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# 3d Lennard-Jones melt
units lj
atom_style atomic
lattice fcc 0.8442
region box block 0 2 0 2 0 2
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 3.0 87287
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.1 bin
neigh_modify every 20 delay 0 check no
python post_force_callback here """
from __future__ import print_function
from lammps import lammps
def post_force_callback(lmp, v):
try:
import os
pid = os.getpid()
pid_prefix = "[{}] ".format(pid)
L = lammps(ptr=lmp)
t = L.extract_global("ntimestep", 0)
print(pid_prefix, "### POST_FORCE ###", t)
#mylist = L.numpy.get_neighlist(0)
idx = L.find_pair_neighlist("lj/cut", reqid=0)
mylist = L.numpy.get_neighlist(idx)
print(pid_prefix, mylist)
nlocal = L.extract_global("nlocal")
nghost = L.extract_global("nghost")
mass = L.numpy.extract_atom("mass")
atype = L.numpy.extract_atom("type", nelem=nlocal+nghost)
x = L.numpy.extract_atom("x", nelem=nlocal+nghost, dim=3)
v = L.numpy.extract_atom("v", nelem=nlocal+nghost, dim=3)
f = L.numpy.extract_atom("f", nelem=nlocal+nghost, dim=3)
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])
else:
print(pid_prefix, " * [GHOST]", jatom, x[jatom], v[jatom], f[jatom])
except Exception as e:
print(e)
"""
fix 1 all nve
fix 3 all python/invoke 50 post_force post_force_callback
#dump id all atom 1 dump.melt
#dump 2 all image 1 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 1 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
thermo 1
run 100
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