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LAMMPS (2 Apr 2025 - Development - patch_2Apr2025-270-g2351418c94-modified)
# 3d Lennard-Jones melt with equal- and atom-style variables which
# use a Python function wrapper in their formulas
variable x index 3
variable y index 3
variable z index 3
units lj
atom_style atomic
lattice fcc 0.8442
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
region box block 0 $x 0 $y 0 $z
region box block 0 3 0 $y 0 $z
region box block 0 3 0 3 0 $z
region box block 0 3 0 3 0 3
create_box 1 box
Created orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 108 atoms
using lattice units in orthogonal box = (0 0 0) to (5.0387886 5.0387886 5.0387886)
create_atoms CPU = 0.000 seconds
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
# define Python truncate() function
variable foo python truncate
python truncate return v_foo input 1 iv_arg format fi here """
def truncate(x):
return int(x)
"""
# use in equal-style variable
variable scalar equal py_foo(4.5)
print "TRUNCATE ${scalar}"
TRUNCATE 4
# use in atom-style variable
# examine dump file to see truncated xyz coords of each atom
variable xtrunc atom py_foo(x)
variable ytrunc atom py_foo(y)
variable ztrunc atom py_foo(z)
dump 1 all custom 100 tmp.dump id x y z v_xtrunc v_ytrunc v_ztrunc
# use in vector-style variable
compute ke all temp
variable ke vector c_ke
variable ketrunc vector py_foo(v_ke)
thermo_style custom step temp epair v_ketrunc[*6]
run 100
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 20 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 4 4 4
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 2.59 | 2.59 | 2.59 Mbytes
Step Temp E_pair v_ketrunc[1] v_ketrunc[2] v_ketrunc[3] v_ketrunc[4] v_ketrunc[5] v_ketrunc[6]
0 1.44 -6.7733681 155 152 154 -10 -4 -6
100 0.82217015 -5.8614684 113 65 84 7 -1 -12
Loop time of 0.00268845 on 4 procs for 100 steps with 108 atoms
Performance: 16068745.964 tau/day, 37196.171 timesteps/s, 4.017 Matom-step/s
66.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00043389 | 0.00051695 | 0.00061255 | 0.0 | 19.23
Neigh | 0.00017121 | 0.00018976 | 0.00019891 | 0.0 | 7.06
Comm | 0.0017423 | 0.0018487 | 0.0019509 | 0.2 | 68.76
Output | 6.7449e-05 | 6.9998e-05 | 7.5195e-05 | 0.0 | 2.60
Modify | 2.1329e-05 | 2.2855e-05 | 2.4821e-05 | 0.0 | 0.85
Other | | 4.018e-05 | | | 1.49
Nlocal: 27 ave 30 max 25 min
Histogram: 1 0 1 0 1 0 0 0 0 1
Nghost: 614 ave 616 max 612 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 1017.75 ave 1149 max 894 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 4071
Ave neighs/atom = 37.694444
Neighbor list builds = 5
Dangerous builds not checked
print "KE TENSOR ${ketrunc}"
KE TENSOR [113,65,84,7,-1,-12]
Total wall time: 0:00:00
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