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 = 3.61496 3.61496 3.61496 Created orthogonal box = (0 -56.4711 0) to (28.2337 56.4711 3.61496) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.09133 5.09133 3.61496 Created 489 atoms create_atoms CPU = 0.000310183 secs 489 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.09133 5.09133 3.61496 Created 489 atoms create_atoms CPU = 0.000172853 secs 489 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 = 8.46629 ghost atom cutoff = 8.46629 binsize = 4.23315, bins = 7 27 1 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 8.46629 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 972 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 = 8.46629 ghost atom cutoff = 8.46629 binsize = 4.23315, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.46629 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) = 5.044 | 5.044 | 5.044 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3402.123 0 -3402.123 10570.994 79 0 -3434.7208 0 -3434.7208 522.85954 Loop time of 0.669179 on 1 procs for 79 steps with 972 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 = -3402.12299963 -3434.71783188 -3434.72078941 Force two-norm initial, final = 29.8035 0.174261 Force max component initial, final = 8.01192 0.0351449 Final line search alpha, max atom move = 1 0.0351449 Iterations, force evaluations = 79 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65234 | 0.65234 | 0.65234 | 0.0 | 97.48 Neigh | 0.0056081 | 0.0056081 | 0.0056081 | 0.0 | 0.84 Comm | 0.0075803 | 0.0075803 | 0.0075803 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003653 | | | 0.55 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8805 ave 8805 max 8805 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: 199608 ave 199608 max 199608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199608 Ave neighs/atom = 205.358 Neighbor list builds = 1 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 : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.425 | 5.425 | 5.425 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3434.7208 0 -3434.7208 522.85954 11527.315 80 0 -3434.7217 0 -3434.7217 305.96137 11529.115 Loop time of 0.0152149 on 1 procs for 1 steps with 972 atoms 131.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3434.72078941 -3434.72078941 -3434.72174258 Force two-norm initial, final = 3.52768 2.81102 Force max component initial, final = 2.9449 2.3263 Final line search alpha, max atom move = 0.00033957 0.000789944 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.014666 | 0.014666 | 0.014666 | 0.0 | 96.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017023 | 0.00017023 | 0.00017023 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003786 | | | 2.49 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8855 ave 8855 max 8855 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: 199766 ave 199766 max 199766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199766 Ave neighs/atom = 205.521 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 = 8.46629 ghost atom cutoff = 8.46629 binsize = 4.23315, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.46629 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) = 5.563 | 5.563 | 5.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3434.7217 0 -3434.7217 305.96137 Loop time of 9.53674e-07 on 1 procs for 0 steps with 972 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: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8835 ave 8835 max 8835 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: 199710 ave 199710 max 199710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199710 Ave neighs/atom = 205.463 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) = 5.563 | 5.563 | 5.563 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 -3434.7217 -3434.7217 28.246596 112.9422 3.6138791 305.96137 305.96137 -218.06397 1459.1328 -323.18474 2.3116454 161.01126 Loop time of 9.53674e-07 on 1 procs for 0 steps with 972 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: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8835 ave 8835 max 8835 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99855 ave 99855 max 99855 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199710 ave 199710 max 199710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199710 Ave neighs/atom = 205.463 Neighbor list builds = 0 Dangerous builds = 0 972 -3434.72174257744 eV 2.31164543621474 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00