Updating SDPD examples
This commit is contained in:
jtclemm
@ -1,6 +1,6 @@
|
|||||||
dimension 2
|
dimension 2
|
||||||
units micro
|
units micro
|
||||||
atom_style meso
|
atom_style sph
|
||||||
|
|
||||||
variable R equal 0.5 # radius of sphere micrometers
|
variable R equal 0.5 # radius of sphere micrometers
|
||||||
variable a equal $R/5 # lattice spacing micrometers
|
variable a equal $R/5 # lattice spacing micrometers
|
||||||
@ -37,12 +37,12 @@ group upper_wall type 3
|
|||||||
group lower_wall type 4
|
group lower_wall type 4
|
||||||
|
|
||||||
mass * ${mass}
|
mass * ${mass}
|
||||||
set group all meso/rho ${rho_0}
|
set group all sph/rho ${rho_0}
|
||||||
|
|
||||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||||
|
|
||||||
fix 1 fluid meso
|
fix 1 fluid sph
|
||||||
fix 2 sphere rigid/meso single
|
fix 2 sphere rigid/meso single
|
||||||
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
||||||
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
||||||
|
|||||||
@ -1,247 +0,0 @@
|
|||||||
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 Lf equal $R*3
|
|
||||||
variable Lf equal 0.5*3
|
|
||||||
variable Lb equal $R*4
|
|
||||||
variable Lb equal 0.5*4
|
|
||||||
variable wall_velocity equal 0.01 # micrometers/microsecond
|
|
||||||
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*$h
|
|
||||||
variable skin equal 0.2*0.45
|
|
||||||
|
|
||||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
|
||||||
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
|
||||||
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
|
|
||||||
region box block -2 2 -2 ${Lb} 0 ${a} units box
|
|
||||||
region box block -2 2 -2 2 0 ${a} units box
|
|
||||||
region box block -2 2 -2 2 0 0.1 units box
|
|
||||||
create_box 4 box
|
|
||||||
Created orthogonal box = (-2 -2 0) to (2 2 0.1)
|
|
||||||
1 by 1 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 1600 atoms
|
|
||||||
Time spent = 0.00169706 secs
|
|
||||||
|
|
||||||
region sphere sphere 0 0 0 $R units box
|
|
||||||
region sphere sphere 0 0 0 0.5 units box
|
|
||||||
set region sphere type 2
|
|
||||||
81 settings made for type
|
|
||||||
|
|
||||||
region upper_wall block INF INF +${Lf} INF INF INF units box
|
|
||||||
region upper_wall block INF INF +1.5 INF INF INF units box
|
|
||||||
set region upper_wall type 3
|
|
||||||
200 settings made for type
|
|
||||||
|
|
||||||
region lower_wall block INF INF INF -${Lf} INF INF units box
|
|
||||||
region lower_wall block INF INF INF -1.5 INF INF units box
|
|
||||||
set region lower_wall type 4
|
|
||||||
240 settings made for type
|
|
||||||
|
|
||||||
group fluid type 1
|
|
||||||
1079 atoms in group fluid
|
|
||||||
group sphere type 2
|
|
||||||
81 atoms in group sphere
|
|
||||||
group upper_wall type 3
|
|
||||||
200 atoms in group upper_wall
|
|
||||||
group lower_wall type 4
|
|
||||||
240 atoms in group lower_wall
|
|
||||||
|
|
||||||
mass * ${mass}
|
|
||||||
mass * 0.001
|
|
||||||
set group all meso/rho ${rho_0}
|
|
||||||
set group all meso/rho 1
|
|
||||||
1600 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 ${h}
|
|
||||||
pair_coeff * * 1 100 0.45
|
|
||||||
|
|
||||||
fix 1 fluid meso
|
|
||||||
fix 2 sphere rigid/meso single
|
|
||||||
1 rigid bodies with 81 atoms
|
|
||||||
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
|
||||||
fix 3 upper_wall meso/move linear +0.01 0 0 units box
|
|
||||||
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
|
||||||
fix 4 lower_wall meso/move linear -0.01 0 0 units box
|
|
||||||
|
|
||||||
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 = 15 15 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) = 6.937 | 6.937 | 6.937 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 0 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 4 0
|
|
||||||
1600 1.6 5 0
|
|
||||||
1700 1.7 5 0
|
|
||||||
1800 1.8 5 0
|
|
||||||
1900 1.9 6 0
|
|
||||||
2000 2 6 0
|
|
||||||
2100 2.1 6 0
|
|
||||||
2200 2.2 7 0
|
|
||||||
2300 2.3 7 0
|
|
||||||
2400 2.4 7 0
|
|
||||||
2500 2.5 8 0
|
|
||||||
2600 2.6 8 0
|
|
||||||
2700 2.7 8 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 14 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 17 0
|
|
||||||
5200 5.2 17 0
|
|
||||||
5300 5.3 17 0
|
|
||||||
5400 5.4 17 0
|
|
||||||
5500 5.5 18 0
|
|
||||||
5600 5.6 18 0
|
|
||||||
5700 5.7 19 0
|
|
||||||
5800 5.8 19 0
|
|
||||||
5900 5.9 19 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 25 0
|
|
||||||
7400 7.4 25 0
|
|
||||||
7500 7.5 25 0
|
|
||||||
7600 7.6 26 0
|
|
||||||
7700 7.7 26 0
|
|
||||||
7800 7.8 26 0
|
|
||||||
7900 7.9 27 0
|
|
||||||
8000 8 27 0
|
|
||||||
8100 8.1 27 0
|
|
||||||
8200 8.2 28 0
|
|
||||||
8300 8.3 28 0
|
|
||||||
8400 8.4 28 0
|
|
||||||
8500 8.5 29 0
|
|
||||||
8600 8.6 29 0
|
|
||||||
8700 8.7 30 0
|
|
||||||
8800 8.8 30 0
|
|
||||||
8900 8.9 30 0
|
|
||||||
9000 9 31 0
|
|
||||||
9100 9.1 31 0
|
|
||||||
9200 9.2 31 0
|
|
||||||
9300 9.3 32 0
|
|
||||||
9400 9.4 32 0
|
|
||||||
9500 9.5 32 0
|
|
||||||
9600 9.6 33 0
|
|
||||||
9700 9.7 33 0
|
|
||||||
9800 9.8 33 0
|
|
||||||
9900 9.9 34 0
|
|
||||||
10000 10 34 0
|
|
||||||
Loop time of 144.208 on 1 procs for 10000 steps with 1600 atoms
|
|
||||||
|
|
||||||
Performance: 5991348.580 ns/day, 0.000 hours/ns, 69.344 timesteps/s
|
|
||||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 143.08 | 143.08 | 143.08 | 0.0 | 99.22
|
|
||||||
Neigh | 0.033195 | 0.033195 | 0.033195 | 0.0 | 0.02
|
|
||||||
Comm | 0.24139 | 0.24139 | 0.24139 | 0.0 | 0.17
|
|
||||||
