==========
Quickstart
==========


Build the engine, read a frame, and print what this binary linked.

The in-tree mixed TIP4P dump is ``input/traj/exampleTraj.lammpstrj``
(750 atoms, 250 waters; type 2 is oxygen).

Install the engine
------------------

Nix flake:

.. code:: bash

    nix build
    ./result/bin/seams --help
    nix develop   # compiler, Eigen, BLAS, Catch2

pixi:

.. code:: bash

    pixi run setup
    pixi run build
    ./bbdir/seams --help

Either path produces ``libyodaLib`` and the ``seams`` CLI. This repository
does not install Python or Lua.

Read a frame
------------

.. code:: bash

    seams read input/traj/exampleTraj.lammpstrj

The line is ``nop 250 frame 1 box ...`` after the oxygen guess (type 2,
then type 1). Pass ``--type 2`` to skip the guess.

Features of this build
----------------------

.. code:: bash

    seams --features

Each line is a compile-time backend: OpenMP, MPI, Highway SIMD, vesin,
chemfiles, readcon-core, IRA/SOFI, sphericart, nauty. The Nix flake
turns Eigen, BLAS/LAPACK, Catch2 and Highway on when nixpkgs provides
them. Optional wrap-git backends stay off unless a package is already
in the closure. ``pixi`` enables what conda-forge put in the environment
(Highway and chemfiles are in the default pixi lock).

CHILL+ and cages
----------------

.. code:: bash

    seams chill-plus input/traj/exampleTraj.lammpstrj --cutoff 3.5 --type 2
    seams cages input/traj/exampleTraj.lammpstrj --type 2

On this fixture the four-neighbour labels are 12 interfacial
clathrate and 238 water. The default bond graph is ``--graph seeded``
(mutual four-nearest seeds, union completions). This mixed frame has
no complete HC or DDC: cage membership is not the CHILL+ star.

Python and Lua
--------------

The engine CLI is not a scripting host. Install
`pydseams <https://github.com/d-SEAMS/PydSEAMSlib>`_ (``pip install pydseams``, compiled module ``yoda``) or
`yodaStruct <https://github.com/d-SEAMS/yodaStruct>`_
(``require("dseams")``). ``import pydseamslib`` is an alias of ``pydseams``.

The Frame tutorial is
`pydseams docs <https://d-seams.github.io/PydSEAMSlib/>`_.
Lua is `dseams docs <https://d-seams.github.io/yodaStruct/>`_.

The full install matrix is `Install <howto/install.rst>`_.
The mixed-frame walkthrough is
`Classify ice on the mixed TIP4P example <tutorials/bulk-ice.rst>`_.