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 -52.0948 0) to (42.5323 52.0948 8.6222) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24371 4.99505 5.74814 Created 1758 atoms create_atoms CPU = 0.000443935 secs 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24371 4.99505 5.74814 Created 1758 atoms create_atoms CPU = 0.000388145 secs 1758 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 28 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 44 atoms, new total = 3472 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 7.425 | 7.425 | 7.425 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15327.061 0 -15327.061 4056.6811 54 0 -15397.153 0 -15397.153 -3827.0531 Loop time of 1.23938 on 1 procs for 54 steps with 3472 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15327.0612868 -15397.1378534 -15397.15315 Force two-norm initial, final = 52.2537 0.42214 Force max component initial, final = 6.18304 0.0695682 Final line search alpha, max atom move = 1 0.0695682 Iterations, force evaluations = 54 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2081 | 1.2081 | 1.2081 | 0.0 | 97.48 Neigh | 0.016369 | 0.016369 | 0.016369 | 0.0 | 1.32 Comm | 0.0072289 | 0.0072289 | 0.0072289 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007674 | | | 0.62 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11393 ave 11393 max 11393 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: 604574 ave 604574 max 604574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 604574 Ave neighs/atom = 174.128 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.425 | 7.425 | 7.425 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -15397.153 0 -15397.153 -3827.0531 38208.64 56 0 -15397.264 0 -15397.264 25.113295 38126.097 Loop time of 0.0495679 on 1 procs for 2 steps with 3472 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15397.15315 -15397.2596209 -15397.2641887 Force two-norm initial, final = 145.612 9.47347 Force max component initial, final = 115.231 9.37363 Final line search alpha, max atom move = 3.8363e-05 0.0003596 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.048084 | 0.048084 | 0.048084 | 0.0 | 97.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035906 | 0.00035906 | 0.00035906 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001125 | | | 2.27 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11389 ave 11389 max 11389 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: 604250 ave 604250 max 604250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 604250 Ave neighs/atom = 174.035 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 7.562 | 7.562 | 7.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15397.264 0 -15397.264 25.113295 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11389 ave 11389 max 11389 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: 604290 ave 604290 max 604290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 604290 Ave neighs/atom = 174.047 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) = 7.562 | 7.562 | 7.562 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 -15397.264 -15397.264 42.475191 104.18954 8.6151513 25.113295 25.113295 -54.550201 -263.69651 393.58659 2.23473 1706.1247 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11389 ave 11389 max 11389 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 302145 ave 302145 max 302145 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 604290 ave 604290 max 604290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 604290 Ave neighs/atom = 174.047 Neighbor list builds = 0 Dangerous builds = 0 3472 -15397.2641887025 eV 2.23472999517529 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01