Updating SDPD examples
This commit is contained in:
jtclemm
@ -1,6 +1,6 @@
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dimension 2
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units micro
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atom_style meso
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atom_style sph
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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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@ -37,12 +37,12 @@ group upper_wall type 3
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group lower_wall type 4
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mass * ${mass}
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set group all meso/rho ${rho_0}
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set group all sph/rho ${rho_0}
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pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
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pair_coeff * * ${rho_0} ${c_0} ${h}
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fix 1 fluid meso
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fix 1 fluid sph
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fix 2 sphere rigid/meso single
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fix 3 upper_wall meso/move linear +${wall_velocity} 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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@ -1,247 +0,0 @@
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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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1 by 1 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 = 0.00169706 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) = 6.937 | 6.937 | 6.937 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 0 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 3 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 7 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 8 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 9 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 10 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 11 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 12 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 13 0
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4100 4.1 13 0
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4200 4.2 14 0
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4300 4.3 14 0
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4400 4.4 14 0
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4500 4.5 15 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 16 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 19 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 21 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 22 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 23 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 24 0
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7200 7.2 24 0
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7300 7.3 25 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 26 0
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7700 7.7 26 0
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7800 7.8 26 0
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7900 7.9 27 0
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8000 8 27 0
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8100 8.1 27 0
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8200 8.2 28 0
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8300 8.3 28 0
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8400 8.4 28 0
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8500 8.5 29 0
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8600 8.6 29 0
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8700 8.7 30 0
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8800 8.8 30 0
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8900 8.9 30 0
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9000 9 31 0
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9100 9.1 31 0
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9200 9.2 31 0
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9300 9.3 32 0
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9400 9.4 32 0
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9500 9.5 32 0
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9600 9.6 33 0
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9700 9.7 33 0
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9800 9.8 33 0
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9900 9.9 34 0
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10000 10 34 0
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Loop time of 144.208 on 1 procs for 10000 steps with 1600 atoms
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Performance: 5991348.580 ns/day, 0.000 hours/ns, 69.344 timesteps/s
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99.7% CPU use with 1 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 | 143.08 | 143.08 | 143.08 | 0.0 | 99.22
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Neigh | 0.033195 | 0.033195 | 0.033195 | 0.0 | 0.02
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Comm | 0.24139 | 0.24139 | 0.24139 | 0.0 | 0.17
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Output | 0.11687 | 0.11687 | 0.11687 | 0.0 | 0.08
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Modify | 0.61566 | 0.61566 | 0.61566 | 0.0 | 0.43
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Other | | 0.117 | | | 0.08
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Nlocal: 1600 ave 1600 max 1600 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 993 ave 993 max 993 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 73236 ave 73236 max 73236 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 73236
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Ave neighs/atom = 45.7725
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Neighbor list builds = 34
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Dangerous builds = 0
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Total wall time: 0:02:24
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@ -1,247 +0,0 @@
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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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|
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fix 2d all enforce2d
|
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|
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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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|
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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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|
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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
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||||
Step Time Nbuild Ndanger
|
||||
0 0 0 0
|
||||
100 0.1 0 0
|
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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
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||||
1000 1 3 0
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||||
1100 1.1 3 0
|
||||
1200 1.2 4 0
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||||
1300 1.3 4 0
|
||||
1400 1.4 4 0
|
||||
1500 1.5 4 0
|
||||
1600 1.6 5 0
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||||
1700 1.7 5 0
|
||||
1800 1.8 5 0
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||||
1900 1.9 6 0
|
||||
2000 2 6 0
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||||
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
|
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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
|
||||
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
|
||||
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
|
||||
Reference in New Issue
Block a user