures tool
Step 7: Metal complexes and ligands
Predefined Metal Complex Geometries
Bidentate Ligands
Modifying the Plane Angle
Step 8: Your own structures library
Defining your structures
Using dummy atoms
Step 9: A sphere of Cu atoms, cut out of the crystal
Tutorial 3: Building Crystals and Slabs
The Crystal Structure Database
Crystal builder (from space group information)
Slicer: building slabs
A three layer slab of the Cu(111) surface
Enlarging the unit cell
Tutorial 4: Excitation energies of ethene
Step 1: Start ADFinput
Step 2: Create your ethene molecule
Step 3: Optimize the geometry
Step 4: Calculate the excitation energies
Select calculations options
Run the calculation
Step 5: Results of your calculation
Logfile: ADFtail
Energy levels: level diagram and DOS
Excitation spectrum: ADFspectra
Orbitals, orbital selection panel: ADFview
Transition density: ADFview
ADF Output
Closing the ADF-GUI modules
Tutorial 5: Vibrational frequencies of ethane
Step 1: Start ADFinput
Step 2: Create your ethane molecule
Step 3: Optimize the geometry
Step 4: Calculate the vibrational frequencies of ethane
Step 5: Results of your calculation
Logfile: ADFtail
IR-spectrum (vibrational spectrum): ADFspectra with normal mode selector and ADFmovie
Advanced ADF-GUI tutorials
Tutorial 6: HCN Isomerization Reaction
Step 1: Prepare the HCN molecule
Step 2: Create a rough approximation for the transition state geometry
Step 3: Finding the transition state: prepare approximate Hessian
Step 4: Search for the transition state
Step 5: Calculating frequencies at the transition state
Step 6: Following the reaction coordinate
Tutorial 7: TlH (thallium hydride) Spin-Orbit Coupling
Step 1: Prepare molecule
Step 2: Set calculation options
Step 3: Run your calculation
Step 4: Results of the calculation
TlH energy diagram
Visualization of spinors
Step 5: Calculate the atomization energy including spin-orbit coupling
The Tl atom
The H atom
TlH atomization energy
Tutorial 8: Multi-Level principles: Regions, QUILD and QMMM
Step 1: Regions
Generate regions
Visualization options per region
Step 2: QUILD
Step 3: QMMM
Generate ethanol in water
Set up the QM/MM calculation
Run the QMMM calculation, and see results
Tutorial 9: ADF Fragment Analysis
Step 1: Build Ni(CO)4
Step 2: Define fragments
Step 3: set up the fragment analysis run
Step 4: Run the fragment analysis and view the results
Step 5: Build PtCl4H22-
Step 6: Define fragments
Step 7: Run the fragment analysis and view the results
Tutorial 10: Basis Set Effects for NH3 (ammonia) Geometry
Step 1: Create and pre-optimize your molecule
Step 2: Set up a single ADF calculation
Step 3: Set up a batch of ADF jobs
Step 4: Run your set of ADF jobs
Step 5: Analyze results of several calculations at once
Tutorial 11: Caffeine Bader (AIM) analysis, Benzene NBO visualization and Occupations
Step 1: Setup and optimize Caffeine
Step 2: Calculation setup
Step 3: Orbitals, Potential and AIM results
Step 4: Benzene Bader charge analysis and NBOs
Step 5: Occupations
Tutorial 12: Spin Coupling in Fe4S4 Cluster
Step 1: Create and pre-optimize the Fe4S4 cubane model
Step 2: Obtain the solution for the high-spin (HS) state of the cubane
Step 3: Couple the spins in Fe4S4 using the SpinFlip option
Step 4: Coupling the spins using the ModifyStartPotential option, use ARH SCF convergence method
Step 5: View the spin density of the broken symmetry (BS) solutions
BAND-GUI tutorials
Tutorial 1: with a grain of salt
Step 1: Start BANDinput
Step 2: Set up the unit cell
Step 3: Add the atoms
Step 4: Running the calculation
Step 5: Examine the band structure
