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Tutorials Tutorials Tutorials
  • 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
  • Tutorials
  • Getting Started with AMS
    • GUI modules
    • Getting started: Geometry optimization of ethanol
    • GUI tour: UV/Vis spectrum of ethene
    • 10 Ways to Get the Energy and Other Properties
    • Run Jobs from the Command Line
    • Run Jobs with Python Scripts
    • Run Jobs with Jupyter Notebooks
  • Building Structures
    • Building Molecules
    • Building Crystals and Slabs
    • Building Liquids and Gases
    • Building Polymers
    • Building Frameworks and Reticular Compounds
  • Structure and Reactivity
    • Transition state search and characterization of a Ziegler Natta Catalyst
    • Lattice Optimization and Phonons
    • Automated reaction pathway discovery for hydrohalogenation
    • Cluster Growth: Cobalt Clusters
    • PES Exploration: Water dissociation on an oxide surface
    • Adsorption Site Study on Pt(111)
    • Oxidation of water on a Pt(111) surface
    • Nudged Elastic Band (NEB)
    • Defect formation energy
    • Proton affinities with DFTB3
    • Accurate XC functionals
    • Basis set superposition error (BSSE)
    • Tips and Tricks for Transition State Searches for Click Reactions
    • Machine Learning Thermochemistry
    • M3GNet: Universal ML Potential
    • QM/MM: Inorganic linker in organic framework
    • Crystals and Surfaces
    • Solvation beyond continuum solvation models: 3D-RISM
    • Gibbs Free Energy in Heterogeneous Catalysis
  • Molecular Dynamics and Monte Carlo
    • Combustion simulation (DFTB)
    • Combustion simulation (ReaxFF)
    • Surface deposition: Bouncing C₆₀
    • Chemical Vapor Deposition
    • Solid-liquid interface
    • ChemTraYzer2: Reactive MD Analysis
    • Diffusion coefficient
    • Ionic Conductivity
    • Viscosity: Green-Kubo relation
    • Thermal conductivity from NEMD
    • Stress-strain curve: Fracture point
    • Young’s modulus, yield point, Poisson’s ratio
    • Glass transition temperature
    • Thermal expansion coefficient
    • Bond boost: Cross-linked polymers
    • CVHD: Bias for Rare Events
    • Voltage profile from Grand-Canonical Monte Carlo
    • Adsorption isotherm from Grand-Canonical Monte Carlo
    • eReaxFF: Electron transfer in MD
    • Ionic liquid with APPLE&P
    • Reaction Boost (targeted MD): bond-making and breaking
    • Reaction Boost (targeted MD): RMSD
  • Vibrational Spectroscopy
    • Vibrational frequencies and IR spectrum of ethane
    • Vibrational circular dichroism (VCD)
    • Resonance Raman
    • Mode Refinement
    • Mode Tracking
    • Vibrationally resolved electronic spectra with ADF
    • Vibrationally resolved electronic spectra with DFTB
  • Optical Properties, Electronic Excitations
    • TDDFT Study of 3 different Dihydroxyanthraquinones
    • GW: Ionization Potential and Electron Affinity
    • Thermally Activated Delayed Fluorescence (TADF)
    • Vibrational progression of an OLED phosphorescent emitter
    • Plasmon Enhanced Two Photon Absorption
    • UV/Vis spectrum of Ir(ppy)3
    • GW-BSE: the singlet-triplet (S0-T1) gap of Benzene
    • CD and CPL for spin-forbidden electronic transitions
    • ROKS-TDA-SOC
    • PolTDDFT: damped complex polarizabilities Au12
    • Eu3+ Luminescence properties with Ligand Field DFT
    • QM/FQ coupled to MD: UV/Vis absorption in aqueous solution
    • Modeling phosphorescent lifetimes of OLED emitters
    • TD-CDFT Response Properties For Crystals (OldResponse)
    • TD-CDFT Response properties for a 2D periodic system (NewResponse)
    • L-Edge X-Ray spectrum NEXAFS
    • Core Ionization Potentials (XPS) of thiophene
  • NMR
    • H-NMR spectrum with spin-spin coupling
    • NMR shifts with relativistic DFT
    • Analysis of NMR parameters with Localized Molecular Orbitals
  • Electronic Structure, Model Hamiltonians
    • TlH (thallium hydride) Spin-Orbit Coupling
    • Spin Coupling in Fe4S4 Cluster
    • QM/MM with polarizable force fields
    • DFT + Hubbard U, PDOS
    • Closing the band gap of a 2D semiconductor with an electric field
    • Benzene molecule in a magnetic field
    • Work functions at interfaces
  • Electronic Transport
    • Electronic transport in a carbon nanotube
    • Electronic transport in a 1D gold chain
    • Gate and Bias potentials
    • Spin transport in Chromium wire
    • NEGF: Create a Molecular Junction
    • Electron and hole mobilities in organic electronics: charge transfer integrals
    • Band Structure and Effective Mass Tensors of Phosphorene
  • Analysis
    • Fragment Analysis in ADF
    • Energy Decomposition Analysis (EDA)
    • QTAIM (Bader), localized orbitals and conceptual DFT
    • Visualization of densities, orbital potentials, etc.
    • Fukui Functions and the Dual Descriptor
    • Interacting Quantum Atoms (IQA)
    • Fragment Orbitals in DFTB
    • Periodic Energy Decomposition Analysis - PEDA
    • PEDA-NOCV - decomposing the orbital relaxation term
    • PEDA-NOCV for Spin Unrestricted Calculations
    • Band Structure and COOP
    • Bands, DOS, and the Fermi surface
    • Restart the DOS or band structure with BAND
    • Periodic Energy Decomposition of the Tetrahydrofuran/Si(001) System
    • Charge Displacement
    • Relative energy gradient (REG) analysis along a PES Scan (1D)
  • COSMO-RS: Fluid Thermodynamics
    • COSMO result files
    • Overview: parameters and analysis
    • Overview: properties
    • The COSMO-RS compound database
    • pKa values
    • Ionic Liquids
    • Polymers
    • Pitzer-Debye-Hückel electrostatic correction
    • COSMO-RS with multi-species components
    • Using the UNIFAC program
    • Python scripting with COSMO-RS using the PLAMS library
  • Bumblebee: Device-level OLED Simulations
  • ParAMS Parametrization
  • Kinetics
    • Microkinetics: CO Oxidation
    • Kinetic Monte Carlo
    • pyZacros Python Library
  • Workflows and Automation
    • Generating a batch of jobs and collecting results: Basis Set Effects for NH3 Geometry
    • Conformers
    • Multiple molecules multiple methods
    • Multiscale modeling of OLED devices
    • ACE Reaction Network
    • Reactions Discovery
    • Simple (MD) Active Learning
  • Optimizing Performance
    • Parallel scalability of Elastic Tensor calculations
  • External Programs: QE and VASP
    • Quantum ESPRESSO: Geometry and Lattice Optimization
    • Quantum ESPRESSO: Magnetism, Band Structure and pDOS
    • Quantum ESPRESSO: Calculating IR and Raman Spectra
    • Quantum ESPRESSO: Phonon Band Structure, DOS, and Thermodynamics
    • Quantum ESPRESSO: Magnetic Anisotropy Energy
    • VASP: TiO₂ surface relaxation
  1. Documentation /
  2. Tutorials /
  3. Python Scripting With PLAMS

Python Scripting With PLAMS¶

This page has moved.

The updated tutorial is now available here: Run Jobs with Python Scripts

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