SOD Documentation

SOD (Site Occupancy Disorder) is a toolkit for modelling site-occupancy disorder in periodic solids using the supercell ensemble method. It enumerates symmetry-inequivalent atomic configurations, generates calculator-specific input files, and provides statistical-mechanical analysis tools.

Source code on GitHub: github.com/rgraucrespo/sod — releases, examples, and issue tracker.

Key Features

  • Symmetry-aware enumeration of inequivalent configurations in supercells

  • Multi-nary and multi-target substitutions on multiple sites

  • Flexible input generation for GULP, LAMMPS, VASP, CASTEP, and Quantum ESPRESSO

  • Statistical analysis in canonical and grand-canonical ensembles

  • Constrained Periodic Motif Expansion (CPME) effective Hamiltonian fitted from ab initio training data

  • Monte Carlo sampling of configuration space at finite temperature using the CPME Hamiltonian

  • Special Quasirandom Structures (SQS) and generalized GQS methods

  • Machine-learning potentials via MACE, with GPU-batched energies and relaxation

  • Comprehensive examples covering diverse disorder models

Quick Start

New users should:

  1. Read the SOD Overview for a high-level introduction

  2. Follow Installation to build the code

  3. Work through Enumerating the configurations — the core of every SOD calculation

  4. Explore Examples — start with example01

How this documentation is organised

Getting started introduces the method and gets SOD built on your machine. Running SOD follows the standard workflow in order: enumerate the configurations, generate and run the calculations, then analyse the ensemble. Alternatives to enumeration covers what to do when enumerating the configurations and averaging over all of them is out of reach: sampling, quasirandom structures, and effective Hamiltonians. Reference holds the worked examples, terminology and citations.

Getting started

Running SOD

Alternatives to enumeration

Reference

Project links