HOOMDArray

class hoomd.data.HOOMDArray(buffer, callback, read_only=None)

A numpy.ndarray-like interface to internal HOOMD-blue data.

HOOMD-blue’s zero copy local snapshot API (hoomd.State.cpu_local_snapshot) returns HOOMDArray objects. HOOMDArray acts like numpy.ndarray through NumPy’s provided interface. Some exceptions are the view, resize, flat and flatiter methods and the data and base properties.

To ensure memory safety, a HOOMDArray object cannot be accessed outside of the context manager in which it was created. Make an explicit copy to use the array elsewhere (e.g. numpy.array(obj, copy=True)).

In general this class should be nearly as fast as a standard NumPy array, but there is some overhead. This is mitigated by returning a numpy.ndarray whenever possible.

Performance Tips

Let a represent a HOOMDArray.

  • Place the HOOMDArray to the left of the expression (e.g. a + b + c is faster than b + a + c). This has to do with the mechanisms HOOMDArray has to do to hook into NumPy’s functionality.

  • Make copies as early as possible. In other words, if you will need access outside the context manager, use numpy.array(a, copy=True) before doing any calculations.

  • If you know that your access of the internal buffer is safe and we cannot detect this (i.e. we return a HOOMDArray), using HOOMDArray._coerce_to_ndarray should help. Note that for large arrays this only gives minimal performance improvements at greater risk of breaking your program.