first commit: added SDPD
This commit is contained in:
Morteza Jalalvand
49
examples/USER/sdpd/2d-diffusion/in.lammps
Normal file
49
examples/USER/sdpd/2d-diffusion/in.lammps
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@ -0,0 +1,49 @@
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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 L equal $R*3
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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*$h
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region box block -$L $L -$L $L 0 $a units box
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create_box 2 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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group fluid type 1
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group sphere type 2
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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 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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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
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@ -0,0 +1,226 @@
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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 L equal $R*3
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variable L equal 0.5*3
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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*$h
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variable skin equal 0.2*0.45
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region box block -$L $L -$L $L 0 $a units box
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region box block -1.5 $L -$L $L 0 $a units box
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region box block -1.5 1.5 -$L $L 0 $a units box
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region box block -1.5 1.5 -1.5 $L 0 $a units box
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region box block -1.5 1.5 -1.5 1.5 0 $a units box
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region box block -1.5 1.5 -1.5 1.5 0 0.1 units box
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create_box 2 box
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Created orthogonal box = (-1.5 -1.5 0) to (1.5 1.5 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 900 atoms
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Time spent = 0.0015769 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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group fluid type 1
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819 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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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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900 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 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 = 12 12 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) = 6.137 | 6.137 | 6.137 Mbytes
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Step Time Nbuild Ndanger
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0 0 0 0
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100 0.1 0 0
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200 0.2 0 0
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300 0.3 0 0
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400 0.4 1 0
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500 0.5 1 0
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600 0.6 1 0
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700 0.7 2 0
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800 0.8 2 0
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900 0.9 2 0
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1000 1 3 0
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1100 1.1 3 0
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1200 1.2 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 6 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 7 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 10 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 11 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 12 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 13 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 17 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 18 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 19 0
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6100 6.1 20 0
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6200 6.2 20 0
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6300 6.3 20 0
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6400 6.4 21 0
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6500 6.5 21 0
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6600 6.6 21 0
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6700 6.7 21 0
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6800 6.8 22 0
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6900 6.9 22 0
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7000 7 22 0
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7100 7.1 23 0
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7200 7.2 23 0
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7300 7.3 23 0
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7400 7.4 24 0
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7500 7.5 24 0
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7600 7.6 24 0
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7700 7.7 25 0
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7800 7.8 25 0
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7900 7.9 26 0
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8000 8 26 0
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8100 8.1 26 0
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8200 8.2 26 0
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8300 8.3 27 0
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8400 8.4 27 0
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8500 8.5 27 0
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8600 8.6 28 0
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8700 8.7 28 0
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8800 8.8 28 0
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8900 8.9 29 0
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9000 9 29 0
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9100 9.1 29 0
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9200 9.2 30 0
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9300 9.3 30 0
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9400 9.4 30 0
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9500 9.5 30 0
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9600 9.6 31 0
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9700 9.7 31 0
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9800 9.8 32 0
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9900 9.9 32 0
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10000 10 32 0
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Loop time of 80.9456 on 1 procs for 10000 steps with 900 atoms
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Performance: 10673829.855 ns/day, 0.000 hours/ns, 123.540 timesteps/s
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99.8% 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 | 80.306 | 80.306 | 80.306 | 0.0 | 99.21
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Neigh | 0.017418 | 0.017418 | 0.017418 | 0.0 | 0.02
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Comm | 0.16939 | 0.16939 | 0.16939 | 0.0 | 0.21
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Output | 0.070281 | 0.070281 | 0.070281 | 0.0 | 0.09
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Modify | 0.3154 | 0.3154 | 0.3154 | 0.0 | 0.39
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Other | | 0.067 | | | 0.08
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Nlocal: 900 ave 900 max 900 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 762 ave 762 max 762 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 40697 ave 40697 max 40697 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 40697
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Ave neighs/atom = 45.2189
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Neighbor list builds = 32
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Dangerous builds = 0
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Total wall time: 0:01:20
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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
|
||||
Reference in New Issue
Block a user