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Scripting Scripting Scripting
  • Installation
    • Windows
    • Linux
    • MacOS
    • Package manager Install optional components
  • Tutorials
    • Getting started
    • All tutorials
  • AMS Driver
    • Geometry and System
    • Geometry Optimization
    • Molecular Dynamics
    • Nudged Elastic Band (NEB)
    • PES Exploration
    • PES Scan, Linear Transit
    • Transition State Search
    • Vibrational Spectroscopy
  • Engines
    • ADF Molecular DFT
    • BAND Periodic DFT
    • DFTB Semi-empirical
    • ForceField AMBER, UFF, APPLE&P...
    • GFNFF Force field
    • Hybrid QM/MM and mixed methods
    • ML Potential Machine Learning potentials
    • MOPAC Semi-empirical
    • Quantum ESPRESSO Periodic DFT
    • VASP Periodic DFT
    • ReaxFF Reactive force field
    • ASE engine Use any ASE calculator
  • Meso/Macro
    • COSMO-RS Thermodynamic properties of fluids
    • Bumblebee OLED device modeling
    • Microkinetics
    • Zacros Kinetic Monte Carlo
  • Tools
    • GUI Graphical User Interface
    • ParAMS Parametrization tool
    • Simple Active Learning On-the-fly training of ML
    • OLED Deposition and Properties Multiscale OLED modeling
    • Reactions Discovery Automatic reaction-discovery workflow
    • ACE Reaction Network Generation of reaction networks
    • Conformers Conformers generation
    • MD Trajectory Analysis Analysis of MD trajectories
    • ChemTraYzer2 Detect reactions from MD simulations
    • Utilities Various utility tools
  • Scripting
    • Python Scripting Examples Examples for Python scripting
    • PLAMS Python Library for Automating Molecular Simulations
    • amspython Python stack shipped with AMS
    • pyCRS Python Scripting with COSMO-RS
    • SCM Base Library Python library with core modules
    • reactmap Atom mapping between reactants and products
    • Command-line tools
    • ASE calculator
    • pyZacros Python Library Zacros (Kinetic Monte Carlo)
  • AMS2026.1
  • Other versions
  • Scripting
  • Getting Started
  • amspython: Python Stack
  • Amsterdam Modeling PySuite
  • Command-Line Tools
    • AMSprep: generate (multiple) ADF jobs
    • Tutorial: Generate structures for substituent effects screening
    • AMSreport: generate reports
    • KF command line utilities
  • Chemical System
    • Overview
    • Read, write, file formats
    • Atoms, Bonds, Elements, Electrostatic Embedding
      • Atoms
      • Bonds
      • Elements
      • Electrostatic Embedding
    • Lattice, Periodic Boundary Conditions
    • Charge, mass, formula
    • Combine and split
    • Geometry Manipulation
    • Comparison of systems
    • Regions
    • Select atoms
    • ASE, RDKit and PLAMS
    • GUI and notebook integration
    • ChemicalSystem Complete API
  • SCM Base Library
    • Units
    • Input File
    • KFFile
  • AKFReader
  • FlexMD
    • Basic philosophy and intended usage
    • FlexMD functionality summary
    • Introduction
    • Molecular Dynamics
    • Multi-scale Molecular Dynamics
    • Biased Molecular Dynamics
    • Working with FlexMD
      • Creating a molecule object
      • Creating a ForceJob
      • Creating and running the MD job
    • Required Citations
    • References
  • AuToGraFS
    • General AuToGraFS Scripting concepts
    • AuToGraFS Examples
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  3. Chemical System

Chemical System¶

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