LAMMPS (12 Mar 2015)
# 3d Lennard-Jones melt

units		lj
atom_style	atomic

lattice		fcc 0.8442
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
region		box block 0 10 0 10 0 10
create_box	1 box
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 4000 atoms
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 1 check yes

fix		1 all nve

run		10
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  master list distance cutoff = 2.8
Memory usage per processor = 2.69271 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0         1.44   -6.7733681            0   -4.6139081   -5.0199732 
      10    1.1259767   -6.3010653            0   -4.6125225   -2.5704638 
Loop time of 0.03213 on 1 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.0242701 (75.5371)
Neigh time (%) = 0.006531 (20.3268)
Comm  time (%) = 0.000502825 (1.56497)
Outpt time (%) = 2.09808e-05 (0.0652998)
Other time (%) = 0.00080514 (2.50588)

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    5841 ave 5841 max 5841 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    155984 ave 155984 max 155984 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 155984
Ave neighs/atom = 38.996
Neighbor list builds = 1
Dangerous builds = 0

# 1st Python function
# example of catching a syntax error

python          simple here """
def simple():
  import exceptions
  print "Inside simple function"
  try:
    foo += 1
  except Exception, e:
    print "FOO error:",e
"""

python          simple invoke

# 2nd Python function
# example of returning the function value to a python-style variable
# invoke it twice

variable        fact python factorial
python          factorial input 1 v_n return v_fact format ii here """
def factorial(n):
  if n == 1: return 1
  return n*factorial(n-1)
"""

variable        n string 10
python          factorial invoke
print           "Factorial of $n = ${fact}"
Factorial of 10 = 3628800

variable        n string 20
python          factorial invoke
print           "Factorial of $n = ${fact}"
Factorial of 20 = 2432902008176640000

# 3rd Python function
# example of calling back to LAMMPS and writing a run loop in Python

variable        cut string 0.0

python          loop input 4 10 1.0 -4.0 SELF format iffp file funcs.py
python          loop invoke
pair_style lj/cut ${cut}
pair_style lj/cut 1.0
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  master list distance cutoff = 1.3
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press 
      10    1.1259767  0.016557378            0    1.7051002    1.2784679 
      20   0.87608998   0.39300382            0    1.7068103    6.0488236 
Loop time of 0.00451207 on 1 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00158691 (35.1704)
Neigh time (%) = 0.00194287 (43.0594)
Comm  time (%) = 0.000257015 (5.69617)
Outpt time (%) = 2.09808e-05 (0.464993)
Other time (%) = 0.000704288 (15.609)

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2083 ave 2083 max 2083 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    17727 ave 17727 max 17727 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 17727
Ave neighs/atom = 4.43175
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.1
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  master list distance cutoff = 1.4
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press 
      20   0.87608998  -0.33042884            0    0.9833776    8.5817494 
      30    1.0155079  -0.83166219            0   0.69121891    7.9905553 
Loop time of 0.00607896 on 1 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00298262 (49.0646)
Neigh time (%) = 0.00210714 (34.6629)
Comm  time (%) = 0.000262499 (4.31816)
Outpt time (%) = 2.00272e-05 (0.329451)
Other time (%) = 0.000706673 (11.6249)

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2087 ave 2087 max 2087 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    21036 ave 21036 max 21036 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 21036
Ave neighs/atom = 5.259
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.2
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  master list distance cutoff = 1.5
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press 
      30    1.0155079   -2.0616558            0  -0.53877467    7.6238572 
      40    1.0490928   -2.1868324            0  -0.61358669    7.2084131 
Loop time of 0.00735807 on 1 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00416398 (56.5906)
Neigh time (%) = 0.00219989 (29.8976)
Comm  time (%) = 0.000262022 (3.56101)
Outpt time (%) = 1.90735e-05 (0.259218)
Other time (%) = 0.00071311 (9.69153)

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2250 ave 2250 max 2250 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    24095 ave 24095 max 24095 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 24095
Ave neighs/atom = 6.02375
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.3
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  master list distance cutoff = 1.6
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press 
      40    1.0490928   -3.0667608            0    -1.493515    6.2796311 
      50    1.0764484   -3.1173704            0   -1.5031014    6.0850409 
Loop time of 0.0085659 on 1 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00486517 (56.7969)
Neigh time (%) = 0.00266886 (31.1568)
Comm  time (%) = 0.000301838 (3.52371)
Outpt time (%) = 2.00272e-05 (0.233801)
Other time (%) = 0.000710011 (8.2888)

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2572 ave 2572 max 2572 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    27137 ave 27137 max 27137 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 27137
Ave neighs/atom = 6.78425
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.4
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  master list distance cutoff = 1.7
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press 
      50    1.0764484   -3.6112241            0   -1.9969552    5.4223348 
      60    1.1101013   -3.6616014            0   -1.9968657    5.2348251 
Loop time of 0.0091939 on 1 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00552583 (60.1032)
Neigh time (%) = 0.00259781 (28.2558)
Comm  time (%) = 0.000323296 (3.51642)
Outpt time (%) = 2.00272e-05 (0.217831)
Other time (%) = 0.000726938 (7.90675)

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    3013 ave 3013 max 3013 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    30887 ave 30887 max 30887 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 30887
Ave neighs/atom = 7.72175
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.5
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  master list distance cutoff = 1.8
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press 
      60    1.1101013   -3.9655053            0   -2.3007696    4.7849008 
      70    1.1122144   -3.9657095            0    -2.297805    4.8014106 
Loop time of 0.0102301 on 1 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00630403 (61.6225)
Neigh time (%) = 0.00282717 (27.6359)
Comm  time (%) = 0.000349283 (3.41428)
Outpt time (%) = 2.00272e-05 (0.195768)
Other time (%) = 0.000729561 (7.13154)

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    3388 ave 3388 max 3388 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    35959 ave 35959 max 35959 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 35959
Ave neighs/atom = 8.98975
Neighbor list builds = 1
Dangerous builds = 0
pair_style lj/cut ${cut}
pair_style lj/cut 1.6
pair_coeff * * 1.0 1.0
run 10
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 0 steps, check yes
  master list distance cutoff = 1.9
Memory usage per processor = 2.78761 Mbytes
Step Temp E_pair E_mol TotEng Press 
      70    1.1122144   -4.1752688            0   -2.5073643    4.4755409 
      80     1.117224   -4.1831357            0   -2.5077187     4.446079 
Loop time of 0.011508 on 1 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00736189 (63.972)
Neigh time (%) = 0.00303006 (26.3301)
Comm  time (%) = 0.000365019 (3.17187)
Outpt time (%) = 2.00272e-05 (0.174028)
Other time (%) = 0.000730991 (6.35203)

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    3612 ave 3612 max 3612 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    43239 ave 43239 max 43239 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 43239
Ave neighs/atom = 10.8097
Neighbor list builds = 1
Dangerous builds = 0
