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 -42.2435 0) to (14.9341 42.2435 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.97803 5.86667 4.97803 Created 292 atoms create_atoms CPU = 0.000351906 secs 292 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.97803 5.86667 4.97803 Created 292 atoms create_atoms CPU = 0.000218868 secs 292 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 20 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 568 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2512.4909 0 -2512.4909 -6028.6067 23 0 -2517.4932 0 -2517.4932 -12859.503 Loop time of 0.139654 on 1 procs for 23 steps with 568 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2512.49088923 -2517.49066404 -2517.49316042 Force two-norm initial, final = 7.8703 0.155384 Force max component initial, final = 1.16056 0.0172785 Final line search alpha, max atom move = 1 0.0172785 Iterations, force evaluations = 23 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13698 | 0.13698 | 0.13698 | 0.0 | 98.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018175 | 0.0018175 | 0.0018175 | 0.0 | 1.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008595 | | | 0.62 Nlocal: 568 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5993 ave 5993 max 5993 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: 125952 ave 125952 max 125952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125952 Ave neighs/atom = 221.746 Neighbor list builds = 0 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 : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -2517.4932 0 -2517.4932 -12859.503 6280.9693 26 0 -2517.5426 0 -2517.5426 -6996.9565 6260.2075 Loop time of 0.016 on 1 procs for 3 steps with 568 atoms 62.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2517.49316042 -2517.54128618 -2517.54259071 Force two-norm initial, final = 39.6762 0.541559 Force max component initial, final = 31.2329 0.367059 Final line search alpha, max atom move = 0.000321337 0.00011795 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015304 | 0.015304 | 0.015304 | 0.0 | 95.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001781 | 0.0001781 | 0.0001781 | 0.0 | 1.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005181 | | | 3.24 Nlocal: 568 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5993 ave 5993 max 5993 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: 126704 ave 126704 max 126704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126704 Ave neighs/atom = 223.07 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2517.5426 0 -2517.5426 -6996.9565 Loop time of 2.14577e-06 on 1 procs for 0 steps with 568 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 | | 2.146e-06 | | |100.00 Nlocal: 568 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5993 ave 5993 max 5993 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: 126720 ave 126720 max 126720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126720 Ave neighs/atom = 223.099 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) = 5.089 | 5.089 | 5.089 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 -2517.5426 -2517.5426 14.897805 84.48704 4.9736629 -6996.9565 -6996.9565 -89.245254 -20807.765 -93.859045 2.3063783 401.29619 Loop time of 2.14577e-06 on 1 procs for 0 steps with 568 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 | | 2.146e-06 | | |100.00 Nlocal: 568 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5993 ave 5993 max 5993 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63360 ave 63360 max 63360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126720 ave 126720 max 126720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126720 Ave neighs/atom = 223.099 Neighbor list builds = 0 Dangerous builds = 0 568 -2517.54259071488 eV 2.30637833249657 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00