forked from lijiext/lammps
228 lines
10 KiB
Groff
228 lines
10 KiB
Groff
|
LAMMPS (27 Nov 2018)
|
||
|
|
using 1 OpenMP thread(s) per MPI task
|
||
|
|
# 3d Lennard-Jones melt
|
||
|
|
|
||
|
|
units lj
|
||
|
|
atom_style atomic
|
||
|
|
processors * 1 1
|
||
|
|
|
||
|
|
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 3 box
|
||
|
|
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||
|
|
2 by 1 by 1 MPI processor grid
|
||
|
|
create_atoms 1 box
|
||
|
|
Created 4000 atoms
|
||
|
|
Time spent = 0.000549078 secs
|
||
|
|
mass * 1.0
|
||
|
|
|
||
|
|
region long block 3 6 0 10 0 10
|
||
|
|
set region long type 2
|
||
|
|
1400 settings made for type
|
||
|
|
|
||
|
|
velocity all create 1.0 87287
|
||
|
|
|
||
|
|
pair_style lj/cut 2.5
|
||
|
|
pair_coeff * * 1.0 1.0 2.5
|
||
|
|
pair_coeff * 2 1.0 1.0 5.0
|
||
|
|
|
||
|
|
neighbor 0.3 bin
|
||
|
|
neigh_modify every 2 delay 4 check yes
|
||
|
|
fix p all property/atom d_WEIGHT
|
||
|
|
compute p all property/atom d_WEIGHT
|
||
|
|
fix 0 all balance 50 1.0 shift x 10 1.0 weight time 1.0 weight store WEIGHT
|
||
|
|
variable maximb equal f_0[1]
|
||
|
|
variable iter equal f_0[2]
|
||
|
|
variable prev equal f_0[3]
|
||
|
|
variable final equal f_0
|
||
|
|
|
||
|
|
#fix 3 all print 50 "${iter} ${prev} ${final} ${maximb}"
|
||
|
|
|
||
|
|
fix 1 all nve
|
||
|
|
|
||
|
|
#dump id all atom 50 dump.melt
|
||
|
|
#dump id all custom 50 dump.lammpstrj id type x y z c_p
|
||
|
|
|
||
|
|
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||
|
|
#dump_modify 2 pad 3
|
||
|
|
|
||
|
|
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||
|
|
#dump_modify 3 pad 3
|
||
|
|
|
||
|
|
thermo 50
|
||
|
|
run 500
|
||
|
|
Neighbor list info ...
|
||
|
|
update every 2 steps, delay 4 steps, check yes
|
||
|
|
max neighbors/atom: 2000, page size: 100000
|
||
|
|
master list distance cutoff = 5.3
|
||
|
|
ghost atom cutoff = 5.3
|
||
|
|
binsize = 2.65, bins = 7 7 7
|
||
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||
|
|
(1) pair lj/cut, 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) = 4.562 | 4.753 | 4.944 Mbytes
|
||
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
||
|
|
0 1 -6.9453205 0 -5.4456955 -5.6812358 4738.2137
|
||
|
|
50 0.49578514 -6.1929216 0 -5.4494298 -1.6668039 4738.2137
|
||
|
|
100 0.53275389 -6.2475932 0 -5.4486622 -1.9063885 4738.2137
|
||
|
|
150 0.53316457 -6.2483202 0 -5.4487733 -1.9476162 4738.2137
|
||
|
|
200 0.536665 -6.2530113 0 -5.448215 -1.933468 4738.2137
|
||
|
|
250 0.55006273 -6.27163 0 -5.4467422 -2.0438847 4738.2137
|
||
|
|
300 0.55111476 -6.2727642 0 -5.4462987 -2.0384873 4738.2137
|
||
|
|
350 0.55211503 -6.274054 0 -5.4460885 -2.0116976 4738.2137
|
||
|
|
400 0.54638463 -6.2661715 0 -5.4467995 -1.992248 4738.2137
|
||
|
|
450 0.55885307 -6.2852263 0 -5.4471563 -2.0669747 4738.2137
|
||
|
|
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
|
||
|
|
Loop time of 3.7099 on 2 procs for 500 steps with 4000 atoms
|
||
|
|
|
||
|
|
Performance: 58222.644 tau/day, 134.775 timesteps/s
|
||
|
|
99.2% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 2.5145 | 2.5951 | 2.6756 | 5.0 | 69.95
|
||
|
|
Neigh | 0.8388 | 0.88634 | 0.93387 | 5.0 | 23.89
|
||
|
|
Comm | 0.17027 | 0.20258 | 0.23489 | 7.2 | 5.46
|
||
