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 = 3.52221 3.52221 3.52221 Created orthogonal box = (0 -37.6104 0) to (26.5921 37.6104 4.98116) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.13181 5.93793 4.98116 Created 458 atoms create_atoms CPU = 0.000412941 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.13181 5.93793 4.98116 Created 458 atoms create_atoms CPU = 0.000258923 secs 458 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 23 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 898 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5159.3096 0 -5159.3096 -2569.5963 46 0 -5169.3082 0 -5169.3082 -11887.536 Loop time of 23.8953 on 1 procs for 46 steps with 898 atoms 75.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5159.30959963 -5169.30340908 -5169.30818029 Force two-norm initial, final = 13.657 0.207266 Force max component initial, final = 4.18978 0.0321285 Final line search alpha, max atom move = 1 0.0321285 Iterations, force evaluations = 46 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 23.891 | 23.891 | 23.891 | 0.0 | 99.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0027642 | 0.0027642 | 0.0027642 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001846 | | | 0.01 Nlocal: 898 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4618 ave 4618 max 4618 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: 116948 ave 116948 max 116948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116948 Ave neighs/atom = 130.232 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -5169.3082 0 -5169.3082 -11887.536 9963.7207 50 0 -5169.4805 0 -5169.4805 -2781.4315 9914.8839 Loop time of 1.96066 on 1 procs for 4 steps with 898 atoms 76.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5169.30818029 -5169.47924652 -5169.48048002 Force two-norm initial, final = 97.1284 0.241686 Force max component initial, final = 73.2185 0.0320151 Final line search alpha, max atom move = 0.000235543 7.54094e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9598 | 1.9598 | 1.9598 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021386 | 0.00021386 | 0.00021386 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006912 | | | 0.04 Nlocal: 898 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4625 ave 4625 max 4625 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: 101624 ave 101624 max 101624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101624 Ave neighs/atom = 113.167 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 9 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.101 | 5.101 | 5.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5169.4805 0 -5169.4805 -2781.4315 Loop time of 2.14577e-06 on 1 procs for 0 steps with 898 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: 898 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4625 ave 4625 max 4625 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: 105960 ave 105960 max 105960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105960 Ave neighs/atom = 117.996 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) = 5.101 | 5.101 | 5.101 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 -5169.4805 -5169.4805 26.508562 75.220885 4.9723653 -2781.4315 -2781.4315 0.87705871 -8340.4417 -4.7299692 2.313825 635.12897 Loop time of 1.90735e-06 on 1 procs for 0 steps with 898 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: 898 ave 898 max 898 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4625 ave 4625 max 4625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52980 ave 52980 max 52980 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105960 ave 105960 max 105960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105960 Ave neighs/atom = 117.996 Neighbor list builds = 0 Dangerous builds = 0 898 -2536.84704606379 eV 2.31382502236645 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27