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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -69.5553 0) to (40.1556 69.5553 6.29691) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9246 5.32089 6.29691 Created 1466 atoms create_atoms CPU = 0.000545025 secs 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9246 5.32089 6.29691 Created 1466 atoms create_atoms CPU = 0.000452042 secs 1466 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 48 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2908 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 48 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.775 | 5.775 | 5.775 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11844.751 0 -11844.751 4390.2803 95 0 -11898.944 0 -11898.944 -4082.588 Loop time of 47.9815 on 1 procs for 95 steps with 2908 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 = -11844.751079 -11898.9340843 -11898.9440253 Force two-norm initial, final = 51.5019 0.264247 Force max component initial, final = 10.7164 0.0664347 Final line search alpha, max atom move = 0.786412 0.052245 Iterations, force evaluations = 95 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 47.936 | 47.936 | 47.936 | 0.0 | 99.90 Neigh | 0.028809 | 0.028809 | 0.028809 | 0.0 | 0.06 Comm | 0.0086296 | 0.0086296 | 0.0086296 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008307 | | | 0.02 Nlocal: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9281 ave 9281 max 9281 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: 223200 ave 223200 max 223200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223200 Ave neighs/atom = 76.7538 Neighbor list builds = 5 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 : 95 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.775 | 5.775 | 5.775 Mbytes Step Temp E_pair E_mol TotEng Press Volume 95 0 -11898.944 0 -11898.944 -4082.588 35174.992 97 0 -11898.984 0 -11898.984 -1967.6288 35122.338 Loop time of 1.63389 on 1 procs for 2 steps with 2908 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11898.9440253 -11898.984181 -11898.984253 Force two-norm initial, final = 75.8612 0.280192 Force max component initial, final = 53.6963 0.0669109 Final line search alpha, max atom move = 0.000640374 4.2848e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6328 | 1.6328 | 1.6328 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002327 | 0.0002327 | 0.0002327 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008607 | | | 0.05 Nlocal: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9285 ave 9285 max 9285 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: 223252 ave 223252 max 223252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223252 Ave neighs/atom = 76.7717 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 14 48 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.913 | 5.913 | 5.913 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11898.984 0 -11898.984 -1967.6288 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2908 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: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9285 ave 9285 max 9285 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: 223280 ave 223280 max 223280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223280 Ave neighs/atom = 76.7813 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) = 5.913 | 5.913 | 5.913 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 -11898.984 -11898.984 40.123742 139.11052 6.2924824 -1967.6288 -1967.6288 -0.79345249 -5899.2198 -2.8731753 2.3620965 1155.7122 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2908 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: 2908 ave 2908 max 2908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9285 ave 9285 max 9285 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111640 ave 111640 max 111640 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223280 ave 223280 max 223280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223280 Ave neighs/atom = 76.7813 Neighbor list builds = 0 Dangerous builds = 0 2908 -10222.7218296287 eV 2.36209648514504 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:50