Output | 0.11687 | 0.11687 | 0.11687 | 0.0 | 0.08
|
|
||||||
Modify | 0.61566 | 0.61566 | 0.61566 | 0.0 | 0.43
|
|
||||||
Other | | 0.117 | | | 0.08
|
|
||||||
|
|
||||||
Nlocal: 1600 ave 1600 max 1600 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 993 ave 993 max 993 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 73236 ave 73236 max 73236 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 73236
|
|
||||||
Ave neighs/atom = 45.7725
|
|
||||||
Neighbor list builds = 34
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:02:24
|
|
||||||
@ -1,247 +0,0 @@
|
|||||||
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 Lf equal $R*3
|
|
||||||
variable Lf equal 0.5*3
|
|
||||||
variable Lb equal $R*4
|
|
||||||
variable Lb equal 0.5*4
|
|
||||||
variable wall_velocity equal 0.01 # micrometers/microsecond
|
|
||||||
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*$h
|
|
||||||
variable skin equal 0.2*0.45
|
|
||||||
|
|
||||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
|
||||||
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
|
||||||
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
|
|
||||||
region box block -2 2 -2 ${Lb} 0 ${a} units box
|
|
||||||
region box block -2 2 -2 2 0 ${a} units box
|
|
||||||
region box block -2 2 -2 2 0 0.1 units box
|
|
||||||
create_box 4 box
|
|
||||||
Created orthogonal box = (-2 -2 0) to (2 2 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 1600 atoms
|
|
||||||
Time spent = 0.000589566 secs
|
|
||||||
|
|
||||||
region sphere sphere 0 0 0 $R units box
|
|
||||||
region sphere sphere 0 0 0 0.5 units box
|
|
||||||
set region sphere type 2
|
|
||||||
81 settings made for type
|
|
||||||
|
|
||||||
region upper_wall block INF INF +${Lf} INF INF INF units box
|
|
||||||
region upper_wall block INF INF +1.5 INF INF INF units box
|
|
||||||
set region upper_wall type 3
|
|
||||||
200 settings made for type
|
|
||||||
|
|
||||||
region lower_wall block INF INF INF -${Lf} INF INF units box
|
|
||||||
region lower_wall block INF INF INF -1.5 INF INF units box
|
|
||||||
set region lower_wall type 4
|
|
||||||
240 settings made for type
|
|
||||||
|
|
||||||
group fluid type 1
|
|
||||||
1079 atoms in group fluid
|
|
||||||
group sphere type 2
|
|
||||||
81 atoms in group sphere
|
|
||||||
group upper_wall type 3
|
|
||||||
200 atoms in group upper_wall
|
|
||||||
group lower_wall type 4
|
|
||||||
240 atoms in group lower_wall
|
|
||||||
|
|
||||||
mass * ${mass}
|
|
||||||
mass * 0.001
|
|
||||||
set group all meso/rho ${rho_0}
|
|
||||||
set group all meso/rho 1
|
|
||||||
1600 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 ${h}
|
|
||||||
pair_coeff * * 1 100 0.45
|
|
||||||
|
|
||||||
fix 1 fluid meso
|
|
||||||
fix 2 sphere rigid/meso single
|
|
||||||
1 rigid bodies with 81 atoms
|
|
||||||
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
|
||||||
fix 3 upper_wall meso/move linear +0.01 0 0 units box
|
|
||||||
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
|
||||||
fix 4 lower_wall meso/move linear -0.01 0 0 units box
|
|
||||||
|
|
||||||
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 = 15 15 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) = 6.854 | 6.854 | 6.854 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 4 0
|
|
||||||
1300 1.3 4 0
|
|
||||||
1400 1.4 4 0
|
|
||||||
1500 1.5 4 0
|
|
||||||
1600 1.6 5 0
|
|
||||||
1700 1.7 5 0
|
|
||||||
1800 1.8 5 0
|
|
||||||
1900 1.9 6 0
|
|
||||||
2000 2 6 0
|
|
||||||
2100 2.1 6 0
|
|
||||||
2200 2.2 6 0
|
|
||||||
2300 2.3 7 0
|
|
||||||
2400 2.4 7 0
|
|
||||||
2500 2.5 7 0
|
|
||||||
2600 2.6 8 0
|
|
||||||
2700 2.7 8 0
|
|
||||||
2800 2.8 8 0
|
|
||||||
2900 2.9 9 0
|
|
||||||
3000 3 9 0
|
|
||||||
3100 3.1 9 0
|
|
||||||
3200 3.2 10 0
|
|
||||||
3300 3.3 10 0
|
|
||||||
3400 3.4 10 0
|
|
||||||
3500 3.5 11 0
|
|
||||||
3600 3.6 11 0
|
|
||||||
3700 3.7 11 0
|
|
||||||
3800 3.8 12 0
|
|
||||||
3900 3.9 12 0
|
|
||||||
4000 4 12 0
|
|
||||||
4100 4.1 13 0
|
|
||||||
4200 4.2 13 0
|
|
||||||
4300 4.3 13 0
|
|
||||||
4400 4.4 14 0
|
|
||||||
4500 4.5 14 0
|
|
||||||
4600 4.6 15 0
|
|
||||||
4700 4.7 15 0
|
|
||||||
4800 4.8 15 0
|
|
||||||
4900 4.9 16 0
|
|
||||||
5000 5 16 0
|
|
||||||
5100 5.1 17 0
|
|
||||||
5200 5.2 17 0
|
|
||||||
5300 5.3 17 0
|
|
||||||
5400 5.4 17 0
|
|
||||||
5500 5.5 18 0
|
|
||||||
5600 5.6 18 0
|
|
||||||
5700 5.7 18 0
|
|
||||||
5800 5.8 19 0
|
|
||||||
5900 5.9 19 0
|
|
||||||
6000 6 20 0
|
|
||||||
6100 6.1 20 0
|
|
||||||
6200 6.2 20 0
|
|
||||||
6300 6.3 21 0
|
|
||||||
6400 6.4 21 0
|
|
||||||
6500 6.5 21 0
|
|
||||||
6600 6.6 22 0
|
|
||||||
6700 6.7 22 0
|
|
||||||
6800 6.8 22 0
|
|
||||||
6900 6.9 23 0
|
|
||||||
7000 7 23 0
|
|
||||||
7100 7.1 23 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 25 0
|
|
||||||
7800 7.8 26 0
|
|
||||||
7900 7.9 26 0
|
|
||||||
8000 8 26 0
|
|
||||||
8100 8.1 27 0
|
|
||||||
8200 8.2 27 0
|
|
||||||
8300 8.3 27 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 32 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 63.2372 on 4 procs for 10000 steps with 1600 atoms
|
|
||||||
|
|
||||||
Performance: 13662841.706 ns/day, 0.000 hours/ns, 158.135 timesteps/s
|
|
||||||
94.3% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 51.576 | 53.662 | 55.484 | 23.9 | 84.86
|
|
||||||
Neigh | 0.011519 | 0.012395 | 0.013405 | 0.7 | 0.02
|
|
||||||
Comm | 6.8389 | 8.5423 | 10.517 | 56.1 | 13.51
|
|
||||||
Output | 0.12342 | 0.12513 | 0.1302 | 0.8 | 0.20
|
|
||||||
Modify | 0.58708 | 0.69128 | 0.78806 | 11.3 | 1.09
|
|
||||||
Other | | 0.2038 | | | 0.32
