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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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Overview

Documentation links for all our modules and tools

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Get started quickly with our Tutorials!
Installation Manual

Quick-start guide and extensive installation manual
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Home > Documentation

Navigate to
  • Documentation
  • Tutorials
  • Installation
  • Index by engine
    • ADF
    • BAND
    • DFTB
    • ReaxFF
    • MLPotential
    • Hybrid
    • MKMCXX
    • Quantum ESPRESSO
    • VASP
    • COSMO-RS
  • Getting Started
    • Keyboard shortcuts
    • GUI modules
    • Getting started: Geometry optimization of ethanol
      • Step 1: Preparations
        • Start AMSjobs
        • Make a directory for the tutorial
        • Start AMSinput
        • 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: AMStail
        • Files
        • Geometry changes: AMSmovie
        • Orbital energy levels: AMSlevels
        • Electron density, potential and orbitals: AMSview
        • Browsing the Output: AMSoutput
        • Convert results to spreadsheet (.xlsx)
        • Close all open GUI windows
    • GUI tour: UV/Vis spectrum of ethene
      • Create your ethene molecule
      • Optimize the geometry
      • Calculate the excitation energies
        • Select calculations options
        • Run the calculation
      • Results of your calculation
        • Logfile: AMStail
        • Energy levels: level diagram and DOS
        • Excitation spectrum: AMSspectra
        • Orbitals, orbital selection panel: AMSview
        • Transition density: AMSview
        • AMSoutput
        • KFBrowser: KF files, copy to Excel, graphs of results
      • Excited state geometry optimization and excited state density
        • Closing the AMS-GUI modules
  • Building structures
    • Building Molecules
      • Start AMSinput
      • Search for ethanol
      • Import XYZ for ethanol
      • Import SMILES string
      • Build ethanol using the structure tool
      • Building a peptide chain using the structures tool
      • Metal complexes and ligands
        • Predefined Metal Complex Geometries
        • Bidentate Ligands
        • Modifying the Plane Angle
      • Your own structures library
        • Defining your structures
        • Using dummy atoms
      • A sphere of Cu atoms, cut out of the crystal
      • A carbon nanotube
    • Building Crystals and Slabs
      • The Crystal Structures Tool
      • The Crystal Structures Database
      • Crystal builder (from space group information)
      • Slicer: building slabs, transform primitive to conventional cell
      • Creating a supercell
    • Building Polymers
      • Loading the monomers from the database
      • Growing polymers
      • Optimizing the structure with UFF
    • Building Frameworks and Reticular Compounds
      • The Export Fragment tool
      • Framework builder : Build a functionalized MOF with defects
  • Structure and Reactivity
    • Transition state search and characterization of a Ziegler Natta Catalyst
      • Introduction
        • Ziegler-Natta catalyzed polymerization
        • Strategy
      • Geometry Setup with AMSinput
      • Settings for the Engine
      • Settings for the AMS Driver
        • Setup PES scan
        • Transition State search
      • Results
        • Energies and barrier height
        • Kinetics and Statistical Thermal Analysis
    • Diamond Lattice Optimization and Phonons
      • Set up the calculation
      • Run the calculation
      • Visualize the Phonons
    • Automated reaction pathway discovery for hydrohalogenation
      • Setup of the process search job
      • Visualization of the results in AMSmovie
      • Restarting a PES exploration
      • Obtaining the reaction path with the IRC (intrinsic reaction coordinate) method
      • Refining an energy landscape at a higher level of theory
    • Cluster Growth: Cobalt Clusters
      • Global Optimization of Co8
      • Growth Mechanism Co8+Co → Co9
    • PES Exploration: Water dissociation on an oxide surface
      • Introduction
      • Step 1: Set up the initial system
        • Import the system into AMSinput
        • Change the default color of Zn atoms
      • Step 2: Basin Hopping
        • ReaxFF settings
        • Basin hopping settings
        • Keep the bottom side of the slab fixed
        • Save and run the basin hopping job
        • View the basin hopping results
      • Step 3: Process search for reaction barriers
    • Reaction path and TS search using NEB
      • Setting up and running the calculation
      • Results of the calculation
    • Proton affinities with DFTB3
      • Step 1: Optimization of the neutral molecule
      • Step 2: Optimization of the acetate and the hydrogen ions
    • Basis set superposition error (BSSE)
      • Method 1: atomic fragments
      • Method 2: molecular fragments
    • Tips and Tricks for Transition State Searches for Click Reactions
      • Introduction
      • 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 – Nudged Elastic Band (NEB)
      • What can possibly go wrong?
