248 lines
9.5 KiB
Groff
248 lines
9.5 KiB
Groff
LAMMPS (24 Oct 2018)
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dimension 2
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units micro
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atom_style meso
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variable R equal 0.5 # radius of sphere micrometers
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variable a equal $R/5 # lattice spacing micrometers
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variable a equal 0.5/5
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variable Lf equal $R*3
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variable Lf equal 0.5*3
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variable Lb equal $R*4
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variable Lb equal 0.5*4
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variable wall_velocity equal 0.01 # micrometers/microsecond
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variable T equal 300.
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variable rho_0 equal 1. # density picograms/micrometer^3
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variable c_0 equal 100. # speed of sound micrometers/microsecond
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variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
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variable h equal $a*4.5 # kernel function cutoff micrometers
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variable h equal 0.1*4.5
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variable mass equal $a*$a*$a*${rho_0}
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variable mass equal 0.1*$a*$a*${rho_0}
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variable mass equal 0.1*0.1*$a*${rho_0}
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variable mass equal 0.1*0.1*0.1*${rho_0}
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variable mass equal 0.1*0.1*0.1*1
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variable dt equal 1e-3 # timestep microseconds
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variable skin equal 0.2*$h
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variable skin equal 0.2*0.45
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region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
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region box block -2 ${Lb} -${Lb} ${Lb} 0 ${a} units box
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region box block -2 2 -${Lb} ${Lb} 0 ${a} units box
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region box block -2 2 -2 ${Lb} 0 ${a} units box
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region box block -2 2 -2 2 0 ${a} units box
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region box block -2 2 -2 2 0 0.1 units box
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create_box 4 box
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Created orthogonal box = (-2 -2 0) to (2 2 0.1)
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2 by 2 by 1 MPI processor grid
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lattice sq $a
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lattice sq 0.1
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Lattice spacing in x,y,z = 0.1 0.1 0.1
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create_atoms 1 box
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Created 1600 atoms
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Time spent = 0.000589566 secs
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region sphere sphere 0 0 0 $R units box
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region sphere sphere 0 0 0 0.5 units box
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set region sphere type 2
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81 settings made for type
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region upper_wall block INF INF +${Lf} INF INF INF units box
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region upper_wall block INF INF +1.5 INF INF INF units box
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set region upper_wall type 3
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200 settings made for type
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region lower_wall block INF INF INF -${Lf} INF INF units box
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region lower_wall block INF INF INF -1.5 INF INF units box
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set region lower_wall type 4
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240 settings made for type
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group fluid type 1
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1079 atoms in group fluid
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group sphere type 2
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81 atoms in group sphere
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group upper_wall type 3
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200 atoms in group upper_wall
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group lower_wall type 4
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240 atoms in group lower_wall
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mass * ${mass}
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mass * 0.001
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set group all meso/rho ${rho_0}
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set group all meso/rho 1
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1600 settings made for meso/rho
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pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
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pair_style sdpd/taitwater/isothermal 300 ${mu} 76787
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pair_style sdpd/taitwater/isothermal 300 1 76787
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pair_coeff * * ${rho_0} ${c_0} ${h}
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pair_coeff * * 1 ${c_0} ${h}
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pair_coeff * * 1 100 ${h}
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pair_coeff * * 1 100 0.45
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fix 1 fluid meso
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fix 2 sphere rigid/meso single
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1 rigid bodies with 81 atoms
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fix 3 upper_wall meso/move linear +${wall_velocity} 0 0 units box
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fix 3 upper_wall meso/move linear +0.01 0 0 units box
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fix 4 lower_wall meso/move linear -${wall_velocity} 0 0 units box
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fix 4 lower_wall meso/move linear -0.01 0 0 units box
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fix 2d all enforce2d
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neighbor ${skin} bin
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neighbor 0.09 bin
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neigh_modify delay 0 every 1 check yes
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timestep ${dt}
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timestep 0.001
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dump dump_id all atom 100 dump.lammpstrj
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thermo 100
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thermo_style custom step time nbuild ndanger
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run 10000
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Neighbor list info ...
