first commit: added SDPD
This commit is contained in:
Morteza Jalalvand
61
examples/USER/sdpd/2d-diffusion-in-shear-flow/in.lammps
Normal file
61
examples/USER/sdpd/2d-diffusion-in-shear-flow/in.lammps
Normal file
@ -0,0 +1,61 @@
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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 Lf equal $R*3
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variable Lb equal $R*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 mass equal $a*$a*$a*${rho_0}
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variable dt equal 1e-3 # timestep microseconds
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variable skin equal 0.2*$h
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region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
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create_box 4 box
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lattice sq $a
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create_atoms 1 box
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region sphere sphere 0 0 0 $R units box
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set region sphere type 2
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region upper_wall block INF INF +${Lf} INF INF INF units box
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set region upper_wall type 3
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region lower_wall block INF INF INF -${Lf} INF INF units box
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set region lower_wall type 4
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group fluid type 1
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group sphere type 2
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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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pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
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pair_coeff * * ${rho_0} ${c_0} ${h}
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fix 1 fluid meso
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fix 2 sphere rigid/meso single
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fix 3 upper_wall meso/move linear +${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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fix 2d all enforce2d
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neighbor ${skin} bin
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neigh_modify delay 0 every 1 check yes
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timestep ${dt}
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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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@ -0,0 +1,247 @@
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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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@ -0,0 +1,247 @@
|
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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
|
||||
49
examples/USER/sdpd/2d-diffusion/in.lammps
Normal file
49
examples/USER/sdpd/2d-diffusion/in.lammps
Normal file
@ -0,0 +1,49 @@
|
||||
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 L equal $R*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 mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -$L $L -$L $L 0 $a units box
|
||||
create_box 2 box
|
||||
lattice sq $a
|
||||
|
||||
create_atoms 1 box
|
||||
|
||||
region sphere sphere 0 0 0 $R units box
|
||||
set region sphere type 2
|
||||
|
||||
group fluid type 1
|
||||
group sphere type 2
|
||||
|
||||
mass * ${mass}
|
||||
set group all meso/rho ${rho_0}
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
|
||||
fix 1 fluid meso
|
||||
fix 2 sphere rigid/meso single
|
||||
|
||||
fix 2d all enforce2d
|
||||
|
||||
neighbor ${skin} bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
timestep ${dt}
|
||||
|
||||
dump dump_id all atom 100 dump.lammpstrj
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step time nbuild ndanger
|
||||
|
||||
run 10000
|
||||
226
examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.1
Normal file
226
examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.1
Normal file
@ -0,0 +1,226 @@
|
||||
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
|
||||
226
examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.4
Normal file
226
examples/USER/sdpd/2d-diffusion/log.24Oct18.2d-diffusion.g++.4
Normal file
@ -0,0 +1,226 @@
|
||||
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
|
||||
24
examples/USER/sdpd/README
Normal file
24
examples/USER/sdpd/README
Normal file
@ -0,0 +1,24 @@
|
||||
Smoothed Dissipative Particle Dynamics examples
|
||||
|
||||
equipartition-verification:
|
||||
This example verifies the equipartition theorem.
|
||||
It simulates a periodic box of water with no solid bodies.
|
||||
If equipartition theorem holds true, the average of each component of
|
||||
translational kinetic energy should be equal to k_B T, and therefore
|
||||
vx_sq_check, vy_sq_check, and vz_sq_check should fluctuate near 1.
|
||||
|
||||
2d-diffusion:
|
||||
This example demonstrates the free diffusion of a disk in 2D.
|
||||
The 3D simulation is similar but takes much longer to complete.
|
||||
As with other statistical experiments you need an ensemble to
|
||||
extract meaningful average quantities.
|
||||
For a more realistic simulation you should increase the resolution
|
||||
of the disk/sphere which also necessitates reduction of timestep.
|
||||
|
||||
2d-diffusion-in-shear-flow:
|
||||
This example demonstrates the diffusion of a disk in shear flow in 2D.
|
||||
The 3D simulation is similar but takes much longer to complete.
|
||||
As with other statistical experiments you need an ensemble to
|
||||
extract meaningful average quantities.
|
||||
For a more realistic simulation you should increase the resolution
|
||||
of the disk/sphere which also necessitates reduction of timestep.
|
||||
45
examples/USER/sdpd/equipartition-verification/in.lammps
Normal file
45
examples/USER/sdpd/equipartition-verification/in.lammps
Normal file
@ -0,0 +1,45 @@
|
||||
dimension 3
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable a equal 0.1 # lattice spacing micrometers
|
||||
variable L equal $a*10
|
||||
variable T equal 300.
