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 = 4.03104 4.03104 4.03104 Created orthogonal box = (0 -49.8652 0) to (16.6204 49.8652 4.03104) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.88835 4.88835 4.03104 Created 206 atoms create_atoms CPU = 0.0002141 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.88835 4.88835 4.03104 Created 206 atoms create_atoms CPU = 7.51019e-05 secs 206 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 5 26 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 7.68732 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1350.154 0 -1350.154 1121.2287 22 0 -1353.1547 0 -1353.1547 -3497.5929 Loop time of 0.051002 on 1 procs for 22 steps with 404 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1350.15403502 -1353.15356104 -1353.15468291 Force two-norm initial, final = 7.152 0.0849443 Force max component initial, final = 2.29902 0.0202406 Final line search alpha, max atom move = 1 0.0202406 Iterations, force evaluations = 22 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049532 | 0.049532 | 0.049532 | 0.0 | 97.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095057 | 0.00095057 | 0.00095057 | 0.0 | 1.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000519 | | | 1.02 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 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: 53040 ave 53040 max 53040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53040 Ave neighs/atom = 131.287 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -1353.1547 0 -1353.1547 -3497.5929 6681.675 24 0 -1353.1674 0 -1353.1674 -1486.4623 6663.5302 Loop time of 0.00541019 on 1 procs for 2 steps with 404 atoms 184.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1353.15468291 -1353.16623048 -1353.167429 Force two-norm initial, final = 13.2551 0.563606 Force max component initial, final = 9.90335 0.457668 Final line search alpha, max atom move = 0.000302119 0.00013827 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0050366 | 0.0050366 | 0.0050366 | 0.0 | 93.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010562 | 0.00010562 | 0.00010562 | 0.0 | 1.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000268 | | | 4.95 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 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: 52912 ave 52912 max 52912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52912 Ave neighs/atom = 130.97 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 = 7.68732 ghost atom cutoff = 7.68732 binsize = 3.84366, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.68732 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1353.1674 0 -1353.1674 -1486.4623 Loop time of 1.19209e-06 on 1 procs for 0 steps with 404 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 | | 1.192e-06 | | |100.00 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 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: 52920 ave 52920 max 52920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52920 Ave neighs/atom = 130.99 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) = 4.603 | 4.603 | 4.603 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 -1353.1674 -1353.1674 16.599974 99.730388 4.0250331 -1486.4623 -1486.4623 109.90625 -4493.5983 -75.694792 2.6157309 227.16837 Loop time of 1.90735e-06 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4026 ave 4026 max 4026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26460 ave 26460 max 26460 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52920 ave 52920 max 52920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52920 Ave neighs/atom = 130.99 Neighbor list builds = 0 Dangerous builds = 0 404 -1353.16742900219 eV 2.61573092414631 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00