Python Library for Automating Molecular Simulations

Table of contents

• Introduction
  • What is PLAMS
  • What can be done with PLAMS
  • Simple example
  • What PLAMS is not
  • About this documentation
• Getting started
  • Library contents
  • Installing PLAMS
  • Updating PLAMS
  • Running PLAMS
  • Defaults file
  • The launch script
    • Working folder location
    • Passing variables
    • Importing past jobs
    • Restarting failed script
    • Multiple input scripts
• Components overview
  • Settings
    • Tree-like structure
    • Dot notation
    • Case sensitivity
    • Global settings
    • API
  • Jobs
    • Preparing a job
    • Running a job
    • Job API
    • Single jobs
    • Multijobs
  • Results
    • Files in the job folder
    • Synchronization of parallel job executions
    • Cleaning job folder
    • API
  • Job runners
    • Local job runner
    • Remote job runner
  • Job manager
    • Rerun prevention
    • Pickling
    • Restarting scripts
    • API
  • Public functions
    • Logging
    • Binding decorators
  • Molecule
    • Molecule
    • Atom
    • Bond
    • RDKit interface
    • ASE interface
  • Utilities
    • Periodic Table
    • Units
    • Geometry tools
    • File format conversion tools
  • Trajectories
    • XYZ trajectory files
    • RKF trajectory files
    • DCD trajectory files
• Interfaces
  • Amsterdam Modeling Suite
    • AMS driver and engines
    • AMS worker
    • Analysis tools: Densf, FCF, analysis
    • KF files
    • COSMO-RS
    • ADF (pre-2020 version)
    • ReaxFF (pre-2019 version)
  • Other programs
    • CP2K
    • Crystal
    • DFTB+
    • Dirac
    • MOPAC (standalone program)
    • ORCA
    • RASPA
• Examples
  • Examples
    • Helium dimer dissociation curve
    • Geometry optimization of water
    • Many jobs in parallel
    • Benchmark accuracy of basis sets
    • Reaction energies with many different engines
    • Workflow: filtering molecules based on excitation energies
    • Charge transfer integrals with ADF
    • Tuning the range separation
    • Oxidation Potential
  • Pre-made recipes
    • ADF and COSMO-RS workflow
    • ADF fragment job
    • Reorganization Energy
    • NBO with ADF
    • Numerical gradients
    • Numerical Hessian
    • ReaxFF molecule gun
    • Global Minimum Search
    • Vibrational analysis with ASE
• Cookbook
  • Settings and input
    • Create an input block with an header
    • Create an empty input block
    • Convert an AMS text input into an AMS job
    • Convert an AMS text input into settings object
    • Convert an AMS .run file into an AMS job
    • Specify paths to files in the input
    • Restart from a previous job
  • Molecules
    • Generate a molecule from a SMILES string
    • Load all files in a folder as molecules
    • Counting rings
  • Extracting Results
    • Directly from Functions
    • From the RKF Interface
    • Finding Section/Variable Pairs
    • From molecular dynamics trajectories
  • Accessing Old Jobs
    • Binding Native PLAMS Jobs
    • Binding old RKF Files
  • Parallelization
• Citations