147 lines
6.2 KiB
Groff
147 lines
6.2 KiB
Groff
LAMMPS (24 Oct 2018)
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dimension 3
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units micro
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atom_style meso
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variable a equal 0.1 # lattice spacing micrometers
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variable L equal $a*10
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variable L equal 0.1*10
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variable T equal 300.
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variable kB equal 1.3806504e-8 # picogram-micrometer^2/(microsecond^2-Kelvin)
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variable rho_0 equal 1. # density picograms/micrometer^3
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variable c_0 equal 10. # 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*4.0 # kernel function cutoff micrometers
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variable h equal 0.1*4.0
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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 5e-4 # timestep microseconds
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variable skin equal 0.1*$h
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variable skin equal 0.1*0.4
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region box block -$L $L -$L $L -$L $L units box
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region box block -1 $L -$L $L -$L $L units box
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region box block -1 1 -$L $L -$L $L units box
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region box block -1 1 -1 $L -$L $L units box
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region box block -1 1 -1 1 -$L $L units box
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region box block -1 1 -1 1 -1 $L units box
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region box block -1 1 -1 1 -1 1 units box
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create_box 1 box
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Created orthogonal box = (-1 -1 -1) to (1 1 1)
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1 by 2 by 2 MPI processor grid
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lattice sc $a
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lattice sc 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 8000 atoms
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Time spent = 0.00252754 secs
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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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8000 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 10 ${h}
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pair_coeff * * 1 10 0.4
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variable vx_sq atom vx*vx
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variable vy_sq atom vy*vy
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variable vz_sq atom vz*vz
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compute v_sq all reduce ave v_vx_sq v_vy_sq v_vz_sq
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variable vx_sq_check equal c_v_sq[1]*${mass}/${kB}/$T
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variable vx_sq_check equal c_v_sq[1]*0.001/${kB}/$T
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variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/$T
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variable vx_sq_check equal c_v_sq[1]*0.001/1.3806504e-08/300
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variable vy_sq_check equal c_v_sq[2]*${mass}/${kB}/$T
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variable vy_sq_check equal c_v_sq[2]*0.001/${kB}/$T
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variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/$T
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variable vy_sq_check equal c_v_sq[2]*0.001/1.3806504e-08/300
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variable vz_sq_check equal c_v_sq[3]*${mass}/${kB}/$T
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variable vz_sq_check equal c_v_sq[3]*0.001/${kB}/$T
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variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/$T
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variable vz_sq_check equal c_v_sq[3]*0.001/1.3806504e-08/300
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fix 1 all meso
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neighbor ${skin} bin
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neighbor 0.04 bin
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timestep ${dt}
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timestep 0.0005
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thermo 10
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thermo_style custom step time v_vx_sq_check v_vy_sq_check v_vz_sq_check
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run 200
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 0.44
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ghost atom cutoff = 0.44
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binsize = 0.22, bins = 10 10 10
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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/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.795 | 5.795 | 5.795 Mbytes
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Step Time v_vx_sq_check v_vy_sq_check v_vz_sq_check
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0 0 0 0 0
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10 0.005 0.71224819 0.71470372 0.7008956
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20 0.01 0.90627589 0.90683966 0.90116506
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30 0.015 0.938505 0.95884272 0.93337542
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40 0.02 0.94394649 0.93668038 0.96468004
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50 0.025 0.97152309 0.97546161 0.95107762
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60 0.03 0.94710871 0.95678322 0.97285504
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70 0.035 0.96253148 0.95838642 0.95450883
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80 0.04 0.97581495 0.95278681 0.95099478
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90 0.045 0.96251614 0.9740684 0.96081505
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100 0.05 0.94191275 0.97137523 0.94084858
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110 0.055 0.953406 0.95739684 0.98574522
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120 0.06 0.99001614 0.99608287 0.9839996
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130 0.065 0.96575225 0.94309655 0.92847798
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140 0.07 0.97642687 0.97458638 0.94696406
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150 0.075 0.99316381 0.96876814 0.95440106
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160 0.08 0.94589744 0.95264791 0.95495169
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170 0.085 0.97599092 0.95336014 0.97687718
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180 0.09 0.97214242 0.9726305 0.9726035
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190 0.095 0.97577583 0.96523645 0.9756968
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200 0.1 0.96386053 0.97268854 0.94582436
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Loop time of 32.5247 on 4 procs for 200 steps with 8000 atoms
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Performance: 265644.515 ns/day, 0.000 hours/ns, 6.149 timesteps/s
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73.9% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 27.385 | 28.409 | 28.761 | 11.1 | 87.34
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 3.582 | 3.9343 | 4.9531 | 29.7 | 12.10
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Output | 0.022267 | 0.026073 | 0.033141 | 2.7 | 0.08
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Modify | 0.031714 | 0.033134 | 0.034367 | 0.6 | 0.10
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Other | | 0.1226 | | | 0.38
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Nlocal: 2000 ave 2000 max 2000 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 8469 ave 8469 max 8469 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Neighs: 364000 ave 376628 max 351184 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Total # of neighbors = 1456000
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Ave neighs/atom = 182
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:32
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