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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
  • 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
    • 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 PtCl4 H2 2-
        • Step 6: Define fragments
        • Step 7: Run the fragment analysis and view the results
      • QTAIM (Bader), (localized) orbitals and conceptual DFT
        • Step 1: QTAIM (Bader) analysis of Caffeine
        • Step 2: Benzene Bader charge analysis and NBOs
        • Step 3: 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 PF5
        • 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 PF5 )
        • 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 Fe4 S4 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 Fe4 S4 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 and transition state search
      • PES Scan
      • Frequencies calculation
      • Transition state search
  • 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 MOPACinput
      • Run interactively
      • Save job and results: charges, 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: MOPAC COSMO result file
      • Step 5: 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 POW )
        • 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
    • 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
    • ReaxFF advanced tutorials
      • Discharge voltage profiles during lithiation using grand canonical monte carlo
        • Overview
        • The System
        • Importing the Sulfur(α) crystal structure
        • Calculating the chemical potential for Li
        • Setting up the GCMC calculation
        • GCMC Troubleshoot
        • Results
      • Li-Ion Diffusion Coefficients in cathode materials
      • Polymer structures with the bond boost acceleration method
        • Overview
        • 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 Logfile
        • Monitoring the bias deposition
        • Improving the CV using the Bias Deposition Plot
        • Analyzing Event Timescales
        • Analyzing the System Composition
        • 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
    • ADF advanced tutorials
      • Tuning the range separation in LC-wPBE for organic electronics
      • Thermally Activated Delayed Flourescence (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 CsPbBr3 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
Tutorials
  • Documentation/
  • Tutorials/
  • GUI tutorials 2018

GUI tutorials 2018¶

  • 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
    • Building Frameworks and Reticular Compounds
  • ADF-GUI tutorials
    • Spectroscopy
    • Analysis
    • Relativistic Effects
    • Multiple Jobs, Multi-Level, Multiple Compounds
    • Structure and Reactivity
  • AMS-GUI tutorials
    • Diamond Lattice Optimization and Phonons
    • PES scan and transition state search
  • BAND-GUI tutorials
    • Getting started with BAND
    • Bonding Analysis
    • TD-CDFT and Linear Response Properties
    • Model Hamiltonians
    • Electronic Transport with NEGF
  • DFTB-GUI tutorials
    • DFTB charges, frequencies and dynamics (MD)
    • Proton affinities with DFTB3
    • UV/Vis spectrum of Ir(ppy)3
    • Electronic transport with DFTB-NEGF
  • MOPAC-GUI tutorial
    • Toluene charges, movies, frequencies and normal modes
  • Quantum ESPRESSO GUI tutorials
    • Geometry and Lattice Optimization
    • Magnetism, Band Structure and pDOS
  • ReaxFF-GUI tutorials
    • Burning methane
    • Water on an aluminum surface
    • The Molecule Gun
  • COSMO-RS GUI Tutorials
    • COSMO result files
    • Overview: parameters and analysis
    • Overview: properties
    • The COSMO-RS compound database
    • pKa values
    • Ionic Liquids
    • Using the UNIFAC program
  • Scripting tutorials
    • PLAMS
  • Advanced tutorials
    • ReaxFF advanced tutorials
    • ADF advanced tutorials
    • BAND advanced tutorials
Next

  • Application Areas

    • Organic Electronics
    • Nanotechnology
    • Polymers
    • Batteries & PVs
    • Inorganic Chemistry
    • Materials Science
    • Catalysis
    • Spectroscopy
    • Oil and Gas
    • Heavy Elements
    • Bonding Analysis
    • Life Sciences
    • Teaching
  • Products

    • ADF
    • BAND
    • COSMO-RS
    • DFTB
    • MOPAC
    • ReaxFF
    • GUI
    • AMS
    • PLAMS
    • Quantum ESPRESSO
  • Support

    • Support Overview
    • Documentation
    • Downloads
    • FAQs
    • ADF Discussion List
    • Release Notes
    • Teaching Materials
    • Workshops
    • Webinars
    • Videos
    • Brochure
    • Papers Citing ADF
    • Literature Highlights
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