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 = 3.52043 3.52043 3.52043 Created orthogonal box = (0 -38.0827 0) to (12.6931 38.0827 3.52043) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.88195 4.88195 3.52043 Created 158 atoms create_atoms CPU = 0.000157833 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.88195 4.88195 3.52043 Created 158 atoms create_atoms CPU = 5.6982e-05 secs 158 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 = 5 26 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 310 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 = 5 26 2 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) = 4.428 | 4.428 | 4.428 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1766.2364 0 -1766.2364 14660.447 45 0 -1785.1727 0 -1785.1727 -1844.0387 Loop time of 3.22106 on 1 procs for 45 steps with 310 atoms 90.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1766.23637953 -1785.17102397 -1785.17266997 Force two-norm initial, final = 19.291 0.147341 Force max component initial, final = 7.18098 0.0282575 Final line search alpha, max atom move = 1 0.0282575 Iterations, force evaluations = 45 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2173 | 3.2173 | 3.2173 | 0.0 | 99.88 Neigh | 0.0016348 | 0.0016348 | 0.0016348 | 0.0 | 0.05 Comm | 0.0013347 | 0.0013347 | 0.0013347 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007555 | | | 0.02 Nlocal: 310 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2768 ave 2768 max 2768 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: 23984 ave 23984 max 23984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23984 Ave neighs/atom = 77.3677 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.428 | 4.428 | 4.428 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -1785.1727 0 -1785.1727 -1844.0387 3403.4576 48 0 -1785.186 0 -1785.186 -740.17627 3401.6127 Loop time of 0.229032 on 1 procs for 3 steps with 310 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1785.17266997 -1785.18562485 -1785.1859752 Force two-norm initial, final = 10.8254 1.13906 Force max component initial, final = 10.7123 1.09987 Final line search alpha, max atom move = 0.000579122 0.000636957 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22834 | 0.22834 | 0.22834 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.8201e-05 | 7.8201e-05 | 7.8201e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006125 | | | 0.27 Nlocal: 310 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772 ave 2772 max 2772 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: 23952 ave 23952 max 23952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23952 Ave neighs/atom = 77.2645 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 = 5 26 2 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) = 4.565 | 4.565 | 4.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1785.186 0 -1785.186 -740.17627 Loop time of 2.14577e-06 on 1 procs for 0 steps with 310 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: 310 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772 ave 2772 max 2772 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: 23952 ave 23952 max 23952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23952 Ave neighs/atom = 77.2645 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) = 4.565 | 4.565 | 4.565 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 -1785.186 -1785.186 12.666781 76.165496 3.5258216 -740.17627 -740.17627 -516.96977 -1590.9256 -112.63343 2.2468971 151.08795 Loop time of 1.90735e-06 on 1 procs for 0 steps with 310 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 | | 1.907e-06 | | |100.00 Nlocal: 310 ave 310 max 310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2772 ave 2772 max 2772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11976 ave 11976 max 11976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23952 ave 23952 max 23952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23952 Ave neighs/atom = 77.2645 Neighbor list builds = 0 Dangerous builds = 0 310 -751.397527690186 eV 2.24689709247242 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03