forked from lijiext/lammps
127 lines
4.2 KiB
Groff
127 lines
4.2 KiB
Groff
LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# 3d rounded cubes
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variable r index 3
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variable steps index 10000
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units lj
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dimension 3
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atom_style body rounded/polyhedron 1 10
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read_data data.cubes
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orthogonal box = (0 0 0) to (6 6 6)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2 atoms
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2 bodies
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replicate $r $r $r
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replicate 3 $r $r
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replicate 3 3 $r
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replicate 3 3 3
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orthogonal box = (0 0 0) to (18 18 18)
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1 by 2 by 2 MPI processor grid
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54 atoms
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Time spent = 0.000776052 secs
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velocity all create 1.2 187287 dist gaussian mom yes rot yes
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variable cut_inner equal 0.5
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variable k_n equal 100
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variable k_na equal 1
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variable c_n equal 20
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variable c_t equal 5
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variable mu equal 0
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variable A_ua equal 1
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pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
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pair_style body/rounded/polyhedron 20 ${c_t} ${mu} ${A_ua} ${cut_inner}
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pair_style body/rounded/polyhedron 20 5 ${mu} ${A_ua} ${cut_inner}
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pair_style body/rounded/polyhedron 20 5 0 ${A_ua} ${cut_inner}
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pair_style body/rounded/polyhedron 20 5 0 1 ${cut_inner}
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pair_style body/rounded/polyhedron 20 5 0 1 0.5
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pair_coeff * * ${k_n} ${k_na}
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pair_coeff * * 100 ${k_na}
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pair_coeff * * 100 1
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comm_modify vel yes
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neighbor 0.5 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.001
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#fix 1 all nve/body
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fix 1 all nvt/body temp 1.2 1.2 0.1
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#fix 1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0
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compute p2 all pressure 1_temp
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#compute 1 all body/local id 1 2 3
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#dump 1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4]
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#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 adiam 1.5 body type 0 0 view 60 15
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#dump_modify 2 pad 6
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thermo_style custom step ke pe etotal c_p2 c_1_temp
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thermo 1000
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run ${steps}
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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 = 3.9641
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ghost atom cutoff = 3.9641
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binsize = 1.98205, bins = 10 10 10
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair body/rounded/polyhedron, 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) = 4.879 | 5.068 | 5.256 Mbytes
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Step KinEng PotEng TotEng c_p2 c_1_temp
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0 1.7666667 0 1.7666667 0.01090535 0.59439252
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1000 3.1462962 0.17392649 3.3202227 0.02361912 1.1654694
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2000 2.9311648 0.13836102 3.0695258 0.021748224 1.1950624
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3000 3.090491 0.16511199 3.255603 0.018691142 1.23672
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4000 2.7401565 0.17792155 2.9180781 0.015093853 1.1180839
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5000 3.0880849 0.17587085 3.2639557 0.030563042 1.2831154
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6000 3.2180776 0.19732251 3.4154001 0.028338151 1.258839
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7000 2.9514882 0.25088882 3.202377 0.025296925 1.1746326
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8000 3.0101226 0.28825968 3.2983823 0.027273454 1.2138056
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9000 3.0164253 0.1901733 3.2065986 0.033228915 1.3095914
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10000 2.3780401 0.34082434 2.7188644 0.031838531 1.0208679
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Loop time of 25.5798 on 4 procs for 10000 steps with 54 atoms
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Performance: 33776.718 tau/day, 390.934 timesteps/s
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97.1% 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 | 9.256 | 13.423 | 24.653 | 177.1 | 52.47
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Neigh | 0.0021949 | 0.0024942 | 0.0031152 | 0.7 | 0.01
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Comm | 0.73678 | 11.948 | 16.096 | 187.4 | 46.71
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Output | 0.00023246 | 0.00041932 | 0.0009768 | 0.0 | 0.00
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Modify | 0.12505 | 0.15661 | 0.18165 | 6.0 | 0.61
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Other | | 0.04968 | | | 0.19
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Nlocal: 13.5 ave 17 max 9 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Nghost: 63.5 ave 68 max 58 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Neighs: 25 ave 38 max 6 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Total # of neighbors = 100
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Ave neighs/atom = 1.85185
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Neighbor list builds = 268
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Dangerous builds = 0
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Total wall time: 0:00:25
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