2.3.10. Neighbor list access — LAMMPS documentation

\(\renewcommand{\AA}{\text{Å}}\)

# 2.3.10. Neighbor list access

Access to neighbor lists is handled through a couple of wrapper classes that allows one to treat it like either a python list or a NumPy array. The access procedure is similar to that of the C-library interface: use one of the “find” functions to look up the index of the neighbor list in the global table of neighbor lists and then get access to the neighbor list data. The code sample below demonstrates reading the neighbor list data using the NumPy access method.

    from lammps import lammps
    import numpy as np

    lmp = lammps()
    lmp.commands_string("""
    region box block -2 2 -2 2 -2 2
    lattice fcc 1.0
    create_box 1 box
    create_atoms 1 box
    mass 1 1.0
    pair_style lj/cut 2.5
    pair_coeff 1 1 1.0 1.0
    run 0 post no""")

    # look up the neighbor list
    nlidx = lmp.find_pair_neighlist('lj/cut')
    nl = lmp.numpy.get_neighlist(nlidx)
    tags = lmp.extract_atom('id')
    print("half neighbor list with {} entries".format(nl.size))
    # print neighbor list contents
    for i in range(0,nl.size):
        idx, nlist  = nl.get(i)
        print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
        if nlist.size > 0:
            for n in np.nditer(nlist):
                print("  atom {} with ID {}".format(n,tags[n]))

Another example for extracting a full neighbor list without evaluating a potential is shown below.

    from lammps import lammps
    import numpy as np

    lmp = lammps()
    lmp.commands_string("""
    newton off
    region box block -2 2 -2 2 -2 2
    lattice fcc 1.0
    create_box 1 box
    create_atoms 1 box
    mass 1 1.0
    pair_style zero 1.0 full
    pair_coeff * *
    run 0 post no""")

    # look up the neighbor list
    nlidx = lmp.find_pair_neighlist('zero')
    nl = lmp.numpy.get_neighlist(nlidx)
    tags = lmp.extract_atom('id')
    print("full neighbor list with {} entries".format(nl.size))
    # print neighbor list contents
    for i in range(0,nl.size):
        idx, nlist  = nl.get(i)
        print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
        if nlist.size > 0:
            for n in np.nditer(nlist):
                pass
                print("  atom {} with ID {}".format(n,tags[n]))

Methods:

- `lammps.get_neighlist()`: Get neighbor list for given index

- `lammps.get_neighlist_size()`: Get number of elements in neighbor list

- `lammps.get_neighlist_element_neighbors()`: Get element in neighbor list and its neighbors

- `lammps.find_pair_neighlist()`: Find neighbor list of pair style

- `lammps.find_fix_neighlist()`: Find neighbor list of fix style

- `lammps.find_compute_neighlist()`: Find neighbor list of compute style

NumPy Methods:

- `lammps.numpy.get_neighlist()`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays

- `lammps.numpy.get_neighlist_element_neighbors()`: Get element in neighbor list and its neighbors (as a numpy array)