LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6063 3.6063 3.6063 Created orthogonal box = (0 -38.5084 0) to (27.227 38.5084 5.10008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.25433 6.0797 5.10008 Created 458 atoms create_atoms CPU = 0.0009799 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.25433 6.0797 5.10008 Created 458 atoms create_atoms CPU = 0.000775099 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 5 13 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 11.9775 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:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 5 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 6.648 | 6.648 | 6.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3690.0392 0 -3690.0392 3058.636 46 0 -3736.1186 0 -3736.1186 -20116.889 Loop time of 1.71399 on 1 procs for 46 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 = -3690.03916131 -3736.11525759 -3736.11855302 Force two-norm initial, final = 38.7772 0.263695 Force max component initial, final = 12.2056 0.0359127 Final line search alpha, max atom move = 1 0.0359127 Iterations, force evaluations = 46 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6897 | 1.6897 | 1.6897 | 0.0 | 98.58 Neigh | 0.012715 | 0.012715 | 0.012715 | 0.0 | 0.74 Comm | 0.0084438 | 0.0084438 | 0.0084438 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003131 | | | 0.18 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11734 ave 11734 max 11734 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: 542788 ave 542788 max 542788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 542788 Ave neighs/atom = 605.79 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) 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) = 6.65 | 6.65 | 6.65 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -3736.1186 0 -3736.1186 -20116.889 10694.538 60 0 -3737.5079 0 -3737.5079 -2903.9278 10582.32 Loop time of 0.32356 on 1 procs for 14 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 = -3736.11855302 -3737.50528227 -3737.50792101 Force two-norm initial, final = 218.641 0.839073 Force max component initial, final = 213.69 0.186855 Final line search alpha, max atom move = 0.00017462 3.26288e-05 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31787 | 0.31787 | 0.31787 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014825 | 0.0014825 | 0.0014825 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004209 | | | 1.30 Nlocal: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11780 ave 11780 max 11780 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: 543160 ave 543160 max 543160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 543160 Ave neighs/atom = 606.205 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 5 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 6.789 | 6.789 | 6.789 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3737.5079 0 -3737.5079 -2903.9278 Loop time of 1.90735e-06 on 1 procs for 0 steps with 896 atoms 157.3% 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: 896 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11835 ave 11835 max 11835 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: 547200 ave 547200 max 547200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 547200 Ave neighs/atom = 610.714 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) = 6.789 | 6.789 | 6.789 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 -3737.5079 -3737.5079 26.858751 77.016762 5.1157558 -2903.9278 -2903.9278 -4.5270697 -8678.8792 -28.377094 2.3308126 760.90668 Loop time of 9.53674e-07 on 1 procs for 0 steps with 896 atoms 314.6% 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: 11835 ave 11835 max 11835 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 273600 ave 273600 max 273600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 547200 ave 547200 max 547200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 547200 Ave neighs/atom = 610.714 Neighbor list builds = 0 Dangerous builds = 0 896 -3737.50792101095 eV 2.33081255917304 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02