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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
Task
XC functional
Basis set
Numerical quality
Geometry Convergence
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
Creating a supercell
Building Frameworks and Reticular Compounds
The Export Fragment tool
Framework builder : Build a pillared, functionalized MOF
Building Polymers
Step 1: Loading the monomers from the database
Step 2: Growing polymers
Step 3: Optimizing the structure with UFF
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 of the VCD spectrum of Oxirane with VCDtools
Step 1. Start ADFinput
Step 2: Create your oxirane molecule
Step 3: Optimize the geometry
Step 4: Calculate the VCD intensities
Step 5: Analyze the VCD Spectra
H-NMR spectrum with spin-spin coupling
Step 1: Start ADFinput
Step 2: Create the molecule
Step 3: Setting up the NMR calculation
Step 4: Results of your calculations
Step 5: Spectrum overlap
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
QTAIM (Bader), localized orbitals and conceptual DFT
QTAIM analysis of an Adenine–Thymine base pair
Benzene QTAIM charge analysis and NBOs
Rationalizing a typical SN2 reaction using condensed Conceptual DFT descriptors
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
Interacting Quantum Atoms (IQA)
Step 1: Build H2O
Step 2: Calculate all inter-atomic interactions in H2O
Step 3: Analyze the results
Step 4: Build PF
5
Step 5: Select two atoms (P and equatorial F) and calculate this specific interaction
Step 6: Analyze the results (a single P-Feq bond in PF
5
)
Step 7: Compare equatorial and axial P-F bonds
Analysis of NMR parameters with Localized Molecular Orbitals
Introduction
Step 1: Preparations
Step 2: Calculation Settings
Step 3: Running the Calculations
NMR Results
NLMO/NBO Analysis
Inspecting NLMOs
Further Reading
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: DRF
Step 5: Quality per region
Multiple molecules, conformers, multiple methods
Multiple 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: Optimize the structure with ADF
Step 3: Obtain the solution for the high-spin (HS) state of the cubane
Step 4: Couple the spins in Fe
4
S
4
using the SpinFlip option
Step 5: Coupling the spins using the ModifyStartPotential option, use ARH SCF convergence method
Step 6: 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: Import the initial and final molecule
Step 2: Set the calculation details
Step 3: Viewing the Results
AMS-GUI tutorials
Diamond Lattice Optimization and Phonons
Set up the calculation
Run the calculation
Visualize the Phonons
PES scan, transition state search and IRC
PES Scan
Frequencies calculation
Transition state search
IRC (Intrinsic Reaction Coordinate) calculation
Molecular dynamics: The Bouncing Buckeyball
Setting up the geometry
Setting up the molecule gun
Visualizing the impact
Molecular dynamics: Burning Isooctane
Building the system
Setting up the calculation
Viewing the results
Battery discharge voltage profiles using Grand Canonical Monte Carlo
Overview
The System
Importing and optimizing the Sulfur(α) crystal structure
Calculating the chemical potential for Li
Setting up the GCMC calculation
GCMC Troubleshoot
Analyzing the results
Mode Refinement
Mode Tracking
BAND-GUI tutorials
Getting started with BAND
Create a work directory and start up ADFInput
Set up the NaCl crystal calculation
Run the calculation
Examine the band structure and DOS
Visualize results with ADFView
Bonding Analysis
Periodic Energy Decomposition 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-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
TD-CDFT and Linear Response Properties
TD-CDFT Response Properties For Crystals (OldResponse)
Step 1: Create the system
Step 2: Run a Single Point Calculation (LDA)
Step 3: Run an OldResponse Calculation (ALDA)
TD-CDFT Response properties for a 2D periodic system (NewResponse)
Step 1: Create the system
Step 2: Run a Singlepoint Calculations (LDA)
Step 3: Run an NewResponse Calculation (ALDA)
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
Benzene molecule in a magnetic field
Step 1: adfinput
Step 2: Setup the system - benzene
Electronic Transport with NEGF
Carbon nanotube
Setting up the system
Running the calculation
Visualizing the results
CO on 1D gold chain
Introduction
Creating the lead file
Gold chain transport calculation
CO on gold chain transport calculation
Au-(4,4’-bipyridine)-Au molecular junction
Using tips
Spin transport in Chromium wire
Gate and Bias potentials
DFTB-GUI tutorials
DFTB charges, frequencies and dynamics (MD)
Step 1: DFTB: Pre-optimization and Charges
Step 2: Frequency evaluation
Step 3: Molecular dynamics
Proton affinities with 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
Electronic transport with DFTB-NEGF
Carbon nanotube
Setting up the system
Running the calculation
Visualizing the results
CO on 1D gold chain
Introduction
Creating the lead file
Gold chain transport calculation
CO on gold chain transport calculation
Au-(4,4’-bipyridine)-Au molecular junction
Using tips
Gate potential
MOPAC-GUI tutorial
Toluene charges, movies, frequencies and normal modes
Set up Toluene in MOPAC
Run interactively
Save job and results: movies, IR spectrum and normal modes
Quantum ESPRESSO GUI tutorials
Geometry and Lattice Optimization
