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 = 3.65836 3.65836 3.65836 Created orthogonal box = (0 -62.5178 0) to (31.2571 62.5178 3.65836) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.70997 4.70997 3.65836 Created 586 atoms create_atoms CPU = 0.000283003 secs 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.70997 4.70997 3.65836 Created 586 atoms create_atoms CPU = 0.000175953 secs 586 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 35 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1167 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4612.345 0 -4612.345 13113.283 261 0 -4665.0063 0 -4665.0063 -4251.5506 Loop time of 1.91482 on 1 procs for 261 steps with 1167 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4612.34502077 -4665.0017792 -4665.00625748 Force two-norm initial, final = 43.0862 0.193532 Force max component initial, final = 9.88819 0.0654186 Final line search alpha, max atom move = 1 0.0654186 Iterations, force evaluations = 261 499 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.861 | 1.861 | 1.861 | 0.0 | 97.19 Neigh | 0.013539 | 0.013539 | 0.013539 | 0.0 | 0.71 Comm | 0.026079 | 0.026079 | 0.026079 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01423 | | | 0.74 Nlocal: 1167 ave 1167 max 1167 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8413 ave 8413 max 8413 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: 161914 ave 161914 max 161914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161914 Ave neighs/atom = 138.744 Neighbor list builds = 3 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 : 261 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press Volume 261 0 -4665.0063 0 -4665.0063 -4251.5506 14297.803 320 0 -4683.8403 0 -4683.8403 -12002.27 14343.452 Loop time of 0.228813 on 1 procs for 59 steps with 1167 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4665.00625748 -4683.83682561 -4683.84032085 Force two-norm initial, final = 548.34 6.51969 Force max component initial, final = 471.549 4.71734 Final line search alpha, max atom move = 0.000226446 0.00106822 Iterations, force evaluations = 59 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21315 | 0.21315 | 0.21315 | 0.0 | 93.15 Neigh | 0.003201 | 0.003201 | 0.003201 | 0.0 | 1.40 Comm | 0.0029073 | 0.0029073 | 0.0029073 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009559 | | | 4.18 Nlocal: 1167 ave 1167 max 1167 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8483 ave 8483 max 8483 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: 162718 ave 162718 max 162718 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162718 Ave neighs/atom = 139.433 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.192 | 5.192 | 5.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4683.8403 0 -4683.8403 -12002.27 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1167 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: 1167 ave 1167 max 1167 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8528 ave 8528 max 8528 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: 163444 ave 163444 max 163444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163444 Ave neighs/atom = 140.055 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) = 5.192 | 5.192 | 5.192 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 -4683.8403 -4683.8403 29.877356 125.03565 3.8395265 -12002.27 -12002.27 503.6718 -36683.515 173.03318 2.2555044 779.03871 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1167 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: 1167 ave 1167 max 1167 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8528 ave 8528 max 8528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81722 ave 81722 max 81722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163444 ave 163444 max 163444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163444 Ave neighs/atom = 140.055 Neighbor list builds = 0 Dangerous builds = 0 1167 -4683.84032084549 eV 2.25550443573609 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02