      • What are the next steps?
    • ANI-1ccx Thermochemistry
      • Set up and run ANI-1ccx calculations
      • Estimating reliability
      • Free energies, vibrational normal modes, and more
      • References
    • Microkinetics: Calculating CO Oxidation
      • Step 1: Specify compounds
      • Step 2: Specify reactions
      • Step 3: Specify properties to calculate
      • Step 4: Run and analyze results
    • QM/MM: Inorganic linker in organic framework
      • Introduction
        • Covalent organic frameworks
        • Solution
      • Setup with AMSinput
        • Define the QM region
        • Setup the Hybrid Engine
        • Results
        • Conclusions
    • Crystals and Surfaces
      • 3D-periodic crystals
        • Files
        • Unit cells
        • When to use primitive cell, conventional cell, or supercell
        • Lattice vectors and lattice parameters
        • Fractional coordinates
        • Rotation of lattice vectors relative to cartesian axes
      • k-space sampling
      • Lattice optimization
        • Run a lattice optimization
        • Convergence criteria for lattice optimizations
        • Tips for lattice optimizations
        • Example: lattice optimization of wurtzite ZnO with DFTB
      • Solid-state properties
      • Surface models in computational chemistry
      • Miller indices
        • Surface Miller indices
        • Crystal directions
      • Generate a slab with AMSinput
      • Surface terminations
      • What makes a good slab model
      • Surface passivation
      • Surface relaxation
      • Surface reconstruction
      • Polar and non-polar surfaces
        • Polar surface stabilization mechanisms
      • Surface unit cells and supercells
        • Create a conventional surface unit cell
        • Create a supercell
      • Surface energy calculations
        • Example: Surface energy of ZnO(\(10\bar{1}0\))
        • Surface energy vs. cleavage energy
      • Adsorption
        • Adsorption on surfaces in AMSinput
        • Example: ontop, bridge, fcc hollow and hcp hollow sites on Cu(111)
        • Adsorption energy
        • Basis set superposition error with BAND
        • In-cell approach for adsorption energies with ReaxFF
        • One-sided vs. two-sided adsorption
        • Fixing the central and/or bottom layers of the slab
      • Solid-solid and solid-liquid interfaces
        • Solid-solid interfaces
        • Solid-liquid interfaces
  • Molecular Dynamics and Monte Carlo
    • Burning Isooctane
      • Building the system
      • Setting up the calculation
      • Viewing the results
    • The Bouncing Buckyball
      • Setting up the geometry
      • Setting up the molecule gun
      • Visualizing the impact
    • Water on an aluminum surface
      • Step 1: Start AMSinput in ReaxFF mode
      • Step 2: Creating the surface
      • Step 3: Add solvent
      • Step 4: Set up the simulation, including a temperature regime
      • Step 5: Run the simulation
    • Burning methane
      • Step 1: Start the GUI
      • 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
      • Troubleshoot
    • Snapping Polyacetylene Chain
      • Step 1: Start the GUI
      • Step 2: Import Structure and Settings
      • Step 3: Run the Calculation
      • Step 4: Evaluate 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
    • 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
    • Polymer structures with the bond boost acceleration method
      • Setting up
      • Execution and visualization
      • Scaling it up: Generate large Polymer structures
      • Analysis: Calculate the density and cross-linking ratio
    • Mechanical properties of epoxy polymers
      • Overview
      • Setting up
      • Setting up the strain rate
      • Results
    • Glass transition temperatures of thermoset polymers
      • Importing the polymer structure
      • Simulated annealing
      • Extraction of Density vs. Temperature profiles
      • Calculation of the glass transition temperature
    • Thermal expansion coefficients of thermoset polymers
      • Importing the polymer structure
      • Annealing the polymer
      • Extracting strain vs. temperature profiles
      • Calculation of the thermal expansion coefficient
    • Li-Ion Diffusion Coefficients in cathode materials
      • Importing the Sulfur(α) crystal structure
      • Generating the Li0.4S system
      • Creating the amorphous systems by simulated annealing
      • Calculating the diffusion coefficients
    • eReaxFF: Electron transfer through a hydrocarbon radical
      • Overview
      • The System
      • Setting up the MD simulation
      • Analyzing the results
  • Vibrational Spectroscopy
    • Vibrational frequencies and IR spectrum of ethane
      • Create an ethane molecule
      • Geometry optimization and vibrational frequencies calculation
      • Visualize the IR-spectrum, normal modes
