LAMMPS (24 Dec 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -33.885977 0.0000000) to (41.498170 33.885977 7.0144709) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7426480 4.3564003 4.6763139 Created 841 atoms create_atoms CPU = 0.002 seconds 841 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7426480 4.3564003 4.6763139 Created 841 atoms create_atoms CPU = 0.002 seconds 841 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 20 3 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 19 atoms, new total = 1663 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.135 | 5.135 | 5.135 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6963.6682 0 -6963.6682 17872.597 87 0 -7091.9503 0 -7091.9503 -7545.0185 Loop time of 12.3109 on 1 procs for 87 steps with 1663 atoms 89.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6963.66822454059 -7091.9443627811 -7091.95032771392 Force two-norm initial, final = 136.10108 0.25586409 Force max component initial, final = 20.442496 0.094164721 Final line search alpha, max atom move = 0.63438697 0.059736872 Iterations, force evaluations = 87 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.288 | 12.288 | 12.288 | 0.0 | 99.81 Neigh | 0.011069 | 0.011069 | 0.011069 | 0.0 | 0.09 Comm | 0.0059911 | 0.0059911 | 0.0059911 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0061 | | | 0.05 Nlocal: 1663.00 ave 1663 max 1663 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6288.00 ave 6288 max 6288 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: 185188.0 ave 185188 max 185188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185188 Ave neighs/atom = 111.35779 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.135 | 5.135 | 5.135 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -7091.9503 0 -7091.9503 -7545.0185 19727.583 90 0 -7092.127 0 -7092.127 -1200.825 19653.583 Loop time of 0.472445 on 1 procs for 3 steps with 1663 atoms 78.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7091.95032771391 -7092.12183699426 -7092.12701569803 Force two-norm initial, final = 128.71560 5.9445191 Force max component initial, final = 107.60793 5.9059470 Final line search alpha, max atom move = 4.9699228e-05 0.00029352101 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4716 | 0.4716 | 0.4716 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001707 | 0.0001707 | 0.0001707 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006701 | | | 0.14 Nlocal: 1663.00 ave 1663 max 1663 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6229.00 ave 6229 max 6229 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: 185170.0 ave 185170 max 185170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185170 Ave neighs/atom = 111.34696 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.273 | 5.273 | 5.273 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7092.127 0 -7092.127 -1200.825 Loop time of 2.0999e-06 on 1 procs for 0 steps with 1663 atoms 142.9% 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 | | 2.1e-06 | | |100.00 Nlocal: 1663.00 ave 1663 max 1663 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6242.00 ave 6242 max 6242 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: 185272.0 ave 185272 max 185272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185272 Ave neighs/atom = 111.40830 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.273 | 5.273 | 5.273 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 -7092.127 -7092.127 41.446469 67.771954 6.9968761 -1200.825 -1200.825 480.85792 -4033.1263 -50.206723 2.2796524 1634.8999 Loop time of 2.30002e-06 on 1 procs for 0 steps with 1663 atoms 173.9% 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 | | 2.3e-06 | | |100.00 Nlocal: 1663.00 ave 1663 max 1663 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6242.00 ave 6242 max 6242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92636.0 ave 92636 max 92636 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 185272.0 ave 185272 max 185272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185272 Ave neighs/atom = 111.40830 Neighbor list builds = 0 Dangerous builds = 0 1663 -7092.12701569803 eV 2.2796524214338 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13