|
||||
variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin)
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 10. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.0 # kernel function cutoff micrometers
|
||||
variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 5e-4 # timestep microseconds
|
||||
variable skin equal 0.1*$h
|
||||
|
||||
region box block -$L $L -$L $L -$L $L units box
|
||||
create_box 1 box
|
||||
lattice sc $a
|
||||
|
||||
create_atoms 1 box
|
||||
|
||||
mass * ${mass}
|
||||
set group all meso/rho ${rho_0}
|
||||
|
||||
pair_style sdpd/taitwater/isothermal $T ${mu} 76787 # temperature viscosity random_seed
|
||||
pair_coeff * * ${rho_0} ${c_0} ${h}
|
||||
|
||||
variable vx_sq atom vx*vx
|
||||
variable vy_sq atom vy*vy
|
||||
variable vz_sq atom vz*vz
|
||||
compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
|
||||
variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
||||
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
||||
|
||||
fix 1 all meso
|
||||
|
||||
neighbor ${skin} bin
|
||||
timestep ${dt}
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
|
||||
run 200
|
||||
@ -0,0 +1,146 @@
|
||||
LAMMPS (24 Oct 2018)
|
||||
dimension 3
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable a equal 0.1 # lattice spacing micrometers
|
||||
variable L equal $a*10
|
||||
variable L equal 0.1*10
|
||||
variable T equal 300.
|
||||
variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin)
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 10. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.0 # kernel function cutoff micrometers
|
||||
variable h equal 0.1*4.0
|
||||
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 5e-4 # timestep microseconds
|
||||
variable skin equal 0.1*$h
|
||||
variable skin equal 0.1*0.4
|
||||
|
||||
region box block -$L $L -$L $L -$L $L units box
|
||||
region box block -1 $L -$L $L -$L $L units box
|
||||
region box block -1 1 -$L $L -$L $L units box
|
||||
region box block -1 1 -1 $L -$L $L units box
|
||||
region box block -1 1 -1 1 -$L $L units box
|
||||
region box block -1 1 -1 1 -1 $L units box
|
||||
region box block -1 1 -1 1 -1 1 units box
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1 -1 -1) to (1 1 1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
lattice sc $a
|
||||
lattice sc 0.1
|
||||
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
||||
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
Time spent = 0.00285411 secs
|
||||
|
||||
mass * ${mass}
|
||||
mass * 0.001
|
||||
set group all meso/rho ${rho_0}
|
||||
set group all meso/rho 1
|
||||
8000 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 10 ${h}
|
||||
pair_coeff * * 1 10 0.4
|
||||
|
||||
variable vx_sq atom vx*vx
|
||||
variable vy_sq atom vy*vy
|
||||
variable vz_sq atom vz*vz
|
||||
compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
|
||||
variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
|
||||
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
|
||||
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
||||
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-08/300
|
||||
|
||||
fix 1 all meso
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.04 bin
|
||||
timestep ${dt}
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
|
||||
run 200
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.44
|
||||
ghost atom cutoff = 0.44
|
||||
binsize = 0.22, bins = 10 10 10
|
||||
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/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.54 | 13.54 | 13.54 Mbytes
|
||||
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
0 0 0 0 0
|
||||
10 0.005 0.70973271 0.71495693 0.71910087
|
||||
20 0.01 0.90418096 0.88845437 0.89659567
|
||||
30 0.015 0.9590736 0.97880338 0.9619016
|
||||
40 0.02 0.98533774 0.96057682 0.95600448
|
||||
50 0.025 0.96433662 0.96650071 0.95509683
|
||||
60 0.03 0.96598029 0.96373656 0.96734888
|
||||
70 0.035 0.95433045 0.98004764 0.96255924
|
||||
80 0.04 0.97872906 0.95987289 0.96623598
|
||||
90 0.045 0.99913888 0.99255731 0.95616142
|
||||
100 0.05 0.98872675 0.97141018 0.95338841
|
||||
110 0.055 0.97794592 0.97389258 0.98473719
|
||||
120 0.06 0.98389266 0.96716284 0.95504862
|
||||
130 0.065 0.98572886 0.96680923 0.95599065
|
||||
140 0.07 0.97602684 0.97580081 0.9886878
|
||||
150 0.075 0.99172003 0.95027467 0.96028033
|
||||
160 0.08 0.96793247 0.94590928 0.95644301
|
||||
170 0.085 0.94167619 0.98048861 0.93439426
|
||||
180 0.09 0.97277934 0.97383622 0.96900866
|
||||
190 0.095 0.96647288 1.0027643 0.96230782
|
||||
200 0.1 0.94864291 0.95902585 0.96398175
|
||||
Loop time of 60.1095 on 1 procs for 200 steps with 8000 atoms
|
||||
|
||||
Performance: 143737.595 ns/day, 0.000 hours/ns, 3.327 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 | 59.92 | 59.92 | 59.92 | 0.0 | 99.68
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.11154 | 0.11154 | 0.11154 | 0.0 | 0.19
|
||||
Output | 0.0063498 | 0.0063498 | 0.0063498 | 0.0 | 0.01
|
||||
Modify | 0.043546 | 0.043546 | 0.043546 | 0.0 | 0.07
|
||||
Other | | 0.02811 | | | 0.05
|
||||
|
||||
Nlocal: 8000 ave 8000 max 8000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 16389 ave 16389 max 16389 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1.456e+06 ave 1.456e+06 max 1.456e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1456000
|
||||
Ave neighs/atom = 182
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:00
|
||||
@ -0,0 +1,146 @@
|
||||
LAMMPS (24 Oct 2018)
|
||||
dimension 3
|
||||
units micro
|
||||
atom_style meso
|
||||
|
||||
variable a equal 0.1 # lattice spacing micrometers
|
||||
variable L equal $a*10
|
||||
variable L equal 0.1*10
|
||||
variable T equal 300.
