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 = 3.49194 3.49194 3.49194 Created orthogonal box = (0 -37.2872 0) to (26.3636 37.2872 4.93835) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.01274 5.8869 4.93835 Created 458 atoms create_atoms CPU = 0.000279903 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.01274 5.8869 4.93835 Created 458 atoms create_atoms CPU = 0.000200033 secs 458 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 8 22 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 6.85342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 904 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 4.971 | 4.971 | 4.971 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3943.6629 0 -3943.6629 22857.554 60 0 -3998.13 0 -3998.13 -6545.5194 Loop time of 0.569795 on 1 procs for 60 steps with 904 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3943.66289382 -3998.12641208 -3998.12996828 Force two-norm initial, final = 81.5122 0.245111 Force max component initial, final = 23.7637 0.0325973 Final line search alpha, max atom move = 1 0.0325973 Iterations, force evaluations = 60 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55814 | 0.55814 | 0.55814 | 0.0 | 97.95 Neigh | 0.0057299 | 0.0057299 | 0.0057299 | 0.0 | 1.01 Comm | 0.0036106 | 0.0036106 | 0.0036106 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002313 | | | 0.41 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5158 ave 5158 max 5158 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: 119668 ave 119668 max 119668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119668 Ave neighs/atom = 132.376 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.971 | 4.971 | 4.971 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -3998.13 0 -3998.13 -6545.5194 9709.0181 62 0 -3998.1388 0 -3998.1388 -5520.7657 9703.428 Loop time of 0.0236149 on 1 procs for 2 steps with 904 atoms 84.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3998.12996828 -3998.13826478 -3998.13880164 Force two-norm initial, final = 17.7673 0.254512 Force max component initial, final = 17.5483 0.0353573 Final line search alpha, max atom move = 0.000197287 6.97554e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023098 | 0.023098 | 0.023098 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013542 | 0.00013542 | 0.00013542 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003819 | | | 1.62 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5146 ave 5146 max 5146 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: 120100 ave 120100 max 120100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120100 Ave neighs/atom = 132.854 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 5.109 | 5.109 | 5.109 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3998.1388 0 -3998.1388 -5520.7657 Loop time of 9.53674e-07 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5146 ave 5146 max 5146 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: 120108 ave 120108 max 120108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120108 Ave neighs/atom = 132.863 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) = 5.109 | 5.109 | 5.109 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 -3998.1388 -3998.1388 26.373323 74.574387 4.9336762 -5520.7657 -5520.7657 -4.5299045 -16556.888 -0.87915809 2.308829 739.43196 Loop time of 9.53674e-07 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5146 ave 5146 max 5146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 60054 ave 60054 max 60054 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 120108 ave 120108 max 120108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 120108 Ave neighs/atom = 132.863 Neighbor list builds = 0 Dangerous builds = 0 904 -3998.13880164087 eV 2.30882902720426 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00