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 = 3.31169 3.31169 3.31169 Created orthogonal box = (0 -65.5714 0) to (40.1521 65.5714 8.11194) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.64344 4.68343 5.40796 Created 2358 atoms create_atoms CPU = 0.000530958 secs 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.64344 4.68343 5.40796 Created 2358 atoms create_atoms CPU = 0.000553131 secs 2358 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 11 35 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 54 atoms, new total = 4662 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 12.8 | 12.8 | 12.8 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17874.472 0 -17874.472 20006.6 143 0 -18166.866 0 -18166.866 206070.5 Loop time of 6.24607 on 1 procs for 143 steps with 4662 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -17874.4723862 -18166.8499872 -18166.8662955 Force two-norm initial, final = 208.737 0.846022 Force max component initial, final = 35.4593 0.0477353 Final line search alpha, max atom move = 0.605665 0.0289116 Iterations, force evaluations = 143 280 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1463 | 6.1463 | 6.1463 | 0.0 | 98.40 Neigh | 0.045484 | 0.045484 | 0.045484 | 0.0 | 0.73 Comm | 0.027818 | 0.027818 | 0.027818 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02648 | | | 0.42 Nlocal: 4662 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15605 ave 15605 max 15605 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: 895608 ave 895608 max 895608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 895608 Ave neighs/atom = 192.108 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 : 143 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.8 | 12.8 | 12.8 Mbytes Step Temp E_pair E_mol TotEng Press Volume 143 0 -18166.866 0 -18166.866 206070.5 42714.701 377 0 -18481.966 0 -18481.966 -9722.3704 50574.313 Loop time of 5.04862 on 1 procs for 234 steps with 4662 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 = -18166.8662955 -18481.9584636 -18481.9659379 Force two-norm initial, final = 6916.12 19.1052 Force max component initial, final = 5534.23 9.84169 Final line search alpha, max atom move = 3.46108e-05 0.000340629 Iterations, force evaluations = 234 246 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7537 | 4.7537 | 4.7537 | 0.0 | 94.16 Neigh | 0.17518 | 0.17518 | 0.17518 | 0.0 | 3.47 Comm | 0.022391 | 0.022391 | 0.022391 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0974 | | | 1.93 Nlocal: 4662 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14856 ave 14856 max 14856 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: 757518 ave 757518 max 757518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 757518 Ave neighs/atom = 162.488 Neighbor list builds = 8 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 13 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 11.54 | 11.54 | 11.54 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18481.966 0 -18481.966 -9722.3704 Loop time of 9.53674e-07 on 1 procs for 0 steps with 4662 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: 4662 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14873 ave 14873 max 14873 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: 760362 ave 760362 max 760362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 760362 Ave neighs/atom = 163.098 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) = 11.54 | 11.54 | 11.54 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 -18481.966 -18481.966 48.196626 131.14276 8.0014559 -9722.3704 -9722.3704 -10.100382 -28849.476 -307.53453 2.2548734 10636.713 Loop time of 9.53674e-07 on 1 procs for 0 steps with 4662 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: 4662 ave 4662 max 4662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14873 ave 14873 max 14873 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 380181 ave 380181 max 380181 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 760362 ave 760362 max 760362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 760362 Ave neighs/atom = 163.098 Neighbor list builds = 0 Dangerous builds = 0 4662 -18481.9659378888 eV 2.25487342241381 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11