User Guide

The guide is ordered as a workflow: first the background and entry points, then how to prepare and run simulations, then analysis, visualisation and reference material.

Start here

• Introduction to PyRETIS and rare event methods
• Obtaining and installing PyRETIS
• Quickstart
• Tutorials
• Main studies performed with PyRETIS

Prepare and run simulations

• Running PyRETIS
• Input reference for sections
• Getting the initial path
• The PyRETIS application

Analyse and visualise

• The PyRETIS analysis application
• The PyVisA application

Concepts and reference

• Monte Carlo moves
• Path types and rejection reasons
• Creating custom order parameters
• Creating custom engines
• Running LAMMPS with PyRETIS
• PyRETIS units
• Some common PyRETIS errors

Advanced use

• Introduction to the PyRETIS library
• LLMs and agents
• PyRETIS exercises