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 = 3.52401 3.52401 3.52401 Created orthogonal box = (0 -63.8261 0) to (22.5647 63.8261 4.9837) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.05394 5.44827 4.9837 Created 658 atoms create_atoms CPU = 0.000542879 secs 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.05394 5.44827 4.9837 Created 658 atoms create_atoms CPU = 0.000444174 secs 658 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5866.9512 0 -5866.9512 3096.4527 29 0 -5893.8819 0 -5893.8819 -5060.2921 Loop time of 0.297752 on 1 procs for 29 steps with 1304 atoms 100.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5866.95122956 -5893.87662051 -5893.88188267 Force two-norm initial, final = 31.4867 0.242054 Force max component initial, final = 7.22486 0.0244616 Final line search alpha, max atom move = 1 0.0244616 Iterations, force evaluations = 29 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28602 | 0.28602 | 0.28602 | 0.0 | 96.06 Neigh | 0.0066481 | 0.0066481 | 0.0066481 | 0.0 | 2.23 Comm | 0.0031707 | 0.0031707 | 0.0031707 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001913 | | | 0.64 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8464 ave 8464 max 8464 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: 227504 ave 227504 max 227504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227504 Ave neighs/atom = 174.466 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -5893.8819 0 -5893.8819 -5060.2921 14355.205 31 0 -5893.9205 0 -5893.9205 -1974.5405 14330.843 Loop time of 0.0224071 on 1 procs for 2 steps with 1304 atoms 89.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5893.88188267 -5893.9149425 -5893.92054187 Force two-norm initial, final = 49.1644 4.30837 Force max component initial, final = 47.9881 4.18031 Final line search alpha, max atom move = 6.01599e-05 0.000251487 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02162 | 0.02162 | 0.02162 | 0.0 | 96.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019383 | 0.00019383 | 0.00019383 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005932 | | | 2.65 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8480 ave 8480 max 8480 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: 227536 ave 227536 max 227536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227536 Ave neighs/atom = 174.491 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.649 | 5.649 | 5.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5893.9205 0 -5893.9205 -1974.5405 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8480 ave 8480 max 8480 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: 227568 ave 227568 max 227568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227568 Ave neighs/atom = 174.515 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) = 5.649 | 5.649 | 5.649 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 -5893.9205 -5893.9205 22.56321 127.65214 4.9755691 -1974.5405 -1974.5405 467.32471 -6503.8996 112.95352 2.301783 378.83428 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8480 ave 8480 max 8480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113784 ave 113784 max 113784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227568 ave 227568 max 227568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227568 Ave neighs/atom = 174.515 Neighbor list builds = 0 Dangerous builds = 0 1304 -5893.9205418707 eV 2.30178301891632 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00