LAMMPS (5 Oct 2016)
# 3d Lennard-Jones melt with Python functions added

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
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 2.8
  ghost atom cutoff = 2.8
  binsize = 1.4 -> bins = 12 12 12
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 0.00930309 on 4 procs for 10 steps with 4000 atoms

Performance: 464361.693 tau/day, 1074.911 timesteps/s
96.7% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0064399  | 0.0064787  | 0.0065157  |   0.0 | 69.64
Neigh   | 0.0017071  | 0.0017205  | 0.0017281  |   0.0 | 18.49
Comm    | 0.00073171 | 0.00077122 | 0.00081086 |   0.1 |  8.29
Output  | 1.9789e-05 | 2.3663e-05 | 2.9087e-05 |   0.1 |  0.25
Modify  | 0.00012827 | 0.00012904 | 0.00013018 |   0.0 |  1.39
Other   |            | 0.0001799  |            |       |  1.93

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
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.3
  ghost atom cutoff = 1.3
  binsize = 0.65 -> bins = 26 26 26
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 0.00152922 on 4 procs for 10 steps with 4000 atoms

Performance: 2824975.566 tau/day, 6539.295 timesteps/s
130.8% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.00040293 | 0.0004105  | 0.00041485 |   0.0 | 26.84
Neigh   | 0.00057507 | 0.00060332 | 0.00062108 |   0.1 | 39.45
Comm    | 0.0002377  | 0.00025356 | 0.00026774 |   0.1 | 16.58
Output  | 1.9073e-05 | 1.9789e-05 | 2.1935e-05 |   0.0 |  1.29
Modify  | 0.00012994 | 0.00013161 | 0.00013328 |   0.0 |  8.61
Other   |            | 0.0001104  |            |       |  7.22

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
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.4
  ghost atom cutoff = 1.4
  binsize = 0.7 -> bins = 24 24 24
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 0.00186676 on 4 procs for 10 steps with 4000 atoms

Performance: 2314172.647 tau/day, 5356.881 timesteps/s
107.1% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.00075388 | 0.00077951 | 0.00079727 |   0.1 | 41.76
Neigh   | 0.00057292 | 0.00058091 | 0.00058484 |   0.0 | 31.12
Comm    | 0.00022578 | 0.00024849 | 0.00028563 |   0.1 | 13.31
Output  | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 |   0.0 |  1.00
Modify  | 0.00012493 | 0.00012845 | 0.00013137 |   0.0 |  6.88
Other   |            | 0.0001107  |            |       |  5.93

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
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.5
  ghost atom cutoff = 1.5
  binsize = 0.75 -> bins = 23 23 23
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 0.00224304 on 4 procs for 10 steps with 4000 atoms

Performance: 1925955.918 tau/day, 4458.231 timesteps/s
89.2% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0010781  | 0.0011036  | 0.0011303  |   0.1 | 49.20
Neigh   | 0.00060606 | 0.00060952 | 0.00061703 |   0.0 | 27.17
Comm    | 0.00023556 | 0.0002715  | 0.00029659 |   0.1 | 12.10
Output  | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 |   0.0 |  0.83
Modify  | 0.00012541 | 0.00012833 | 0.00013351 |   0.0 |  5.72
Other   |            | 0.0001114  |            |       |  4.97

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
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.6
  ghost atom cutoff = 1.6
  binsize = 0.8 -> bins = 21 21 21
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 0.00257862 on 4 procs for 10 steps with 4000 atoms

Performance: 1675317.210 tau/day, 3878.049 timesteps/s
77.6% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0012422  | 0.0012776  | 0.0013103  |   0.1 | 49.55
Neigh   | 0.0007019  | 0.00072145 | 0.00073099 |   0.0 | 27.98
Comm    | 0.00027132 | 0.00031221 | 0.00036168 |   0.2 | 12.11
Output  | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 |   0.0 |  0.74
Modify  | 0.00012279 | 0.00012654 | 0.00012875 |   0.0 |  4.91
Other   |            | 0.0001217  |            |       |  4.72

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
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.7
  ghost atom cutoff = 1.7
  binsize = 0.85 -> bins = 20 20 20
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 0.00283062 on 4 procs for 10 steps with 4000 atoms

Performance: 1526164.943 tau/day, 3532.789 timesteps/s
97.1% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0014381  | 0.0014688  | 0.0015128  |   0.1 | 51.89
Neigh   | 0.00070405 | 0.000714   | 0.00071907 |   0.0 | 25.22
Comm    | 0.00032473 | 0.00037426 | 0.0004046  |   0.2 | 13.22
Output  | 1.8835e-05 | 1.961e-05  | 2.1935e-05 |   0.0 |  0.69
Modify  | 0.00012612 | 0.00012892 | 0.00013089 |   0.0 |  4.55
Other   |            | 0.000125   |            |       |  4.42

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
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.8
  ghost atom cutoff = 1.8
  binsize = 0.9 -> bins = 19 19 19
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 0.00313491 on 4 procs for 10 steps with 4000 atoms

Performance: 1378031.621 tau/day, 3189.888 timesteps/s
87.7% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0016167  | 0.001663   | 0.0016985  |   0.1 | 53.05
Neigh   | 0.00075388 | 0.00076818 | 0.00078201 |   0.0 | 24.50
Comm    | 0.00037456 | 0.00042272 | 0.00048018 |   0.2 | 13.48
Output  | 1.7881e-05 | 1.9133e-05 | 2.1935e-05 |   0.0 |  0.61
Modify  | 0.00012636 | 0.00012881 | 0.00013304 |   0.0 |  4.11
Other   |            | 0.0001331  |            |       |  4.25

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
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 1.9
  ghost atom cutoff = 1.9
  binsize = 0.95 -> bins = 18 18 18
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 0.00345927 on 4 procs for 10 steps with 4000 atoms

Performance: 1248816.671 tau/day, 2890.779 timesteps/s
79.5% CPU use with 4 MPI tasks x no OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.0019331  | 0.0019561  | 0.0019834  |   0.0 | 56.55
Neigh   | 0.00081587 | 0.00081897 | 0.00082588 |   0.0 | 23.67
Comm    | 0.00037837 | 0.00040215 | 0.00041842 |   0.1 | 11.63
Output  | 1.812e-05  | 1.9312e-05 | 2.1935e-05 |   0.0 |  0.56
Modify  | 0.00012708 | 0.00013059 | 0.00013423 |   0.0 |  3.78
Other   |            | 0.0001321  |            |       |  3.82

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
Total wall time: 0:00:00
