176 lines
7.8 KiB
Groff
176 lines
7.8 KiB
Groff
LAMMPS (24 Dec 2020)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Big colloid particles and small LJ particles
|
|
|
|
units lj
|
|
atom_style sphere
|
|
dimension 2
|
|
|
|
lattice sq 0.5
|
|
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
|
region box block 0 60 0 60 -0.5 0.5
|
|
create_box 2 box
|
|
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
|
1 by 1 by 1 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 3600 atoms
|
|
create_atoms CPU = 0.001 seconds
|
|
change_box all triclinic
|
|
Changing box ...
|
|
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
|
|
|
# remove two spheres of small particles and add large particles in the voids
|
|
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
|
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
|
delete_atoms region sphere1
|
|
Deleted 154 atoms, new total = 3446
|
|
delete_atoms region sphere2
|
|
Deleted 158 atoms, new total = 3288
|
|
create_atoms 2 single 20.0 20.0 0.0 units box
|
|
Created 1 atoms
|
|
create_atoms CPU = 0.000 seconds
|
|
create_atoms 2 single 60.0 60.0 0.0 units box
|
|
Created 1 atoms
|
|
create_atoms CPU = 0.000 seconds
|
|
|
|
set type 2 mass 400
|
|
Setting atom values ...
|
|
2 settings made for mass
|
|
set type 1 mass 1
|
|
Setting atom values ...
|
|
3288 settings made for mass
|
|
set type 2 diameter 20
|
|
Setting atom values ...
|
|
2 settings made for diameter
|
|
set type 1 diameter 1
|
|
Setting atom values ...
|
|
3288 settings made for diameter
|
|
|
|
velocity all create 1.44 87287 loop geom
|
|
|
|
# multi neighbor and comm for efficiency
|
|
|
|
neighbor 1 multi/old #multi
|
|
neigh_modify delay 0 #collection/interval 2 1 20
|
|
comm_modify mode multi/old vel yes #reduce/multi
|
|
|
|
# colloid potential
|
|
|
|
pair_style granular
|
|
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
|
|
|
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
|
fix 2 all enforce2d
|
|
fix 3 all deform 1 xy erate 1e-3
|
|
|
|
#dump 1 all custom 1000 dump.granular id x y z radius
|
|
|
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
|
|
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
|
|
|
thermo_style custom step temp epair etotal press vol
|
|
thermo 1000
|
|
|
|
timestep 0.005
|
|
|
|
run 50000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 21
|
|
ghost atom cutoff = 21
|
|
binsize = 1, bins = 85 85 2
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair granular, perpetual
|
|
attributes: half, newton on, size, history
|
|
pair build: half/size/multi/old/newton/tri
|
|
stencil: half/multi/old/2d/tri
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes
|
|
Step Temp E_pair TotEng Press Volume
|
|
0 1.44 0 1.4395623 0.66837658 7200
|
|
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
|
|
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
|
|
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
|
|
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
|
|
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
|
|
6000 0.025856 0 0.025848141 0.021241317 7603.5534
|
|
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
|
|
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
|
|
9000 0.016370159 0 0.016365184 0.020261904 6515.3445
|
|
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
|
|
11000 0.014156551 0 0.014152248 0.021324815 5815.4665
|
|
12000 0.013725406 0 0.013721235 0.021159958 5483.6304
|
|
13000 0.013215746 0 0.013211729 0.021685712 5165.4758
|
|
14000 0.012398153 0 0.012394384 0.024155434 4862.8657
|
|
15000 0.011842796 0 0.011839196 0.028503991 4577.9008
|
|
16000 0.011433182 0 0.011429706 0.033564839 4309.8792
|
|
17000 0.011166574 0 0.01116318 0.040592677 4058.9964
|
|
18000 0.01100067 0 0.010997326 0.04899206 3825.155
|
|
19000 0.010224474 0 0.010221366 0.063670337 3607.6577
|
|
20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658
|
|
21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002
|
|
22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986
|
|
23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014
|
|
24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113
|
|
25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604
|
|
26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564
|
|
27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379
|
|
28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461
|
|
29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308
|
|
30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316
|
|
31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683
|
|
32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093
|
|
33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574
|
|
34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254
|
|
35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217
|
|
36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654
|
|
37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901
|
|
38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136
|
|
39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531
|
|
40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834
|
|
41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027
|
|
42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714
|
|
43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408
|
|
44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677
|
|
45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144
|
|
46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355
|
|
47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285
|
|
48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043
|
|
49000 0.00018879338 0 0.000188736 0.95775166 1780.0323
|
|
50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442
|
|
Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms
|
|
|
|
Performance: 289297.713 tau/day, 669.671 timesteps/s
|
|
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 56.696 | 56.696 | 56.696 | 0.0 | 75.93
|
|
Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98
|
|
Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29
|
|
Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00
|
|
Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29
|
|
Other | | 1.125 | | | 1.51
|
|
|
|
Nlocal: 3290.00 ave 3290 max 3290 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 6295.00 ave 6295 max 6295 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 53729.0 ave 53729 max 53729 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 53729
|
|
Ave neighs/atom = 16.331003
|
|
Neighbor list builds = 348
|
|
Dangerous builds = 0
|
|
|
|
Please see the log.cite file for references relevant to this simulation
|
|
|
|
Total wall time: 0:01:14
|