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Amsterdam Modeling Suite
Atomistic Scale
Electronic Structure
ADF

Understand and predict chemical properties with our fast and accurate molecular DFT code.

Periodic DFT

BAND & Quantum Espresso: Calculate reactivity, band gaps, optical response, and other properties for periodic systems.

DFTB & MOPAC

Model larger molecules and periodic systems, or prescreen many candidates, with the fast electronic structure methods DFTB and MOPAC.
Interatomic Potentials
ReaxFF

Study large, chemically evolving systems with ReaxFF molecular dynamics.

Machine Learning Potentials

Use preparametrized ML potentials M3GNET, ANI-1ccx or your own models.

Force Fields

GFN-FF, Apple&P, UFF, and more- (polarizable) force fields.
Meso- & Macroscale
kMC and Microkinetics

Predict catalytic turn-over frequencies with microkinetics and kinetic Monte Carlo.
Bumblebee: OLED stacks

3D kinetic Monte Carlo for simulating OLED device-level physics
Fluid Thermodynamics
COSMO-RS

Quick physical property predictions, thermodynamic properties in solution, and solvent screening.

Amsterdam Modeling Suite: computational chemistry with expert support to advance your chemistry & materials R&D

Discover the Suite Pricing & licensing
Tools
Workflows and Utilities
OLED workflows

Automatic workflows to simulate physical vapor deposition and calculate properties for OLED device modeling.
ChemTraYzer2

Automatically extract reaction pathways and reaction rates from reactive MD trajectories.
Conformers

Easily generate, screen, refine, and select conformers. Pass on to other modules for conformational averaging.
Reactions Discovery

Predict chemical (side) reactions from nothing but constituent molecules.
AMS Driver
Properties

Calculate frequencies, phonons, and more. Use forces and energies from AMS or external engines.
PES Exploration

Minimize structures, find transitions states, scan multiple coordinates.
Molecular Dynamics

Use advanced thermo- and barostats, non-equilibrium and accelerated MD, molecule gun.

Monte Carlo

Grand Canonical Monte Carlo to study absorption, (dis)charge processes.
Interfaces
ParAMS

Versatile graphical and python scripting tools to create training sets and parametrize DFTB, ReaxFF, and machine learned potentials.
PLAMS

Versatile python scripting interface to create your own computational chemistry workflows
GUI

Powerful graphical interface to set up, run, and analyze calculations. Even across different platforms.
VASP

Interface to popular plane-wave code VASP. Easily set up PES Scans to create training data.

The SCM team wants to make computational chemistry work for you!

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ams2025.102
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ams2025.102
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Documentation links for all our modules and tools

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Quick-start guide and extensive installation manual
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Home > Documentation

Navigate to
  • Documentation
  • Tutorials
  • Installation
  • 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
AMS Modules
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Interatomic Potentials
ReaxFF ML Potentials Force Fields
Kinetics
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Macroscale
COSMO-RS
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Research Topics
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