Step 6: Visualizing the results
Plotting the orbitals
Plotting the partial density-of-states
Plotting the deformation density
Step 7: Check the charges
Tutorial 2: a transition state search
Step 1: Create the H3 toy system
Step 2: Optimize the geometry
Step 3: Calculate the Hessian
Step 4: Search the transition state
Tutorial 3: a transition state search with a partial Hessian*
Step 1: Create the system
Step 2: Calculate a partial Hessian
Step 3: Transition state search with a frozen substrate
DFTB-GUI tutorials
Tutorial 1: DFTB charges, frequencies and dynamics (MD)
Step 1: DFTB: Pre-optimization and Charges
Step 2: Frequency evaluation
Step 3: Molecular dynamics
Tutorial 2: Periodic DFTB, Lattice Optimization, DOS, band structure and phonons
Step 1: Lattice optimization - input setup
Step 2: Lattice optimization - execution
Step 3: DOS and Band Structure
Step 4: Phonons
Tutorial 3: Proton affinities with third order DFTB (DFTB3)
Step 1: Optimization of the neutral molecule
Step 2: Optimization of the acetate and the hydrogen ions
MOPAC-GUI tutorial
Tutorial 1: Toluene charges, movies, frequencies and normal modes
Set up Toluene in MOPACinput
Run interactively
Save job and results: charges and movies
IR spectrum and normal modes
ReaxFF-GUI tutorials
Tutorial 1: Burning methane
Step 1: Start ReaxFFinput
Step 2: Create a methane / oxygen mixture
Step 3: Prepare for burning: set up the simulation
Step 4: Burn it: run the simulation
Tutorial 2: Water on an aluminum surface
Step 1: Start ReaxFFinput
Step 2: Creating the surface
Step 3: Add solvent
Step 4: Set up the simulation, including a temperature regime
Step 5: Run the simulation
COSMO-RS GUI Tutorials
Tutorial 1: COSMO result files
Step 1: Start ADFinput
Step 2: Create the molecule
Step 3: Optimize the gas phase geometry
Step 4: Set up the ADF COSMO parameters
Step 5: Perform the ADF COSMO calculation and obtain the ADF COSMO result file
Step 6: MOPAC COSMO result file
Tutorial 2: COSMO-RS overview: analysis
Step 1: Copy COSMO result Files
Step 2: Start ADFcrs
Step 3: Add Compounds
Step 4: Set pure compound parameters
Step 5: Set the COSMO-RS parameters
Step 6: COSMO-RS or COSMO-SAC
Step 7: Visualize the COSMO surface: ADFview
Step 8: Analysis: The sigma profile
Step 9: Analysis: The sigma potential
Tutorial 3: COSMO-RS overview: properties
Step 1: Start ADFcrs
Step 2: Calculate the vapor pressure of a solvent
Step 3: Calculate the boiling point of a solvent
Step 4: Calculate the flash point of a solvent
Step 5: Calculate activity coefficients
Step 6: Calculate partition coefficients (log P)
Step 7: Calculate solubility
Solubility liquid in a solvent
Solubility solid in a solvent
Solubility gas in a solvent
Step 8: Calculate binary mixtures VLE/LLE
Isothermal
Isothermal, input pure compound vapor pressure
Isothermal, miscibility gap, LLE
Isobaric
Step 9: Calculate ternary mixtures VLE/LLE
Isothermal
Isobaric
Step 10: Calculate a composition line between solvents s1 and s2
Tutorial 4: Examples using the COSMO-RS database
4.1: How to use the COSMO-RS database
Step 1: Add compounds
Step 2: Select a compound
Step 3: Visualize the COSMO surface: ADFview
4.2: Octanol-Water partition coefficients (log POW)
4.3: Henry's law constants
4.4: Solubility of Vanillin in organic solvents
4.5: Binary mixture of Methanol and Hexane
4.6: Large infinite dilution activity coefficients in Water
4.7: Parametrization of ADF COSMO-RS: ΔGhydr, vapor pressures, partition coefficients
Tutorial 5: pKa values
5.1: Empirical pKa calculation method
5.2: Relative pKa calculation method
