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 = 3.65334 3.65334 3.65334 Created orthogonal box = (0 -39.0107 0) to (27.5821 39.0107 5.16661) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.32287 6.15901 5.16661 Created 458 atoms create_atoms CPU = 0.00104904 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.32287 6.15901 5.16661 Created 458 atoms create_atoms CPU = 0.000858784 secs 458 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 18 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 900 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.395 | 5.395 | 5.395 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2885.7589 0 -2885.7589 4319.2475 50 0 -2923.5434 0 -2923.5434 -13591.491 Loop time of 0.730564 on 1 procs for 50 steps with 900 atoms 68.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2885.75887086 -2923.54095616 -2923.54336542 Force two-norm initial, final = 38.9784 0.188763 Force max component initial, final = 11.2175 0.0257569 Final line search alpha, max atom move = 1 0.0257569 Iterations, force evaluations = 50 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70372 | 0.70372 | 0.70372 | 0.0 | 96.32 Neigh | 0.018237 | 0.018237 | 0.018237 | 0.0 | 2.50 Comm | 0.0055463 | 0.0055463 | 0.0055463 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003066 | | | 0.42 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7200 ave 7200 max 7200 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: 200232 ave 200232 max 200232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200232 Ave neighs/atom = 222.48 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.395 | 5.395 | 5.395 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2923.5434 0 -2923.5434 -13591.491 11118.527 67 0 -2924.5905 0 -2924.5905 -697.39193 10980.021 Loop time of 0.176526 on 1 procs for 17 steps with 900 atoms 69.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2923.54336542 -2924.59036117 -2924.59052974 Force two-norm initial, final = 161.824 1.01613 Force max component initial, final = 157.796 0.557904 Final line search alpha, max atom move = 0.00100331 0.00055975 Iterations, force evaluations = 17 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17113 | 0.17113 | 0.17113 | 0.0 | 96.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001183 | 0.001183 | 0.001183 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00421 | | | 2.38 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7200 ave 7200 max 7200 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: 200244 ave 200244 max 200244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200244 Ave neighs/atom = 222.493 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.534 | 5.534 | 5.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2924.5905 0 -2924.5905 -697.39193 Loop time of 9.53674e-07 on 1 procs for 0 steps with 900 atoms 419.4% 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: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7263 ave 7263 max 7263 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: 200856 ave 200856 max 200856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200856 Ave neighs/atom = 223.173 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) = 5.534 | 5.534 | 5.534 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 -2924.5905 -2924.5905 27.138234 78.021387 5.1857064 -697.39193 -697.39193 -53.419382 -1957.0476 -81.70883 2.3442879 737.23863 Loop time of 2.14577e-06 on 1 procs for 0 steps with 900 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: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7263 ave 7263 max 7263 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100428 ave 100428 max 100428 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200856 ave 200856 max 200856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200856 Ave neighs/atom = 223.173 Neighbor list builds = 0 Dangerous builds = 0 900 -2924.59052973773 eV 2.34428792935553 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01