|
||||
variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin)
|
||||
variable rho_0 equal 1. # density picograms/micrometer^3
|
||||
variable c_0 equal 10. # speed of sound micrometers/microsecond
|
||||
variable mu equal 1. # dynamic viscosity picogram/(micrometer-microsecond)
|
||||
variable h equal $a*4.0 # kernel function cutoff micrometers
|
||||
variable h equal 0.1*4.0
|
||||
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 5e-4 # timestep microseconds
|
||||
variable skin equal 0.1*$h
|
||||
variable skin equal 0.1*0.4
|
||||
|
||||
region box block -$L $L -$L $L -$L $L units box
|
||||
region box block -1 $L -$L $L -$L $L units box
|
||||
region box block -1 1 -$L $L -$L $L units box
|
||||
region box block -1 1 -1 $L -$L $L units box
|
||||
region box block -1 1 -1 1 -$L $L units box
|
||||
region box block -1 1 -1 1 -1 $L units box
|
||||
region box block -1 1 -1 1 -1 1 units box
|
||||
create_box 1 box
|
||||
Created orthogonal box = (-1 -1 -1) to (1 1 1)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
lattice sc $a
|
||||
lattice sc 0.1
|
||||
Lattice spacing in x,y,z = 0.1 0.1 0.1
|
||||
|
||||
create_atoms 1 box
|
||||
Created 8000 atoms
|
||||
Time spent = 0.00252754 secs
|
||||
|
||||
mass * ${mass}
|
||||
mass * 0.001
|
||||
set group all meso/rho ${rho_0}
|
||||
set group all meso/rho 1
|
||||
8000 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 10 ${h}
|
||||
pair_coeff * * 1 10 0.4
|
||||
|
||||
variable vx_sq atom vx*vx
|
||||
variable vy_sq atom vy*vy
|
||||
variable vz_sq atom vz*vz
|
||||
compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
|
||||
variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
|
||||
variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
|
||||
variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
|
||||
variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
|
||||
variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
|
||||
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-08/300
|
||||
|
||||
fix 1 all meso
|
||||
|
||||
neighbor ${skin} bin
|
||||
neighbor 0.04 bin
|
||||
timestep ${dt}
|
||||
timestep 0.0005
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
|
||||
run 200
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 0.44
|
||||
ghost atom cutoff = 0.44
|
||||
binsize = 0.22, bins = 10 10 10
|
||||
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/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes
|
||||
Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
|
||||
0 0 0 0 0
|
||||
10 0.005 0.71224819 0.71470372 0.7008956
|
||||
20 0.01 0.90627589 0.90683966 0.90116506
|
||||
30 0.015 0.938505 0.95884272 0.93337542
|
||||
40 0.02 0.94394649 0.93668038 0.96468004
|
||||
50 0.025 0.97152309 0.97546161 0.95107762
|
||||
60 0.03 0.94710871 0.95678322 0.97285504
|
||||
70 0.035 0.96253148 0.95838642 0.95450883
|
||||
80 0.04 0.97581495 0.95278681 0.95099478
|
||||
90 0.045 0.96251614 0.9740684 0.96081505
|
||||
100 0.05 0.94191275 0.97137523 0.94084858
|
||||
110 0.055 0.953406 0.95739684 0.98574522
|
||||
120 0.06 0.99001614 0.99608287 0.9839996
|
||||
130 0.065 0.96575225 0.94309655 0.92847798
|
||||
140 0.07 0.97642687 0.97458638 0.94696406
|
||||
150 0.075 0.99316381 0.96876814 0.95440106
|
||||
160 0.08 0.94589744 0.95264791 0.95495169
|
||||
170 0.085 0.97599092 0.95336014 0.97687718
|
||||
180 0.09 0.97214242 0.9726305 0.9726035
|
||||
190 0.095 0.97577583 0.96523645 0.9756968
|
||||
200 0.1 0.96386053 0.97268854 0.94582436
|
||||
Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms
|
||||
|
||||
Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s
|
||||
73.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 27.385 | 28.409 | 28.761 | 11.1 | 87.34
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 3.582 | 3.9343 | 4.9531 | 29.7 | 12.10
|
||||
Output | 0.022267 | 0.026073 | 0.033141 | 2.7 | 0.08
|
||||
Modify | 0.031714 | 0.033134 | 0.034367 | 0.6 | 0.10
|
||||
Other | | 0.1226 | | | 0.38
|
||||
|
||||
Nlocal: 2000 ave 2000 max 2000 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8469 ave 8469 max 8469 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 364000 ave 376628 max 351184 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 1456000
|
||||
Ave neighs/atom = 182
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:32
|
||||
Reference in New Issue
Block a user