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

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Model larger molecules and periodic systems, or prescreen many candidates, with the fast electronic structure methods DFTB and MOPAC.
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Study large, chemically evolving systems with ReaxFF molecular dynamics.

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

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Predict catalytic turn-over frequencies with microkinetics and kinetic Monte Carlo.
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3D kinetic Monte Carlo for simulating OLED device-level physics
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Quick physical property predictions, thermodynamic properties in solution, and solvent screening.

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Automatically extract reaction pathways and reaction rates from reactive MD trajectories.
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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.
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Use advanced thermo- and barostats, non-equilibrium and accelerated MD, molecule gun.

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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.
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Versatile python scripting interface to create your own computational chemistry workflows
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Powerful graphical interface to set up, run, and analyze calculations. Even across different platforms.
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Interface to popular plane-wave code VASP. Easily set up PES Scans to create training data.

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Home > Documentation

Navigate to
  • Documentation
  • Tutorials
  • Installation
  • Keywords Index
  • General
    • Overview
    • What’s new in the AMS2019 driver?
      • New in AMS2019.3
      • New in AMS2019.1
    • Motivation and progress
    • Input, execution and output
  • System definition
    • System geometry
    • Additional system properties
    • Restoring a system from disk
  • Exploring the PES: Tasks
    • Single point calculations
    • Geometry optimization
      • Constrained optimization
      • Optimization under pressure / external stress
      • Optimization methods
        • Quasi-Newton
        • FIRE
        • SCMGO
        • Limited-memory BFGS
        • Conjugate gradients
      • Troubleshooting
        • Failure to converge
        • Restarting a geometry optimization
    • Transition state search
    • PES scan
      • Troubleshooting
    • Nudged Elastic Band (NEB)
      • Input
      • Frozen atom constraints
      • Optimizations and convergence criteria
      • Output
      • Troubleshooting
    • Intrinsic Reaction Coordinate (IRC) Scan
      • Method details
      • Input
      • Output
    • Molecular dynamics
      • General
      • Constrained molecular dynamics
      • (Re-)Starting a simulation
      • Thermostats and barostats
        • Temperature and pressure regimes
      • Trajectory sampling and output
      • Molecule Gun: adding molecules during simulation
      • Removing molecules during simulation
      • The PLUMED library support in AMS
      • Collective Variable-driven HyperDynamics (CVHD)
      • Non-equilibrium MD (NEMD): heat exchange
      • Temperature Replica Exchange
    • Vibrational analysis
      • All vibrational modes
      • Vibrational Analysis Tools
        • Mode Selective Analysis
        • Vibrationally resolved electronic spectra
        • VG-FC Resonance Raman
        • Selecting modes
        • Overview of input options
    • Grand Canonical Monte Carlo (GCMC)
      • General info
      • Method Details
      • Input
      • Output
  • PES point properties
    • Nuclear gradients and stress tensor
    • Hessian and normal modes of vibration
      • Thermodynamics (ideal gas)
      • Partial Vibrational Spectra (PVDOS)
    • PES point character
    • Elastic tensor
    • Phonons
    • Numerical differentiation options
    • Other Properties
  • Engines
    • Available engines
    • External programs as engines
    • Toy engines
    • Engine add-ons
      • Dispersion corrections
      • Pressure
      • Non-isotropic external stress
  • Technical topics
    • Input syntax
      • General remarks on input structure and parsing
      • Keys
      • Blocks
      • Units
    • Driver level parallelism
    • Running AMS on compute clusters
    • Python interface
    • Pipe interface
      • AMSPipe protocol specification
        • Low-level message encoding
        • Return messages and error handling
        • Methods
      • AMS as a pipe master
      • AMS as a pipe worker
  • Utilities
    • Trajectory Analysis
      • Radial Distribution
        • Description
        • Options
      • Histogram
  • Examples
    • Geometry optimization
      • Example: Simple geometry optimization
      • Example: Two-stage geometry optimization with initial Hessian
      • Example: Periodic lattice optimization under pressure
      • Example: Phase Transition Due To External Nonuniform Stress
      • Example: Boron nitride optimization under external stress
      • Example: Graphene optimization under external stress
      • Example: Constrained optimizations
    • Transition state search
      • Example: TS search starting from initial Hessian
      • Example: PES scan and TS search for H2 on graphene
    • Nudged Elastic Band (NEB)
      • Nudged Elastic Band (NEB) Examples
        • HCN isomerization reaction with NEB
        • H2 dissociation on graphene
        • Running multiple NEB calculations using PLAMS
    • Intrinsic reaction coordinate (IRC)
      • Example: IRC for HCN
      • Example: TS and IRC for Claisen reaction
    • PES scan
      • Example: Linear transit
      • Example: 2D PES scan
    • Molecular dynamics
      • Example: Simple MD for H2
      • Example: MD for a box of water
    • Vibrational analysis
      • Example: Mode Refinement
      • Example: Mode Tracking
      • Example: Vibronic-Structure Tracking
    • PES point properties
      • Example: Phonons for graphene
      • Example: Phonons with isotopes
      • Example: User-defined Brillouin zone for phonon dispersion
      • Example: Elastic tensor
    • Pipe interface
      • Example: ASE calculator as a pipe worker
      • Example: AMS as a pipe worker
  • Appendices
    • Environment variables
    • Extended XYZ file format
    • Developer options
  • Required citations
    • General references
    • Feature references
      • Vibrational analysis
        • Mode tracking
        • Mode refinement
  • Keywords
    • Links to manual entries
    • Summary of all keywords
AMS
  • Documentation/
  • AMS/
  • AMS Manual 2019.3

