2.3.7. Per-atom properties — LAMMPS documentation

\(\renewcommand{\AA}{\text{Å}}\)

# 2.3.7. Per-atom properties

Similar to what is described in Per-atom properties, the instances of `lammps` can be used to extract atom quantities and modify some of them.

In some cases the data returned is a direct reference to the original data inside LAMMPS cast to `ctypes` pointers. Where possible, the wrappers will determine the `ctypes` data type and cast pointers accordingly. If `numpy` is installed arrays can also be extracted as numpy arrays, which will access the C arrays directly and have the correct dimensions to protect against invalid accesses.

Warning

When accessing per-atom data, please note that this data is the per-processor local data and indexed accordingly. These arrays can change sizes and order at every neighbor list rebuild and atom sort event as atoms are migrating between subdomains.

    from lammps import lammps

    lmp = lammps()
    lmp.file("in.sysinit")

    # Read/Write access via ctypes
    nlocal = lmp.extract_global("nlocal")
    x = lmp.extract_atom("x")

    for i in range(nlocal):
       print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")

    # Read/Write access via NumPy arrays
    atom_id = L.numpy.extract_atom("id")
    atom_type = L.numpy.extract_atom("type")
    x = L.numpy.extract_atom("x")
    v = L.numpy.extract_atom("v")
    f = L.numpy.extract_atom("f")

    # set position in 2D simulation
    x[0] = (1.0, 0.0)

    # set position in 3D simulation
    x[0] = (1.0, 0.0, 1.)

    lmp.close()

Methods:

- `extract_atom()`: extract a per-atom quantity

Numpy Methods:

- `numpy.extract_atom()`: extract a per-atom quantity as numpy array