Commit 3f7821ba authored by sjplimp's avatar sjplimp
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15707 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent 2a93bca2

examples/python/log.lammps

deleted100644 → 0
+0 −396
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 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 0.00927401 on 4 procs for 10 steps with 4000 atoms



Performance: 465818.121 tau/day, 1078.283 timesteps/s

97.0% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.0063918  | 0.0064297  | 0.0064912  |   0.1 | 69.33

Neigh   | 0.00175    | 0.001769   | 0.001781   |   0.0 | 19.07

Comm    | 0.00068188 | 0.00074887 | 0.0007844  |   0.1 |  8.07

Output  | 1.812e-05  | 1.9312e-05 | 2.1935e-05 |   0.0 |  0.21

Modify  | 0.00012898 | 0.00013059 | 0.00013304 |   0.0 |  1.41

Other   |            | 0.0001765  |            |       |  1.90



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 0.00150609 on 4 procs for 10 steps with 4000 atoms



Performance: 2868354.168 tau/day, 6639.709 timesteps/s

132.8% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.00040388 | 0.00040805 | 0.00041318 |   0.0 | 27.09

Neigh   | 0.00054407 | 0.00057578 | 0.00058794 |   0.1 | 38.23

Comm    | 0.00023937 | 0.00025755 | 0.00029469 |   0.1 | 17.10

Output  | 1.9073e-05 | 1.9789e-05 | 2.0981e-05 |   0.0 |  1.31

Modify  | 0.00012827 | 0.00012988 | 0.00013113 |   0.0 |  8.62

Other   |            | 0.000115   |            |       |  7.64



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 0.00186372 on 4 procs for 10 steps with 4000 atoms



Performance: 2317947.202 tau/day, 5365.619 timesteps/s

93.9% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.00075579 | 0.00077468 | 0.00078678 |   0.0 | 41.57

Neigh   | 0.00057006 | 0.00057727 | 0.00058198 |   0.0 | 30.97

Comm    | 0.00023437 | 0.00025171 | 0.0002768  |   0.1 | 13.51

Output  | 1.7166e-05 | 1.9073e-05 | 2.1935e-05 |   0.0 |  1.02

Modify  | 0.00012541 | 0.00013083 | 0.00013685 |   0.0 |  7.02

Other   |            | 0.0001101  |            |       |  5.91



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 0.00224113 on 4 procs for 10 steps with 4000 atoms



Performance: 1927595.030 tau/day, 4462.026 timesteps/s

78.1% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.0010741  | 0.0010966  | 0.0011258  |   0.1 | 48.93

Neigh   | 0.00059891 | 0.00060576 | 0.00061202 |   0.0 | 27.03

Comm    | 0.00024176 | 0.00027955 | 0.00030494 |   0.2 | 12.47

Output  | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 |   0.0 |  0.83

Modify  | 0.00012755 | 0.00013041 | 0.00013423 |   0.0 |  5.82

Other   |            | 0.0001101  |            |       |  4.91



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 0.00257301 on 4 procs for 10 steps with 4000 atoms



Performance: 1678965.278 tau/day, 3886.494 timesteps/s

77.7% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.0012639  | 0.0012798  | 0.001297   |   0.0 | 49.74

Neigh   | 0.00069809 | 0.00072157 | 0.00073504 |   0.1 | 28.04

Comm    | 0.000283   | 0.00030494 | 0.00033665 |   0.1 | 11.85

Output  | 1.6928e-05 | 1.8239e-05 | 1.9789e-05 |   0.0 |  0.71

Modify  | 0.00012851 | 0.00013149 | 0.00013351 |   0.0 |  5.11

Other   |            | 0.000117   |            |       |  4.55



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 0.00281382 on 4 procs for 10 steps with 4000 atoms



Performance: 1535281.586 tau/day, 3553.893 timesteps/s

71.1% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.001436   | 0.0014526  | 0.0014732  |   0.0 | 51.62

Neigh   | 0.00070786 | 0.00071573 | 0.00072408 |   0.0 | 25.44

Comm    | 0.00035024 | 0.00036937 | 0.00038791 |   0.1 | 13.13

Output  | 1.812e-05  | 1.955e-05  | 2.2888e-05 |   0.0 |  0.69

Modify  | 0.00012541 | 0.00012916 | 0.00013518 |   0.0 |  4.59

Other   |            | 0.0001274  |            |       |  4.53



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 0.00315809 on 4 procs for 10 steps with 4000 atoms



Performance: 1367914.335 tau/day, 3166.468 timesteps/s

95.0% CPU use with 4 MPI tasks x no OpenMP threads



MPI task timing breakdown:

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

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

Pair    | 0.0016134  | 0.0016503  | 0.0016952  |   0.1 | 52.26

Neigh   | 0.00075412 | 0.00077403 | 0.00078702 |   0.0 | 24.51

Comm    | 0.0003922  | 0.00044894 | 0.00050783 |   0.2 | 14.22

Output  | 1.7881e-05 | 1.8656e-05 | 2.0981e-05 |   0.0 |  0.59

Modify  | 0.00012779 | 0.00013137 | 0.00013638 |   0.0 |  4.16

Other   |            | 0.0001348  |            |       |  4.27



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 0.00346923 on 4 procs for 10 steps with 4000 atoms



Performance: 1245233.543 tau/day, 2882.485 timesteps/s

86.5% 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  | 0.001945   | 0.0019629  |   0.0 | 56.06

Neigh   | 0.00082707 | 0.0008325  | 0.0008409  |   0.0 | 24.00

Comm    | 0.0003984  | 0.00040597 | 0.0004189  |   0.0 | 11.70

Output  | 1.8835e-05 | 1.961e-05  | 2.1935e-05 |   0.0 |  0.57

Modify  | 0.00012946 | 0.00013238 | 0.00013733 |   0.0 |  3.82

Other   |            | 0.0001338  |            |       |  3.86



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

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