|
|
||||||
|
|
||||||
Nlocal: 400 ave 411 max 388 min
|
|
||||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
||||||
Nghost: 552.25 ave 567 max 539 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
|
||||||
Neighs: 18298.8 ave 18781 max 17829 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 73195
|
|
||||||
Ave neighs/atom = 45.7469
|
|
||||||
Neighbor list builds = 33
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:01:03
|
|
||||||
@ -0,0 +1,253 @@
|
|||||||
|
LAMMPS (28 Mar 2023 - Development)
|
||||||
|
dimension 2
|
||||||
|
units micro
|
||||||
|
atom_style sph
|
||||||
|
|
||||||
|
variable R equal 0.5 # radius of sphere micrometers
|
||||||
|
variable a equal $R/5 # lattice spacing micrometers
|
||||||
|
variable a equal 0.5/5
|
||||||
|
variable Lf equal $R*3
|
||||||
|
variable Lf equal 0.5*3
|
||||||
|
variable Lb equal $R*4
|
||||||
|
variable Lb equal 0.5*4
|
||||||
|
variable wall_velocity equal 0.01 # micrometers/microsecond
|
||||||
|
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*$h
|
||||||
|
variable skin equal 0.2*0.45
|
||||||
|
|
||||||
|
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||||
|
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||||
|
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
|
||||||
|
region box block -2 2 -2 ${Lb} 0 ${a} units box
|
||||||
|
region box block -2 2 -2 2 0 ${a} units box
|
||||||
|
region box block -2 2 -2 2 0 0.1 units box
|
||||||
|
create_box 4 box
|
||||||
|
Created orthogonal box = (-2 -2 0) to (2 2 0.1)
|
||||||
|
1 by 1 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 1600 atoms
|
||||||
|
using lattice units in orthogonal box = (-2 -2 0) to (2 2 0.1)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
region sphere sphere 0 0 0 $R units box
|
||||||
|
region sphere sphere 0 0 0 0.5 units box
|
||||||
|
set region sphere type 2
|
||||||
|
Setting atom values ...
|
||||||
|
81 settings made for type
|
||||||
|
|
||||||
|
region upper_wall block INF INF +${Lf} INF INF INF units box
|
||||||
|
region upper_wall block INF INF +1.5 INF INF INF units box
|
||||||
|
set region upper_wall type 3
|
||||||
|
Setting atom values ...
|
||||||
|
200 settings made for type
|
||||||
|
|
||||||
|
region lower_wall block INF INF INF -${Lf} INF INF units box
|
||||||
|
region lower_wall block INF INF INF -1.5 INF INF units box
|
||||||
|
set region lower_wall type 4
|
||||||
|
Setting atom values ...
|
||||||
|
240 settings made for type
|
||||||
|
|
||||||
|
group fluid type 1
|
||||||
|
1079 atoms in group fluid
|
||||||
|
group sphere type 2
|
||||||
|
81 atoms in group sphere
|
||||||
|
group upper_wall type 3
|
||||||
|
200 atoms in group upper_wall
|
||||||
|
group lower_wall type 4
|
||||||
|
240 atoms in group lower_wall
|
||||||
|
|
||||||
|
mass * ${mass}
|
||||||
|
mass * 0.001
|
||||||
|
set group all sph/rho ${rho_0}
|
||||||
|
set group all sph/rho 1
|
||||||
|
Setting atom values ...
|
||||||
|
1600 settings made for sph/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 ${h}
|
||||||
|
pair_coeff * * 1 100 0.45
|
||||||
|
|
||||||
|
fix 1 fluid sph
|
||||||
|
fix 2 sphere rigid/meso single
|
||||||
|
1 rigid bodies with 81 atoms
|
||||||
|
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
||||||
|
fix 3 upper_wall meso/move linear +0.01 0 0 units box
|
||||||
|
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
||||||
|
fix 4 lower_wall meso/move linear -0.01 0 0 units box
|
||||||
|
|
||||||
|
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
|
||||||
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
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 = 15 15 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
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.313 | 7.313 | 7.313 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 0 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 4 0
|
||||||
|
1600 1.6 5 0
|
||||||
|
1700 1.7 5 0
|
||||||
|
1800 1.8 5 0
|
||||||
|
1900 1.9 6 0
|
||||||
|
2000 2 6 0
|
||||||
|
2100 2.1 6 0
|
||||||
|
2200 2.2 7 0
|
||||||
|
2300 2.3 7 0
|
||||||
|
2400 2.4 7 0
|
||||||
|
2500 2.5 8 0
|
||||||
|
2600 2.6 8 0
|
||||||
|
2700 2.7 8 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 14 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 17 0
|
||||||
|
5200 5.2 17 0
|
||||||
|
5300 5.3 17 0
|
||||||
|
5400 5.4 17 0
|
||||||
|
5500 5.5 18 0
|
||||||
|
5600 5.6 18 0
|
||||||
|
5700 5.7 19 0
|
||||||
|
5800 5.8 19 0
|
||||||
|
5900 5.9 19 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 25 0
|
||||||
|
7400 7.4 25 0
|
||||||
|
7500 7.5 25 0
|
||||||
|
7600 7.6 26 0
|
||||||
|
7700 7.7 26 0
|
||||||
|
7800 7.8 26 0
|
||||||
|
7900 7.9 27 0
|
||||||
|
8000 8 27 0
|
||||||
|
8100 8.1 27 0
|
||||||
|
8200 8.2 28 0
|
||||||
|
8300 8.3 28 0
|
||||||
|
8400 8.4 28 0
|
||||||
|
8500 8.5 29 0
|
||||||
|
8600 8.6 29 0
|
||||||
|
8700 8.7 30 0
|
||||||
|
8800 8.8 30 0
|
||||||
|
8900 8.9 30 0
|
||||||
|
9000 9 31 0
|
||||||
|
9100 9.1 31 0
|
||||||
|
9200 9.2 31 0
|
||||||
|
9300 9.3 32 0
|
||||||
|
9400 9.4 32 0
|
||||||
|
9500 9.5 32 0
|
||||||
|
9600 9.6 33 0
|
||||||
|
9700 9.7 33 0
|
||||||
|
9800 9.8 33 0
|
||||||
|
9900 9.9 34 0
|
||||||
|
10000 10 34 0
|
||||||
|
Loop time of 131.724 on 1 procs for 10000 steps with 1600 atoms
|
||||||
|
|
||||||
|
Performance: 6559168.339 ns/day, 0.000 hours/ns, 75.916 timesteps/s, 121.466 katom-step/s
|
||||||
|
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 130.89 | 130.89 | 130.89 | 0.0 | 99.37
|
||||||
|
Neigh | 0.02884 | 0.02884 | 0.02884 | 0.0 | 0.02
