=============
Paper figures
=============


The 2020 JCIM figures are drawn from figshare project 73545.
This page is the same calls on the dumps that are in the tree.
The runnable copy is ``docs/tutorials/test_paper_figures.py``.
Python is ``pip install pydseamslib``.

.. table::

    +-------------------+----------------------------------------+-------------------------------+--------------------------------------------+
    | figure            | dump in this tree                      | call                          | result                                     |
    +===================+========================================+===============================+============================================+
    | cubic ice, CHILL+ | ``mW_cubic.lammpstrj`` frame 1, type 1 | ``chill_plus()``              | 4096 cubic                                 |
    +-------------------+----------------------------------------+-------------------------------+--------------------------------------------+
    | cubic ice, cages  | the same frame                         | ``cages()``                   | ``n_ic`` 4096                              |
    +-------------------+----------------------------------------+-------------------------------+--------------------------------------------+
    | sI 5^12 cages     | ``genice_sI.lammpstrj``, type 1        | ``cages_by_signature("512")`` | 2 cages, 40 atoms                          |
    +-------------------+----------------------------------------+-------------------------------+--------------------------------------------+
    | mixed frame       | ``exampleTraj.lammpstrj``, type 2      | cutoff CHILL+ versus cages    | 12 interfacial clathrate, no complete cage |
    +-------------------+----------------------------------------+-------------------------------+--------------------------------------------+

The R and Julia fronts also report 4096 cubic on the first row.
They call ``libseams_lang`` with the mutual four-neighbour list.
On this lattice that list and the cutoff list agree.

The nucleation, nanotube, monolayer, and in-plane RDF figures need the figshare dumps.
Point the same functions at those files.

.. code:: python

    import pydseams as ds

    ice = ds.read("input/traj/mW_cubic.lammpstrj", frame=1, atom_type=1)
    print(ice.chill_plus().cubic, ice.cages().n_ic)

    guest = ds.read("input/traj/genice_sI.lammpstrj", atom_type=1)
    print(len(guest.cages_by_signature("512")))