    • Analysis of the VCD spectrum of Oxirane with VCDtools
      • Create your oxirane molecule
      • Set up and run the calculation
      • Analyze the VCD Spectra
    • Resonance Raman
    • Mode Refinement
    • Mode Tracking
    • Vibrationally resolved electronic spectra with ADF
      • Step 1: Geometry Optimization
      • Step 2: Excited state gradient
      • Step 3: Vibronic-Structure Tracking
    • Vibrationally resolved electronic spectra with DFTB
      • Step 1: Geometry Optimization
      • Step 2: Excited state gradient
      • Step 3: Vibronic-Structure Tracking
      • Step 4: Increase spectral resolution
  • Optical Properties, Electronic Excitations
    • TDDFT Study of 3 different Dihydroxyanthraquinones
      • Scientific Questions
      • Model Questions
      • Prerequisites
      • 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
    • Accurate Ionization Potential and Electron Affinity with G0W0
      • Set up and run the calculation
      • Results
    • Thermally Activated Delayed Fluorescence (TADF)
      • General Remarks on Modelling OLED Emitters
        • Electronic Structure of OLED Materials
      • Computational Description of TADF 1: Electronic Structure
        • Excited States Geometry Optimizations
        • Vertical Absorption
      • Computational Description of TADF 2: Spin-Orbit Coupling
        • Calculating Spin-Orbit Couplings
      • Computational Description of TADF 3: Vibrations
        • Marcus Theory
        • Franck-Condon Principle and Marcus-Levich-Jortner Theory
        • Effective Modes and Huang-Rhys Factors from DFTB and FCF
      • Computational Description of TADF 4: Solvent Effects
    • Vibrational progression of an OLED phosphorescent emitter
      • 1. Optimize lowest singlet state (S0)
      • 2. Optimize lowest triplet state (T1)
      • 3. Calculation of the Franck-Condon Spectrum
      • References
    • Plasmon Enhanced Two Photon Absorption
      • Model and Methods
      • Workflow and Calculation Script
      • Calculation and Results
    • UV/Vis spectrum of Ir(ppy)3
    • 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)
  • NMR
    • H-NMR spectrum with spin-spin coupling
      • Start AMSinput and copy the molecule
      • Setting up the NMR calculation
      • Results of your calculations
        • Logfile: AMStail
        • View the 1 H-NMR spectrum
        • Average chemical shifts and couplings for equivalent atoms
        • Comparison of calculated and experimental spectrum
      • Spectrum overlap
    • NMR shifts with relativistic DFT
      • Scalar relativistic & spin-orbit coupling calculations of NMR chemical shifts
      • Geometry optimization and NMR chemical shifts for the H-X series
      • Run calculations for the other hydrogen halides
      • Vary the relativistic approach and density functional (XC)
      • Analyze multiple jobs with ADFreport
    • 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
  • Electronic Structure, Model Hamiltonians
    • TlH (thallium hydride) Spin-Orbit Coupling
      • Prepare the molecule
      • Set calculation options
      • Run your calculation
      • Results of the calculation
        • TlH energy diagram
        • Visualization of spinors
      • Calculate the atomization energy including spin-orbit coupling
        • The Tl atom
        • The H atom
        • TlH atomization energy
    • Spin Coupling in Fe4S4 Cluster
      • Create the Fe4 S4 cubane model
      • Optimize the structure with ADF
      • Obtain the solution for the high-spin (HS) state of the cubane
      • Couple the spins in Fe4 S4 using the SpinFlip option
      • Coupling the spins using the ModifyStartPotential option
      • View the spin density of the broken symmetry (BS) solutions
    • QM/MM with polarizable force fields
      • DRF
      • QM/FQ
    • NiO and DFT+U
      • Step 1: amsinput
      • Step 2: Setup the system - NiO
      • Step 3: BP86 without Hubbard
        • Step 3a: Run the calculation
        • Step 3b: Checking the results
      • Step 4: Run the calculation - BP86+U
        • Step 4a: Run the calculation
        • Step 4b: Checking the results
    • Closing the band gap of a 2D semiconductor with an electric field
      • Create the MoS2 monolayer
      • Analyze the DOS and band structure
      • Electron-hole transport
      • Fix the band gap
      • Applying an electric field
      • Analyzing the charge
      • Improving the accuracy
      • References
    • Benzene molecule in a magnetic field
      • Step 1: amsinput
      • Step 2: Setup the system - benzene
        • Step 3: Run the calculation
        • Step 4a: Magnetic current: vectors
        • Step 4b: Magnetic current: streamlines
  • Electronic Transport
    • Electronic transport in a carbon nanotube
      • Setting up the calculation
      • Run the calculation and visualize the results
