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 = 3.63857 3.63857 3.63857 Created orthogonal box = (0 -47.5841 0) to (22.4296 47.5841 5.14571) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.72203 5.84321 5.14571 Created 462 atoms create_atoms CPU = 0.000375032 secs 462 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.72203 5.84321 5.14571 Created 462 atoms create_atoms CPU = 0.000251055 secs 462 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 = 5 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 912 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 = 5 20 2 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) = 5.442 | 5.442 | 5.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3062.1556 0 -3062.1556 17278.828 41 0 -3093.3377 0 -3093.3377 4467.4444 Loop time of 0.56865 on 1 procs for 41 steps with 912 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3062.15559982 -3093.33459977 -3093.33767672 Force two-norm initial, final = 49.7413 0.148751 Force max component initial, final = 9.8672 0.0108864 Final line search alpha, max atom move = 1 0.0108864 Iterations, force evaluations = 41 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56255 | 0.56255 | 0.56255 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0040154 | 0.0040154 | 0.0040154 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002087 | | | 0.37 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8241 ave 8241 max 8241 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: 290836 ave 290836 max 290836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290836 Ave neighs/atom = 318.899 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.442 | 5.442 | 5.442 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -3093.3377 0 -3093.3377 4467.4444 10983.979 43 0 -3093.3481 0 -3093.3481 2820.803 10996.488 Loop time of 0.0298641 on 1 procs for 2 steps with 912 atoms 100.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3093.33767672 -3093.34514865 -3093.34805219 Force two-norm initial, final = 17.293 0.152164 Force max component initial, final = 15.6466 0.0111023 Final line search alpha, max atom move = 0.000218209 2.42263e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.029081 | 0.029081 | 0.029081 | 0.0 | 97.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019956 | 0.00019956 | 0.00019956 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005832 | | | 1.95 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8268 ave 8268 max 8268 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: 289344 ave 289344 max 289344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289344 Ave neighs/atom = 317.263 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 = 5 20 2 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) = 5.58 | 5.58 | 5.58 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3093.3481 0 -3093.3481 2820.803 Loop time of 9.53674e-07 on 1 procs for 0 steps with 912 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: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8250 ave 8250 max 8250 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: 289176 ave 289176 max 289176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289176 Ave neighs/atom = 317.079 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) = 5.58 | 5.58 | 5.58 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 -3093.3481 -3093.3481 22.463152 95.16819 5.1438877 2820.803 2820.803 -0.005197622 8461.7258 0.68844613 2.2716222 333.16992 Loop time of 1.90735e-06 on 1 procs for 0 steps with 912 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 | | 1.907e-06 | | |100.00 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8250 ave 8250 max 8250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144588 ave 144588 max 144588 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 289176 ave 289176 max 289176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289176 Ave neighs/atom = 317.079 Neighbor list builds = 0 Dangerous builds = 0 912 -3093.34805219233 eV 2.27162218334187 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00