|
||||||
|
Comm | 0.17863 | 0.17863 | 0.17863 | 0.0 | 0.14
|
||||||
|
Output | 0.095497 | 0.095497 | 0.095497 | 0.0 | 0.07
|
||||||
|
Modify | 0.42063 | 0.42063 | 0.42063 | 0.0 | 0.32
|
||||||
|
Other | | 0.1069 | | | 0.08
|
||||||
|
|
||||||
|
Nlocal: 1600 ave 1600 max 1600 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 993 ave 993 max 993 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 73236 ave 73236 max 73236 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 73236
|
||||||
|
Ave neighs/atom = 45.7725
|
||||||
|
Neighbor list builds = 34
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:02:11
|
||||||
@ -0,0 +1,253 @@
|
|||||||
|
LAMMPS (28 Mar 2023 - Development)
|
||||||
|
dimension 2
|
||||||
|
units micro
|
||||||
|
atom_style sph
|
||||||
|
|
||||||
|
variable R equal 0.5 # radius of sphere micrometers
|
||||||
|
variable a equal $R/5 # lattice spacing micrometers
|
||||||
|
variable a equal 0.5/5
|
||||||
|
variable Lf equal $R*3
|
||||||
|
variable Lf equal 0.5*3
|
||||||
|
variable Lb equal $R*4
|
||||||
|
variable Lb equal 0.5*4
|
||||||
|
variable wall_velocity equal 0.01 # micrometers/microsecond
|
||||||
|
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*$h
|
||||||
|
variable skin equal 0.2*0.45
|
||||||
|
|
||||||
|
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||||
|
region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||||
|
region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
|
||||||
|
region box block -2 2 -2 ${Lb} 0 ${a} units box
|
||||||
|
region box block -2 2 -2 2 0 ${a} units box
|
||||||
|
region box block -2 2 -2 2 0 0.1 units box
|
||||||
|
create_box 4 box
|
||||||
|
Created orthogonal box = (-2 -2 0) to (2 2 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 1600 atoms
|
||||||
|
using lattice units in orthogonal box = (-2 -2 0) to (2 2 0.1)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
region sphere sphere 0 0 0 $R units box
|
||||||
|
region sphere sphere 0 0 0 0.5 units box
|
||||||
|
set region sphere type 2
|
||||||
|
Setting atom values ...
|
||||||
|
81 settings made for type
|
||||||
|
|
||||||
|
region upper_wall block INF INF +${Lf} INF INF INF units box
|
||||||
|
region upper_wall block INF INF +1.5 INF INF INF units box
|
||||||
|
set region upper_wall type 3
|
||||||
|
Setting atom values ...
|
||||||
|
200 settings made for type
|
||||||
|
|
||||||
|
region lower_wall block INF INF INF -${Lf} INF INF units box
|
||||||
|
region lower_wall block INF INF INF -1.5 INF INF units box
|
||||||
|
set region lower_wall type 4
|
||||||
|
Setting atom values ...
|
||||||
|
240 settings made for type
|
||||||
|
|
||||||
|
group fluid type 1
|
||||||
|
1079 atoms in group fluid
|
||||||
|
group sphere type 2
|
||||||
|
81 atoms in group sphere
|
||||||
|
group upper_wall type 3
|
||||||
|
200 atoms in group upper_wall
|
||||||
|
group lower_wall type 4
|
||||||
|
240 atoms in group lower_wall
|
||||||
|
|
||||||
|
mass * ${mass}
|
||||||
|
mass * 0.001
|
||||||
|
set group all sph/rho ${rho_0}
|
||||||
|
set group all sph/rho 1
|
||||||
|
Setting atom values ...
|
||||||
|
1600 settings made for sph/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 ${h}
|
||||||
|
pair_coeff * * 1 100 0.45
|
||||||
|
|
||||||
|
fix 1 fluid sph
|
||||||
|
fix 2 sphere rigid/meso single
|
||||||
|
1 rigid bodies with 81 atoms
|
||||||
|
fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
|
||||||
|
fix 3 upper_wall meso/move linear +0.01 0 0 units box
|
||||||
|
fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
|
||||||
|
fix 4 lower_wall meso/move linear -0.01 0 0 units box
|
||||||
|
|
||||||
|
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
|
||||||
|
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
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 = 15 15 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
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 7.23 | 7.23 | 7.23 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 4 0
|
||||||
|
1600 1.6 5 0
|
||||||
|
1700 1.7 5 0
|
||||||
|
1800 1.8 5 0
|
||||||
|
1900 1.9 6 0
|
||||||
|
2000 2 6 0
|
||||||
|
2100 2.1 6 0
|
||||||
|
2200 2.2 7 0
|
||||||
|
2300 2.3 7 0
|
||||||
|
2400 2.4 7 0
|
||||||
|
2500 2.5 8 0
|
||||||
|
2600 2.6 8 0
|
||||||
|
2700 2.7 8 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 14 0
|
||||||
|
4600 4.6 14 0
|
||||||
|
4700 4.7 15 0
|
||||||
|
4800 4.8 15 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 17 0
|
||||||
|
5500 5.5 18 0
|
||||||
|
5600 5.6 18 0
|
||||||
|
5700 5.7 18 0
|
||||||
|
5800 5.8 19 0
|
||||||
|
5900 5.9 19 0
|
||||||
|
6000 6 20 0
|
||||||
|
6100 6.1 20 0
|
||||||
|
6200 6.2 20 0
|
||||||
|
6300 6.3 21 0
|
||||||
|
6400 6.4 21 0
|
||||||
|
6500 6.5 21 0
|
||||||
|
6600 6.6 22 0
|
||||||
|
6700 6.7 22 0
|
||||||
|
6800 6.8 22 0
|
||||||
|
6900 6.9 23 0
|
||||||
|
7000 7 23 0
|
||||||
|
7100 7.1 23 0
|
||||||
|
7200 7.2 24 0
|
||||||
|
7300 7.3 24 0
|
||||||
|
7400 7.4 24 0
|
||||||
|
7500 7.5 25 0
|
||||||
|
7600 7.6 25 0
|
||||||
|
7700 7.7 25 0
|
||||||
|
7800 7.8 25 0
|
||||||
|
7900 7.9 26 0
|
||||||
|
8000 8 26 0
|
||||||
|
8100 8.1 26 0
|
||||||
|
8200 8.2 27 0
|
||||||
|
8300 8.3 27 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 30 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 32 0
|
||||||
|
10000 10 33 0
|
||||||
|
Loop time of 24.8261 on 4 procs for 10000 steps with 1600 atoms
|
||||||
|
|
||||||
|
Performance: 34802055.618 ns/day, 0.000 hours/ns, 402.802 timesteps/s, 644.483 katom-step/s
|