    • Electronic transport in a 1D gold chain
      • Introduction
      • Creating the lead file
      • Gold chain transport calculation
      • CO on gold chain transport calculation
    • Gate and Bias potentials
    • Spin transport in Chromium wire
    • Au-(4,4’-bipyridine)-Au molecular junction
      • Instructions
      • Gate potential
    • Electron and hole mobilities in organic electronics: charge transfer integrals
      • Calculation of charge mobilities
      • Define the fragments for charge transfer
        • Transport properties and settings
        • Generalized Charge Transfer Integrals
      • Reorganization energies
      • Hopping rates from Marcus theory
      • Further considerations for charge mobilities
      • References
    • Band Structure and Effective Mass Tensors of Phosphorene
      • Effective Mass Tensors
      • Black Phosphorus and Phosphorene
      • Settings
      • Results
        • Optimized Structures
        • Band Gaps
        • Band Structures
        • Effective Masses
  • Analysis
    • Fragment Analysis
      • Ni(CO)4
        • Build the Structure
        • Define fragments
        • Set up the fragment analysis run
        • Run the fragment analysis and view the results
      • PtCl4 H2 2-
        • Build the structure
        • Define fragments
        • Run the fragment analysis and view the results
      • CH3I
        • Set up the calculation
        • Prepared for bonding
        • Run the calculation
    • Energy Decomposition Analysis (EDA)
      • EDA with restricted fragments
        • Geometry Optimizations of NH3, BH3 and H3N-BH3
        • EDA: single-point calculation with molecular fragments
        • Bond energy, preparation energy, interaction energy
        • EDA Analysis
      • EDA with unrestricted fragments
        • Geometry Optimization
        • EDA
        • Analysis
      • Dispersion correction
      • EDA-NOCV: natural orbitals for chemical valence
        • 1. Dative bonding
        • 2. Electron-sharing bonding
        • 3. Dative/Electron‐sharing bonding
        • EDA
        • EDA-NOCV Fischer‐type carbyne complex
        • EDA-NOCV Schrock‐type carbyne complex
    • 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 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
    • Periodic Energy Decomposition Analysis - PEDA
      • Set up the system - CO@MgO(100) (√2×√2)-R45°
      • Set up the PEDA calculation
      • Run the calculation check the results
      • Plot the deformation density with respect to the fragments
    • PEDA-NOCV - decomposing the orbital relaxation term
      • Setting up the System and the Calculation
        • Preparations for the PEDA-NOCV calculation
        • Save and run the calculation
      • Step 2: Checking the results
      • Step 3: Plotting NOCV orbitals and deformation densities
        • Step 3a: Plotting NOCV deformation densities
        • Step 3b: Plotting NOCV orbitals
    • PEDA-NOCV for Spin Unrestricted Calculations
      • Step 1: Start AMSinput
      • Step 2: Set up the system - Ethane
      • Step 3: Running the PEDA-NOCV calculation
        • Step 3a: Setting up the fragments
        • Step 3b: Details for the calculation
        • Step 3c: Enabling the PEDA-NOCV
        • Step 3d: Save and run the calculation
      • Step 4: Checking the results
      • Step 5: Plotting NOCV orbitals and deformation densities
        • Step 5a: Plotting NOCV deformation densities
    • 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
    • Charge Displacement
      • Case 1: CT in closed-shell interacting fragments: Xe—AuF
        • 1. Fragment Calculation
        • 2. Density SCF
        • 3. Generate CD function
      • Case 2: Dewar-Chatt-Duncanson bonding components in a transition metal complex (NOCV-CD)
        • 1. Fragment Calculation
        • 2. Visualize NOCV deformation densities
        • 3. Generate a CUBE file
        • 4. CD functions for the NOCV deformation densities
      • Case 3: Open-Shell CD in the HAT mechanism of the TauD-J intermediate
        • 1. Unrestricted Calculations
        • 2. Generate CUBE files
        • 3. Obtain density differences
        • 4: Generate the CD functions
      • References
  • COSMO-RS: Fluid Thermodynamics
    • COSMO result files
      • Step 1: Start AMSinput
      • 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 AMScrs
      • 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: AMSview
      • Step 6: Analysis: The sigma profile
      • Step 7: Analysis: The sigma potential
    • Overview: properties
      • Step 1: Start AMScrs
      • 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
      • Install and use the COSMO-RS compound database
        • Step 1: Install database
        • Step 2: Add or search compounds
        • Step 3: Set pure compound data
        • Step 4: Visualize the COSMO surface: AMSview
