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 -51.4177 0) to (25.707 51.4177 3.63552) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.11312 4.11312 3.63552 Created 402 atoms create_atoms CPU = 0.000239134 secs 402 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.11312 4.11312 3.63552 Created 402 atoms create_atoms CPU = 0.000110865 secs 402 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 = 9 35 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 = 796 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 = 9 35 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3231.6932 0 -3231.6932 11133.484 18 0 -3254.9046 0 -3254.9046 -1043.6648 Loop time of 3.2561 on 1 procs for 18 steps with 796 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 = -3231.69316241 -3254.90203333 -3254.90459405 Force two-norm initial, final = 33.2959 0.153138 Force max component initial, final = 9.60196 0.0266341 Final line search alpha, max atom move = 1 0.0266341 Iterations, force evaluations = 18 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2546 | 3.2546 | 3.2546 | 0.0 | 99.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085497 | 0.00085497 | 0.00085497 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006015 | | | 0.02 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4963 ave 4963 max 4963 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: 61544 ave 61544 max 61544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61544 Ave neighs/atom = 77.3166 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -3254.9046 0 -3254.9046 -1043.6648 9610.8308 20 0 -3254.9099 0 -3254.9099 -1034.7534 9610.7957 Loop time of 0.473629 on 1 procs for 2 steps with 796 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3254.90459405 -3254.9088408 -3254.90985559 Force two-norm initial, final = 6.21166 1.67173 Force max component initial, final = 5.37444 1.65026 Final line search alpha, max atom move = 0.000181511 0.000299541 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46679 | 0.46679 | 0.46679 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006713 | | | 1.42 Nlocal: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4973 ave 4973 max 4973 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: 61000 ave 61000 max 61000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61000 Ave neighs/atom = 76.6332 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 = 9 35 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) = 4.68 | 4.68 | 4.68 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3254.9099 0 -3254.9099 -1034.7534 Loop time of 9.53674e-07 on 1 procs for 0 steps with 796 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: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4973 ave 4973 max 4973 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: 61032 ave 61032 max 61032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61032 Ave neighs/atom = 76.6734 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) = 4.68 | 4.68 | 4.68 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 -3254.9099 -3254.9099 25.679777 102.83535 3.6393654 -1034.7534 -1034.7534 -274.81731 -2793.5276 -35.915386 2.3594455 207.59027 Loop time of 9.53674e-07 on 1 procs for 0 steps with 796 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: 796 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4973 ave 4973 max 4973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30516 ave 30516 max 30516 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61032 ave 61032 max 61032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61032 Ave neighs/atom = 76.6734 Neighbor list builds = 0 Dangerous builds = 0 796 -2796.07048522462 eV 2.35944552134352 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04