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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -29.458521 0.0000000) to (25.511828 29.458521 5.0032811) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5790460 4.5320802 5.0032811 Created 310 atoms using lattice units in orthogonal box = (0.0000000 -29.458521 0.0000000) to (25.511828 29.458521 5.0032811) create_atoms CPU = 0.002 seconds 310 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5790460 4.5320802 5.0032811 Created 317 atoms using lattice units in orthogonal box = (0.0000000 -29.458521 0.0000000) to (25.511828 29.458521 5.0032811) create_atoms CPU = 0.002 seconds 317 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 23 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 627 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_608695023236_000#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.864 | 4.864 | 4.864 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2335.5077 0 -2335.5077 109333.25 54 0 -2598.2291 0 -2598.2291 14911.753 Loop time of 10.5375 on 1 procs for 54 steps with 627 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 = -2335.50766135151 -2598.22748786365 -2598.22910992722 Force two-norm initial, final = 440.42438 0.16120259 Force max component initial, final = 223.00450 0.044540543 Final line search alpha, max atom move = 0.88354992 0.039353793 Iterations, force evaluations = 54 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.499 | 10.499 | 10.499 | 0.0 | 99.64 Neigh | 0.02396 | 0.02396 | 0.02396 | 0.0 | 0.23 Comm | 0.0065014 | 0.0065014 | 0.0065014 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007961 | | | 0.08 Nlocal: 627.000 ave 627 max 627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2666.00 ave 2666 max 2666 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: 36012.0 ave 36012 max 36012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36012 Ave neighs/atom = 57.435407 Neighbor list builds = 1 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.864 | 4.864 | 4.864 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -2598.2291 0 -2598.2291 14911.753 7520.339 63 0 -2598.7476 0 -2598.7476 -120.75635 7580.0207 Loop time of 1.20451 on 1 procs for 9 steps with 627 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 = -2598.22910992722 -2598.74727668907 -2598.74762625041 Force two-norm initial, final = 141.21555 1.3608465 Force max component initial, final = 129.12019 0.64439945 Final line search alpha, max atom move = 0.00048790808 0.00031440770 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.201 | 1.201 | 1.201 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064396 | 0.00064396 | 0.00064396 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002888 | | | 0.24 Nlocal: 627.000 ave 627 max 627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 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: 36036.0 ave 36036 max 36036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 36036 Ave neighs/atom = 57.473684 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.002 | 5.002 | 5.002 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2598.7476 0 -2598.7476 -120.75635 Loop time of 6.696e-06 on 1 procs for 0 steps with 627 atoms 194.1% 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 | | 6.696e-06 | | |100.00 Nlocal: 627.000 ave 627 max 627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 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: 35986.0 ave 35986 max 35986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35986 Ave neighs/atom = 57.393939 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.002 | 5.002 | 5.002 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 -2598.7476 -2598.7476 25.499528 59.400899 5.0043219 -120.75635 -120.75635 -104.23881 -137.32424 -120.70599 2.309119 691.61364 Loop time of 6.405e-06 on 1 procs for 0 steps with 627 atoms 265.4% 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 | | 6.405e-06 | | |100.00 Nlocal: 627.000 ave 627 max 627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17993.0 ave 17993 max 17993 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35986.0 ave 35986 max 35986 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35986 Ave neighs/atom = 57.393939 Neighbor list builds = 0 Dangerous builds = 0 627 -2598.74762625041 eV 2.30911904611236 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12