Notebooks
=========

The repository ships executed Jupyter notebooks under `notebooks/
<https://github.com/farrisric/mcpy/tree/main/notebooks>`_.
Every cell output is included, so they read as worked case studies without
running anything.

- `gcmc_basics_lj.ipynb
  <https://github.com/farrisric/mcpy/blob/main/notebooks/gcmc_basics_lj.ipynb>`_:
  GCMC fundamentals on a Lennard-Jones system, no MLIP or GPU required.
- `grand_canonical_simulation_ag.ipynb
  <https://github.com/farrisric/mcpy/blob/main/notebooks/grand_canonical_simulation_ag.ipynb>`_:
  oxygen on silver with MACE, the notebook form of :doc:`getting_started`.
- `molecular_gcmc.ipynb
  <https://github.com/farrisric/mcpy/blob/main/notebooks/molecular_gcmc.ipynb>`_:
  whole-molecule insertion, deletion, and displacement step by step
  (see :doc:`molecular_adsorbates`).
- `phase_diagram.ipynb
  <https://github.com/farrisric/mcpy/blob/main/notebooks/phase_diagram.ipynb>`_:
  building a phase diagram from swept trajectories
  (see :doc:`phase_diagrams`).
- `co_on_cupd_replica_exchange.ipynb
  <https://github.com/farrisric/mcpy/blob/main/notebooks/co_on_cupd_replica_exchange.ipynb>`_:
  CO on a CuPd nanoparticle with batched replica exchange, ending in the
  molecular phase diagram.