|
|
Output | 0.00029612 | 0.00032723 | 0.00035834 | 0.0 | 0.01
|
||
|
|
Modify | 0.016136 | 0.017057 | 0.017979 | 0.7 | 0.46
|
||
|
|
Other | | 0.008504 | | | 0.23
|
||
|
|
|
||
|
|
Nlocal: 2000 ave 2157 max 1843 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
Nghost: 10465.5 ave 10840 max 10091 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
Neighs: 298070 ave 305706 max 290433 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
|
||
|
|
Total # of neighbors = 596139
|
||
|
|
Ave neighs/atom = 149.035
|
||
|
|
Neighbor list builds = 51
|
||
|
|
Dangerous builds = 0
|
||
|
|
run 500
|
||
|
|
Per MPI rank memory allocation (min/avg/max) = 4.944 | 4.947 | 4.951 Mbytes
|
||
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
||
|
|
500 0.54587069 -6.2662849 0 -5.4476836 -2.0078802 4738.2137
|
||
|
|
550 0.54137926 -6.2592773 0 -5.4474115 -1.9770236 4738.2137
|
||
|
|
600 0.54022886 -6.2573307 0 -5.44719 -1.9619637 4738.2137
|
||
|
|
650 0.54709009 -6.2678862 0 -5.4474562 -1.9958342 4738.2137
|
||
|
|
700 0.54590044 -6.2656903 0 -5.4470444 -1.9957108 4738.2137
|
||
|
|
750 0.55098488 -6.2724831 0 -5.4462124 -2.0287523 4738.2137
|
||
|
|
800 0.5520987 -6.2739184 0 -5.4459774 -2.0084991 4738.2137
|
||
|
|
850 0.54963958 -6.2702473 0 -5.445994 -1.9740031 4738.2137
|
||
|
|
900 0.54390586 -6.2615476 0 -5.4458927 -1.9400871 4738.2137
|
||
|
|
950 0.54741732 -6.2665755 0 -5.4456548 -1.9466417 4738.2137
|
||
|
|
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
|
||
|
|
Loop time of 3.70634 on 2 procs for 500 steps with 4000 atoms
|
||
|
|
|
||
|
|
Performance: 58278.514 tau/day, 134.904 timesteps/s
|
||
|
|
99.0% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 2.5536 | 2.6173 | 2.6811 | 3.9 | 70.62
|
||
|
|
Neigh | 0.82942 | 0.88683 | 0.94424 | 6.1 | 23.93
|
||
|
|
Comm | 0.16927 | 0.17474 | 0.1802 | 1.3 | 4.71
|
||
|
|
Output | 0.00030422 | 0.00033307 | 0.00036192 | 0.0 | 0.01
|
||
|
|
Modify | 0.016714 | 0.017824 | 0.018933 | 0.8 | 0.48
|
||
|
|
Other | | 0.009277 | | | 0.25
|
||
|
|
|
||
|
|
Nlocal: 2000 ave 2136 max 1864 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
Nghost: 10413.5 ave 10877 max 9950 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
Neighs: 300836 ave 312313 max 289358 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
|
||
|
|
Total # of neighbors = 601671
|
||
|
|
Ave neighs/atom = 150.418
|
||
|
|
Neighbor list builds = 51
|
||
|
|
Dangerous builds = 0
|
||
|
|
fix 0 all balance 50 1.0 shift x 5 1.0 weight neigh 0.5 weight time 0.66 weight store WEIGHT
|
||
|
|
run 500
|
||
|
|
Per MPI rank memory allocation (min/avg/max) = 4.951 | 5.142 | 5.334 Mbytes
|
||
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
||
|
|
1000 0.54200867 -6.2591246 0 -5.4463148 -1.8881624 4738.2137
|
||
|
|
1050 0.54633412 -6.2656384 0 -5.4463421 -1.9012895 4738.2137
|
||
|
|
1100 0.54325667 -6.2612166 0 -5.4465353 -1.8870463 4738.2137
|
||
|
|
1150 0.55057583 -6.2719187 0 -5.4462614 -1.9575881 4738.2137
|
||
|
|
1200 0.53728175 -6.251744 0 -5.4460228 -1.8124097 4738.2137
|
||
|
|
1250 0.54077561 -6.2567544 0 -5.4457938 -1.8418133 4738.2137
|
||
|
|
1300 0.54430333 -6.260995 0 -5.4447442 -1.856351 4738.2137
|
||
|
|
1350 0.55097839 -6.2715909 0 -5.4453299 -1.9014337 4738.2137
|
