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 = 3.58984 3.58984 3.58984 Created orthogonal box = (0 -68.6812 0) to (39.651 68.6812 6.21778) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.85015 5.25403 6.21778 Created 1466 atoms create_atoms CPU = 0.000823021 secs 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.85015 5.25403 6.21778 Created 1466 atoms create_atoms CPU = 0.000683069 secs 1466 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 11 37 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2902 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 6.989 | 6.989 | 6.989 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10138.133 0 -10138.133 3398.3418 80 0 -10177.394 0 -10177.394 -6500.6507 Loop time of 3.81456 on 1 procs for 80 steps with 2902 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10138.133138 -10177.384483 -10177.3941945 Force two-norm initial, final = 51.2082 0.322977 Force max component initial, final = 12.7291 0.0753372 Final line search alpha, max atom move = 1 0.0753372 Iterations, force evaluations = 80 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7549 | 3.7549 | 3.7549 | 0.0 | 98.44 Neigh | 0.038361 | 0.038361 | 0.038361 | 0.0 | 1.01 Comm | 0.011997 | 0.011997 | 0.011997 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009308 | | | 0.24 Nlocal: 2902 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11968 ave 11968 max 11968 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: 443360 ave 443360 max 443360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 443360 Ave neighs/atom = 152.777 Neighbor list builds = 3 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 : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.989 | 6.989 | 6.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -10177.394 0 -10177.394 -6500.6507 33865.522 83 0 -10177.512 0 -10177.512 -3109.7399 33778.884 Loop time of 0.163819 on 1 procs for 3 steps with 2902 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10177.3941945 -10177.5109978 -10177.5124219 Force two-norm initial, final = 121.008 0.338489 Force max component initial, final = 101.652 0.0728998 Final line search alpha, max atom move = 0.000110124 8.02805e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16187 | 0.16187 | 0.16187 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004375 | 0.0004375 | 0.0004375 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001513 | | | 0.92 Nlocal: 2902 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11977 ave 11977 max 11977 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: 443264 ave 443264 max 443264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 443264 Ave neighs/atom = 152.744 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 6.746 | 6.746 | 6.746 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10177.512 0 -10177.512 -3109.7399 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2902 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 | | 2.146e-06 | | |100.00 Nlocal: 2902 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11984 ave 11984 max 11984 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: 460916 ave 460916 max 460916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460916 Ave neighs/atom = 158.827 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) = 6.746 | 6.746 | 6.746 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 -10177.512 -10177.512 39.576511 137.36241 6.2135513 -3109.7399 -3109.7399 -0.75771223 -9326.8846 -1.577429 2.3348148 1116.8988 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2902 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 | | 2.146e-06 | | |100.00 Nlocal: 2902 ave 2902 max 2902 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11984 ave 11984 max 11984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230458 ave 230458 max 230458 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 460916 ave 460916 max 460916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460916 Ave neighs/atom = 158.827 Neighbor list builds = 0 Dangerous builds = 0 2902 -10177.5124219046 eV 2.33481481723027 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04