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 = 3.52 3.52 3.52 Created orthogonal box = (0 -43.1145 0) to (6.09682 43.1145 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.09682 5.74814 4.97803 Created 122 atoms create_atoms CPU = 0.000178814 secs 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.09682 5.74814 4.97803 Created 122 atoms create_atoms CPU = 8.2016e-05 secs 122 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 2 21 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 240 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 2 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 4.498 | 4.498 | 4.498 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1056.5864 0 -1056.5864 12712.974 26 0 -1064.2782 0 -1064.2782 6658.5905 Loop time of 0.0622609 on 1 procs for 26 steps with 240 atoms 96.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1056.58635897 -1064.27727348 -1064.27822545 Force two-norm initial, final = 13.688 0.101842 Force max component initial, final = 4.55998 0.0138428 Final line search alpha, max atom move = 1 0.0138428 Iterations, force evaluations = 26 46 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060509 | 0.060509 | 0.060509 | 0.0 | 97.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011947 | 0.0011947 | 0.0011947 | 0.0 | 1.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005572 | | | 0.89 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4467 ave 4467 max 4467 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: 53528 ave 53528 max 53528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53528 Ave neighs/atom = 223.033 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.498 | 4.498 | 4.498 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -1064.2782 0 -1064.2782 6658.5905 2617.0663 29 0 -1064.2923 0 -1064.2923 1568.6885 2624.5008 Loop time of 0.00931501 on 1 procs for 3 steps with 240 atoms 107.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1064.27822545 -1064.2922799 -1064.29229324 Force two-norm initial, final = 14.0396 0.113095 Force max component initial, final = 10.0487 0.0339572 Final line search alpha, max atom move = 0.00488478 0.000165874 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0086737 | 0.0086737 | 0.0086737 | 0.0 | 93.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001626 | 0.0001626 | 0.0001626 | 0.0 | 1.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004787 | | | 5.14 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4512 ave 4512 max 4512 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: 53136 ave 53136 max 53136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53136 Ave neighs/atom = 221.4 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.1436, bins = 2 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 4.636 | 4.636 | 4.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1064.2923 0 -1064.2923 1568.6885 Loop time of 9.53674e-07 on 1 procs for 0 steps with 240 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: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4512 ave 4512 max 4512 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: 53060 ave 53060 max 53060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53060 Ave neighs/atom = 221.083 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) = 4.636 | 4.636 | 4.636 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 -1064.2923 -1064.2923 6.1048075 86.22908 4.9856408 1568.6885 1568.6885 13.743798 4713.0833 -20.7615 2.3632608 120.18688 Loop time of 9.53674e-07 on 1 procs for 0 steps with 240 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: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4512 ave 4512 max 4512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26530 ave 26530 max 26530 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53060 ave 53060 max 53060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53060 Ave neighs/atom = 221.083 Neighbor list builds = 0 Dangerous builds = 0 240 -1058.88114843713 eV 2.36326076292616 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00