Python Library for Automating Molecular Simulations

Table of Contents

• 1. Introduction
  • 1.1. What is PLAMS
  • 1.2. What can be done with PLAMS
  • 1.3. Simple example
  • 1.4. What PLAMS is not
  • 1.5. About this documentation
• 2. Getting started
  • 2.1. Library contents
  • 2.2. Installing PLAMS
  • 2.3. Running PLAMS
  • 2.4. Defaults file
  • 2.5. Master script
    • 2.5.1. Working folder location
    • 2.5.2. Passing variables
    • 2.5.3. Importing past jobs
    • 2.5.4. Restarting failed script
    • 2.5.5. Multiple input scripts
• 3. Components overview
  • 3.1. Settings
    • 3.1.1. Tree-like structure
    • 3.1.2. Dot notation
    • 3.1.3. Global settings
    • 3.1.4. API
  • 3.2. Jobs
    • 3.2.1. Preparing a job
    • 3.2.2. Running a job
    • 3.2.3. Job API
    • 3.2.4. Single jobs
    • 3.2.5. Multijobs
  • 3.3. Results
    • 3.3.1. Files in the job folder
    • 3.3.2. Synchronization of parallel job executions
    • 3.3.3. Cleaning job folder
    • 3.3.4. API
  • 3.4. Job runners
    • 3.4.1. Local job runner
    • 3.4.2. Remote job runner
  • 3.5. Job manager
    • 3.5.1. Rerun prevention
    • 3.5.2. Pickling
    • 3.5.3. Restarting crashed scripts
    • 3.5.4. API
  • 3.6. Public functions
    • 3.6.1. Logging
    • 3.6.2. Binding decorators
  • 3.7. Molecule
    • 3.7.1. Molecule
    • 3.7.2. Atom
    • 3.7.3. Bond
  • 3.8. Utilities
    • 3.8.1. Periodic Table
    • 3.8.2. Units
    • 3.8.3. Geometry tools
• 4. Interfaces
  • 4.1. ADF Suite
    • 4.1.1. ADF, BAND and DFTB
    • 4.1.2. Other tools: Densf, FCF
    • 4.1.3. KF files
  • 4.2. MOPAC
    • 4.2.1. Preparing input
    • 4.2.2. API
  • 4.3. Dirac
    • 4.3.1. Preparing a calculation
    • 4.3.2. Results extraction
    • 4.3.3. API