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 = 3.52 3.52 3.52 Created orthogonal box = (0 -39.8278 0) to (17.2444 39.8278 6.09682) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.74814 4.97803 6.09682 Created 396 atoms create_atoms CPU = 0.000315189 secs 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.74814 4.97803 6.09682 Created 396 atoms create_atoms CPU = 0.000169992 secs 396 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 21 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 25 atoms, new total = 767 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3238.6052 0 -3238.6052 85492.873 113 0 -3398.6969 0 -3398.6969 9887.9761 Loop time of 0.562302 on 1 procs for 113 steps with 767 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3238.60520578 -3398.69355982 -3398.69690732 Force two-norm initial, final = 172.264 0.224826 Force max component initial, final = 28.2208 0.0433068 Final line search alpha, max atom move = 1 0.0433068 Iterations, force evaluations = 113 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.54492 | 0.54492 | 0.54492 | 0.0 | 96.91 Neigh | 0.006397 | 0.006397 | 0.006397 | 0.0 | 1.14 Comm | 0.0064709 | 0.0064709 | 0.0064709 | 0.0 | 1.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004511 | | | 0.80 Nlocal: 767 ave 767 max 767 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5009 ave 5009 max 5009 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: 133004 ave 133004 max 133004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133004 Ave neighs/atom = 173.408 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 : 113 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press Volume 113 0 -3398.6969 0 -3398.6969 9887.9761 8374.6752 117 0 -3398.7932 0 -3398.7932 3318.4242 8405.2011 Loop time of 0.0241649 on 1 procs for 4 steps with 767 atoms 124.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3398.69690732 -3398.79252664 -3398.79319821 Force two-norm initial, final = 63.6157 0.252915 Force max component initial, final = 58.5182 0.0469991 Final line search alpha, max atom move = 0.00023707 1.11421e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023164 | 0.023164 | 0.023164 | 0.0 | 95.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020432 | 0.00020432 | 0.00020432 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000797 | | | 3.30 Nlocal: 767 ave 767 max 767 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4963 ave 4963 max 4963 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: 133060 ave 133060 max 133060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133060 Ave neighs/atom = 173.481 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 5 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3398.7932 0 -3398.7932 3318.4242 Loop time of 9.53674e-07 on 1 procs for 0 steps with 767 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: 767 ave 767 max 767 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4960 ave 4960 max 4960 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: 132962 ave 132962 max 132962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132962 Ave neighs/atom = 173.353 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) = 5.125 | 5.125 | 5.125 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 -3398.7932 -3398.7932 17.254552 79.65557 6.1154478 3318.4242 3318.4242 -0.43355139 9956.3198 -0.61380456 2.2884465 383.11606 Loop time of 9.53674e-07 on 1 procs for 0 steps with 767 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: 767 ave 767 max 767 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4960 ave 4960 max 4960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66481 ave 66481 max 66481 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132962 ave 132962 max 132962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132962 Ave neighs/atom = 173.353 Neighbor list builds = 0 Dangerous builds = 0 767 -3370.83434811462 eV 2.28844647322402 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00