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 = 3.51812 3.51812 3.51812 Created orthogonal box = (0 -54.9583 0) to (27.4774 54.9583 3.51812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.95494 4.95494 3.51812 Created 490 atoms create_atoms CPU = 0.000291109 secs 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.95494 4.95494 3.51812 Created 490 atoms create_atoms CPU = 0.000193119 secs 490 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 23 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 972 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.841 | 5.841 | 5.841 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4212.9576 0 -4212.9576 23995.972 66 0 -4253.4342 0 -4253.4342 -1927.1872 Loop time of 0.939157 on 1 procs for 66 steps with 972 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4212.95761358 -4253.43066049 -4253.43423121 Force two-norm initial, final = 58.1824 0.179696 Force max component initial, final = 18.2473 0.0294418 Final line search alpha, max atom move = 1 0.0294418 Iterations, force evaluations = 66 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92309 | 0.92309 | 0.92309 | 0.0 | 98.29 Neigh | 0.0052881 | 0.0052881 | 0.0052881 | 0.0 | 0.56 Comm | 0.007442 | 0.007442 | 0.007442 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003341 | | | 0.36 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10704 ave 10704 max 10704 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: 316720 ave 316720 max 316720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316720 Ave neighs/atom = 325.844 Neighbor list builds = 1 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.841 | 5.841 | 5.841 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -4253.4342 0 -4253.4342 -1927.1872 10625.515 68 0 -4253.4457 0 -4253.4457 -1078.992 10620.531 Loop time of 0.0373449 on 1 procs for 2 steps with 972 atoms 107.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4253.43423121 -4253.44317839 -4253.44572651 Force two-norm initial, final = 15.4464 2.92078 Force max component initial, final = 15.2304 2.72535 Final line search alpha, max atom move = 0.000110994 0.000302496 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036427 | 0.036427 | 0.036427 | 0.0 | 97.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025201 | 0.00025201 | 0.00025201 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006661 | | | 1.78 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10638 ave 10638 max 10638 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: 316756 ave 316756 max 316756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316756 Ave neighs/atom = 325.881 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.978 | 5.978 | 5.978 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4253.4457 0 -4253.4457 -1078.992 Loop time of 2.14577e-06 on 1 procs for 0 steps with 972 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: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10638 ave 10638 max 10638 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: 317012 ave 317012 max 317012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317012 Ave neighs/atom = 326.144 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) = 5.978 | 5.978 | 5.978 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 -4253.4457 -4253.4457 27.497904 109.91665 3.5138493 -1078.992 -1078.992 -156.27215 -2670.0669 -410.63694 2.2016914 128.55223 Loop time of 9.53674e-07 on 1 procs for 0 steps with 972 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: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10638 ave 10638 max 10638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 158506 ave 158506 max 158506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 317012 ave 317012 max 317012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317012 Ave neighs/atom = 326.144 Neighbor list builds = 0 Dangerous builds = 0 972 -4253.44572651359 eV 2.20169143869728 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01