LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal boundary s s p atom_style atomic lattice fcc 3.52 Lattice spacing in x,y,z = 3.52 3.52 3.52 region box block 0 16.0 0 10.0 0 2.828427 create_box 3 box Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) 2 by 2 by 1 MPI processor grid lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 Lattice spacing in x,y,z = 3.52 4.97803 4.97803 create_atoms 1 box Created 1912 atoms Time spent = 0.000400543 secs pair_style eam pair_coeff * * Ni_u3.eam Reading potential file Ni_u3.eam with DATE: 2007-06-11 neighbor 0.3 bin neigh_modify delay 5 region lower block INF INF INF 0.9 INF INF region upper block INF INF 6.1 INF INF INF group lower region lower 264 atoms in group lower group upper region upper 264 atoms in group upper group boundary union lower upper 528 atoms in group boundary group mobile subtract all boundary 1384 atoms in group mobile set group lower type 2 264 settings made for type set group upper type 3 264 settings made for type # void region void cylinder z 8 3.535534 2.5 INF INF delete_atoms region void Deleted 204 atoms, new total = 1708 # temp controllers compute new3d mobile temp compute new2d mobile temp/partial 0 1 1 # equilibrate velocity mobile create 300.0 5812775 temp new3d fix 1 all nve fix 2 boundary setforce 0.0 0.0 0.0 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) timestep 0.001 run 100 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.1 ghost atom cutoff = 5.1 binsize = 2.55, bins = 23 14 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair eam, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 3.356 | 3.356 | 3.356 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -7358.6159 0 -7312.8966 -9600.8353 19547.02 25 220.57465 -7320.4003 0 -7286.7852 832.69858 19547.02 50 300 -7292.1121 0 -7246.3928 7101.9213 19686.075 75 295.2793 -7286.9013 0 -7241.9014 5282.1114 19746.39 100 300 -7301.0026 0 -7255.2833 -1939.7714 19790.975 Loop time of 0.0688287 on 4 procs for 100 steps with 1708 atoms Performance: 125.529 ns/day, 0.191 hours/ns, 1452.882 timesteps/s 96.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059247 | 0.060771 | 0.062449 | 0.5 | 88.29 Neigh | 0.0022693 | 0.0023552 | 0.0024772 | 0.2 | 3.42 Comm | 0.0018966 | 0.0037905 | 0.005276 | 2.1 | 5.51 Output | 8.297e-05 | 0.00011259 | 0.00019741 | 0.0 | 0.16 Modify | 0.00082994 | 0.00084907 | 0.00086927 | 0.0 | 1.23 Other | | 0.0009506 | | | 1.38 Nlocal: 427 ave 437 max 419 min Histogram: 1 1 0 0 0 0 1 0 0 1 Nghost: 780 ave 788 max 774 min Histogram: 1 1 0 0 0 1 0 0 0 1 Neighs: 9859.75 ave 10248 max 9544 min Histogram: 1 0 1 0 0 1 0 0 0 1 Total # of neighbors = 39439 Ave neighs/atom = 23.0907 Neighbor list builds = 4 Dangerous builds = 0 # shear velocity upper set 1.0 0 0 velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes unfix 3 fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 fix_modify 3 temp new2d #dump 1 all atom 100 dump.shear.void #dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 #dump_modify 2 pad 4 #dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 #dump_modify 3 pad 4 thermo 100 thermo_modify temp new2d WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:488) reset_timestep 0 run 3000 Per MPI rank memory allocation (min/avg/max) = 3.356 | 3.356 | 3.356 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 298.93143 -7301.0026 0 -7270.6316 -2766.8643 19799.958 100 301.13545 -7308.1131 0 -7277.5182 -8902.3332 19851.054 200 296.29577 -7306.2042 0 -7276.101 -9974.9354 19977.713 300 301.05914 -7303.6788 0 -7273.0916 -9862.4944 20024.1 400 303.0153 -7299.731 0 -7268.9451 -7947.0168 20095.075 500 298.65447 -7297.2717 0 -7266.9288 -5763.5283 20168.398 600 296.11526 -7292.6719 0 -7262.5871 -1784.5157 20265.23 700 305.84406 -7287.3611 0 -7256.2878 -1047.7333 20413.775 800 297.24737 -7280.1938 0 -7249.9939 -1482.5729 20516.847 900 305.15166 -7272.5442 0 -7241.5412 -806.41836 20629.22 1000 303.27519 -7264.3603 0 -7233.548 -2138.7382 20763.579 1100 297.64923 -7258.2644 0 -7228.0237 -768.39318 20890.609 1200 309.57038 -7254.7251 0 -7223.2732 826.2357 20995.654 1300 300 -7251.8391 0 -7221.3595 -1913.381 21121.462 1400 300 -7258.6892 0 -7228.2096 -5149.1767 21253.378 1500 304.55119 -7269.4714 0 -7238.5294 -8459.0382 21376.744 1600 302.21492 -7270.4103 0 -7239.7057 -10281.182 21489.117 1700 300 -7273.5589 0 -7243.0794 -11327.559 21616.147 1800 306.43021 -7269.3385 0 -7238.2057 -14197.412 21741.956 1900 306.23041 -7271.5332 0 -7240.4207 -19223.302 21854.329 2000 302.23263 -7267.091 0 -7236.3847 -20191.798 21975.252 2100 308.71627 -7268.4269 0 -7237.0618 -25282.39 22097.397 2200 306.77342 -7266.6664 0 -7235.4987 -27060.48 22230.534 2300 300 -7262.0978 0 -7231.6182 -24060.909 22351.457 2400 300 -7261.4125 0 -7230.9329 -20517.199 22462.608 2500 300.21813 -7260.6381 0 -7230.1364 -15407.463 22589.639 2600 296.24006 -7257.2142 0 -7227.1167 -13436.36 22711.783 2700 300 -7256.4647 0 -7225.9852 -15922.92 22830.263 2800 298.94765 -7255.6331 0 -7225.2605 -20555.015 22959.736 2900 294.98551 -7249.0201 0 -7219.05 -23986.374 23079.438 3000 291.21483 -7244.1837 0 -7214.5967 -25356.925 23197.918 Loop time of 2.21357 on 4 procs for 3000 steps with 1708 atoms Performance: 117.096 ns/day, 0.205 hours/ns, 1355.278 timesteps/s 96.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8072 | 1.86 | 1.9192 | 3.7 | 84.03 Neigh | 0.11667 | 0.12264 | 0.13213 | 1.7 | 5.54 Comm | 0.10804 | 0.17878 | 0.23557 | 13.3 | 8.08 Output | 0.00073075 | 0.0012527 | 0.002811 | 2.5 | 0.06 Modify | 0.024781 | 0.025831 | 0.02754 | 0.7 | 1.17 Other | | 0.02508 | | | 1.13 Nlocal: 427 ave 450 max 403 min Histogram: 1 1 0 0 0 0 0 0 1 1 Nghost: 785.25 ave 844 max 723 min Histogram: 1 0 1 0 0 0 0 0 1 1 Neighs: 9581.25 ave 10185 max 9102 min Histogram: 2 0 0 0 0 0 0 1 0 1 Total # of neighbors = 38325 Ave neighs/atom = 22.4385 Neighbor list builds = 215 Dangerous builds = 0 Total wall time: 0:00:02