||||||
|
99.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 21.84 | 22.879 | 23.944 | 21.4 | 92.16
|
||||||
|
Neigh | 0.007446 | 0.0079435 | 0.0084435 | 0.6 | 0.03
|
||||||
|
Comm | 0.5271 | 1.5894 | 2.6259 | 80.9 | 6.40
|
||||||
|
Output | 0.034799 | 0.035302 | 0.036437 | 0.4 | 0.14
|
||||||
|
Modify | 0.20079 | 0.21033 | 0.2202 | 1.7 | 0.85
|
||||||
|
Other | | 0.1041 | | | 0.42
|
||||||
|
|
||||||
|
Nlocal: 400 ave 414 max 390 min
|
||||||
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||||
|
Nghost: 555.5 ave 564 max 543 min
|
||||||
|
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||||
|
Neighs: 18299.2 ave 18820 max 17906 min
|
||||||
|
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 73197
|
||||||
|
Ave neighs/atom = 45.748125
|
||||||
|
Neighbor list builds = 33
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:24
|
||||||
@ -1,6 +1,6 @@
|
|||||||
dimension 2
|
dimension 2
|
||||||
units micro
|
units micro
|
||||||
atom_style meso
|
atom_style sph
|
||||||
|
|
||||||
variable R equal 0.5 # radius of sphere micrometers
|
variable R equal 0.5 # radius of sphere micrometers
|
||||||
variable a equal $R/5 # lattice spacing micrometers
|
variable a equal $R/5 # lattice spacing micrometers
|
||||||
@ -27,12 +27,12 @@ group fluid type 1
|
|||||||
group sphere type 2
|
group sphere type 2
|
||||||
|
|
||||||
mass * ${mass}
|
mass * ${mass}
|
||||||
set group all meso/rho ${rho_0}
|
set group all sph/rho ${rho_0}
|
||||||
|
|
||||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||||
|
|
||||||
fix 1 fluid meso
|
fix 1 fluid sph
|
||||||
fix 2 sphere rigid/meso single
|
fix 2 sphere rigid/meso single
|
||||||
|
|
||||||
fix 2d all enforce2d
|
fix 2d all enforce2d
|
||||||
|
|||||||
@ -1,226 +0,0 @@
|
|||||||
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)
|
|
||||||
1 by 1 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 = 0.0015769 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) = 6.137 | 6.137 | 6.137 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 4 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 7 0
|
|
||||||
2500 2.5 8 0
|
|
||||||
2600 2.6 8 0
|
|
||||||
2700 2.7 8 0
|
|
||||||
2800 2.8 9 0
|
|
||||||
2900 2.9 9 0
|
|
||||||
3000 3 10 0
|
|
||||||
3100 3.1 10 0
|
|
||||||
3200 3.2 10 0
|
|
||||||
3300 3.3 11 0
|
|
||||||
3400 3.4 11 0
|
|
||||||
3500 3.5 11 0
|
|
||||||
3600 3.6 12 0
|
|
||||||
3700 3.7 12 0
|
|
||||||
3800 3.8 12 0
|
|
||||||
3900 3.9 13 0
|
|
||||||
4000 4 13 0
|
|
||||||
4100 4.1 13 0
|
|
||||||
4200 4.2 14 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 17 0
|
|
||||||
5100 5.1 17 0
|
|
||||||
5200 5.2 17 0
|
|
||||||
5300 5.3 17 0
|
|
||||||
5400 5.4 18 0
|
|
||||||
5500 5.5 18 0
|
|
||||||
5600 5.6 18 0
|
|
||||||
5700 5.7 19 0
|
|
||||||
5800 5.8 19 0
|
|
||||||
5900 5.9 19 0
|
|
||||||
6000 6 19 0
|
|
||||||
6100 6.1 20 0
|
|
||||||
6200 6.2 20 0
|
|
||||||
6300 6.3 20 0
|
|
||||||
6400 6.4 21 0
|
|
||||||
6500 6.5 21 0
|
|
||||||
6600 6.6 21 0
|
|
||||||
6700 6.7 21 0
|
|
||||||
6800 6.8 22 0
|
|
||||||
6900 6.9 22 0
|
|
||||||
7000 7 22 0
|
|
||||||
7100 7.1 23 0
|
|
||||||
7200 7.2 23 0
|
|
||||||
7300 7.3 23 0
|
|
||||||
7400 7.4 24 0
|
|
||||||
7500 7.5 24 0
|
|
||||||
7600 7.6 24 0
|
|
||||||
7700 7.7 25 0
|
|
||||||
7800 7.8 25 0
|
|
||||||
7900 7.9 26 0
|
|
||||||
8000 8 26 0
|
|
||||||
8100 8.1 26 0
|
|
||||||
8200 8.2 26 0
|
|
||||||
8300 8.3 27 0
|
|
||||||
8400 8.4 27 0
|
|
||||||
8500 8.5 27 0
|
|
||||||
8600 8.6 28 0
|
|
||||||
8700 8.7 28 0
|
|
||||||
8800 8.8 28 0
|
|
||||||
8900 8.9 29 0
|
|
||||||
9000 9 29 0
|
|
||||||
9100 9.1 29 0
|
|
||||||
9200 9.2 30 0
|
|
||||||
9300 9.3 30 0
|
|
||||||
9400 9.4 30 0
|
|
||||||
9500 9.5 30 0
|
|
||||||
9600 9.6 31 0
|
|
||||||
9700 9.7 31 0
|
|
||||||
9800 9.8 32 0
|
|
||||||
9900 9.9 32 0
|
|
||||||
10000 10 32 0
|
|
||||||
Loop time of 80.9456 on 1 procs for 10000 steps with 900 atoms
|
|
||||||
|
|
||||||
Performance: 10673829.855 ns/day, 0.000 hours/ns, 123.540 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 80.306 | 80.306 | 80.306 | 0.0 | 99.21
|
|
||||||
Neigh | 0.017418 | 0.017418 | 0.017418 | 0.0 | 0.02
|
|
||||||
Comm | 0.16939 | 0.16939 | 0.16939 | 0.0 | 0.21
|
|
||||||
Output | 0.070281 | 0.070281 | 0.070281 | 0.0 | 0.09
|
|
||||||
Modify | 0.3154 | 0.3154 | 0.3154 | 0.0 | 0.39
|
|
||||||
Other | | 0.067 | | | 0.08
|
|
||||||
|
|
||||||
Nlocal: 900 ave 900 max 900 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 762 ave 762 max 762 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 40697 ave 40697 max 40697 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 40697
|
|
||||||
Ave neighs/atom = 45.2189
|
|
||||||
Neighbor list builds = 32
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:01:20
|
|
||||||
@ -1,226 +0,0 @@
|
|||||||
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
|
|
||||||
@ -0,0 +1,230 @@
|
|||||||
|
LAMMPS (28 Mar 2023 - Development)
|
||||||
|
dimension 2
|
||||||
|
units micro
|
||||||
|
atom_style sph
|
||||||
|
|
||||||
|
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)
|
||||||
|
1 by 1 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
|
||||||
|
using lattice units in orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
region sphere sphere 0 0 0 $R units box
|
||||||
|
region sphere sphere 0 0 0 0.5 units box
|
||||||
|
set region sphere type 2
|
||||||
|
Setting atom values ...
|
||||||
|
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 sph/rho ${rho_0}
|
||||||
|
set group all sph/rho 1
|
||||||
|
Setting atom values ...
