lammps/examples/python/log.27Nov18.pair_python_hybrid.g++.1

LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# 3d Lennard-Jones hybrid

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	2 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
  Time spent = 0.00073123 secs
mass		* 1.0
region          half block -0.1 4.9 0 10 0 10
set region half type 2
  2000 settings made for type

velocity	all create 3.0 87287

pair_style	hybrid lj/cut 2.5 python 2.5
pair_coeff	* * python py_pot.LJCutMelt lj NULL
pair_coeff      * 2 lj/cut 1.0 1.0

neighbor	0.3 bin
neigh_modify	every 20 delay 0 check no

fix		1 all nve

thermo		50
run		250
Neighbor list info ...
  update every 20 steps, delay 0 steps, check no
  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
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair lj/cut, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair python, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.484 | 4.484 | 4.484 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0            3   -6.7733681            0   -2.2744931   -3.7033504 
      50    1.6758903   -4.7955425            0   -2.2823355     5.670064 
     100    1.6458363   -4.7492704            0   -2.2811332    5.8691042 
     150    1.6324555   -4.7286791            0    -2.280608    5.9589514 
     200    1.6630725   -4.7750988            0   -2.2811136    5.7364886 
     250    1.6275257   -4.7224992            0    -2.281821    5.9567365 
Loop time of 5.56562 on 1 procs for 250 steps with 4000 atoms

Performance: 19404.856 tau/day, 44.919 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.4305     | 5.4305     | 5.4305     |   0.0 | 97.57
Neigh   | 0.10441    | 0.10441    | 0.10441    |   0.0 |  1.88
Comm    | 0.013915   | 0.013915   | 0.013915   |   0.0 |  0.25
Output  | 0.00019979 | 0.00019979 | 0.00019979 |   0.0 |  0.00
Modify  | 0.014502   | 0.014502   | 0.014502   |   0.0 |  0.26
Other   |            | 0.002061   |            |       |  0.04

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    5499 ave 5499 max 5499 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    85978 ave 85978 max 85978 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 85978
Ave neighs/atom = 21.4945
Neighbor list builds = 12
Dangerous builds not checked

write_data      hybrid.data
Neighbor list info ...
  update every 20 steps, delay 0 steps, check no
  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
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair lj/cut, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair python, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
write_restart   hybrid.restart
Neighbor list info ...
  update every 20 steps, delay 0 steps, check no
  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
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair lj/cut, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair python, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard

clear
  using 1 OpenMP thread(s) per MPI task

read_restart    hybrid.restart
  restoring atom style atomic from restart
  orthogonal box = (0 0 0) to (16.796 16.796 16.796)
  1 by 1 by 1 MPI processor grid
  restoring pair style hybrid from restart
  4000 atoms

pair_style	hybrid lj/cut 2.5 python 2.5
pair_coeff	* * python py_pot.LJCutMelt lj NULL
pair_coeff      * 2 lj/cut 1.0 1.0

fix		1 all nve

thermo		50
run		250
Neighbor list info ...
  update every 1 steps, delay 10 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
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair lj/cut, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair python, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.281 | 4.281 | 4.281 Mbytes
Step Temp E_pair E_mol TotEng Press 
     250    1.6275257   -4.7224992            0    -2.281821    5.9567365 
     300     1.645592   -4.7496711            0   -2.2819002    5.8734193 
     350    1.6514972   -4.7580756            0   -2.2814491     5.810167 
     400    1.6540555   -4.7622999            0    -2.281837    5.8200413 
     450    1.6264734   -4.7200865            0   -2.2809863    5.9546991 
     500    1.6366891   -4.7350979            0   -2.2806781    5.9369284 
Loop time of 5.56525 on 1 procs for 250 steps with 4000 atoms

Performance: 19406.123 tau/day, 44.922 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.3122     | 5.3122     | 5.3122     |   0.0 | 95.45
Neigh   | 0.21918    | 0.21918    | 0.21918    |   0.0 |  3.94
Comm    | 0.015959   | 0.015959   | 0.015959   |   0.0 |  0.29
Output  | 0.00018764 | 0.00018764 | 0.00018764 |   0.0 |  0.00
Modify  | 0.014443   | 0.014443   | 0.014443   |   0.0 |  0.26
Other   |            | 0.00326    |            |       |  0.06

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    5472 ave 5472 max 5472 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    86930 ave 86930 max 86930 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 86930
Ave neighs/atom = 21.7325
Neighbor list builds = 25
Dangerous builds = 25

clear
  using 1 OpenMP thread(s) per MPI task

units		lj
atom_style	atomic

read_data       hybrid.data
  orthogonal box = (0 0 0) to (16.796 16.796 16.796)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  4000 atoms
  reading velocities ...
  4000 velocities

pair_style	hybrid lj/cut 2.5 python 2.5
pair_coeff	* * python py_pot.LJCutMelt lj NULL
pair_coeff      * 2 lj/cut 1.0 1.0

neighbor	0.3 bin
neigh_modify	every 20 delay 0 check no

fix		1 all nve

thermo		50
run		250
Neighbor list info ...
  update every 20 steps, delay 0 steps, check no
  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
  3 neighbor lists, perpetual/occasional/extra = 3 0 0
  (1) pair lj/cut, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (2) pair python, perpetual, skip from (3)
      attributes: half, newton on
      pair build: skip
      stencil: none
      bin: none
  (3) neighbor class addition, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 3.781 | 3.781 | 3.781 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    1.6275257   -4.7224992            0    -2.281821    5.9567365 
      50    1.6454666   -4.7497515            0   -2.2821686    5.8729175 
     100    1.6512008   -4.7582693            0   -2.2820874    5.8090548 
     150    1.6537193   -4.7627023            0   -2.2827434    5.8177704 
     200    1.6258731   -4.7205017            0   -2.2823017     5.952511 
     250    1.6370862   -4.7373176            0   -2.2823022     5.925807 
Loop time of 5.44427 on 1 procs for 250 steps with 4000 atoms

Performance: 19837.379 tau/day, 45.920 timesteps/s
99.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 5.3082     | 5.3082     | 5.3082     |   0.0 | 97.50
Neigh   | 0.10536    | 0.10536    | 0.10536    |   0.0 |  1.94
Comm    | 0.01346    | 0.01346    | 0.01346    |   0.0 |  0.25
Output  | 0.00019431 | 0.00019431 | 0.00019431 |   0.0 |  0.00
Modify  | 0.015079   | 0.015079   | 0.015079   |   0.0 |  0.28
Other   |            | 0.002012   |            |       |  0.04

Nlocal:    4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    5487 ave 5487 max 5487 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    86831 ave 86831 max 86831 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 86831
Ave neighs/atom = 21.7078
Neighbor list builds = 12
Dangerous builds not checked

shell rm hybrid.data hybrid.restart
Total wall time: 0:00:16