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 0.54
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ghost atom cutoff = 0.54
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binsize = 0.27, bins = 15 15 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair sdpd/taitwater/isothermal, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/2d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.854 | 6.854 | 6.854 Mbytes
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Step Time Nbuild Ndanger
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0 0 0 0
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100 0.1 0 0
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200 0.2 0 0
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300 0.3 0 0
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400 0.4 1 0
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500 0.5 1 0
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600 0.6 1 0
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700 0.7 2 0
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800 0.8 2 0
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900 0.9 2 0
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1000 1 3 0
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1100 1.1 3 0
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1200 1.2 4 0
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1300 1.3 4 0
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1400 1.4 4 0
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1500 1.5 4 0
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1600 1.6 5 0
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1700 1.7 5 0
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1800 1.8 5 0
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1900 1.9 6 0
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2000 2 6 0
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2100 2.1 6 0
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2200 2.2 6 0
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2300 2.3 7 0
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2400 2.4 7 0
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2500 2.5 7 0
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2600 2.6 8 0
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2700 2.7 8 0
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2800 2.8 8 0
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2900 2.9 9 0
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3000 3 9 0
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3100 3.1 9 0
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3200 3.2 10 0
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3300 3.3 10 0
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3400 3.4 10 0
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3500 3.5 11 0
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3600 3.6 11 0
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3700 3.7 11 0
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3800 3.8 12 0
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3900 3.9 12 0
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4000 4 12 0
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4100 4.1 13 0
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4200 4.2 13 0
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4300 4.3 13 0
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4400 4.4 14 0
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4500 4.5 14 0
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4600 4.6 15 0
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4700 4.7 15 0
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4800 4.8 15 0
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4900 4.9 16 0
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5000 5 16 0
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5100 5.1 17 0
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5200 5.2 17 0
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5300 5.3 17 0
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5400 5.4 17 0
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5500 5.5 18 0
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5600 5.6 18 0
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5700 5.7 18 0
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5800 5.8 19 0
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5900 5.9 19 0
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6000 6 20 0
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6100 6.1 20 0
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6200 6.2 20 0
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6300 6.3 21 0
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6400 6.4 21 0
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6500 6.5 21 0
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6600 6.6 22 0
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6700 6.7 22 0
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6800 6.8 22 0
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6900 6.9 23 0
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7000 7 23 0
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7100 7.1 23 0
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7200 7.2 24 0
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7300 7.3 24 0
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7400 7.4 25 0
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7500 7.5 25 0
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7600 7.6 25 0
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7700 7.7 25 0
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7800 7.8 26 0
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7900 7.9 26 0
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8000 8 26 0
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8100 8.1 27 0
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8200 8.2 27 0
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8300 8.3 27 0
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8400 8.4 28 0
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8500 8.5 28 0
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8600 8.6 28 0
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8700 8.7 29 0
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8800 8.8 29 0
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8900 8.9 29 0
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9000 9 30 0
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9100 9.1 30 0
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9200 9.2 31 0
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9300 9.3 31 0
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9400 9.4 31 0
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9500 9.5 32 0
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9600 9.6 32 0
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9700 9.7 32 0
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9800 9.8 32 0
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9900 9.9 33 0
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10000 10 33 0
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Loop time of 63.2372 on 4 procs for 10000 steps with 1600 atoms
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Performance: 13662841.706 ns/day, 0.000 hours/ns, 158.135 timesteps/s
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94.3% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 51.576 | 53.662 | 55.484 | 23.9 | 84.86
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Neigh | 0.011519 | 0.012395 | 0.013405 | 0.7 | 0.02
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Comm | 6.8389 | 8.5423 | 10.517 | 56.1 | 13.51
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Output | 0.12342 | 0.12513 | 0.1302 | 0.8 | 0.20
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Modify | 0.58708 | 0.69128 | 0.78806 | 11.3 | 1.09
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Other | | 0.2038 | | | 0.32
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Nlocal: 400 ave 411 max 388 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 552.25 ave 567 max 539 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Neighs: 18298.8 ave 18781 max 17829 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 73195
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Ave neighs/atom = 45.7469
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Neighbor list builds = 33
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Dangerous builds = 0
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Total wall time: 0:01:03
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