|
||||||
|
900 settings made for sph/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 sph
|
||||||
|
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
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
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
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.512 | 6.512 | 6.512 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 4 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 7 0
|
||||||
|
2500 2.5 8 0
|
||||||
|
2600 2.6 8 0
|
||||||
|
2700 2.7 8 0
|
||||||
|
2800 2.8 9 0
|
||||||
|
2900 2.9 9 0
|
||||||
|
3000 3 10 0
|
||||||
|
3100 3.1 10 0
|
||||||
|
3200 3.2 10 0
|
||||||
|
3300 3.3 11 0
|
||||||
|
3400 3.4 11 0
|
||||||
|
3500 3.5 11 0
|
||||||
|
3600 3.6 12 0
|
||||||
|
3700 3.7 12 0
|
||||||
|
3800 3.8 12 0
|
||||||
|
3900 3.9 13 0
|
||||||
|
4000 4 13 0
|
||||||
|
4100 4.1 13 0
|
||||||
|
4200 4.2 14 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 17 0
|
||||||
|
5100 5.1 17 0
|
||||||
|
5200 5.2 17 0
|
||||||
|
5300 5.3 17 0
|
||||||
|
5400 5.4 18 0
|
||||||
|
5500 5.5 18 0
|
||||||
|
5600 5.6 18 0
|
||||||
|
5700 5.7 19 0
|
||||||
|
5800 5.8 19 0
|
||||||
|
5900 5.9 19 0
|
||||||
|
6000 6 19 0
|
||||||
|
6100 6.1 20 0
|
||||||
|
6200 6.2 20 0
|
||||||
|
6300 6.3 20 0
|
||||||
|
6400 6.4 21 0
|
||||||
|
6500 6.5 21 0
|
||||||
|
6600 6.6 21 0
|
||||||
|
6700 6.7 21 0
|
||||||
|
6800 6.8 22 0
|
||||||
|
6900 6.9 22 0
|
||||||
|
7000 7 22 0
|
||||||
|
7100 7.1 23 0
|
||||||
|
7200 7.2 23 0
|
||||||
|
7300 7.3 23 0
|
||||||
|
7400 7.4 24 0
|
||||||
|
7500 7.5 24 0
|
||||||
|
7600 7.6 24 0
|
||||||
|
7700 7.7 25 0
|
||||||
|
7800 7.8 25 0
|
||||||
|
7900 7.9 26 0
|
||||||
|
8000 8 26 0
|
||||||
|
8100 8.1 26 0
|
||||||
|
8200 8.2 26 0
|
||||||
|
8300 8.3 27 0
|
||||||
|
8400 8.4 27 0
|
||||||
|
8500 8.5 27 0
|
||||||
|
8600 8.6 28 0
|
||||||
|
8700 8.7 28 0
|
||||||
|
8800 8.8 28 0
|
||||||
|
8900 8.9 29 0
|
||||||
|
9000 9 29 0
|
||||||
|
9100 9.1 29 0
|
||||||
|
9200 9.2 30 0
|
||||||
|
9300 9.3 30 0
|
||||||
|
9400 9.4 30 0
|
||||||
|
9500 9.5 30 0
|
||||||
|
9600 9.6 31 0
|
||||||
|
9700 9.7 31 0
|
||||||
|
9800 9.8 32 0
|
||||||
|
9900 9.9 32 0
|
||||||
|
10000 10 32 0
|
||||||
|
Loop time of 78.0094 on 1 procs for 10000 steps with 900 atoms
|
||||||
|
|
||||||
|
Performance: 11075589.479 ns/day, 0.000 hours/ns, 128.190 timesteps/s, 115.371 katom-step/s
|
||||||
|
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 77.441 | 77.441 | 77.441 | 0.0 | 99.27
|
||||||
|
Neigh | 0.016471 | 0.016471 | 0.016471 | 0.0 | 0.02
|
||||||
|
Comm | 0.14821 | 0.14821 | 0.14821 | 0.0 | 0.19
|
||||||
|
Output | 0.062415 | 0.062415 | 0.062415 | 0.0 | 0.08
|
||||||
|
Modify | 0.25323 | 0.25323 | 0.25323 | 0.0 | 0.32
|
||||||
|
Other | | 0.0877 | | | 0.11
|
||||||
|
|
||||||
|
Nlocal: 900 ave 900 max 900 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 762 ave 762 max 762 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 40697 ave 40697 max 40697 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 40697
|
||||||
|
Ave neighs/atom = 45.218889
|
||||||
|
Neighbor list builds = 32
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:01:18
|
||||||
@ -0,0 +1,230 @@
|
|||||||
|
LAMMPS (28 Mar 2023 - Development)
|
||||||
|
dimension 2
|
||||||
|
units micro
|
||||||
|
atom_style sph
|
||||||
|
|
||||||
|
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
|
||||||
|
using lattice units in orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 0.1)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
region sphere sphere 0 0 0 $R units box
|
||||||
|
region sphere sphere 0 0 0 0.5 units box
|
||||||
|
set region sphere type 2
|
||||||
|
Setting atom values ...
|
||||||
|
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 sph/rho ${rho_0}
|
||||||
|
set group all sph/rho 1
|
||||||
|
Setting atom values ...
