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 = 0.000388622 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 5 2.5 INF INF #delete_atoms region void # 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) = 3.371 | 3.371 | 3.371 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -8317.4367 0 -8263.8067 -7100.7667 19547.02 25 219.81848 -8272.1577 0 -8232.8615 5206.8057 19547.02 50 300 -8238.3413 0 -8184.7112 13308.809 19688.933 75 294.78636 -8232.2217 0 -8179.5237 13192.782 19748.176 100 300 -8248.1223 0 -8194.4923 7352.0246 19816.321 Loop time of 0.0884107 on 4 procs for 100 steps with 1912 atoms Performance: 97.726 ns/day, 0.246 hours/ns, 1131.084 timesteps/s 94.9% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072181 | 0.073453 | 0.074266 | 0.3 | 83.08 Neigh | 0.0026526 | 0.0028275 | 0.0029895 | 0.2 | 3.20 Comm | 0.0081384 | 0.0091963 | 0.0099204 | 0.7 | 10.40 Output | 9.8705e-05 | 0.00012231 | 0.00018597 | 0.0 | 0.14 Modify | 0.00092363 | 0.00094259 | 0.00096059 | 0.0 | 1.07 Other | | 0.001869 | | | 2.11 Nlocal: 478 ave 490 max 466 min Histogram: 1 0 1 0 0 0 0 1 0 1 Nghost: 1036.25 ave 1046 max 1027 min Histogram: 1 1 0 0 0 0 0 1 0 1 Neighs: 11488 ave 11948 max 11157 min Histogram: 1 0 1 0 1 0 0 0 0 1 Total # of neighbors = 45952 Ave neighs/atom = 24.0335 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 #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) = 3.371 | 3.371 | 3.371 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 302.29407 -8248.1223 0 -8212.0956 6393.6774 19845.81 100 291.61298 -8259.5472 0 -8224.7933 -1300.9229 19874.36 200 293.36405 -8256.9998 0 -8222.0373 -799.49219 19965.148 300 305.94188 -8252.9181 0 -8216.4566 -1335.0012 20062.063 400 309.95918 -8247.5756 0 -8210.6354 -1062.2448 20094.446 500 301.94062 -8239.3596 0 -8203.375 797.08496 20172.635 600 302.21507 -8230.7027 0 -8194.6854 3987.1988 20265.23 700 296.32595 -8221.2036 0 -8185.8881 5409.7911 20394.703 800 291.23487 -8207.8671 0 -8173.1583 10667.09 20510.74 900 297.88948 -8196.1164 0 -8160.6146 13967.96 20646.32 1000 301.54921 -8182.0007 0 -8146.0627 17939.885 20752.586 1100 308.95153 -8164.9247 0 -8128.1046 22823.971 20889.388 1200 301.95399 -8153.476 0 -8117.4898 25618.698 21000.539 1300 300 -8143.3818 0 -8107.6284 26668.263 21122.684 1400 300 -8136.2928 0 -8100.5395 26328.325 21252.157 1500 300 -8132.5465 0 -8096.7931 23584.447 21379.187 1600 300 -8129.9298 0 -8094.1764 20684.486 21497.667 1700 300 -8131.655 0 -8095.9016 15384.272 21617.369 1800 300 -8149.3135 0 -8113.5601 9698.7054 21738.292 1900 300 -8156.1776 0 -8120.4243 9887.2669 21861.658 2000 300 -8161.9857 0 -8126.2324 8382.4517 21988.688 2100 300 -8163.9644 0 -8128.211 5288.1872 22107.168 2200 309.9432 -8171.1806 0 -8134.2422 331.97612 22234.198 2300 300 -8173.679 0 -8137.9256 -2756.1784 22346.571 2400 300 -8183.2429 0 -8147.4895 -6494.1612 22472.38 2500 309.13407 -8186.7918 0 -8149.9499 -8827.4368 22599.41 2600 299.71761 -8177.7445 0 -8142.0248 -7906.1647 22721.555 2700 300 -8174.4672 0 -8138.7138 -8920.5441 22832.706 2800 306.09492 -8173.4147 0 -8136.935 -10981.226 22960.958 2900 303.27397 -8168.2141 0 -8132.0706 -8905.5017 23078.216 3000 301.48023 -8165.8151 0 -8129.8854 -10668.385 23201.582 Loop time of 2.66845 on 4 procs for 3000 steps with 1912 atoms Performance: 97.135 ns/day, 0.247 hours/ns, 1124.248 timesteps/s 96.3% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1584 | 2.2278 | 2.3244 | 4.0 | 83.49 Neigh | 0.14134 | 0.15172 | 0.1614 | 2.0 | 5.69 Comm | 0.11957 | 0.22852 | 0.30416 | 14.2 | 8.56 Output | 0.00077462 | 0.0013641 | 0.0031083 | 2.7 | 0.05 Modify | 0.028383 | 0.029401 | 0.030651 | 0.5 | 1.10 Other | | 0.02965 | | | 1.11 Nlocal: 478 ave 509 max 446 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 1009.5 ave 1054 max 963 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 11210.5 ave 12215 max 10197 min Histogram: 1 0 1 0 0 0 0 1 0 1 Total # of neighbors = 44842 Ave neighs/atom = 23.4529 Neighbor list builds = 225 Dangerous builds = 0 Total wall time: 0:00:02