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 = 4.08165 4.08165 4.08165 Created orthogonal box = (0 -70.7004 0) to (28.8617 70.7004 9.99797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9268 6.12702 6.66531 Created 1203 atoms create_atoms CPU = 0.00068903 secs 1203 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9268 6.12702 6.66531 Created 1203 atoms create_atoms CPU = 0.000528097 secs 1203 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 24 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, cut 12.1025 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 2384 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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) = 12.87 | 12.87 | 12.87 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8508.3598 0 -8508.3598 -113.23184 20 0 -8523.2927 0 -8523.2927 -3157.9386 Loop time of 0.809129 on 1 procs for 20 steps with 2384 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 = -8508.35981473 -8523.28583973 -8523.29269076 Force two-norm initial, final = 12.4015 0.161761 Force max component initial, final = 1.84292 0.0224965 Final line search alpha, max atom move = 1 0.0224965 Iterations, force evaluations = 20 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78566 | 0.78566 | 0.78566 | 0.0 | 97.10 Neigh | 0.017976 | 0.017976 | 0.017976 | 0.0 | 2.22 Comm | 0.0035279 | 0.0035279 | 0.0035279 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00197 | | | 0.24 Nlocal: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15046 ave 15046 max 15046 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: 1.01625e+06 ave 1.01625e+06 max 1.01625e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1016254 Ave neighs/atom = 426.281 Neighbor list builds = 1 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 : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.87 | 12.87 | 12.87 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -8523.2927 0 -8523.2927 -3157.9386 40802.35 23 0 -8523.4092 0 -8523.4092 -404.20902 40682.703 Loop time of 0.16175 on 1 procs for 3 steps with 2384 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8523.29269076 -8523.40862968 -8523.40916445 Force two-norm initial, final = 110.628 0.176672 Force max component initial, final = 83.089 0.0450364 Final line search alpha, max atom move = 0.000310356 1.39773e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15967 | 0.15967 | 0.15967 | 0.0 | 98.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053835 | 0.00053835 | 0.00053835 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001542 | | | 0.95 Nlocal: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15060 ave 15060 max 15060 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: 1.01641e+06 ave 1.01641e+06 max 1.01641e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1016414 Ave neighs/atom = 426.348 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1025 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) = 12.39 | 12.39 | 12.39 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8523.4092 0 -8523.4092 -404.20902 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2384 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: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15067 ave 15067 max 15067 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: 1.0168e+06 ave 1.0168e+06 max 1.0168e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1016800 Ave neighs/atom = 426.51 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) = 12.39 | 12.39 | 12.39 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 -8523.4092 -8523.4092 28.828446 141.40084 9.9801388 -404.20902 -404.20902 -1.7715927 -1209.4505 -1.4049519 2.6716449 758.50598 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2384 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: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15067 ave 15067 max 15067 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 508400 ave 508400 max 508400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.0168e+06 ave 1.0168e+06 max 1.0168e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1016800 Ave neighs/atom = 426.51 Neighbor list builds = 0 Dangerous builds = 0 2384 -8523.40916444624 eV 2.67164486691561 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01