.. Copyright (c) 2016-2024 The Regents of the University of Michigan
.. Part of GSD, released under the BSD 2-Clause License.

.. _hoomd-examples:

HOOMD examples
--------------

`gsd.hoomd` provides high-level access to **HOOMD** schema **GSD** files.

View the page source to find unformatted example code.

Import the module
^^^^^^^^^^^^^^^^^

.. ipython:: python

    import gsd.hoomd

Define a frame
^^^^^^^^^^^^^^^^^

.. ipython:: python

    frame = gsd.hoomd.Frame()
    frame.particles.N = 4
    frame.particles.types = ['A', 'B']
    frame.particles.typeid = [0,0,1,1]
    frame.particles.position = [[0,0,0],[1,1,1], [-1,-1,-1], [1,-1,-1]]
    frame.configuration.box = [3, 3, 3, 0, 0, 0]

`gsd.hoomd.Frame` stores the state of a single system configuration, or frame, in the file.
Instantiate this class to create a system configuration. All fields default to `None`. Each field is
written to the file when not `None` **and** when the data does not match the data in the first frame
or defaults specified in the schema.

Create a hoomd gsd file
^^^^^^^^^^^^^^^^^^^^^^^

.. ipython:: python

    f = gsd.hoomd.open(name='file.gsd', mode='w')
    @suppress
    f.close()

Use `gsd.hoomd.open` to open a **GSD** file as a `gsd.hoomd.HOOMDTrajectory` instance.

Write frames to a gsd file
^^^^^^^^^^^^^^^^^^^^^^^^^^^

.. ipython:: python

    def create_frame(i):
        frame = gsd.hoomd.Frame()
        frame.configuration.step = i
        frame.particles.N = 4+i
        frame.particles.position = numpy.random.random(size=(4+i,3))
        return frame

    f = gsd.hoomd.open(name='example.gsd', mode='w')
    f.extend( (create_frame(i) for i in range(10)) )
    f.append( create_frame(10) )
    len(f)
    @suppress
    f.close()

`gsd.hoomd.HOOMDTrajectory` is similar to a sequence of `gsd.hoomd.Frame` objects. The
`append <gsd.hoomd.HOOMDTrajectory.append>` and `extend <gsd.hoomd.HOOMDTrajectory.extend>` methods
add frames to the trajectory.

.. tip:: When using `extend <gsd.hoomd.HOOMDTrajectory.extend>`, pass in a
         generator or generator expression to avoid storing the entire
         trajectory in memory before writing it out.

Randomly index frames
^^^^^^^^^^^^^^^^^^^^^

.. ipython:: python

    f = gsd.hoomd.open(name='example.gsd', mode='r')
    frame = f[5]
    frame.configuration.step
    frame.particles.N
    frame.particles.position
    @suppress
    f.close()

`gsd.hoomd.HOOMDTrajectory` supports random indexing of frames in the file.
Indexing into a trajectory returns a `gsd.hoomd.Frame`.

Slicing and selection
^^^^^^^^^^^^^^^^^^^^^

Use the slicing operator to select individual frames or a subset of a
trajectory.

.. ipython:: python

    f = gsd.hoomd.open(name='example.gsd', mode='r')

    for frame in f[5:-2]:
        print(frame.configuration.step, end=' ')

    every_2nd_frame = f[::2]  # create a view of a trajectory subset
    for frame in every_2nd_frame[:4]:
        print(frame.configuration.step, end=' ')
    @suppress
    f.close()

Slicing a trajectory creates a trajectory view, which can then be queried for
length or sliced again.

Pure python reader
^^^^^^^^^^^^^^^^^^

.. ipython:: python

    f = gsd.pygsd.GSDFile(open('example.gsd', 'rb'))
    trajectory = gsd.hoomd.HOOMDTrajectory(f);
    trajectory[3].particles.position
    @suppress
    f.close()

You can use **GSD** without needing to compile C code to read **GSD** files
using `gsd.pygsd.GSDFile` in combination with `gsd.hoomd.HOOMDTrajectory`. It
only supports the ``rb`` mode and does not read files as fast as the C
implementation. It takes in a python file-like object, so it can be used with
in-memory IO classes, and grid file classes that access data over the internet.

.. warning::

    `gsd.pygsd` is **slow**. Use `gsd.hoomd.open` whenever possible.

Access logged data
^^^^^^^^^^^^^^^^^^

.. ipython:: python

    with gsd.hoomd.open(name='log-example.gsd', mode='w') as f:
        frame = gsd.hoomd.Frame()
        frame.particles.N = 4
        for i in range(10):
            frame.configuration.step = i*100
            frame.log['particles/net_force'] = numpy.array([[-1,2,-3+i],
                                                               [0,2,-4],
                                                               [-3,2,1],
                                                               [1,2,3]],
                                                              dtype=numpy.float32)
            frame.log['value/potential_energy'] = 1.5+i
            f.append(frame)

Logged data is stored in the ``log`` dictionary as numpy arrays. Place data into
this dictionary directly without the ``'log/'`` prefix and gsd will include it in
the output. Store per-particle quantities with the prefix ``particles/``. Choose
another prefix for other quantities.

.. ipython:: python

    log = gsd.hoomd.read_log(name='log-example.gsd', scalar_only=True)
    list(log.keys())
    log['log/value/potential_energy']
    log['configuration/step']

Read logged data from the ``log`` dictionary.

.. note::

    Logged data must be a convertible to a numpy array of a supported type.

    .. ipython:: python
        :okexcept:

        with gsd.hoomd.open(name='example.gsd', mode='w') as f:
            frame = gsd.hoomd.Frame()
            frame.particles.N = 4
            frame.log['invalid'] = dict(a=1, b=5)
            f.append(frame)

Use multiprocessing
^^^^^^^^^^^^^^^^^^^

.. code:: python

   import multiprocessing

   def count_particles(args):
      t, frame_idx = args
      return len(t[frame_idx].particles.position)

   with gsd.hoomd.open(name='example.gsd', mode='r') as t:
      with multiprocessing.Pool(processes=multiprocessing.cpu_count()) as pool:
         result = pool.map(count_particles, [(t, frame_idx) for frame_idx in range(len(t))])

    result

`gsd.hoomd.HOOMDTrajectory` can be pickled when in read mode to allow for multiprocessing through
Python's :py:mod:`multiprocessing` library. Here ``count_particles`` finds the number of particles
in each frame and appends it to a list.

Using the command line
^^^^^^^^^^^^^^^^^^^^^^

The GSD library provides a command line interface for reading files with
first-class support for reading HOOMD GSD files. The CLI opens a Python
interpreter with a file opened in a specified mode.

.. code-block:: console

   $ gsd read -s hoomd 'example.gsd'
   ...
   File: example.gsd
   Number of frames: 11

   The GSD file handle is available via the "handle" variable.
   For supported schema, you may access the trajectory using the "traj" variable.
   Type "help(handle)" or "help(traj)" for more information.
   The gsd and gsd.fl packages are always loaded.
   Schema-specific modules (e.g. gsd.hoomd) are loaded if available.

   >>> len(traj)
   11
   >>> traj[0].particles.position.shape == (4, 3)
   True
   >>> handle.read_chunk(0, 'particles/N')
   array([4], dtype=uint32)
