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 = 4.04527 4.04527 4.04527 Created orthogonal box = (0 -59.8686 0) to (48.8792 59.8686 9.90885) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0262 5.74043 6.6059 Created 1759 atoms create_atoms CPU = 0.00075078 secs 1759 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0262 5.74043 6.6059 Created 1759 atoms create_atoms CPU = 0.000643015 secs 1759 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 11 26 3 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 47 atoms, new total = 3471 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11775.776 0 -11775.776 133.47538 44 0 -11806.238 0 -11806.238 -2970.8068 Loop time of 1.2937 on 1 procs for 44 steps with 3471 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 = -11775.7757462 -11806.2265066 -11806.237952 Force two-norm initial, final = 27.2295 0.218551 Force max component initial, final = 4.63112 0.0260759 Final line search alpha, max atom move = 1 0.0260759 Iterations, force evaluations = 44 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2812 | 1.2812 | 1.2812 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064023 | 0.0064023 | 0.0064023 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00612 | | | 0.47 Nlocal: 3471 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12746 ave 12746 max 12746 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: 767984 ave 767984 max 767984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 767984 Ave neighs/atom = 221.257 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.79 | 11.79 | 11.79 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -11806.238 0 -11806.238 -2970.8068 57993.076 47 0 -11806.439 0 -11806.439 -250.64606 57793.255 Loop time of 0.0865538 on 1 procs for 3 steps with 3471 atoms 92.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11806.237952 -11806.4368213 -11806.4390165 Force two-norm initial, final = 158.321 0.922545 Force max component initial, final = 123.25 0.659759 Final line search alpha, max atom move = 0.000134686 8.88604e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.084684 | 0.084684 | 0.084684 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003767 | 0.0003767 | 0.0003767 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001493 | | | 1.72 Nlocal: 3471 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12775 ave 12775 max 12775 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: 739610 ave 739610 max 739610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739610 Ave neighs/atom = 213.083 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 11.31 | 11.31 | 11.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11806.439 0 -11806.439 -250.64606 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3471 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: 3471 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12786 ave 12786 max 12786 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: 752840 ave 752840 max 752840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752840 Ave neighs/atom = 216.894 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) = 11.31 | 11.31 | 11.31 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 -11806.439 -11806.439 48.767032 119.73716 9.8974171 -250.64606 -250.64606 -18.248222 -717.15028 -16.539696 2.5220668 2123.9167 Loop time of 3.09944e-06 on 1 procs for 0 steps with 3471 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 | | 3.099e-06 | | |100.00 Nlocal: 3471 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12786 ave 12786 max 12786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 376420 ave 376420 max 376420 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 752840 ave 752840 max 752840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 752840 Ave neighs/atom = 216.894 Neighbor list builds = 0 Dangerous builds = 0 3471 -11806.4390165103 eV 2.5220668357402 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01