      • Octanol-Water partition coefficients (log POW )
      • Henry’s law constants
      • Solubility of Vanillin in organic solvents
      • Binary mixture of Methanol and Hexane
      • Large infinite dilution activity coefficients in Water
      • Parametrization of ADF COSMO-RS: solvation energies, vapor pressures, partition coefficients
        • Table: Parametrization of COSMO-RS
      • COSMO-SAC 2013-ADF
      • Optimize solvents for LLE of Acetic acid and Water
    • pKa values
      • Empirical pKa calculation method
      • Relative pKa calculation method
    • Ionic Liquids
      • Using the ADF COSMO-RS ionic liquid database
        • Reparameterization of COSMO-RS for ionic liquids
        • References
      • Ionic liquid volumes and densities
        • References
      • Activity coefficient calculation
        • References
      • Henry’s law constants
        • References
      • Gas solubility and selectivity in ionic liquids
        • References
      • VLE for systems containing ionic liquids
    • Polymers
      • The ADFCRS Polymer Database
      • Selecting/inputting database compounds
      • Inputting your own polymers (optional)
        • Method 1: Using ADF
        • Method 2: Using FastSigma to estimate a polymer’s sigma profile
      • 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 \(\chi\)
    • COSMO-RS with multi-species components
      • Building multi-species compounds
      • Enthalpy and entropy corrections
      • Example multi-species calculations
        • Acetic acid dimerization
        • NaCl in Water
    • 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
    • Python scripting with COSMO-RS using the PLAMS library
  • Workflows and Automation
    • Python Scripting With PLAMS
      • First steps with PLAMS
        • Running a PLAMS script
        • Molecule
        • Settings class
        • Creating and running the Job
        • Results
    • 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
    • Multiple molecules, conformers, multiple methods
      • Multiple molecules
        • Step 1: Set up methane and ethane in AMSinput
        • Step 2: H-NMR calculation
      • Conformers
        • Step 3: Set up propanoic acid in AMSinput
        • Step 4: Generate the conformers
        • Step 5: Refine the conformer geometries with ADF
        • Step 6: Calculate the IR spectrum
        • Step 7: Visualize the Boltzmann weighted IR spectrum
        • Step 8: H-NMR, UV/Vis
      • Multiple Methods
        • Step 9: Set up a series of calculations
        • Step 10: Run a series of calculations for a single molecule
        • Step 11: Create an SDF file, and Run a series of calculations for a set of molecules
  • Optimizing Performance
    • Parallel scalability of Elastic Tensor calculations
      • Setting up the job
      • Measuring parallel scalability
      • Looking at the results
  • Parametrization
    • Force Field editing with AMStrain
      • Load a force field into AMStrain
      • Inspect the parameters
      • Edit the parameters
    • Training sets for ReaxFF Reparametrization
      • Co.ff
        • Weighting of individual entries
        • General energies, Cluster models and the Co2 dimer
        • Description of crystalline phases
        • Description of Co-surfaces
        • Adatoms
        • Vacancies and defects
        • Elastic strain moduli
    • Reparametrizing ReaxFF with the CMA-ES optimizer
      • Overview of the workflow
      • Generating reference data
        • Introduction
        • Preparation
        • Preparation: Set up a DFTB3 preset
        • Optimized geometries
        • PES/Bond Scans
        • Conformers
        • Transition states / Trajectory snapshots
        • Before you continue…
      • Preparing the training data
        • Assigning weights
        • Splitting 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
        • Errors and Cross-validation
        • Refine the training set
  • External Programs: QE and VASP
    • Geometry and Lattice Optimization
      • Step 1: Start AMSinput
      • 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 AMSinput
      • 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
        • Output
        • AMSbandstructure
        • AMSview
    • TiO2 surface relaxation
      • Step 1: Check the VASP installation
      • Step 2: Locate the POTCAR library
      • Step 3: Set up the system - a TiO2(001) slab
      • Step 4: Set the VASP settings
      • Step 5: Set the AMS settings
      • Step 6: Run your job
Tutorials
  • Documentation/
  • Tutorials/
  • Workflows and Automation

Workflows and Automation¶

  • Python Scripting With PLAMS
  • Generating a batch of jobs and collecting results: Basis Set Effects for NH3 Geometry
  • Multiple molecules, conformers, multiple methods
Next Previous
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