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Create ctypes only neighbor list API variant

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This moves the lammps.get_neighlist() method to lammps.numpy.get_neighlist().
lammps.get_neighlist() now returns a NeighList object, while the NumPy variants
returns a NumPyNeighList object. The main difference between the two is that while
the ctypes variant returns neighlist elements as

atom idx (int), numneighs (int), neighbors (POINTER(c_int))

the NumPy variant returns

atom idx (int), neighbors (numpy.array)
This commit is contained in:
Richard Berger
2020-10-05 16:21:37 -04:00
parent 68147306e7
commit 02b10380bc
3 changed files with 137 additions and 42 deletions
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9
examples/python/in.fix_python_invoke_neighlist
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@ -32,8 +32,9 @@ def post_force_callback(lmp, v):
t = L.extract_global("ntimestep", 0)
print(pid_prefix, "### POST_FORCE ###", t)
#mylist = L.get_neighlist(0)
mylist = L.find_pair_neighlist("lj/cut", request=0)
#mylist = L.numpy.get_neighlist(0)
idx = L.find_pair_neighlist("lj/cut", request=0)
mylist = L.numpy.get_neighlist(idx)
print(pid_prefix, mylist)
nlocal = L.extract_global("nlocal")
nghost = L.extract_global("nghost")
@ -43,8 +44,8 @@ def post_force_callback(lmp, v):
v = L.numpy.extract_atom("v", nelem=nlocal+nghost, dim=3)
f = L.numpy.extract_atom("f", nelem=nlocal+nghost, dim=3)
for iatom, numneigh, neighs in mylist:
print(pid_prefix, "- {}".format(iatom), x[iatom], v[iatom], f[iatom], " : ", numneigh, "Neighbors")
for iatom, neighs in mylist:
print(pid_prefix, "- {}".format(iatom), x[iatom], v[iatom], f[iatom], " : ", len(neighs), "Neighbors")
for jatom in neighs:
if jatom < nlocal:
print(pid_prefix, " * ", jatom, x[jatom], v[jatom], f[jatom])