forked from lijiext/lammps
148 lines
7.3 KiB
Groff
148 lines
7.3 KiB
Groff
LAMMPS (4 May 2022)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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units real
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atom_style hybrid sphere bond
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WARNING: Atom style hybrid defines both, per-type and per-atom masses; both must be set, but only per-atom masses will be used (src/atom_vec_hybrid.cpp:130)
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lattice sc 5.0
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Lattice spacing in x,y,z = 5 5 5
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region box block 50 250 50 250 50 250 units box
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create_box 2 box
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Created orthogonal box = (50 50 50) to (250 250 250)
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1 by 2 by 2 MPI processor grid
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region particles block 110 190 110 190 110 190 units box
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create_atoms 1 region particles
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Created 4913 atoms
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using lattice units in orthogonal box = (50 50 50) to (250 250 250)
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create_atoms CPU = 0.001 seconds
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region lid block 100 110 50 250 50 250 units box
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group mobile type 1
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4913 atoms in group mobile
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set type 1 diameter 7.0
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Setting atom values ...
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4913 settings made for diameter
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# create_atoms 2 mesh open_box.stl meshmode bisect 4.0 units box
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create_atoms 2 mesh open_box.stl meshmode qrand 0.1 units box
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Reading STL object Open Box from file open_box.stl
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read 10 triangles with 2000.00 atoms per triangle added in quasi-random mode
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Created 5000 atoms
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using box units in orthogonal box = (50 50 50) to (250 250 250)
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create_atoms CPU = 0.001 seconds
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group mesh type 2
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5000 atoms in group mesh
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pair_style lj/cut 8.76
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pair_coeff 1 1 0.2339 3.504
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pair_coeff 1 2 0.2339 7.008 $(7.008*2^(1.0/6.0))
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pair_coeff 1 2 0.2339 7.008 7.8662140345520858986
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pair_coeff 2 2 0.0 1.0
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mass * 39.95
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neigh_modify exclude type 2 2
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timestep 1.0
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run 0 post no
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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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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 = 10.76
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ghost atom cutoff = 10.76
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binsize = 5.38, bins = 38 38 38
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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/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.455 | 5.474 | 5.491 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 -1778.6527 0 -1778.6527 -27.271044
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Loop time of 2.8725e-06 on 4 procs for 0 steps with 9913 atoms
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fix dir mobile oneway 10 lid x
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fix move mobile nve
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fix load all balance 1000 1.1 shift xyz 10 1.01 weight neigh 0.5 weight group 2 mesh 0.1 mobile 1.0
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fix rot mesh move rotate 150.0 150.0 150.0 1.0 0.0 0.0 500000.0 units box
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reset_timestep 0 time 0.0
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velocity mobile create 150.0 54634234
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compute ptemp mobile temp
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thermo_modify temp ptemp
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WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:520)
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thermo 200
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compute ke all ke/atom
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#dump 2 all movie 200 mesh.mkv c_ke radius size 960 1440 zoom 1.5 box no 0.0 view 120 180
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#dump_modify 2 bitrate 4000 framerate 12 color orange 1.0 0.5 0.0 amap min max cf 0.0 6 min blue 0.1 fuchsia 0.2 red 0.4 orange 0.6 yellow max white
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#dump 1 all custom 500 open_box.lammpstrj id type mol x y z vx vy vz
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run 5000
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 6.011 | 6.046 | 6.072 Mbytes
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Step Temp E_pair E_mol TotEng Press Volume
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0 150 -1778.6527 0 417.60814 -14.721534 8000000
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200 178.90737 -2298.4303 0 321.08483 15.681113 8000000
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400 182.18748 -2339.8994 0 327.64208 13.983929 8000000
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600 182.78421 -2363.0316 0 313.24702 15.533691 8000000
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800 185.27077 -2397.561 0 315.12532 14.162041 8000000
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1000 185.59249 -2394.3379 0 323.05898 14.45888 8000000
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1200 184.9041 -2365.2474 0 342.07022 14.281891 8000000
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1400 186.59058 -2397.5471 0 334.46342 15.095686 8000000
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1600 184.44411 -2386.6701 0 313.91242 16.825132 8000000
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1800 188.29985 -2432.366 0 324.6713 15.109591 8000000
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2000 187.05565 -2423.8405 0 314.97946 15.67693 8000000
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2200 187.02332 -2411.5557 0 326.79085 14.702305 8000000
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2400 185.67262 -2386.3932 0 332.17677 15.796702 8000000
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2600 185.97931 -2411.0423 0 312.01823 16.15444 8000000
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2800 187.2186 -2403.7584 0 337.44748 15.197009 8000000
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3000 185.18778 -2388.9601 0 322.51107 16.289848 8000000
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3200 186.38078 -2396.9152 0 332.02344 15.860688 8000000
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3400 184.95984 -2386.3632 0 321.77041 16.513329 8000000
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3600 187.94957 -2408.3205 0 343.58806 13.931044 8000000
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3800 187.1454 -2413.0585 0 327.07559 14.801401 8000000
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4000 186.12517 -2394.4218 0 330.77436 14.257144 8000000
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4200 186.91955 -2407.2113 0 329.61591 14.869086 8000000
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4400 184.72142 -2382.9411 0 321.70176 15.898793 8000000
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4600 186.8458 -2408.8059 0 326.94154 14.766765 8000000
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4800 187.28977 -2397.6811 0 344.56676 15.301534 8000000
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5000 185.17839 -2378.709 0 332.62466 16.043707 8000000
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Loop time of 3.41925 on 4 procs for 5000 steps with 9913 atoms
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Performance: 126.344 ns/day, 0.190 hours/ns, 1462.309 timesteps/s
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99.3% 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 | 1.011 | 1.4158 | 1.8652 | 31.9 | 41.41
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Bond | 0.00026998 | 0.00029559 | 0.00031513 | 0.0 | 0.01
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Neigh | 0.60535 | 0.82114 | 1.0415 | 21.6 | 24.02
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Comm | 0.19046 | 0.88593 | 1.5316 | 63.7 | 25.91
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Output | 0.00067893 | 0.00085803 | 0.001033 | 0.0 | 0.03
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Modify | 0.20164 | 0.23804 | 0.27649 | 6.5 | 6.96
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Other | | 0.05722 | | | 1.67
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Nlocal: 2478.25 ave 2954 max 2037 min
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Histogram: 1 1 0 0 0 0 0 0 1 1
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Nghost: 1043.25 ave 1146 max 940 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 24605.8 ave 32065 max 17721 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Total # of neighbors = 98423
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Ave neighs/atom = 9.9286795
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Ave special neighs/atom = 0
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Neighbor list builds = 371
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Dangerous builds = 0
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Total wall time: 0:00:03
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