LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.5226425 3.5226425 3.5226425 Created orthogonal box = (0.0000000 -35.924046 0.0000000) to (31.111136 35.924046 6.1013958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5840501 5.5267762 6.1013958 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -35.924046 0.0000000) to (31.111136 35.924046 6.1013958) create_atoms CPU = 0.001 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5840501 5.5267762 6.1013958 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -35.924046 0.0000000) to (31.111136 35.924046 6.1013958) create_atoms CPU = 0.001 seconds 630 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 6 13 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1254 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_381861218831_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 6 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 7.905 | 7.905 | 7.905 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4530.725 0 -4530.725 114302.74 72 0 -5269.1114 0 -5269.1114 20051.635 Loop time of 4.47377 on 1 procs for 72 steps with 1254 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4530.72502588246 -5269.10663226537 -5269.11141129493 Force two-norm initial, final = 760.60136 0.32165530 Force max component initial, final = 139.15815 0.059601245 Final line search alpha, max atom move = 0.87642817 0.052236210 Iterations, force evaluations = 72 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3244 | 4.3244 | 4.3244 | 0.0 | 96.66 Neigh | 0.11863 | 0.11863 | 0.11863 | 0.0 | 2.65 Comm | 0.018933 | 0.018933 | 0.018933 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0118 | | | 0.26 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13333.0 ave 13333 max 13333 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 782012.0 ave 782012 max 782012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 782012 Ave neighs/atom = 623.61404 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 6 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.523 | 7.523 | 7.523 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -5269.1114 0 -5269.1114 20051.635 13638.302 83 0 -5270.6955 0 -5270.6955 -66.421841 13783.873 Loop time of 0.502505 on 1 procs for 11 steps with 1254 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5269.11141129492 -5270.69534801292 -5270.6955123018 Force two-norm initial, final = 347.22148 1.4048582 Force max component initial, final = 313.66459 0.68962607 Final line search alpha, max atom move = 0.00038904249 0.00026829384 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4941 | 0.4941 | 0.4941 | 0.0 | 98.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014287 | 0.0014287 | 0.0014287 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006973 | | | 1.39 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13369.0 ave 13369 max 13369 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 782548.0 ave 782548 max 782548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 782548 Ave neighs/atom = 624.04147 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 6 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.661 | 7.661 | 7.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5270.6955 0 -5270.6955 -66.421841 Loop time of 2.55e-06 on 1 procs for 0 steps with 1254 atoms 156.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.55e-06 | | |100.00 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13264.0 ave 13264 max 13264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 779000.0 ave 779000 max 779000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 779000 Ave neighs/atom = 621.21212 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.75476 ghost atom cutoff = 11.75476 binsize = 5.87738, bins = 6 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.75476 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 7.661 | 7.661 | 7.661 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -5270.6955 -5270.6955 31.147016 72.554366 6.0994582 -66.421841 -66.421841 -80.251534 -78.261704 -40.752286 2.2294161 941.84988 Loop time of 2.705e-06 on 1 procs for 0 steps with 1254 atoms 258.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.705e-06 | | |100.00 Nlocal: 1254.00 ave 1254 max 1254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13264.0 ave 13264 max 13264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 389500.0 ave 389500 max 389500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 779000.0 ave 779000 max 779000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 779000 Ave neighs/atom = 621.21212 Neighbor list builds = 0 Dangerous builds = 0 1254 -5270.6955123018 eV 2.22941614587788 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05