LAMMPS (24 Jan 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 = 3.52043 3.52043 3.52043 Created orthogonal box = (0 -41.6578 0) to (51.0158 41.6578 8.62325) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.83038 5.35555 5.74883 Created 1695 atoms create_atoms CPU = 0.00117803 secs 1695 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.83038 5.35555 5.74883 Created 1695 atoms create_atoms CPU = 0.000950098 secs 1695 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 = 18 29 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 78 atoms, new total = 3312 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) 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 = 18 29 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) = 5.665 | 5.665 | 5.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18971.5 0 -18971.5 -3519.7665 69 0 -19084.924 0 -19084.924 -17680.549 Loop time of 53.6932 on 1 procs for 69 steps with 3312 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 = -18971.499876 -19084.9060087 -19084.9235885 Force two-norm initial, final = 53.8447 0.438442 Force max component initial, final = 5.42906 0.0446966 Final line search alpha, max atom move = 1 0.0446966 Iterations, force evaluations = 69 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 53.656 | 53.656 | 53.656 | 0.0 | 99.93 Neigh | 0.016952 | 0.016952 | 0.016952 | 0.0 | 0.03 Comm | 0.0089312 | 0.0089312 | 0.0089312 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01128 | | | 0.02 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7621 ave 7621 max 7621 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: 255692 ave 255692 max 255692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255692 Ave neighs/atom = 77.2017 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.666 | 5.666 | 5.666 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -19084.924 0 -19084.924 -17680.549 36652.33 74 0 -19086.25 0 -19086.25 -3855.3329 36398.007 Loop time of 3.39132 on 1 procs for 5 steps with 3312 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 = -19084.9235885 -19086.2494544 -19086.2502211 Force two-norm initial, final = 529.992 0.605509 Force max component initial, final = 412.472 0.0460924 Final line search alpha, max atom move = 0.000137559 6.34044e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3892 | 3.3892 | 3.3892 | 0.0 | 99.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039506 | 0.00039506 | 0.00039506 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001727 | | | 0.05 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7660 ave 7660 max 7660 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: 255580 ave 255580 max 255580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255580 Ave neighs/atom = 77.1679 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 = 18 29 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) = 5.802 | 5.802 | 5.802 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19086.25 0 -19086.25 -3855.3329 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3312 atoms 209.7% 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7667 ave 7667 max 7667 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: 255762 ave 255762 max 255762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255762 Ave neighs/atom = 77.2228 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) = 5.802 | 5.802 | 5.802 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 -19086.25 -19086.25 50.807883 83.315521 8.5984584 -3855.3329 -3855.3329 1.5023272 -11565.478 -2.0230734 2.3671006 2557.8992 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3312 atoms 209.7% 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7667 ave 7667 max 7667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127881 ave 127881 max 127881 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255762 ave 255762 max 255762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255762 Ave neighs/atom = 77.2228 Neighbor list builds = 0 Dangerous builds = 0 3312 -8041.38783991908 eV 2.36710056916618 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:59