||
|
|
1400 0.53858139 -6.2526781 0 -5.445008 -1.7965773 4738.2137
|
||
|
|
1450 0.5421844 -6.2574683 0 -5.444395 -1.7901189 4738.2137
|
||
|
|
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
|
||
|
|
Loop time of 4.8272 on 2 procs for 500 steps with 4000 atoms
|
||
|
|
|
||
|
|
Performance: 44746.478 tau/day, 103.580 timesteps/s
|
||
|
|
98.5% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 1.9951 | 2.6814 | 3.3676 | 41.9 | 55.55
|
||
|
|
Neigh | 0.82826 | 0.90961 | 0.99095 | 8.5 | 18.84
|
||
|
|
Comm | 0.44043 | 1.2083 | 1.9762 | 69.9 | 25.03
|
||
|
|
Output | 0.00034881 | 0.0003655 | 0.00038218 | 0.0 | 0.01
|
||
|
|
Modify | 0.016762 | 0.01755 | 0.018337 | 0.6 | 0.36
|
||
|
|
Other | | 0.01001 | | | 0.21
|
||
|
|
|
||
|
|
Nlocal: 2000 ave 2564 max 1436 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
Nghost: 10334 ave 10752 max 9916 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
Neighs: 302958 ave 499873 max 106044 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
|
||
|
|
Total # of neighbors = 605917
|
||
|
|
Ave neighs/atom = 151.479
|
||
|
|
Neighbor list builds = 51
|
||
|
|
Dangerous builds = 0
|
||
|
|
run 500
|
||
|
|
Per MPI rank memory allocation (min/avg/max) = 4.955 | 5.336 | 5.717 Mbytes
|
||
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
||
|
|
1500 0.54200617 -6.2571433 0 -5.4443373 -1.8000344 4738.2137
|
||
|
|
1550 0.53713591 -6.2504068 0 -5.4449044 -1.7647087 4738.2137
|
||
|
|
1600 0.5467956 -6.2646482 0 -5.4446599 -1.8115778 4738.2137
|
||
|
|
1650 0.53806575 -6.2519004 0 -5.4450036 -1.7409135 4738.2137
|
||
|
|
1700 0.5347949 -6.2468958 0 -5.444904 -1.7162322 4738.2137
|
||
|
|
1750 0.53714528 -6.2506529 0 -5.4451365 -1.7340402 4738.2137
|
||
|
|
1800 0.5274989 -6.2358675 0 -5.444817 -1.6874989 4738.2137
|
||
|
|
1850 0.54585906 -6.2629475 0 -5.4443636 -1.7758918 4738.2137
|
||
|
|
1900 0.5301071 -6.2387551 0 -5.4437932 -1.6381903 4738.2137
|
||
|
|
1950 0.54288149 -6.2582818 0 -5.4441632 -1.7367819 4738.2137
|
||
|
|
2000 0.52766162 -6.2348587 0 -5.4435642 -1.5589151 4738.2137
|
||
|
|
Loop time of 4.90351 on 2 procs for 500 steps with 4000 atoms
|
||
|
|
|
||
|
|
Performance: 44050.062 tau/day, 101.968 timesteps/s
|
||
|
|
98.1% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||
|
|
|
||
|
|
MPI task timing breakdown:
|
||
|
|
Section | min time | avg time | max time |%varavg| %total
|
||
|
|
---------------------------------------------------------------
|
||
|
|
Pair | 1.9937 | 2.6502 | 3.3067 | 40.3 | 54.05
|
||
|
|
Neigh | 0.81645 | 0.88655 | 0.95664 | 7.4 | 18.08
|
||
|
|
Comm | 0.61197 | 1.3389 | 2.0659 | 62.8 | 27.31
|
||
|
|
Output | 0.00036287 | 0.0003773 | 0.00039172 | 0.0 | 0.01
|
||
|
|
Modify | 0.016585 | 0.017429 | 0.018274 | 0.6 | 0.36
|
||
|
|
Other | | 0.01003 | | | 0.20
|
||
|
|
|
||
|
|
Nlocal: 2000 ave 2564 max 1436 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
Nghost: 10256 ave 10620 max 9892 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
Neighs: 303988 ave 502064 max 105911 min
|
||
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||
|
|
|
||
|
|
Total # of neighbors = 607975
|
||
|
|
Ave neighs/atom = 151.994
|
||
|
|
Neighbor list builds = 51
|
||
|
|
Dangerous builds = 0
|
||
|
|
Total wall time: 0:00:17
|