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Introduction
Starting the GUI: start ADFjobs
UNIX (such as Linux) users
Windows users
Macintosh users
GUI modules
Keyboard shortcuts
GUI overview tutorials
Getting started: 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
Viewing the molecule
Molecular conformation
Getting and setting geometry parameters
Extending and changing your molecule
Step 3: Select calculation options
Preset
Title
XC functional
Basis set
Numerical quality
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
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
Step 10: A carbon nanotube
Building Crystals and Slabs
The Crystal Structures Tool
The Crystal Structures Database
Crystal builder (from space group information)
Slicer: building slabs
A three layer slab of the Cu(111) surface
Enlarging the unit cell
ADF-GUI tutorials
Spectroscopy
Excitation energies and UV/Vis spectrum of ethene
Step 1: Start ADFinput
Step 2: Create your ethene molecule
Step 3: Optimize the geometry
Step 4: Calculate the excitation energies
Step 5: Results of your calculation
Step 6: Excited state geometry optimization and excited state density
Vibrational frequencies and IR spectrum 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
Analysis
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 PtCl
4
H
2
2-
Step 6: Define fragments
Step 7: Run the fragment analysis and view the results
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
Visualization of densities, orbitals potentials, ...
Step 1: Get Single-Point calculation results with ADF on Anthracene
Step 2: Details: Divergent and Rainbow Colormap, scalar range of field on isosurface
Step 3: Multi Isosurface
Step 4: Combining visualization techniques
Step 5: Play with lights
Step 6: Special fields
Fukui Functions and the Dual Descriptor
Step 1: Setting up the calculation
Step 2: The output
Step 3: Visualizing the Fukui functions and Dual Descriptor
Relativistic Effects
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
Step 5: Calculate the atomization energy including spin-orbit coupling
Multiple Jobs, Multi-Level, Multiple Compounds
Generating a batch of jobs and collecting results: Basis Set Effects for NH3 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
Multi-Level principles: Regions, QUILD, QMMM, Quality per region
Step 1: Regions for multi-level calculations, visualization and grouping
Step 2: QUILD
Step 3: QMMM
Step 4: Quality per region
Multiple molecules, conformers, multiple methods
Multipe molecules
Conformers
Multiple Methods
Structure and Reactivity
Spin Coupling in Fe4S4 Cluster
Step 1: Create and pre-optimize the Fe
4
S
4
cubane model
Step 2: Obtain the solution for the high-spin (HS) state of the cubane
Step 3: Couple the spins in Fe
4
S
4
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
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
Step 7: Following orbitals along the IRC: reporting from .t21 files
Step 8: Following orbitals for the LT afterwards: generating jobs for many geometries
Transition State Search with ASE using the Nudged Elastic Band method
Step 1: Build the initial and final molecule
Step 2: Set the calculation details
Step 3: Viewing the Results
BAND-GUI tutorials
Bonding Analysis
Bandstructure/DOS/Charges/Orbitals/Densities - With a Grain of Salt
Step 1: Start ADFinput
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
Step 7: Check the charges
Periodic Energy Decompositon Analysis - PEDA
Step 1: Start ADFinput
Step 2: Set up the system - CO@MgO(sqrt(2)xsqrt(2))
Step 3: Running the PEDA calculation
Step 4: Checking the results
PEDA for Spin Unrestricted Calculations
Step 1: Start ADFinput
Step 2: Set up the system - Ethane
Step 3: Running the PEDA calculation
Step 4: Checking the results
PEDA + NOCV - decomposing the orbital relaxation term
Step 1: Setting up the System and the Calculation
Step 2: Checking the results
Step 3: Plotting NOCV orbitals and deformation densities
PEDA-NOCV for Spin Unrestricted Calculations
Step 1: Start ADFinput
Step 2: Set up the system - Ethane
Step 3: Running the PEDA-NOCV calculation
Step 4: Checking the results
Step 5: Plotting NOCV orbitals and deformation densities
Model Hamiltonians