AMS Manual 2019.3¶

  • (PDF) AMS Manual

Table of Contents:

  • General
    • Overview
    • What’s new in the AMS2019 driver?
    • Motivation and progress
    • Input, execution and output
  • System definition
    • System geometry
    • Additional system properties
    • Restoring a system from disk
  • Exploring the PES: Tasks
    • Single point calculations
    • Geometry optimization
    • Transition state search
    • PES scan
    • Nudged Elastic Band (NEB)
    • Intrinsic Reaction Coordinate (IRC) Scan
    • Molecular dynamics
    • Vibrational analysis
    • Grand Canonical Monte Carlo (GCMC)
  • PES point properties
    • Nuclear gradients and stress tensor
    • Hessian and normal modes of vibration
    • PES point character
    • Elastic tensor
    • Phonons
    • Numerical differentiation options
    • Other Properties
  • Engines
    • Available engines
    • External programs as engines
    • Toy engines
    • Engine add-ons
  • Technical topics
    • Input syntax
    • Driver level parallelism
    • Running AMS on compute clusters
    • Python interface
    • Pipe interface
  • Utilities
    • Trajectory Analysis
  • Examples
    • Geometry optimization
    • Transition state search
    • Nudged Elastic Band (NEB)
    • Intrinsic reaction coordinate (IRC)
    • PES scan
    • Molecular dynamics
    • Vibrational analysis
    • PES point properties
    • Pipe interface
  • Appendices
    • Environment variables
    • Extended XYZ file format
    • Developer options
  • Required citations
    • General references
    • Feature references
  • Keywords
    • Links to manual entries
    • Summary of all keywords
  • Index
Next
AMS Modules
Electronic Structure
ADF: molecular DFT Periodic DFT DFTB & MOPAC
Interatomic Potentials
ReaxFF ML Potentials Force Fields
Kinetics
kMC and Microkinetics Bumblebee: OLEDs
Macroscale
COSMO-RS
Application Areas
Research Topics
Batteries Biotechnology Bonding Analysis Catalysis Heavy Elements Inorganic Chemistry Materials Science Nanoscience Oil & Gas OLEDs Perovskites Polymers Semiconductors Spectroscopy
Where to use AMS?
Industry Government Lab National Supercomputer Academic Research Teaching
Tools
Workflows
Conformers OLED workflows Reaction analysis Reaction discovery
AMS Driver
Hybrid Engine Molecular Dynamics Monte Carlo PES Exploration Properties
Python Utilities
ACErxn ParAMS PLAMS pyZacros
Interfaces
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Documentation & Support
Downloads Documentation Videos Release notes Changelog Previous releases Webinars Workshops AMS Literature Brochure
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