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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 PtCl4 H2 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 Fe4 S4 cubane model
        • Step 2: Obtain the solution for the high-spin (HS) state of the cubane
        • Step 3: Couple the spins in Fe4 S4 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 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
    • 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 tutorialsΒΆ

  • 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
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    • Organic Electronics
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