147 lines
6.2 KiB
Groff
147 lines
6.2 KiB
Groff
LAMMPS (3 Aug 2023 - Development - patch_2Aug2023-790-g0fbe388cbd)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
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 = 1.6795962 1.6795962 1.6795962
|
|
region box block 0 10 0 10 0 10
|
|
create_box 3 box
|
|
Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
|
|
2 by 1 by 1 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 4000 atoms
|
|
using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962)
|
|
create_atoms CPU = 0.001 seconds
|
|
mass * 1.0
|
|
|
|
region long block 3 6 0 10 0 10
|
|
set region long type 2
|
|
Setting atom values ...
|
|
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
|
|
|
|
comm_style tiled
|
|
|
|
neighbor 0.3 bin
|
|
neigh_modify every 2 delay 4 check yes
|
|
fix p all property/atom d_WEIGHT
|
|
fix 0 all balance 50 1.0 rcb weight neigh 0.8 weight store WEIGHT
|
|
compute p all property/atom d_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 250
|
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
|
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
|
|
bin: standard
|
|
WARNING: Balance weight neigh skipped b/c no suitable list found (src/imbalance_neigh.cpp:65)
|
|
Per MPI rank memory allocation (min/avg/max) = 4.138 | 4.329 | 4.52 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
|
|
Loop time of 0.963489 on 2 procs for 250 steps with 4000 atoms
|
|
|
|
Performance: 112092.660 tau/day, 259.474 timesteps/s, 1.038 Matom-step/s
|
|
97.7% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.64566 | 0.66162 | 0.67758 | 2.0 | 68.67
|
|
Neigh | 0.23969 | 0.24019 | 0.24069 | 0.1 | 24.93
|
|
Comm | 0.037375 | 0.052867 | 0.068358 | 6.7 | 5.49
|
|
Output | 0.0001635 | 0.00017861 | 0.00019372 | 0.0 | 0.02
|
|
Modify | 0.0055964 | 0.0056409 | 0.0056853 | 0.1 | 0.59
|
|
Other | | 0.002991 | | | 0.31
|
|
|
|
Nlocal: 2000 ave 2000 max 2000 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
Nghost: 10412.5 ave 10414 max 10411 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Neighs: 298332 ave 299797 max 296867 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 596664
|
|
Ave neighs/atom = 149.166
|
|
Neighbor list builds = 25
|
|
Dangerous builds = 0
|
|
run 250
|
|
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
|
Per MPI rank memory allocation (min/avg/max) = 4.932 | 4.933 | 4.933 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press Volume
|
|
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 0.986357 on 2 procs for 250 steps with 4000 atoms
|
|
|
|
Performance: 109493.776 tau/day, 253.458 timesteps/s, 1.014 Matom-step/s
|
|
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.68342 | 0.68352 | 0.68362 | 0.0 | 69.30
|
|
Neigh | 0.25726 | 0.25795 | 0.25864 | 0.1 | 26.15
|
|
Comm | 0.035415 | 0.036212 | 0.037009 | 0.4 | 3.67
|
|
Output | 0.00016727 | 0.00018288 | 0.00019849 | 0.0 | 0.02
|
|
Modify | 0.0054242 | 0.005429 | 0.0054338 | 0.0 | 0.55
|
|
Other | | 0.003066 | | | 0.31
|
|
|
|
Nlocal: 2000 ave 2000 max 2000 min
|
|
Histogram: 2 0 0 0 0 0 0 0 0 0
|
|
Nghost: 10466.5 ave 10470 max 10463 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
Neighs: 298070 ave 349236 max 246903 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 596139
|
|
Ave neighs/atom = 149.03475
|
|
Neighbor list builds = 26
|
|
Dangerous builds = 0
|
|
|
|
Total wall time: 0:00:02
|