Python Library for Automating Molecular Simulations¶

Table of contents

• General
  • What’s new in PLAMS for AMS2024?
  • What’s new in PLAMS for AMS2023?
• 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
    • Packmol interface
  • Utilities
    • Periodic Table
    • Units
    • Geometry tools
    • File format conversion tools
    • Reaction energies
    • Plotting tools
    • Postprocess results
  • Trajectories
    • XYZ trajectory files
    • RKF trajectory files
    • DCD trajectory files
    • Trajectory class
• Interfaces
  • Amsterdam Modeling Suite
    • AMS driver and engines
    • AMS worker
    • ASE Calculator for AMS
    • Quick jobs
    • Analysis tools: Densf, FCF, analysis
    • KF files
    • COSMO-RS
    • ParAMS, Simple Active Learning
    • Conformers
    • Reactions Discovery
    • Zacros
    • ADF (pre-2020 version)
    • ReaxFF (pre-2019 version)
  • Other programs
    • CP2K
    • Crystal
    • DFTB+
    • Dirac
    • MOPAC (standalone program)
    • ORCA
    • RASPA
    • VASP
• Examples
  • Getting Started
    • Geometry optimization of water
    • AMS Settings: Chemical System (Molecule)
    • Helium dimer dissociation curve
    • Many jobs in parallel
  • Molecule analysis
    • PLAMS Molecule: store/load many file formats, convert to/from ASE, RDKit, pymatgen, and more
    • Extract frames from ams.rkf trajectory
    • Table molecule counts and bond count from reactive MD ams.rkf
    • Molecule substitution: Attach ligands to substrates
    • Convert to ams.rkf trajectory with bond guessing
    • Correlation plots for output from different AMS jobs
    • Convert RKF to DCD while mapping all atoms into molecules
    • Hydrogen bonds from MD
  • MD trajectory analysis
    • Ionic conductivity from ams.rkf trajectory
    • IR spectrum from MD
    • IR spectrum H2O dimer from MD
  • Benchmarks
    • Benchmark accuracy of basis sets
    • Reaction energies with many different engines
  • Workflows
    • Reduction and oxidation potentials
    • Workflow: filtering molecules based on excitation energies
    • AMS transition state workflow
    • Charge transfer integrals with ADF
    • Tuning the range separation
    • Conformers Generation
    • Conformers Generation with Multiple Molecules
    • Reactions Discovery
  • COSMO-RS and property prediction
    • Property Prediction
    • ADF and COSMO-RS workflow
  • Packmol and AMS-ASE interfaces
    • Packmol example
    • Engine ASE: AMS geometry optimizer with forces from any ASE calculator
    • AMSCalculator: ASE geometry optimizer with AMS forces
    • AMSCalculator: Access results files & Charged systems
    • i-PI path integral MD with AMS
    • Sella transition state search with AMS
  • ParAMS, Simple Active Learning, and pyZacros
  • Other AMS calculations
    • BAND: NiO with DFT+U
    • Band structure
    • AMS biased MD / PLUMED
    • Quantum ESPRESSO as an AMS engine: Antiferromagnetic FeO
    • Basic molecular dynamics analysis
    • Hybrid engine: Use lowest energy
    • Universal Potential: M3GNet-UP-2022
  • Pymatgen
    • X-Ray Diffraction (XRD)
  • Pre-made recipes
    • ADF: Task COSMO-RS Compound
    • Generating multiple conformers for use with COSMO-RS
    • AMS Molecular Dynamics PLAMS jobs
    • ADF fragment job
    • Reorganization Energy
    • NBO with ADF
    • Numerical gradients
    • Numerical Hessian
    • Vibronic Density of States using the AH-FC method
    • Vibronic Density of States with ADF
    • Reuse force field atom types and charges
• Cookbook
  • init and finish
    • Get the workdir created by plams.init
    • Load job results from a plams work dir
  • Settings and input
    • Create an input block with an header
    • Create an empty input block
    • Create an input block with repeating keys
    • Repeating input block
    • Create a “free” 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
    • Generate a liquid or gas mixture
    • Write an ams.rkf-like trajectory
    • Convert a trajectory to ams.rkf with bond guessing
    • Pre-optimize a molecule
    • 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
    • Parallel job execution
    • PLAMS scripts under Slurm
• Citations

• FAQ