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 = 4.0398 4.0398 4.0398 Created orthogonal box = (0 -52.8313 0) to (24.903 52.8313 5.71314) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24273 6.48755 5.71314 Created 458 atoms create_atoms CPU = 0.00028801 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24273 6.48755 5.71314 Created 458 atoms create_atoms CPU = 0.000159979 secs 458 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 5 18 1 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 896 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 5 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 5.862 | 5.862 | 5.862 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2542.2131 0 -2542.2131 587.25815 66 0 -2570.5921 0 -2570.5921 -9855.2204 Loop time of 1.11026 on 1 procs for 66 steps with 896 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 = -2542.21308902 -2570.58996467 -2570.59210724 Force two-norm initial, final = 14.6664 0.145391 Force max component initial, final = 2.03286 0.0252609 Final line search alpha, max atom move = 1 0.0252609 Iterations, force evaluations = 66 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0861 | 1.0861 | 1.0861 | 0.0 | 97.83 Neigh | 0.0089729 | 0.0089729 | 0.0089729 | 0.0 | 0.81 Comm | 0.0087655 | 0.0087655 | 0.0087655 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006397 | | | 0.58 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10190 ave 10190 max 10190 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: 350116 ave 350116 max 350116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350116 Ave neighs/atom = 390.754 Neighbor list builds = 1 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.862 | 5.862 | 5.862 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -2570.5921 0 -2570.5921 -9855.2204 15033.052 81 0 -2571.3513 0 -2571.3513 -3134.5071 14893.518 Loop time of 0.145386 on 1 procs for 15 steps with 896 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2570.59210724 -2571.34914042 -2571.35126443 Force two-norm initial, final = 107.855 0.446706 Force max component initial, final = 107.261 0.0560852 Final line search alpha, max atom move = 0.000269613 1.51213e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14146 | 0.14146 | 0.14146 | 0.0 | 97.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097537 | 0.00097537 | 0.00097537 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002947 | | | 2.03 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10182 ave 10182 max 10182 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: 350396 ave 350396 max 350396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 350396 Ave neighs/atom = 391.067 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 5 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 6.001 | 6.001 | 6.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2571.3513 0 -2571.3513 -3134.5071 Loop time of 9.53674e-07 on 1 procs for 0 steps with 896 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: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10282 ave 10282 max 10282 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: 358148 ave 358148 max 358148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 358148 Ave neighs/atom = 399.719 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) = 6.001 | 6.001 | 6.001 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 -2571.3513 -2571.3513 24.536233 105.66252 5.7447146 -3134.5071 -3134.5071 2.8554906 -9400.31 -6.0667386 2.5889719 570.67664 Loop time of 9.53674e-07 on 1 procs for 0 steps with 896 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: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10282 ave 10282 max 10282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 179074 ave 179074 max 179074 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 358148 ave 358148 max 358148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 358148 Ave neighs/atom = 399.719 Neighbor list builds = 0 Dangerous builds = 0 896 -2571.35126442501 eV 2.5889719437743 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01