Commit 47b3de25 authored by sjplimp's avatar sjplimp
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15711 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent e5165066

examples/python/log.python.5Oct16.linux.1

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Original line number Diff line number Diff line 
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 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

  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 = 2.69271 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 0.0323398 on 1 procs for 10 steps with 4000 atoms



Performance: 133581.484 tau/day, 309.216 timesteps/s

102.0% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.024638   | 0.024638   | 0.024638   |   0.0 | 76.18

Neigh   | 0.0063899  | 0.0063899  | 0.0063899  |   0.0 | 19.76

Comm    | 0.00049949 | 0.00049949 | 0.00049949 |   0.0 |  1.54

Output  | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 |   0.0 |  0.06

Modify  | 0.00050044 | 0.00050044 | 0.00050044 |   0.0 |  1.55

Other   |            | 0.0002944  |            |       |  0.91



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

  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 = 2.78761 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 0.0046258 on 1 procs for 10 steps with 4000 atoms



Performance: 933893.067 tau/day, 2161.790 timesteps/s

86.4% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.001574   | 0.001574   | 0.001574   |   0.0 | 34.03

Neigh   | 0.0020421  | 0.0020421  | 0.0020421  |   0.0 | 44.14

Comm    | 0.00025463 | 0.00025463 | 0.00025463 |   0.0 |  5.50

Output  | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 |   0.0 |  0.39

Modify  | 0.00049615 | 0.00049615 | 0.00049615 |   0.0 | 10.73

Other   |            | 0.000241   |            |       |  5.21



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

  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 = 2.78761 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 0.00619817 on 1 procs for 10 steps with 4000 atoms



Performance: 696980.162 tau/day, 1613.380 timesteps/s

96.8% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0029786  | 0.0029786  | 0.0029786  |   0.0 | 48.06

Neigh   | 0.002203   | 0.002203   | 0.002203   |   0.0 | 35.54

Comm    | 0.00025678 | 0.00025678 | 0.00025678 |   0.0 |  4.14

Output  | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 |   0.0 |  0.29

Modify  | 0.00049472 | 0.00049472 | 0.00049472 |   0.0 |  7.98

Other   |            | 0.0002472  |            |       |  3.99



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

  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 = 2.78761 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 0.00750899 on 1 procs for 10 steps with 4000 atoms



Performance: 575310.153 tau/day, 1331.736 timesteps/s

93.2% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.004189   | 0.004189   | 0.004189   |   0.0 | 55.79

Neigh   | 0.0022991  | 0.0022991  | 0.0022991  |   0.0 | 30.62

Comm    | 0.0002594  | 0.0002594  | 0.0002594  |   0.0 |  3.45

Output  | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 |   0.0 |  0.24

Modify  | 0.00049615 | 0.00049615 | 0.00049615 |   0.0 |  6.61

Other   |            | 0.0002475  |            |       |  3.30



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

  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 = 2.78761 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 0.00869107 on 1 procs for 10 steps with 4000 atoms



Performance: 497061.786 tau/day, 1150.606 timesteps/s

103.5% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0049038  | 0.0049038  | 0.0049038  |   0.0 | 56.42

Neigh   | 0.0027289  | 0.0027289  | 0.0027289  |   0.0 | 31.40

Comm    | 0.00028753 | 0.00028753 | 0.00028753 |   0.0 |  3.31

Output  | 2.0027e-05 | 2.0027e-05 | 2.0027e-05 |   0.0 |  0.23

Modify  | 0.00049758 | 0.00049758 | 0.00049758 |   0.0 |  5.73

Other   |            | 0.0002532  |            |       |  2.91



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

  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 = 2.78761 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 0.00934482 on 1 procs for 10 steps with 4000 atoms



Performance: 462288.386 tau/day, 1070.112 timesteps/s

96.3% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0055761  | 0.0055761  | 0.0055761  |   0.0 | 59.67

Neigh   | 0.002676   | 0.002676   | 0.002676   |   0.0 | 28.64

Comm    | 0.00032163 | 0.00032163 | 0.00032163 |   0.0 |  3.44

Output  | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 |   0.0 |  0.19

Modify  | 0.00049901 | 0.00049901 | 0.00049901 |   0.0 |  5.34

Other   |            | 0.0002542  |            |       |  2.72



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

  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 = 2.78761 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 0.0103869 on 1 procs for 10 steps with 4000 atoms



Performance: 415906.746 tau/day, 962.747 timesteps/s

96.3% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0063703  | 0.0063703  | 0.0063703  |   0.0 | 61.33

Neigh   | 0.002893   | 0.002893   | 0.002893   |   0.0 | 27.85

Comm    | 0.00034499 | 0.00034499 | 0.00034499 |   0.0 |  3.32

Output  | 1.7881e-05 | 1.7881e-05 | 1.7881e-05 |   0.0 |  0.17

Modify  | 0.00050139 | 0.00050139 | 0.00050139 |   0.0 |  4.83

Other   |            | 0.0002594  |            |       |  2.50



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

  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 = 2.78761 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 0.0116282 on 1 procs for 10 steps with 4000 atoms



Performance: 371512.205 tau/day, 859.982 timesteps/s

103.2% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.0074186  | 0.0074186  | 0.0074186  |   0.0 | 63.80

Neigh   | 0.0030658  | 0.0030658  | 0.0030658  |   0.0 | 26.37

Comm    | 0.00036025 | 0.00036025 | 0.00036025 |   0.0 |  3.10

Output  | 1.7166e-05 | 1.7166e-05 | 1.7166e-05 |   0.0 |  0.15

Modify  | 0.0005033  | 0.0005033  | 0.0005033  |   0.0 |  4.33

Other   |            | 0.000263   |            |       |  2.26



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

Total wall time: 0:00:00

examples/python/log.python.5Oct16.linux.4

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