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 = 3.60735 3.60735 3.60735 Created orthogonal box = (0 -40.335 0) to (19.7583 40.335 8.83617) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.26888 4.83977 5.89078 Created 612 atoms create_atoms CPU = 0.000825882 secs 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.26888 4.83977 5.89078 Created 612 atoms create_atoms CPU = 0.000595093 secs 612 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 14 2 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 1188 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.597 | 7.597 | 7.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4116.5425 0 -4116.5425 7918.6716 64 0 -4162.6858 0 -4162.6858 -5635.4475 Loop time of 3.88757 on 1 procs for 64 steps with 1188 atoms 78.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4116.54250916 -4162.68292309 -4162.68581579 Force two-norm initial, final = 33.9398 0.225727 Force max component initial, final = 5.86349 0.0151188 Final line search alpha, max atom move = 1 0.0151188 Iterations, force evaluations = 64 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8512 | 3.8512 | 3.8512 | 0.0 | 99.06 Neigh | 0.019053 | 0.019053 | 0.019053 | 0.0 | 0.49 Comm | 0.012068 | 0.012068 | 0.012068 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005232 | | | 0.13 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11712 ave 11712 max 11712 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: 741912 ave 741912 max 741912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 741912 Ave neighs/atom = 624.505 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.597 | 7.597 | 7.597 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -4162.6858 0 -4162.6858 -5635.4475 14083.997 67 0 -4162.756 0 -4162.756 -1573.7424 14042.031 Loop time of 0.164718 on 1 procs for 3 steps with 1188 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 = -4162.68581579 -4162.75575475 -4162.75596147 Force two-norm initial, final = 62.8742 0.271965 Force max component initial, final = 53.7007 0.0333826 Final line search alpha, max atom move = 0.000479713 1.60141e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16257 | 0.16257 | 0.16257 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057769 | 0.00057769 | 0.00057769 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001567 | | | 0.95 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11696 ave 11696 max 11696 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: 741504 ave 741504 max 741504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 741504 Ave neighs/atom = 624.162 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 4 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 7.735 | 7.735 | 7.735 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4162.756 0 -4162.756 -1573.7424 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1188 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: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11728 ave 11728 max 11728 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: 741888 ave 741888 max 741888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 741888 Ave neighs/atom = 624.485 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) = 7.735 | 7.735 | 7.735 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 -4162.756 -4162.756 19.739301 80.670073 8.8183172 -1573.7424 -1573.7424 -3.8052463 -4719.2136 1.7917242 2.2587938 709.73376 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1188 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: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11728 ave 11728 max 11728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 370944 ave 370944 max 370944 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 741888 ave 741888 max 741888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 741888 Ave neighs/atom = 624.485 Neighbor list builds = 0 Dangerous builds = 0 1188 -4162.75596147402 eV 2.25879375284757 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04