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  • 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
      • 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/
  • Examples

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

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
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