Components overview

This chapter contains description of all components (classes, functions, decorators) that can be used within PLAMS scripts. In each part you can find API specification of a particular component, an explanation of its role in the whole environment and examples of usage.

• Settings
  • Tree-like structure
  • Dot notation
  • Case sensitivity
  • Global settings
  • API
• Jobs
  • Preparing a job
    • Contents of job settings
    • Default settings
  • Running a job
    • Name conflicts
    • Prerun and postrun methods
    • Preview mode
  • Job API
  • Single jobs
    • Subclassing SingleJob
  • Multijobs
    • Using MultiJob
• Results
  • Files in the job folder
  • Synchronization of parallel job executions
    • Examples
  • Cleaning job folder
    • Cleaning for multijobs
  • 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 labeling
  • Atom
  • Bond
  • RDKit interface
  • ASE interface
• Utilities
  • Periodic Table
  • Units
  • Geometry tools
  • File format conversion tools
• Trajectories
  • XYZ trajectory files
    • XYZ history files
  • RKF trajectory files
    • RKF history files
  • DCD trajectory files