add an example for looking up and looping over a neighbor list
This commit is contained in:
@ -1,6 +1,43 @@
|
||||
Neighbor list access
|
||||
====================
|
||||
|
||||
Access to neighbor lists is handled through a couple of wrapper classes
|
||||
that allows 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 neigbor list
|
||||
data. The code sample below demonstrates reading the neighbor list data
|
||||
using the NumPy access method.
|
||||
|
||||
.. code-block:: python
|
||||
|
||||
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]))
|
||||
|
||||
**Methods:**
|
||||
|
||||
* :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index
|
||||
|
||||
Reference in New Issue
Block a user