|
||||||
|
900 settings made for sph/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 sph
|
||||||
|
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
|
||||||
|
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
|
||||||
|
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
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.463 | 6.463 | 6.463 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 4 0
|
||||||
|
1600 1.6 5 0
|
||||||
|
1700 1.7 5 0
|
||||||
|
1800 1.8 5 0
|
||||||
|
1900 1.9 6 0
|
||||||
|
2000 2 6 0
|
||||||
|
2100 2.1 6 0
|
||||||
|
2200 2.2 7 0
|
||||||
|
2300 2.3 7 0
|
||||||
|
2400 2.4 7 0
|
||||||
|
2500 2.5 8 0
|
||||||
|
2600 2.6 8 0
|
||||||
|
2700 2.7 8 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 11 0
|
||||||
|
3400 3.4 11 0
|
||||||
|
3500 3.5 11 0
|
||||||
|
3600 3.6 12 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 14 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 17 0
|
||||||
|
5200 5.2 17 0
|
||||||
|
5300 5.3 17 0
|
||||||
|
5400 5.4 17 0
|
||||||
|
5500 5.5 18 0
|
||||||
|
5600 5.6 18 0
|
||||||
|
5700 5.7 18 0
|
||||||
|
5800 5.8 19 0
|
||||||
|
5900 5.9 19 0
|
||||||
|
6000 6 19 0
|
||||||
|
6100 6.1 20 0
|
||||||
|
6200 6.2 20 0
|
||||||
|
6300 6.3 20 0
|
||||||
|
6400 6.4 21 0
|
||||||
|
6500 6.5 21 0
|
||||||
|
6600 6.6 21 0
|
||||||
|
6700 6.7 22 0
|
||||||
|
6800 6.8 22 0
|
||||||
|
6900 6.9 22 0
|
||||||
|
7000 7 23 0
|
||||||
|
7100 7.1 23 0
|
||||||
|
7200 7.2 23 0
|
||||||
|
7300 7.3 24 0
|
||||||
|
7400 7.4 24 0
|
||||||
|
7500 7.5 24 0
|
||||||
|
7600 7.6 25 0
|
||||||
|
7700 7.7 25 0
|
||||||
|
7800 7.8 26 0
|
||||||
|
7900 7.9 26 0
|
||||||
|
8000 8 26 0
|
||||||
|
8100 8.1 26 0
|
||||||
|
8200 8.2 27 0
|
||||||
|
8300 8.3 27 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 30 0
|
||||||
|
9300 9.3 30 0
|
||||||
|
9400 9.4 31 0
|
||||||
|
9500 9.5 31 0
|
||||||
|
9600 9.6 31 0
|
||||||
|
9700 9.7 32 0
|
||||||
|
9800 9.8 32 0
|
||||||
|
9900 9.9 32 0
|
||||||
|
10000 10 33 0
|
||||||
|
Loop time of 13.5306 on 4 procs for 10000 steps with 900 atoms
|
||||||
|
|
||||||
|
Performance: 63855371.888 ns/day, 0.000 hours/ns, 739.067 timesteps/s, 665.160 katom-step/s
|
||||||
|
98.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 12.327 | 12.56 | 12.738 | 4.3 | 92.83
|
||||||
|
Neigh | 0.0043391 | 0.0044297 | 0.0045381 | 0.1 | 0.03
|
||||||
|
Comm | 0.53746 | 0.71463 | 0.94685 | 18.1 | 5.28
|
||||||
|
Output | 0.021884 | 0.02228 | 0.023428 | 0.4 | 0.16
|
||||||
|
Modify | 0.14457 | 0.14548 | 0.14643 | 0.2 | 1.08
|
||||||
|
Other | | 0.08351 | | | 0.62
|
||||||
|
|
||||||
|
Nlocal: 225 ave 228 max 222 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
Nghost: 438.25 ave 442 max 434 min
|
||||||
|
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||||
|
Neighs: 10152.2 ave 10328 max 9853 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 40609
|
||||||
|
Ave neighs/atom = 45.121111
|
||||||
|
Neighbor list builds = 33
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:13
|
||||||
@ -1,6 +1,6 @@
|
|||||||
dimension 3
|
dimension 3
|
||||||
units micro
|
units micro
|
||||||
atom_style meso
|
atom_style sph
|
||||||
|
|
||||||
variable a equal 0.1 # lattice spacing micrometers
|
variable a equal 0.1 # lattice spacing micrometers
|
||||||
variable L equal $a*10
|
variable L equal $a*10
|
||||||
@ -21,7 +21,7 @@ lattice sc $a
|
|||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
|
|
||||||
mass * ${mass}
|
mass * ${mass}
|
||||||
set group all meso/rho ${rho_0}
|
set group all sph/rho ${rho_0}
|
||||||
|
|
||||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||||
@ -34,7 +34,7 @@ variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
|
|||||||
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
||||||
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
||||||
|
|
||||||
fix 1 all meso
|
fix 1 all sph
|
||||||
|
|
||||||
neighbor ${skin} bin
|
neighbor ${skin} bin
|
||||||
timestep ${dt}
|
timestep ${dt}
|
||||||
|
|||||||
@ -1,7 +1,7 @@
|
|||||||
LAMMPS (24 Oct 2018)
|
LAMMPS (28 Mar 2023 - Development)
|
||||||
dimension 3
|
dimension 3
|
||||||
units micro
|
units micro
|
||||||
atom_style meso
|
atom_style sph
|
||||||
|
|
||||||
variable a equal 0.1 # lattice spacing micrometers
|
variable a equal 0.1 # lattice spacing micrometers
|
||||||
variable L equal $a*10
|
variable L equal $a*10
|
||||||
@ -38,13 +38,15 @@ Lattice spacing in x,y,z = 0.1 0.1 0.1
|
|||||||
|
|
||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
Created 8000 atoms
|
Created 8000 atoms
|
||||||
Time spent = 0.00285411 secs
|
using lattice units in orthogonal box = (-1 -1 -1) to (1 1 1)
|
||||||
|
create_atoms CPU = 0.002 seconds
|
||||||
|
|
||||||
mass * ${mass}
|
mass * ${mass}
|
||||||
mass * 0.001
|
mass * 0.001
|
||||||
set group all meso/rho ${rho_0}
|
set group all sph/rho ${rho_0}
|
||||||
set group all meso/rho 1
|
set group all sph/rho 1
|
||||||
8000 settings made for meso/rho
|
Setting atom values ...
|
||||||
|
8000 settings made for sph/rho
|
||||||
|
|
||||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
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 ${mu} 76787
|
||||||
@ -71,7 +73,7 @@ variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
|
|||||||
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
|
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
|
||||||
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
|
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
|
||||||
|
|
||||||
fix 1 all meso
|
fix 1 all sph
|
||||||
|
|
||||||
neighbor ${skin} bin
|
neighbor ${skin} bin
|
||||||
neighbor 0.04 bin
|
neighbor 0.04 bin
|
||||||
@ -82,8 +84,9 @@ thermo 10
|
|||||||
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||||
|
|
||||||
run 200
|
run 200
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 10 steps, check yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 0.44
|
master list distance cutoff = 0.44
|
||||||
ghost atom cutoff = 0.44
|
ghost atom cutoff = 0.44
|
||||||
@ -92,9 +95,9 @@ Neighbor list info ...
