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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -44.2317 0) to (22.114 44.2317 3.63552) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.18373 4.18373 3.63552 Created 298 atoms create_atoms CPU = 0.000188112 secs 298 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.18373 4.18373 3.63552 Created 298 atoms create_atoms CPU = 5.6982e-05 secs 298 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 8 30 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 588 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.487 | 4.487 | 4.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2387.3478 0 -2387.3478 9481.7517 18 0 -2402.8249 0 -2402.8249 -2091.1947 Loop time of 2.38706 on 1 procs for 18 steps with 588 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 = -2387.34784582 -2402.82294693 -2402.82491868 Force two-norm initial, final = 26.8047 0.130712 Force max component initial, final = 8.54581 0.0254457 Final line search alpha, max atom move = 1 0.0254457 Iterations, force evaluations = 18 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.386 | 2.386 | 2.386 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064564 | 0.00064564 | 0.00064564 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000458 | | | 0.02 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3468 ave 3468 max 3468 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: 45332 ave 45332 max 45332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45332 Ave neighs/atom = 77.0952 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 : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.487 | 4.487 | 4.487 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -2402.8249 0 -2402.8249 -2091.1947 7112.0965 21 0 -2402.8311 0 -2402.8311 -1195.3183 7107.5906 Loop time of 0.561903 on 1 procs for 3 steps with 588 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2402.82491868 -2402.83110538 -2402.83113561 Force two-norm initial, final = 8.26802 0.533072 Force max component initial, final = 8.15702 0.502546 Final line search alpha, max atom move = 0.00175797 0.000883464 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56136 | 0.56136 | 0.56136 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012207 | 0.00012207 | 0.00012207 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004251 | | | 0.08 Nlocal: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3492 ave 3492 max 3492 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: 45008 ave 45008 max 45008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45008 Ave neighs/atom = 76.5442 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.625 | 4.625 | 4.625 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2402.8311 0 -2402.8311 -1195.3183 Loop time of 1.90735e-06 on 1 procs for 0 steps with 588 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: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3492 ave 3492 max 3492 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: 45016 ave 45016 max 45016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45016 Ave neighs/atom = 76.5578 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) = 4.625 | 4.625 | 4.625 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 -2402.8311 -2402.8311 22.078769 88.463332 3.6390184 -1195.3183 -1195.3183 -113.1023 -3447.4619 -25.390849 2.3590667 204.32875 Loop time of 9.53674e-07 on 1 procs for 0 steps with 588 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: 588 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3492 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22508 ave 22508 max 22508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 45016 ave 45016 max 45016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 45016 Ave neighs/atom = 76.5578 Neighbor list builds = 0 Dangerous builds = 0 588 -2063.88949015917 eV 2.35906665146782 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03