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 2 by 2 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 = 2.60344 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 0.00962114 on 4 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00643039 (66.836)
Neigh time (%) = 0.00174427 (18.1296)
Comm  time (%) = 0.00106865 (11.1073)
Outpt time (%) = 3.48091e-05 (0.361798)
Other time (%) = 0.000343025 (3.56532)

Nlocal:    1000 ave 1013 max 989 min
Histogram: 1 0 1 0 0 1 0 0 0 1
Nghost:    2901 ave 2912 max 2888 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs:    38996 ave 39269 max 38365 min
Histogram: 1 0 0 0 0 0 0 0 1 2

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 = 2.63679 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 0.00155491 on 4 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.000403821 (25.9708)
Neigh time (%) = 0.00049901 (32.0926)
Comm  time (%) = 0.000386357 (24.8476)
Outpt time (%) = 2.87294e-05 (1.84766)
Other time (%) = 0.000236988 (15.2413)

Nlocal:    1000 ave 1015 max 987 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost:    943 ave 956 max 928 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Neighs:    4431.75 ave 4498 max 4325 min
Histogram: 1 0 0 0 0 0 1 0 1 1

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 = 2.63679 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 0.00199097 on 4 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.000789523 (39.6551)
Neigh time (%) = 0.000541985 (27.2221)
Comm  time (%) = 0.000392973 (19.7377)
Outpt time (%) = 2.49147e-05 (1.25138)
Other time (%) = 0.000241578 (12.1336)

Nlocal:    1000 ave 1019 max 983 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Nghost:    945.25 ave 962 max 925 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs:    5259 ave 5343 max 5125 min
Histogram: 1 0 0 0 0 1 0 0 0 2

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 = 2.63679 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 0.00233454 on 4 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00106812 (45.7528)
Neigh time (%) = 0.000583589 (24.9981)
Comm  time (%) = 0.000406563 (17.4152)
Outpt time (%) = 2.41399e-05 (1.03403)
Other time (%) = 0.000252128 (10.7999)

Nlocal:    1000 ave 1013 max 984 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost:    1023 ave 1035 max 1005 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs:    6023.75 ave 6093 max 5953 min
Histogram: 2 0 0 0 0 0 0 0 0 2

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 = 2.63679 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 0.00265193 on 4 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00123417 (46.5387)
Neigh time (%) = 0.000687182 (25.9125)
Comm  time (%) = 0.000449538 (16.9514)
Outpt time (%) = 2.40803e-05 (0.908028)
Other time (%) = 0.000256956 (9.68938)

Nlocal:    1000 ave 1013 max 974 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Nghost:    1184.75 ave 1200 max 1165 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Neighs:    6784.25 ave 6922 max 6577 min
Histogram: 1 0 0 0 0 1 0 0 1 1

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 = 2.63679 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 0.00285125 on 4 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00141847 (49.7491)
Neigh time (%) = 0.000675321 (23.6851)
Comm  time (%) = 0.000490129 (17.19)
Outpt time (%) = 2.77162e-05 (0.972071)
Other time (%) = 0.000239611 (8.40371)

Nlocal:    1000 ave 1016 max 981 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Nghost:    1402.25 ave 1408 max 1390 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs:    7721.75 ave 7798 max 7615 min
Histogram: 1 0 0 1 0 0 0 0 0 2

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 = 2.63679 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 0.00325108 on 4 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00161421 (49.6517)
Neigh time (%) = 0.000730813 (22.4791)
Comm  time (%) = 0.000600517 (18.4713)
Outpt time (%) = 2.87294e-05 (0.88369)
Other time (%) = 0.000276804 (8.51423)

Nlocal:    1000 ave 1022 max 982 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost:    1595.75 ave 1604 max 1588 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs:    8989.75 ave 9204 max 8776 min
Histogram: 1 0 0 0 1 1 0 0 0 1

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 = 2.63679 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 0.00360203 on 4 procs for 10 steps with 4000 atoms

Pair  time (%) = 0.00191045 (53.0381)
Neigh time (%) = 0.000787675 (21.8676)
Comm  time (%) = 0.000629485 (17.4758)
Outpt time (%) = 2.46167e-05 (0.683413)
Other time (%) = 0.000249803 (6.93507)

Nlocal:    1000 ave 1013 max 987 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost:    1706 ave 1720 max 1693 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Neighs:    10809.8 ave 10831 max 10761 min
Histogram: 1 0 0 0 0 0 0 0 1 2

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