===============
Classify a dump
===============


You have a LAMMPS water dump and want counts. Flags and the full
surface live on `seams CLI <../reference/cli.rst>`_. Measured
numbers for the in-tree mixed frame live in
`the mixed TIP4P tutorial <../tutorials/bulk-ice.rst>`_.

One frame
---------

.. code:: bash

    seams read FILE
    seams chill-plus FILE --cutoff 3.5 --type 2
    seams cages FILE --type 2

``chill`` is the original CHILL rule. ``chill-plus`` is CHILL+.
``chill_plus`` is a CLI alias of ``chill-plus``.

Type
----

``--type 0`` (default) guesses type 2 then type 1. Mixed water dumps in
this tree use type 2 oxygen. Single-site mW dumps use type 1.

.. code:: bash

    seams chill-plus FILE --type 2
    seams cages input/traj/mW_cubic.lammpstrj --type 1

Frame range
-----------

Frames are 1-based. ``--last`` is inclusive. ``--jobs`` walks the range
via ``forEachLammpsFrame`` (``--jobs 1`` is serial).

.. code:: bash

    seams chill-plus FILE --frame 1 --last 10 --jobs 4

Bond graph for cages
--------------------

.. code:: bash

    seams cages FILE --graph seeded
    seams cages FILE --graph cutoff --cutoff 3.5
    seams cages FILE --graph knn -k 4
    seams cages FILE --graph knn-union -k 4

``seeded`` is the CLI default: mutual four-nearest seeds, union
completions. On a perfect cubic crystal the four graphs coincide.

Features of this binary
-----------------------

.. code:: bash

    seams --features