227 lines
8.5 KiB
Groff
227 lines
8.5 KiB
Groff
LAMMPS (24 Oct 2018)
|
|
dimension 2
|
|
units micro
|
|
atom_style meso
|
|
|
|
variable R equal 0.5 # radius of sphere micrometers
|
|
variable a equal $R/5 # lattice spacing micrometers
|
|
variable a equal 0.5/5
|
|
variable L equal $R*3
|
|
variable L equal 0.5*3
|
|
variable T equal 300.
|
|
variable rho_0 equal 1. # density picograms/micrometer^3
|
|
variable c_0 equal 100. # speed of sound micrometers/microsecond
|
|
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
|
variable h equal $a*4.5 # kernel function cutoff micrometers
|
|
variable h equal 0.1*4.5
|
|
variable mass equal $a*$a*$a*${rho_0}
|
|
variable mass equal 0.1*$a*$a*${rho_0}
|
|
variable mass equal 0.1*0.1*$a*${rho_0}
|
|
variable mass equal 0.1*0.1*0.1*${rho_0}
|
|
variable mass equal 0.1*0.1*0.1*1
|
|
variable dt equal 1e-3 # timestep microseconds
|
|
variable skin equal 0.2*$h
|
|
variable skin equal 0.2*0.45
|
|
|
|
region box block -$L $L -$L $L 0 $a units box
|
|
region box block -1.5 $L -$L $L 0 $a units box
|
|
region box block -1.5 1.5 -$L $L 0 $a units box
|
|
region box block -1.5 1.5 -1.5 $L 0 $a units box
|
|
region box block -1.5 1.5 -1.5 1.5 0 $a units box
|
|
region box block -1.5 1.5 -1.5 1.5 0 0.1 units box
|
|
create_box 2 box
|
|
Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
|
|
2 by 2 by 1 MPI processor grid
|
|
lattice sq $a
|
|
lattice sq 0.1
|
|
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
|
|
|
create_atoms 1 box
|
|
Created 900 atoms
|
|
Time spent = 0.0010246 secs
|
|
|
|
region sphere sphere 0 0 0 $R units box
|
|
region sphere sphere 0 0 0 0.5 units box
|
|
set region sphere type 2
|
|
81 settings made for type
|
|
|
|
group fluid type 1
|
|
819 atoms in group fluid
|
|
group sphere type 2
|
|
81 atoms in group sphere
|
|
|
|
mass * ${mass}
|
|
mass * 0.001
|
|
set group all meso/rho ${rho_0}
|
|
set group all meso/rho 1
|
|
900 settings made for meso/rho
|
|
|
|
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
|
pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
|
|
pair_style sdpd/taitwater/isothermal 300 1 76787
|
|
pair_coeff * * ${rho_0} ${c_0} ${h}
|
|
pair_coeff * * 1 ${c_0} ${h}
|
|
pair_coeff * * 1 100 ${h}
|
|
pair_coeff * * 1 100 0.45
|
|
|
|
fix 1 fluid meso
|
|
fix 2 sphere rigid/meso single
|
|
1 rigid bodies with 81 atoms
|
|
|
|
fix 2d all enforce2d
|
|
|
|
neighbor ${skin} bin
|
|
neighbor 0.09 bin
|
|
neigh_modify delay 0 every 1 check yes
|
|
timestep ${dt}
|
|
timestep 0.001
|
|
|
|
dump dump_id all atom 100 dump.lammpstrj
|
|
|
|
thermo 100
|
|
thermo_style custom step time nbuild ndanger
|
|
|
|
run 10000
|
|
Neighbor list info ...
