2019-09-13 01:43:14 +08:00
|
|
|
# 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:
|
2019-09-13 01:53:29 +08:00
|
|
|
import os
|
|
|
|
|
pid = os.getpid()
|
|
|
|
|
pid_prefix = "[{}] ".format(pid)
|
|
|
|
|
|
2019-09-13 01:43:14 +08:00
|
|
|
L = lammps(ptr=lmp)
|
|
|
|
|
t = L.extract_global("ntimestep", 0)
|
2019-09-13 01:53:29 +08:00
|
|
|
print(pid_prefix, "### POST_FORCE ###", t)
|
2019-09-13 01:43:14 +08:00
|
|
|
|
|
|
|
|
#mylist = L.get_neighlist(0)
|
|
|
|
|
mylist = L.find_pair_neighlist("lj/cut", request=0)
|
2019-09-13 01:53:29 +08:00
|
|
|
print(pid_prefix, mylist)
|
2019-09-13 01:43:14 +08:00
|
|
|
nlocal = L.extract_global("nlocal", 0)
|
|
|
|
|
nghost = L.extract_global("nghost", 0)
|
|
|
|
|
ntypes = L.extract_global("ntypes", 0)
|
|
|
|
|
mass = L.numpy.extract_atom_darray("mass", ntypes+1)
|
|
|
|
|
atype = L.numpy.extract_atom_iarray("type", nlocal+nghost)
|
|
|
|
|
x = L.numpy.extract_atom_darray("x", nlocal+nghost, dim=3)
|
|
|
|
|
v = L.numpy.extract_atom_darray("v", nlocal+nghost, dim=3)
|
|
|
|
|
f = L.numpy.extract_atom_darray("f", nlocal+nghost, dim=3)
|
|
|
|
|
|
|
|
|
|
for iatom, numneigh, neighs in mylist:
|
2019-09-13 01:53:29 +08:00
|
|
|
print(pid_prefix, "- {}".format(iatom), x[iatom], v[iatom], f[iatom], " : ", numneigh, "Neighbors")
|
2019-09-13 01:43:14 +08:00
|
|
|
for jatom in neighs:
|
|
|
|
|
if jatom < nlocal:
|
2019-09-13 01:53:29 +08:00
|
|
|
print(pid_prefix, " * ", jatom, x[jatom], v[jatom], f[jatom])
|
2019-09-13 01:43:14 +08:00
|
|
|
else:
|
2019-09-13 01:53:29 +08:00
|
|
|
print(pid_prefix, " * [GHOST]", jatom, x[jatom], v[jatom], f[jatom])
|
2019-09-13 01:43:14 +08:00
|
|
|
except Exception as e:
|
|
|
|
|
print(e)
|
|
|
|
|
"""
|
|
|
|
|
|
|
|
|
|
fix 1 all nve
|
2019-09-13 01:53:29 +08:00
|
|
|
fix 3 all python/invoke 50 post_force post_force_callback
|
2019-09-13 01:43:14 +08:00
|
|
|
|
|
|
|
|
#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
|
2019-09-13 01:53:29 +08:00
|
|
|
run 100
|
