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LAMMPS (27 Nov 2018)
using 1 OpenMP thread(s) per MPI task
# 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 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000694513 secs
mass * 1.0
velocity all create 3.0 87287
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, 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) = 3.221 | 3.221 | 3.221 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 11.5979 on 1 procs for 250 steps with 4000 atoms
Performance: 9312.020 tau/day, 21.556 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.474 | 11.474 | 11.474 | 0.0 | 98.94
Neigh | 0.092903 | 0.092903 | 0.092903 | 0.0 | 0.80
Comm | 0.01373 | 0.01373 | 0.01373 | 0.0 | 0.12
Output | 0.00021935 | 0.00021935 | 0.00021935 | 0.0 | 0.00
Modify | 0.014506 | 0.014506 | 0.014506 | 0.0 | 0.13
Other | | 0.002072 | | | 0.02
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: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 12
Dangerous builds not checked
write_data melt.data
write_restart melt.restart
clear
using 1 OpenMP thread(s) per MPI task
read_restart melt.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
pair style python stores no restart info
4000 atoms
pair_style python 2.5
pair_coeff * * py_pot.LJCutMelt lj
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, 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) = 3.396 | 3.396 | 3.396 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 11.6299 on 1 procs for 250 steps with 4000 atoms
Performance: 9286.409 tau/day, 21.496 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.403 | 11.403 | 11.403 | 0.0 | 98.05
Neigh | 0.19289 | 0.19289 | 0.19289 | 0.0 | 1.66
Comm | 0.015828 | 0.015828 | 0.015828 | 0.0 | 0.14
Output | 0.00018644 | 0.00018644 | 0.00018644 | 0.0 | 0.00
Modify | 0.014582 | 0.014582 | 0.014582 | 0.0 | 0.13
Other | | 0.003107 | | | 0.03
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: 151513 ave 151513 max 151513 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151513
Ave neighs/atom = 37.8783
Neighbor list builds = 25
Dangerous builds = 25
clear
using 1 OpenMP thread(s) per MPI task
units lj
atom_style atomic
read_data melt.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 python 2.5
pair_coeff * * py_pot.LJCutMelt lj
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
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair python, 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) = 2.896 | 2.896 | 2.896 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 11.6243 on 1 procs for 250 steps with 4000 atoms
Performance: 9290.855 tau/day, 21.507 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.501 | 11.501 | 11.501 | 0.0 | 98.94
Neigh | 0.093333 | 0.093333 | 0.093333 | 0.0 | 0.80
Comm | 0.013483 | 0.013483 | 0.013483 | 0.0 | 0.12
Output | 0.00020981 | 0.00020981 | 0.00020981 | 0.0 | 0.00
Modify | 0.014475 | 0.014475 | 0.014475 | 0.0 | 0.12
Other | | 0.001968 | | | 0.02
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: 151490 ave 151490 max 151490 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 151490
Ave neighs/atom = 37.8725
Neighbor list builds = 12
Dangerous builds not checked
shell rm melt.data melt.restart
Total wall time: 0:00:35
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