|
|
update every 1 steps, delay 0 steps, check yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 0.54
|
|
ghost atom cutoff = 0.54
|
|
binsize = 0.27, bins = 12 12 1
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair sdpd/taitwater/isothermal, perpetual
|
|
attributes: half, newton on
|
|
pair build: half/bin/atomonly/newton
|
|
stencil: half/bin/2d/newton
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 6.087 | 6.087 | 6.087 Mbytes
|
|
Step Time Nbuild Ndanger
|
|
0 0 0 0
|
|
100 0.1 0 0
|
|
200 0.2 0 0
|
|
300 0.3 0 0
|
|
400 0.4 1 0
|
|
500 0.5 1 0
|
|
600 0.6 1 0
|
|
700 0.7 2 0
|
|
800 0.8 2 0
|
|
900 0.9 2 0
|
|
1000 1 3 0
|
|
1100 1.1 3 0
|
|
1200 1.2 3 0
|
|
1300 1.3 4 0
|
|
1400 1.4 4 0
|
|
1500 1.5 5 0
|
|
1600 1.6 5 0
|
|
1700 1.7 5 0
|
|
1800 1.8 6 0
|
|
1900 1.9 6 0
|
|
2000 2 6 0
|
|
2100 2.1 7 0
|
|
2200 2.2 7 0
|
|
2300 2.3 7 0
|
|
2400 2.4 8 0
|
|
2500 2.5 8 0
|
|
2600 2.6 8 0
|
|
2700 2.7 9 0
|
|
2800 2.8 9 0
|
|
2900 2.9 9 0
|
|
3000 3 9 0
|
|
3100 3.1 10 0
|
|
3200 3.2 10 0
|
|
3300 3.3 10 0
|
|
3400 3.4 11 0
|
|
3500 3.5 11 0
|
|
3600 3.6 11 0
|
|
3700 3.7 12 0
|
|
3800 3.8 12 0
|
|
3900 3.9 12 0
|
|
4000 4 13 0
|
|
4100 4.1 13 0
|
|
4200 4.2 13 0
|
|
4300 4.3 14 0
|
|
4400 4.4 14 0
|
|
4500 4.5 15 0
|
|
4600 4.6 15 0
|
|
4700 4.7 15 0
|
|
4800 4.8 16 0
|
|
4900 4.9 16 0
|
|
5000 5 16 0
|
|
5100 5.1 16 0
|
|
5200 5.2 17 0
|
|
5300 5.3 17 0
|
|
5400 5.4 18 0
|
|
5500 5.5 18 0
|
|
5600 5.6 19 0
|
|
5700 5.7 19 0
|
|
5800 5.8 19 0
|
|
5900 5.9 20 0
|
|
6000 6 20 0
|
|
6100 6.1 20 0
|
|
6200 6.2 21 0
|
|
6300 6.3 21 0
|
|
6400 6.4 21 0
|
|
6500 6.5 22 0
|
|
6600 6.6 22 0
|
|
6700 6.7 22 0
|
|
6800 6.8 23 0
|
|
6900 6.9 23 0
|
|
7000 7 23 0
|
|
7100 7.1 24 0
|
|
7200 7.2 24 0
|
|
7300 7.3 24 0
|
|
7400 7.4 25 0
|
|
7500 7.5 25 0
|
|
7600 7.6 25 0
|
|
7700 7.7 26 0
|
|
7800 7.8 26 0
|
|
7900 7.9 26 0
|
|
8000 8 27 0
|
|
8100 8.1 27 0
|
|
8200 8.2 27 0
|
|
8300 8.3 28 0
|
|
8400 8.4 28 0
|
|
8500 8.5 28 0
|
|
8600 8.6 28 0
|
|
8700 8.7 29 0
|
|
8800 8.8 29 0
|
|
8900 8.9 29 0
|
|
9000 9 30 0
|
|
9100 9.1 30 0
|
|
9200 9.2 31 0
|
|
9300 9.3 31 0
|
|
9400 9.4 31 0
|
|
9500 9.5 31 0
|
|
9600 9.6 32 0
|
|
9700 9.7 32 0
|
|
9800 9.8 32 0
|
|
9900 9.9 33 0
|
|
10000 10 33 0
|
|
Loop time of 69.01 on 4 procs for 10000 steps with 900 atoms
|
|
|
|
Performance: 12519931.275 ns/day, 0.000 hours/ns, 144.907 timesteps/s
|
|
48.7% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 56.528 | 57.936 | 58.729 | 11.0 | 83.95
|
|
Neigh | 0.013157 | 0.013382 | 0.013551 | 0.1 | 0.02
|
|
Comm | 8.9594 | 9.7555 | 11.113 | 26.7 | 14.14
|
|
Output | 0.14644 | 0.15009 | 0.15809 | 1.2 | 0.22
|
|
Modify | 0.72913 | 0.91574 | 1.0524 | 12.4 | 1.33
|
|
Other | | 0.2389 | | | 0.35
|
|
|
|
Nlocal: 225 ave 229 max 223 min
|
|
Histogram: 1 2 0 0 0 0 0 0 0 1
|
|
Nghost: 442 ave 444 max 439 min
|
|
Histogram: 1 0 0 0 1 0 0 0 0 2
|
|
Neighs: 10188.8 ave 10437 max 9932 min
|
|
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
|
|
Total # of neighbors = 40755
|
|
Ave neighs/atom = 45.2833
|
|
Neighbor list builds = 33
|
|
Dangerous builds = 0
|
|
Total wall time: 0:01:09
|