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 = 3.63366 3.63366 3.63366 Created orthogonal box = (0 -39.8084 0) to (8.12512 39.8084 8.90062) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.87507 5.3073 5.93375 Created 242 atoms create_atoms CPU = 0.000203133 secs 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.87507 5.3073 5.93375 Created 242 atoms create_atoms CPU = 7.39098e-05 secs 242 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 3 28 4 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 472 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 3 28 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.447 | 4.447 | 4.447 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1919.579 0 -1919.579 -4349.3958 19 0 -1928.2973 0 -1928.2973 -12416.081 Loop time of 1.37591 on 1 procs for 19 steps with 472 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1919.57903294 -1928.29569048 -1928.29730839 Force two-norm initial, final = 12.6323 0.103589 Force max component initial, final = 4.36157 0.0195757 Final line search alpha, max atom move = 1 0.0195757 Iterations, force evaluations = 19 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3752 | 1.3752 | 1.3752 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038671 | 0.00038671 | 0.00038671 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002995 | | | 0.02 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2537 ave 2537 max 2537 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: 25280 ave 25280 max 25280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25280 Ave neighs/atom = 53.5593 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.447 | 4.447 | 4.447 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -1928.2973 0 -1928.2973 -12416.081 5757.7725 24 0 -1928.4689 0 -1928.4689 -1625.694 5712.002 Loop time of 0.300267 on 1 procs for 5 steps with 472 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1928.29730839 -1928.46759868 -1928.46885764 Force two-norm initial, final = 60.5196 1.64623 Force max component initial, final = 44.6062 1.58356 Final line search alpha, max atom move = 0.000214659 0.000339924 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29989 | 0.29989 | 0.29989 | 0.0 | 99.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 8.2493e-05 | 8.2493e-05 | 8.2493e-05 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002992 | | | 0.10 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2494 ave 2494 max 2494 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: 26212 ave 26212 max 26212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26212 Ave neighs/atom = 55.5339 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 3 28 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1928.4689 0 -1928.4689 -1625.694 Loop time of 0 on 1 procs for 0 steps with 472 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 | | 0 | | | 0.00 Nlocal: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2537 ave 2537 max 2537 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: 26352 ave 26352 max 26352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26352 Ave neighs/atom = 55.8305 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) = 4.585 | 4.585 | 4.585 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 -1928.4689 -1928.4689 8.0884946 79.616815 8.8698413 -1625.694 -1625.694 -109.34902 -5210.3735 442.64057 2.3414491 320.07296 Loop time of 9.53674e-07 on 1 procs for 0 steps with 472 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: 472 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2537 ave 2537 max 2537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13176 ave 13176 max 13176 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26352 ave 26352 max 26352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26352 Ave neighs/atom = 55.8305 Neighbor list builds = 0 Dangerous builds = 0 472 -1203.8379283786 eV 2.34144907930853 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01