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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 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000420809 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) = 3.968 | 3.968 | 3.968 Mbytes
Step Temp E_pair E_mol TotEng Press
0 3 -6.7733681 0 -2.2744931 -3.7033504
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
Loop time of 1.53377 on 4 procs for 250 steps with 4000 atoms
Performance: 70414.718 tau/day, 162.997 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3644 | 1.406 | 1.4448 | 3.2 | 91.67
Neigh | 0.027066 | 0.027591 | 0.028437 | 0.3 | 1.80
Comm | 0.055296 | 0.095109 | 0.13733 | 12.4 | 6.20
Output | 0.00022817 | 0.00030088 | 0.00042033 | 0.0 | 0.02
Modify | 0.0037878 | 0.0038549 | 0.0040336 | 0.2 | 0.25
Other | | 0.0008861 | | | 0.06
Nlocal: 1000 ave 1010 max 982 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 2703.75 ave 2713 max 2689 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Neighs: 21469.8 ave 22167 max 20546 min
Histogram: 1 0 0 0 0 1 1 0 0 1
Total # of neighbors = 85879
Ave neighs/atom = 21.4698
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 2 by 2 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) = 3.626 | 3.626 | 3.626 Mbytes
Step Temp E_pair E_mol TotEng Press
250 1.6323462 -4.7292062 0 -2.2812991 5.9762168
300 1.6451788 -4.7488091 0 -2.2816578 5.8375485
350 1.6171909 -4.7064928 0 -2.2813129 6.0094235
400 1.6388136 -4.7387093 0 -2.2811035 5.9331084
450 1.6431295 -4.7452215 0 -2.2811435 5.8929898
500 1.643316 -4.7454222 0 -2.2810644 5.8454817
Loop time of 1.51785 on 4 procs for 250 steps with 4000 atoms
Performance: 71153.411 tau/day, 164.707 timesteps/s
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2893 | 1.3741 | 1.416 | 4.2 | 90.53
Neigh | 0.055474 | 0.056676 | 0.057363 | 0.3 | 3.73
Comm | 0.039187 | 0.081666 | 0.16742 | 17.6 | 5.38
Output | 0.00014877 | 0.0002687 | 0.00061893 | 0.0 | 0.02
Modify | 0.003741 | 0.0037862 | 0.0038075 | 0.0 | 0.25
Other | | 0.001315 | | | 0.09
Nlocal: 1000 ave 1012 max 983 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Nghost: 2699 ave 2706 max 2693 min
Histogram: 1 1 0 0 0 0 1 0 0 1
Neighs: 21802 ave 22700 max 21236 min
Histogram: 1 1 0 1 0 0 0 0 0 1
Total # of neighbors = 87208
Ave neighs/atom = 21.802
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 2 by 2 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) = 3.126 | 3.126 | 3.126 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.6323462 -4.7292062 0 -2.2812991 5.9762168
50 1.6450626 -4.7488948 0 -2.2819177 5.8370409
100 1.6169004 -4.7066969 0 -2.2819526 6.0082546
150 1.6384234 -4.7389689 0 -2.2819482 5.9315273
200 1.6428814 -4.7460743 0 -2.2823683 5.8888228
250 1.6432631 -4.7466603 0 -2.2823818 5.8398819
Loop time of 1.53622 on 4 procs for 250 steps with 4000 atoms
Performance: 70302.534 tau/day, 162.737 timesteps/s
97.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2893 | 1.3875 | 1.4506 | 5.1 | 90.32
Neigh | 0.026512 | 0.02714 | 0.027651 | 0.2 | 1.77
Comm | 0.053684 | 0.11665 | 0.21515 | 17.6 | 7.59
Output | 0.00017214 | 0.00029582 | 0.0006547 | 0.0 | 0.02
Modify | 0.0037682 | 0.0037964 | 0.0038147 | 0.0 | 0.25
Other | | 0.0008581 | | | 0.06
Nlocal: 1000 ave 1013 max 989 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 2695.5 ave 2706 max 2682 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Neighs: 21792 ave 22490 max 21457 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 87168
Ave neighs/atom = 21.792
Neighbor list builds = 12
Dangerous builds not checked
shell rm hybrid.data hybrid.restart
Total wall time: 0:00:04
|
