251 lines
8.4 KiB
Groff
251 lines
8.4 KiB
Groff
LAMMPS (4 May 2017)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
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
|
|
mass * 1.0
|
|
|
|
velocity all create 3.0 87287
|
|
|
|
pair_style hybrid lj/cut 2.5 python 2.5
|
|
pair_coeff * * python potentials.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) = 3.953 | 3.953 | 3.953 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 11.1422 on 4 procs for 250 steps with 4000 atoms
|
|
|
|
Performance: 9692.888 tau/day, 22.437 timesteps/s
|
|
35.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 10.448 | 10.772 | 10.937 | 5.9 | 96.67
|
|
Neigh | 0.062061 | 0.062949 | 0.06439 | 0.4 | 0.56
|
|
Comm | 0.12929 | 0.29444 | 0.61802 | 35.8 | 2.64
|
|
Output | 0.000301 | 0.000684 | 0.001824 | 0.0 | 0.01
|
|
Modify | 0.009803 | 0.0098622 | 0.010014 | 0.1 | 0.09
|
|
Other | | 0.002618 | | | 0.02
|
|
|
|
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: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 0
|
|
Ave neighs/atom = 0
|
|
Neighbor list builds = 12
|
|
Dangerous builds not checked
|
|
|
|
write_data hybrid.data
|
|
write_restart hybrid.restart
|
|
|
|
clear
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
|
|
read_restart hybrid.restart
|
|
orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
|
1 by 2 by 2 MPI processor grid
|
|
4000 atoms
|
|
|
|
pair_style hybrid lj/cut 2.5 python 2.5
|
|
pair_coeff * * python potentials.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) = 3.612 | 3.612 | 3.612 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 11.287 on 4 procs for 250 steps with 4000 atoms
|
|
|
|
Performance: 9568.520 tau/day, 22.149 timesteps/s
|
|
34.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 10.274 | 10.76 | 11.02 | 8.8 | 95.33
|
|
Neigh | 0.12639 | 0.1291 | 0.13056 | 0.5 | 1.14
|
|
Comm | 0.12094 | 0.38226 | 0.87078 | 46.7 | 3.39
|
|
Output | 0.000297 | 0.0006965 | 0.001867 | 0.0 | 0.01
|
|
Modify | 0.010445 | 0.010638 | 0.011054 | 0.2 | 0.09
|
|
Other | | 0.003901 | | | 0.03
|
|
|
|
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: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 0
|
|
Ave neighs/atom = 0
|
|
Neighbor list builds = 25
|
|
Dangerous builds = 25
|
|
|
|
clear
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
|
|
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 potentials.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) = 3.112 | 3.112 | 3.112 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 11.1573 on 4 procs for 250 steps with 4000 atoms
|
|
|
|
Performance: 9679.760 tau/day, 22.407 timesteps/s
|
|
35.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 10.166 | 10.713 | 10.932 | 9.7 | 96.01
|
|
Neigh | 0.060687 | 0.062175 | 0.063163 | 0.4 | 0.56
|
|
Comm | 0.14931 | 0.36938 | 0.91686 | 52.5 | 3.31
|
|
Output | 0.00036 | 0.00058175 | 0.001228 | 0.0 | 0.01
|
|
Modify | 0.009918 | 0.010237 | 0.010388 | 0.2 | 0.09
|
|
Other | | 0.002356 | | | 0.02
|
|
|
|
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: 0 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 0
|
|
Ave neighs/atom = 0
|
|
Neighbor list builds = 12
|
|
Dangerous builds not checked
|
|
|
|
shell rm hybrid.data hybrid.restart
|
|
Total wall time: 0:00:35
|