\(\renewcommand{\AA}{\text{Å}}\)

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:

NumPy Methods: