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 = 4.03204 4.03204 4.03204 Created orthogonal box = (0 -44.1728 0) to (9.01591 44.1728 9.87644) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.40955 5.88917 6.58429 Created 242 atoms create_atoms CPU = 0.000268936 secs 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.40955 5.88917 6.58429 Created 242 atoms create_atoms CPU = 0.000132084 secs 242 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 3 21 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 476 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 3 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 4.555 | 4.555 | 4.555 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1575.2268 0 -1575.2268 8567.3151 48 0 -1594.52 0 -1594.52 -1073.352 Loop time of 0.181401 on 1 procs for 48 steps with 476 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1575.22680017 -1594.5185235 -1594.51995416 Force two-norm initial, final = 30.4555 0.0998655 Force max component initial, final = 8.66462 0.0222724 Final line search alpha, max atom move = 1 0.0222724 Iterations, force evaluations = 48 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17774 | 0.17774 | 0.17774 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022078 | 0.0022078 | 0.0022078 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001455 | | | 0.80 Nlocal: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4207 ave 4207 max 4207 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: 82560 ave 82560 max 82560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82560 Ave neighs/atom = 173.445 Neighbor list builds = 0 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.555 | 4.555 | 4.555 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -1594.52 0 -1594.52 -1073.352 7866.7402 51 0 -1594.5318 0 -1594.5318 469.78496 7852.175 Loop time of 0.00918102 on 1 procs for 3 steps with 476 atoms 108.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1594.51995416 -1594.5312077 -1594.53175901 Force two-norm initial, final = 13.1053 0.104404 Force max component initial, final = 12.077 0.0177261 Final line search alpha, max atom move = 0.000398507 7.06399e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0087266 | 0.0087266 | 0.0087266 | 0.0 | 95.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010943 | 0.00010943 | 0.00010943 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000345 | | | 3.76 Nlocal: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4300 ave 4300 max 4300 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: 82080 ave 82080 max 82080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82080 Ave neighs/atom = 172.437 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 3 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 4.696 | 4.696 | 4.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1594.5318 0 -1594.5318 469.78496 Loop time of 1.19209e-06 on 1 procs for 0 steps with 476 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 | | 1.192e-06 | | |100.00 Nlocal: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4321 ave 4321 max 4321 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: 82108 ave 82108 max 82108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82108 Ave neighs/atom = 172.496 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) = 4.696 | 4.696 | 4.696 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 -1594.5318 -1594.5318 9.0171995 88.345595 9.856742 469.78496 469.78496 -2.8346842 1413.2328 -1.0432083 2.5647827 392.31714 Loop time of 9.53674e-07 on 1 procs for 0 steps with 476 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: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4321 ave 4321 max 4321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41054 ave 41054 max 41054 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82108 ave 82108 max 82108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82108 Ave neighs/atom = 172.496 Neighbor list builds = 0 Dangerous builds = 0 476 -1594.53175901093 eV 2.56478267626971 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00