Step 1: Start ADFinput
Step 2: Set up the system - Silicon
Step 3: Setting up the calculation
Step 4: Running your job
Step 5: Checking the results
Magnetism, Band Structure and pDOS
Step 1: Start ADFinput
Step 2: Set up the system - Iron supercell
Step 3: Set up the anti-ferromagnetic iron calculation
Step 4: Set up the ferromagnetic iron calculation
Step 5: Run the calculations
Step 6: Examine the results
KFBrowser
BANDstructure
ADFview
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
The Molecule Gun
The bouncing buckyball
Setting up the system
Setting up the calculation
Running the calculation and visualizing the results
COSMO-RS GUI Tutorials
COSMO result files
Step 1: Start ADFinput
Step 2: Create the molecule
Step 3: ADF COSMO result file
Step 4: Lowest Conformer
Step 5: Polymers
Step 6: MOPAC COSMO result file
Step 7: Fast Sigma: QSPR 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, COSMO-SAC, and UNIFAC 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
Step 11: Pure Compound Properties
Step 12: Solvent Optimizations: Optimize Solubility
Step 13: Solvent Optimizations: Optimize Liquid-Liquid Extraction
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
4.9: Optimize solvents for LLE of Acetic acid and Water
pKa values
5.1: Empirical pKa calculation method
5.2: Relative pKa calculation method
Ionic Liquids
6.1: Using the ADF COSMO-RS ionic liquid database
Reparameterization of COSMO-RS for ionic liquids
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
Polymers
The ADFCRS Polymer Database
Selecting/inputting database compounds
Inputting your own polymers
Inputting necessary property values
Polymer/Average Molecular Weight
Density
Example polymer calculations
Activity coefficients
Vapor pressure of a mixture
Partition Coefficients (LogP)
Solubility in Pure Solvents
Binary Mixture and Flory-Huggins
\(\chi\)
Using the UNIFAC program
Selecting/inputting compounds
Inputting property values
Calculations with the UNIFAC program
Vapor Pressure Mixture
Activity Coefficients
Partition Coefficients (LogP)
Solubility in Pure Solvents
Solubility in Mixture
Binary Mixture VLE/LLE
Ternary Mixture VLE/LLE
Common issues
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
Advanced tutorials
AMS advanced tutorials
Tips and Tricks for Transition State Searches for Click Reactions
Contents
Tools
Pre-requisites
Setting up the Structure
Setting up the calculations
Follow your intuition
What can possibly go wrong?
What are the next steps?
Starting from reactant and product – Nudge Elastic Band (NEB)s
What can possibly go wrong?
What are the next steps?
ReaxFF advanced tutorials
Li-Ion Diffusion Coefficients in cathode materials
Polymer structures with the bond boost acceleration method
Setting up
Running and analyzing
Polymerization workflow
Description of the workflow
Realistic-temperature fuel pyrolysis with collective variable-driven hyperdynamics (CVHD)
Overview
Background information
The System
Preparation
CVHD events in the output
Analyzing the System Composition
Monitoring the bias deposition
Improving the CV using the Bias Deposition Plot
Analyzing Event Timescales
Discussion
Summary
Mechanical properties of epoxy polymers
Overview
Setting up
Setting up the strain rate
Results
Training sets for ReaxFF Reparametrization
Co.ff
Reparametrizing ReaxFF with the CMA-ES optimizer
Overview of the workflow
Generating reference data
Preparing the training data
How to run the optimizer
How to monitor a running optimization
How to change optimizer settings
How to cross-validate a fitted force field
Running the optimizer
Force Field editing with ADFtrain
Load a force field into ADFtrain
Inspect the parameters
Edit the parameters
ADF advanced tutorials
Tuning the range separation for range separated hybrids
Thermally Activated Delayed Fluorescence (TADF)
General Remarks on Modelling OLED Emitters
Computational Description of TADF 1: Electronic Structure
Computational Description of TADF 2: Spin-Orbit Coupling
Computational Description of TADF 3: Vibrations
Computational Description of TADF 4: Solvent Effects
TDDFT Study of 3 different Dihydroxyanthraquinones
Scientific Questions
Model Questions
Pre-requisities
Overview
0. What functional, What basis set?
1. Geometry Optimization
2. TDDFT Calculations
3. Analyzing TDDFT Calculations
4. Faster TDDFT variant: sTDDFT
5. Analyzing the Orbitals
6. Analyzing the NTOs
7. Localized Analysis of Canonical Molecular Orbitals (CMO) with NBO6
13
C - NMR chemical shifts in substituted benzenes w. ADF & NBO
Plasmon Enhanced Two Photon Absorption
Model and Methods
Workflow and Calculation Script
Calculation and Results
BAND advanced tutorials
Calculation of Band Structure and COOP of CsPbBr
3
with BAND
Step 1: Preparations
Step 2: Calculations
Step 3: Inspecting the Band Structure
Interpretation of Results
Periodic Energy Decomposition of the Tetrahydrofuran/Si(001) System
Model
Settings
PEDA Terms
NOCV Orbitals
Theory Overview
Density Functional Theory
XC Functionals and How to Tame Them
Introduction
Classes of Functionals
Overview of Available Functionals
Properties – Accuracy of Different Types of Functionals
System Classes – Applicability of Different Types of Functionals
Tutorials
Documentation
/
Tutorials
/
Theory Overview
Theory Overview
¶
Density Functional Theory
¶
XC Functionals and How to Tame Them