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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -38.133706 0.0000000) to (12.711235 38.133706 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7385986 3.7385986 3.0829274 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -38.133706 0.0000000) to (12.711235 38.133706 3.0829274) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7385986 3.7385986 3.0829274 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -38.133706 0.0000000) to (12.711235 38.133706 3.0829274) create_atoms CPU = 0.000 seconds 103 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 1 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 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 205 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.783 | 4.783 | 4.783 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1117.9063 0 -1117.9063 214382.28 58 0 -1328.156 0 -1328.156 21524.342 Loop time of 5.8712 on 1 procs for 58 steps with 205 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 = -1117.90633634741 -1328.15471812781 -1328.15600229049 Force two-norm initial, final = 1037.4397 0.16767312 Force max component initial, final = 702.67211 0.043605814 Final line search alpha, max atom move = 1.0000000 0.043605814 Iterations, force evaluations = 58 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8665 | 5.8665 | 5.8665 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024524 | 0.0024524 | 0.0024524 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00222 | | | 0.04 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2230.00 ave 2230 max 2230 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: 13610.0 ave 13610 max 13610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13610 Ave neighs/atom = 66.390244 Neighbor list builds = 0 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.783 | 4.783 | 4.783 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -1328.156 0 -1328.156 21524.342 2988.7532 86 0 -1328.8298 0 -1328.8298 710.42278 3013.416 Loop time of 1.70107 on 1 procs for 28 steps with 205 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 = -1328.15600229049 -1328.82934988455 -1328.82981040959 Force two-norm initial, final = 82.396846 2.6756492 Force max component initial, final = 76.095149 1.6070176 Final line search alpha, max atom move = 0.00077077973 0.0012386566 Iterations, force evaluations = 28 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6861 | 1.6861 | 1.6861 | 0.0 | 99.12 Neigh | 0.011667 | 0.011667 | 0.011667 | 0.0 | 0.69 Comm | 0.00059751 | 0.00059751 | 0.00059751 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002755 | | | 0.16 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2255.00 ave 2255 max 2255 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: 15552.0 ave 15552 max 15552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15552 Ave neighs/atom = 75.863415 Neighbor list builds = 1 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.921 | 4.921 | 4.921 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1328.8298 0 -1328.8298 710.42278 Loop time of 1.602e-06 on 1 procs for 0 steps with 205 atoms 124.8% 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 | | 1.602e-06 | | |100.00 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2255.00 ave 2255 max 2255 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: 15466.0 ave 15466 max 15466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15466 Ave neighs/atom = 75.443902 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 4 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 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) = 4.921 | 4.921 | 4.921 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 -1328.8298 -1328.8298 12.737529 77.982106 3.0337441 710.42278 710.42278 856.18837 854.23295 420.84703 2.5891209 305.73634 Loop time of 1.494e-06 on 1 procs for 0 steps with 205 atoms 133.9% 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 | | 1.494e-06 | | |100.00 Nlocal: 205.000 ave 205 max 205 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2255.00 ave 2255 max 2255 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7733.00 ave 7733 max 7733 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15466.0 ave 15466 max 15466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15466 Ave neighs/atom = 75.443902 Neighbor list builds = 0 Dangerous builds = 0 205 -1328.82981040959 eV 2.58912091293771 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07