NiO and DFT+U
Step 1: adfinput
Step 2: Setup the system - NiO
Step 3: BP86 without Hubbard
Step 4: Run the calculation - BP86+U
Structure and Reactivity
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
DFTB charges, frequencies and dynamics (MD)
Step 1: DFTB: Pre-optimization and Charges
Step 2: Frequency evaluation
Step 3: Molecular dynamics
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
Proton affinities with third order DFTB (DFTB3)
Step 1: Optimization of the neutral molecule
Step 2: Optimization of the acetate and the hydrogen ions
UV/Vis spectrum of Ir(ppy)3
MOPAC-GUI tutorial
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
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
Step 5: Analyze it: Create a reaction network
Step 6: Analyze it: Browse a reaction network
Step 7: Analyze it: Filter a reaction network
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
COSMO result files
Step 1: Start ADFinput
Step 2: Create the molecule
Step 3: ADF COSMO result file
Step 4: MOPAC COSMO result file
Overview: parameters and analysis
Step 1: Start ADFcrs
Step 2: Add Compounds
Step 3: Set pure compound parameters
Step 4: COSMO-RS and COSMO-SAC parameters
Step 5: Visualize the COSMO surface: ADFview
Step 6: Analysis: The sigma profile
Step 7: Analysis: The sigma potential
Overview: properties
Step 1: Start ADFcrs
Step 2: Vapor pressure
Step 3: Boiling point
Step 4: Flash point
Step 5: Activity coefficients, Henry coefficients, Solvation free energies
Step 6: Partition coefficients (log P)
Step 7: Solubility
Solubility liquid in a solvent
Solubility solid in a solvent
Solubility gas in a solvent
Step 8: Binary mixtures VLE/LLE
Isothermal
Isothermal, input pure compound vapor pressure
Isothermal, miscibility gap, LLE
Isobaric
Step 9: Ternary mixtures VLE/LLE
Isothermal
Isobaric
Step 10: A composition line between solvents s1 and s2
The COSMO-RS compound database
4.1: Install and use the COSMO-RS compound database
Step 1: Install database
Step 2: Add or search compounds
Step 3: Set pure compound data
References
Step 4: Visualize the COSMO surface: ADFview
4.2: Octanol-Water partition coefficients (log P
OW
)
References
4.3: Henry’s law constants
References
4.4: Solubility of Vanillin in organic solvents
References
4.5: Binary mixture of Methanol and Hexane
References
4.6: Large infinite dilution activity coefficients in Water
References
4.7: Parametrization of ADF COSMO-RS: solvation energies, vapor pressures, partition coefficients
Table: Parametrization of COSMO-RS
References
4.8: COSMO-SAC 2013-ADF
References
pKa values
5.1: Empirical pKa calculation method
5.2: Relative pKa calculation method
Ionic Liquids
6.1: Install and use the ADF COSMO-RS ionic liquid database
References
6.2: Ionic liquid volumes and densities
References
6.3: Activity coefficient calculation
References
6.4: Henry’s law constants
References
6.5: Gas solubility and selectivity in ionic liquids
References
6.6: VLE for systems containing ionic liquids
Scripting tutorials
PLAMS
First steps with PLAMS
Running the script
Molecule
Settings class
Creating and running the Job
Results
Automating Workflows
Introducing the case study
Workflow script
Settings library
Miscellaneous remarks
Tutorials
Documentation
/
Tutorials
/
GUI tutorials
GUI tutorials
ΒΆ
Introduction
Starting the GUI: start ADFjobs
GUI modules
Keyboard shortcuts
GUI overview tutorials
Getting started: Geometry optimization of ethanol
Building Molecules
Building Crystals and Slabs
ADF-GUI tutorials
Spectroscopy
Analysis
Relativistic Effects
Multiple Jobs, Multi-Level, Multiple Compounds
Structure and Reactivity
BAND-GUI tutorials
Bonding Analysis
Model Hamiltonians
Structure and Reactivity
DFTB-GUI tutorials
DFTB charges, frequencies and dynamics (MD)
Periodic DFTB, Lattice Optimization, DOS, band structure and phonons
Proton affinities with third order DFTB (DFTB3)
UV/Vis spectrum of Ir(ppy)3
MOPAC-GUI tutorial
Toluene charges, movies, frequencies and normal modes
ReaxFF-GUI tutorials
Burning methane
Water on an aluminum surface
COSMO-RS GUI Tutorials
COSMO result files
Overview: parameters and analysis
Overview: properties
The COSMO-RS compound database
pKa values
Ionic Liquids
Scripting tutorials
PLAMS