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 = 4.06121 4.06121 4.06121 Created orthogonal box = (0 -69.4021 0) to (34.699 69.4021 4.06121) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.22862 5.22862 4.06121 Created 586 atoms create_atoms CPU = 0.000755072 secs 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.22862 5.22862 4.06121 Created 586 atoms create_atoms CPU = 0.000499964 secs 586 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 29 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1160 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.481 | 5.481 | 5.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3095.1578 0 -3095.1578 2054.1655 26 0 -3115.0461 0 -3115.0461 -1685.7005 Loop time of 0.409397 on 1 procs for 26 steps with 1160 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 = -3095.15775998 -3115.04355266 -3115.04609521 Force two-norm initial, final = 20.7675 0.143628 Force max component initial, final = 4.77016 0.0213895 Final line search alpha, max atom move = 1 0.0213895 Iterations, force evaluations = 26 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39478 | 0.39478 | 0.39478 | 0.0 | 96.43 Neigh | 0.0092571 | 0.0092571 | 0.0092571 | 0.0 | 2.26 Comm | 0.0034952 | 0.0034952 | 0.0034952 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00186 | | | 0.45 Nlocal: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10178 ave 10178 max 10178 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: 258908 ave 258908 max 258908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258908 Ave neighs/atom = 223.197 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -3115.0461 0 -3115.0461 -1685.7005 19560.31 30 0 -3115.0796 0 -3115.0796 -290.97949 19523.664 Loop time of 0.093219 on 1 procs for 4 steps with 1160 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3115.04609521 -3115.07960659 -3115.07960983 Force two-norm initial, final = 32.8969 0.318416 Force max component initial, final = 30.277 0.209231 Final line search alpha, max atom move = 0.0117166 0.00245147 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090302 | 0.090302 | 0.090302 | 0.0 | 96.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073981 | 0.00073981 | 0.00073981 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002177 | | | 2.34 Nlocal: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10178 ave 10178 max 10178 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: 259168 ave 259168 max 259168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259168 Ave neighs/atom = 223.421 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 8 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.619 | 5.619 | 5.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3115.0796 0 -3115.0796 -290.97949 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1160 atoms 209.7% 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: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10184 ave 10184 max 10184 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: 259200 ave 259200 max 259200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259200 Ave neighs/atom = 223.448 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) = 5.619 | 5.619 | 5.619 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 -3115.0796 -3115.0796 34.614764 138.80422 4.0634723 -290.97949 -290.97949 -17.128466 -841.08134 -14.728676 2.5775832 596.91432 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1160 atoms 139.8% 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: 1160 ave 1160 max 1160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10184 ave 10184 max 10184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129600 ave 129600 max 129600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 259200 ave 259200 max 259200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259200 Ave neighs/atom = 223.448 Neighbor list builds = 0 Dangerous builds = 0 1160 -3115.07960982524 eV 2.57758321386615 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00