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 1 by 1 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) = 2.598 | 2.598 | 2.598 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 0.00278186 on 1 procs for 100 steps with 108 atoms

Performance: 15529161.573 tau/day, 35947.133 timesteps/s, 3.882 Matom-step/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0018161  | 0.0018161  | 0.0018161  |   0.0 | 65.29
Neigh   | 0.00057543 | 0.00057543 | 0.00057543 |   0.0 | 20.68
Comm    | 0.00019634 | 0.00019634 | 0.00019634 |   0.0 |  7.06
Output  | 0.00012056 | 0.00012056 | 0.00012056 |   0.0 |  4.33
Modify  | 4.8221e-05 | 4.8221e-05 | 4.8221e-05 |   0.0 |  1.73
Other   |            | 2.516e-05  |            |       |  0.90

Nlocal:            108 ave         108 max         108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:            980 ave         980 max         980 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:           4071 ave        4071 max        4071 min
Histogram: 1 0 0 0 0 0 0 0 0 0

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