|
|||||||
(1) pair sdpd/taitwater/isothermal, perpetual
|
(1) pair sdpd/taitwater/isothermal, perpetual
|
||||||
attributes: half, newton on
|
attributes: half, newton on
|
||||||
pair build: half/bin/atomonly/newton
|
pair build: half/bin/atomonly/newton
|
||||||
stencil: half/bin/3d/newton
|
stencil: half/bin/3d
|
||||||
bin: standard
|
bin: standard
|
||||||
Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 14.29 | 14.29 | 14.29 Mbytes
|
||||||
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||||
0 0 0 0 0
|
0 0 0 0 0
|
||||||
10 0.005 0.70973271 0.71495693 0.71910087
|
10 0.005 0.70973271 0.71495693 0.71910087
|
||||||
@ -117,20 +120,20 @@ Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
|||||||
180 0.09 0.97277934 0.97383622 0.96900866
|
180 0.09 0.97277934 0.97383622 0.96900866
|
||||||
190 0.095 0.96647288 1.0027643 0.96230782
|
190 0.095 0.96647288 1.0027643 0.96230782
|
||||||
200 0.1 0.94864291 0.95902585 0.96398175
|
200 0.1 0.94864291 0.95902585 0.96398175
|
||||||
Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms
|
Loop time of 55.7542 on 1 procs for 200 steps with 8000 atoms
|
||||||
|
|
||||||
Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 timesteps/s
|
Performance: 154965.922 ns/day, 0.000 hours/ns, 3.587 timesteps/s, 28.697 katom-step/s
|
||||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
99.6% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 59.92 | 59.92 | 59.92 | 0.0 | 99.68
|
Pair | 55.642 | 55.642 | 55.642 | 0.0 | 99.80
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Comm | 0.11154 | 0.11154 | 0.11154 | 0.0 | 0.19
|
Comm | 0.060977 | 0.060977 | 0.060977 | 0.0 | 0.11
|
||||||
Output | 0.0063498 | 0.0063498 | 0.0063498 | 0.0 | 0.01
|
Output | 0.0066393 | 0.0066393 | 0.0066393 | 0.0 | 0.01
|
||||||
Modify | 0.043546 | 0.043546 | 0.043546 | 0.0 | 0.07
|
Modify | 0.028354 | 0.028354 | 0.028354 | 0.0 | 0.05
|
||||||
Other | | 0.02811 | | | 0.05
|
Other | | 0.01623 | | | 0.03
|
||||||
|
|
||||||
Nlocal: 8000 ave 8000 max 8000 min
|
Nlocal: 8000 ave 8000 max 8000 min
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
@ -143,4 +146,4 @@ Total # of neighbors = 1456000
|
|||||||
Ave neighs/atom = 182
|
Ave neighs/atom = 182
|
||||||
Neighbor list builds = 0
|
Neighbor list builds = 0
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
Total wall time: 0:01:00
|
Total wall time: 0:00:56
|
||||||
@ -1,7 +1,7 @@
|
|||||||
LAMMPS (24 Oct 2018)
|
LAMMPS (28 Mar 2023 - Development)
|
||||||
dimension 3
|
dimension 3
|
||||||
units micro
|
units micro
|
||||||
atom_style meso
|
atom_style sph
|
||||||
|
|
||||||
variable a equal 0.1 # lattice spacing micrometers
|
variable a equal 0.1 # lattice spacing micrometers
|
||||||
variable L equal $a*10
|
variable L equal $a*10
|
||||||
@ -38,13 +38,15 @@ Lattice spacing in x,y,z = 0.1 0.1 0.1
|
|||||||
|
|
||||||
create_atoms 1 box
|
create_atoms 1 box
|
||||||
Created 8000 atoms
|
Created 8000 atoms
|
||||||
Time spent = 0.00252754 secs
|
using lattice units in orthogonal box = (-1 -1 -1) to (1 1 1)
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
mass * ${mass}
|
mass * ${mass}
|
||||||
mass * 0.001
|
mass * 0.001
|
||||||
set group all meso/rho ${rho_0}
|
set group all sph/rho ${rho_0}
|
||||||
set group all meso/rho 1
|
set group all sph/rho 1
|
||||||
8000 settings made for meso/rho
|
Setting atom values ...
|
||||||
|
8000 settings made for sph/rho
|
||||||
|
|
||||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
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 ${mu} 76787
|
||||||
@ -71,7 +73,7 @@ variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
|
|||||||
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
|
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
|
||||||
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
|
variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
|
||||||
|
|
||||||
fix 1 all meso
|
fix 1 all sph
|
||||||
|
|
||||||
neighbor ${skin} bin
|
neighbor ${skin} bin
|
||||||
neighbor 0.04 bin
|
neighbor 0.04 bin
|
||||||
@ -82,8 +84,9 @@ thermo 10
|
|||||||
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||||
|
|
||||||
run 200
|
run 200
|
||||||
|
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
|
||||||
Neighbor list info ...
|
Neighbor list info ...
|
||||||
update every 1 steps, delay 10 steps, check yes
|
update: every = 1 steps, delay = 0 steps, check = yes
|
||||||
max neighbors/atom: 2000, page size: 100000
|
max neighbors/atom: 2000, page size: 100000
|
||||||
master list distance cutoff = 0.44
|
master list distance cutoff = 0.44
|
||||||
ghost atom cutoff = 0.44
|
ghost atom cutoff = 0.44
|
||||||
@ -92,9 +95,9 @@ Neighbor list info ...
|
|||||||
(1) pair sdpd/taitwater/isothermal, perpetual
|
(1) pair sdpd/taitwater/isothermal, perpetual
|
||||||
attributes: half, newton on
|
attributes: half, newton on
|
||||||
pair build: half/bin/atomonly/newton
|
pair build: half/bin/atomonly/newton
|
||||||
stencil: half/bin/3d/newton
|
stencil: half/bin/3d
|
||||||
bin: standard
|
bin: standard
|
||||||
Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes
|
Per MPI rank memory allocation (min/avg/max) = 6.172 | 6.172 | 6.172 Mbytes
|
||||||
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||||
0 0 0 0 0
|
0 0 0 0 0
|
||||||
10 0.005 0.71224819 0.71470372 0.7008956
|
10 0.005 0.71224819 0.71470372 0.7008956
|
||||||
@ -117,20 +120,20 @@ Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
|||||||
180 0.09 0.97214242 0.9726305 0.9726035
|
180 0.09 0.97214242 0.9726305 0.9726035
|
||||||
190 0.095 0.97577583 0.96523645 0.9756968
|
190 0.095 0.97577583 0.96523645 0.9756968
|
||||||
200 0.1 0.96386053 0.97268854 0.94582436
|
200 0.1 0.96386053 0.97268854 0.94582436
|
||||||
Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms
|
Loop time of 9.59181 on 4 procs for 200 steps with 8000 atoms
|
||||||
|
|
||||||
Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s
|
Performance: 900768.333 ns/day, 0.000 hours/ns, 20.851 timesteps/s, 166.809 katom-step/s
|
||||||
73.9% CPU use with 4 MPI tasks x no OpenMP threads
|
98.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
MPI task timing breakdown:
|
MPI task timing breakdown:
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
---------------------------------------------------------------
|
---------------------------------------------------------------
|
||||||
Pair | 27.385 | 28.409 | 28.761 | 11.1 | 87.34
|
Pair | 8.9729 | 9.2147 | 9.4383 | 5.5 | 96.07
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||||
Comm | 3.582 | 3.9343 | 4.9531 | 29.7 | 12.10
|
Comm | 0.13739 | 0.36068 | 0.60216 | 27.6 | 3.76
|
||||||
Output | 0.022267 | 0.026073 | 0.033141 | 2.7 | 0.08
|
Output | 0.0022724 | 0.002394 | 0.0026506 | 0.3 | 0.02
|
||||||
Modify | 0.031714 | 0.033134 | 0.034367 | 0.6 | 0.10
|
Modify | 0.0068559 | 0.0069926 | 0.0070974 | 0.1 | 0.07
|
||||||
Other | | 0.1226 | | | 0.38
|
Other | | 0.007004 | | | 0.07
|
||||||
|
|
||||||
Nlocal: 2000 ave 2000 max 2000 min
|
Nlocal: 2000 ave 2000 max 2000 min
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
@ -143,4 +146,4 @@ Total # of neighbors = 1456000
|
|||||||
Ave neighs/atom = 182
|
Ave neighs/atom = 182
|
||||||
Neighbor list builds = 0
|
Neighbor list builds = 0
|
||||||
Dangerous builds = 0
|
Dangerous builds = 0
|
||||||
Total wall time: 0:00:32
|
Total wall time: 0:00:09
|
||||||
Reference in New Issue
Block a user