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 1 by 1 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 500.00 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) = 5.64 | 5.64 | 5.64 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 1.514e-06 on 1 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) = 6.155 | 6.155 | 6.155 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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200 179.67539 -2344.2923 0 286.46789 14.546173 8000000
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400 181.6261 -2331.1731 0 328.14895 15.522647 8000000
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600 183.6116 -2362.5284 0 325.86464 14.828678 8000000
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800 187.69451 -2422.3021 0 325.87189 14.99914 8000000
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1000 186.32256 -2393.187 0 334.89931 14.49224 8000000
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1200 186.57797 -2406.6141 0 325.21184 15.514285 8000000
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1400 188.39717 -2403.2075 0 355.25478 14.282381 8000000
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1600 185.774 -2391.15 0 328.90446 16.025507 8000000
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1800 186.95292 -2423.2897 0 314.02613 15.51055 8000000
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2000 186.0637 -2414.6095 0 309.68668 14.894421 8000000
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2200 187.03262 -2409.2253 0 329.25754 14.90094 8000000
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2400 186.66862 -2409.987 0 323.16626 15.497536 8000000
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2600 184.98646 -2386.3118 0 322.21161 14.935837 8000000
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2800 185.83051 -2392.5258 0 328.35604 14.863905 8000000
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3000 184.68382 -2397.8429 0 306.24943 15.696458 8000000
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3200 187.56974 -2409.8941 0 336.45315 14.352166 8000000
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3400 187.5721 -2425.0188 0 321.36292 14.7297 8000000
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3600 185.97304 -2391.4399 0 331.52886 15.586758 8000000
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3800 185.40034 -2401.6336 0 312.94973 15.742308 8000000
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4000 187.71377 -2409.3588 0 339.09729 15.102297 8000000
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4200 186.4676 -2394.1921 0 336.01789 15.312368 8000000
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4400 186.98262 -2396.3842 0 341.36649 14.764489 8000000
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4600 185.98808 -2397.7342 0 325.45468 15.379472 8000000
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4800 187.6927 -2422.0727 0 326.07474 14.252141 8000000
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5000 188.21075 -2428.1325 0 327.60023 14.694135 8000000
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Loop time of 9.49245 on 1 procs for 5000 steps with 9913 atoms
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Performance: 45.510 ns/day, 0.527 hours/ns, 526.734 timesteps/s
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99.8% CPU use with 1 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 | 5.3698 | 5.3698 | 5.3698 | 0.0 | 56.57
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Bond | 0.00036337 | 0.00036337 | 0.00036337 | 0.0 | 0.00
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Neigh | 3.0911 | 3.0911 | 3.0911 | 0.0 | 32.56
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Comm | 0.039329 | 0.039329 | 0.039329 | 0.0 | 0.41
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Output | 0.0010197 | 0.0010197 | 0.0010197 | 0.0 | 0.01
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Modify | 0.86293 | 0.86293 | 0.86293 | 0.0 | 9.09
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Other | | 0.1279 | | | 1.35
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Nlocal: 9913 ave 9913 max 9913 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 97756 ave 97756 max 97756 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 97756
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Ave neighs/atom = 9.8613941
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Ave special neighs/atom = 0
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Neighbor list builds = 375
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Dangerous builds = 1
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Total wall time: 0:00:09
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