LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.51623 3.51623 3.51623 Created orthogonal box = (0 -60.4991 0) to (30.2478 60.4991 3.51623) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.90505 4.90505 3.51623 Created 594 atoms create_atoms CPU = 0.00031805 secs 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.90505 4.90505 3.51623 Created 594 atoms create_atoms CPU = 0.000200987 secs 594 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 28 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, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1178 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.514 | 5.514 | 5.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5664.735 0 -5664.735 29584.312 88 0 -5728.8582 0 -5728.8582 -3337.7971 Loop time of 1.25897 on 1 procs for 88 steps with 1178 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5664.73501093 -5728.85310307 -5728.85816125 Force two-norm initial, final = 83.2566 0.272105 Force max component initial, final = 29.1128 0.0433751 Final line search alpha, max atom move = 1 0.0433751 Iterations, force evaluations = 88 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2241 | 1.2241 | 1.2241 | 0.0 | 97.23 Neigh | 0.017878 | 0.017878 | 0.017878 | 0.0 | 1.42 Comm | 0.011858 | 0.011858 | 0.011858 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005098 | | | 0.40 Nlocal: 1178 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12741 ave 12741 max 12741 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 297888 ave 297888 max 297888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 297888 Ave neighs/atom = 252.876 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.895 | 5.895 | 5.895 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -5728.8582 0 -5728.8582 -3337.7971 12869.148 91 0 -5728.8853 0 -5728.8853 -1357.349 12854.915 Loop time of 0.0575371 on 1 procs for 3 steps with 1178 atoms 104.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5728.85816125 -5728.88522811 -5728.88525299 Force two-norm initial, final = 36.1128 0.28781 Force max component initial, final = 34.8181 0.0565958 Final line search alpha, max atom move = 0.00107922 6.10795e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055782 | 0.055782 | 0.055782 | 0.0 | 96.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046945 | 0.00046945 | 0.00046945 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001285 | | | 2.23 Nlocal: 1178 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12768 ave 12768 max 12768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 295888 ave 295888 max 295888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295888 Ave neighs/atom = 251.178 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 6.034 | 6.034 | 6.034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5728.8853 0 -5728.8853 -1357.349 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1178 atoms 0.0% 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 | | 2.146e-06 | | |100.00 Nlocal: 1178 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12786 ave 12786 max 12786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 296124 ave 296124 max 296124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296124 Ave neighs/atom = 251.379 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) = 6.034 | 6.034 | 6.034 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 -5728.8853 -5728.8853 30.195842 120.99815 3.518385 -1357.349 -1357.349 -7.0417278 -4059.3387 -5.6666513 2.2238986 295.77882 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1178 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 1178 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12786 ave 12786 max 12786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 148062 ave 148062 max 148062 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 296124 ave 296124 max 296124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296124 Ave neighs/atom = 251.379 Neighbor list builds = 0 Dangerous builds = 0 1178 -5728.88525298932 eV 2.22389858692654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01