forked from lijiext/lammps
175 lines
6.0 KiB
Groff
175 lines
6.0 KiB
Groff
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 2d friction simulation
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dimension 2
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boundary p s p
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atom_style atomic
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neighbor 0.3 bin
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neigh_modify delay 5
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# create geometry
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lattice hex 0.9
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Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
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region box block 0 50 0 22 -0.25 0.25
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create_box 4 box
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Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
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2 by 2 by 1 MPI processor grid
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mass 1 1.0
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mass 2 1.0
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mass 3 1.0
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mass 4 1.0
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# atom regions
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region lo-fixed block INF INF INF 1.1 INF INF
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region lo-slab block INF INF INF 7 INF INF
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region above-lo block INF INF INF 7 INF INF side out
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region hi-fixed block INF INF 20.9 INF INF INF
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region hi-slab block INF INF 15 INF INF INF
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region below-hi block INF INF 15 INF INF INF side out
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region lo-asperity sphere 32 7 0 8
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region hi-asperity sphere 18 15 0 8
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region lo-half-sphere intersect 2 lo-asperity above-lo
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region hi-half-sphere intersect 2 hi-asperity below-hi
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# create 2 surfaces with asperities
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create_atoms 1 region lo-slab
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Created 750 atoms
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Time spent = 0.000427008 secs
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create_atoms 1 region hi-slab
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Created 750 atoms
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Time spent = 0.000396729 secs
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create_atoms 2 region lo-half-sphere
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Created 112 atoms
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Time spent = 0.000207663 secs
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create_atoms 3 region hi-half-sphere
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Created 112 atoms
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Time spent = 0.000194788 secs
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# LJ potentials
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pair_style lj/cut 2.5
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pair_coeff * * 1.0 1.0 2.5
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# define groups
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group lo region lo-slab
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750 atoms in group lo
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group lo type 2
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862 atoms in group lo
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group hi region hi-slab
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750 atoms in group hi
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group hi type 3
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862 atoms in group hi
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group lo-fixed region lo-fixed
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150 atoms in group lo-fixed
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group hi-fixed region hi-fixed
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150 atoms in group hi-fixed
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group boundary union lo-fixed hi-fixed
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300 atoms in group boundary
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group mobile subtract all boundary
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1424 atoms in group mobile
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set group lo-fixed type 4
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150 settings made for type
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set group hi-fixed type 4
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150 settings made for type
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# initial velocities
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compute new mobile temp/partial 0 1 0
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velocity mobile create 0.1 482748 temp new
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velocity hi set 1.0 0.0 0.0 sum yes
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# fixes
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fix 1 all nve
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fix 2 boundary setforce 0.0 0.0 0.0
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fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
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fix_modify 3 temp new
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fix 4 all enforce2d
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# Run
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timestep 0.0025
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thermo 1000
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thermo_modify temp new
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488)
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#dump 1 all atom 500 dump.friction
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#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
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#dump_modify 2 pad 5
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#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
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#dump_modify 3 pad 5
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run 20000
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 41 31 1
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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) = 3.051 | 3.051 | 3.052 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 0.1 -3.1333672 0 -3.0920969 -1.1437663 2444.9333
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1000 0.081947197 -3.0926906 0 -3.0588707 -0.021905504 2444.9333
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2000 0.082643627 -3.0850391 0 -3.0509318 -0.44951926 2444.9333
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3000 0.09228068 -3.0747307 0 -3.0366461 -0.25332113 2444.9333
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4000 0.096009906 -3.0564001 0 -3.0167765 -0.026756079 2444.9333
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5000 0.11991393 -3.0463606 0 -2.9968718 -0.095571711 2444.9333
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6000 0.11344201 -3.0428779 0 -2.9960601 -0.28750906 2444.9333
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7000 0.11932053 -3.0297394 0 -2.9804955 -0.44411602 2444.9333
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8000 0.11472412 -3.0260173 0 -2.9786703 -0.45505281 2444.9333
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9000 0.1153823 -3.0172996 0 -2.969681 -0.54699367 2444.9333
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10000 0.1110096 -3.0180324 0 -2.9722184 -0.28712224 2444.9333
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11000 0.10553488 -3.0281386 0 -2.984584 -0.40414683 2444.9333
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12000 0.10913279 -3.0339553 0 -2.9889159 -0.23876138 2444.9333
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13000 0.10791089 -3.036479 0 -2.9919439 -0.4066437 2444.9333
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14000 0.11089726 -3.0434547 0 -2.9976871 -0.25931118 2444.9333
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15000 0.10791244 -3.0452052 0 -3.0006694 -0.31309363 2444.9333
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16000 0.11451836 -3.0490643 0 -3.0018023 -0.28317436 2444.9333
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17000 0.10861713 -3.044417 0 -2.9995904 -0.39120148 2444.9333
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18000 0.11086121 -3.0462098 0 -3.0004571 -0.19272619 2444.9333
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19000 0.11407977 -3.046791 0 -2.99971 -0.29824356 2444.9333
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20000 0.11532037 -3.0463959 0 -2.9988028 -0.3435294 2444.9333
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Loop time of 1.98982 on 4 procs for 20000 steps with 1724 atoms
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Performance: 2171051.815 tau/day, 10051.166 timesteps/s
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97.5% CPU use with 4 MPI tasks x 1 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 | 1.0746 | 1.214 | 1.3479 | 8.9 | 61.01
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Neigh | 0.073977 | 0.083197 | 0.096277 | 2.9 | 4.18
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Comm | 0.22466 | 0.37933 | 0.52711 | 17.6 | 19.06
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Output | 0.00045776 | 0.00078875 | 0.0017807 | 0.0 | 0.04
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Modify | 0.16952 | 0.18621 | 0.20218 | 2.8 | 9.36
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Other | | 0.1263 | | | 6.35
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Nlocal: 431 ave 479 max 377 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 99.25 ave 120 max 81 min
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Histogram: 1 1 0 0 0 0 1 0 0 1
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Neighs: 3597 ave 4064 max 3146 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 14388
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Ave neighs/atom = 8.34571
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Neighbor list builds = 717
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Dangerous builds = 0
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Total wall time: 0:00:01
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