LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.06121 4.06121 4.06121 Created orthogonal box = (0 -49.0759 0) to (60.1005 49.0759 9.9479) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.76306 6.04995 6.63193 Created 1756 atoms create_atoms CPU = 0.00196218 secs 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.76306 6.04995 6.63193 Created 1756 atoms create_atoms CPU = 0.00185013 secs 1756 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 13 21 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 80 atoms, new total = 3432 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 7.904 | 7.904 | 7.904 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9115.6976 0 -9115.6976 -893.37586 82 0 -9219.3626 0 -9219.3626 -11143.385 Loop time of 3.81596 on 1 procs for 82 steps with 3432 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 = -9115.69757293 -9219.35436875 -9219.36262332 Force two-norm initial, final = 23.5678 0.265164 Force max component initial, final = 2.13473 0.014155 Final line search alpha, max atom move = 1 0.014155 Iterations, force evaluations = 82 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7539 | 3.7539 | 3.7539 | 0.0 | 98.37 Neigh | 0.030191 | 0.030191 | 0.030191 | 0.0 | 0.79 Comm | 0.015908 | 0.015908 | 0.015908 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01598 | | | 0.42 Nlocal: 3432 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12421 ave 12421 max 12421 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: 761922 ave 761922 max 761922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 761922 Ave neighs/atom = 222.005 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.905 | 7.905 | 7.905 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -9219.3626 0 -9219.3626 -11143.385 58682.351 94 0 -9222.9318 0 -9222.9318 -1058.1093 57843.523 Loop time of 0.328019 on 1 procs for 12 steps with 3432 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 = -9219.36262332 -9222.93087554 -9222.93176956 Force two-norm initial, final = 627.302 0.626166 Force max component initial, final = 546.741 0.0690554 Final line search alpha, max atom move = 9.82676e-05 6.78591e-06 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32071 | 0.32071 | 0.32071 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014429 | 0.0014429 | 0.0014429 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005863 | | | 1.79 Nlocal: 3432 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12631 ave 12631 max 12631 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: 766538 ave 766538 max 766538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 766538 Ave neighs/atom = 223.35 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 8.044 | 8.044 | 8.044 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9222.9318 0 -9222.9318 -1058.1093 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3432 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 3432 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12689 ave 12689 max 12689 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: 769516 ave 769516 max 769516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 769516 Ave neighs/atom = 224.218 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) = 8.044 | 8.044 | 8.044 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 -9222.9318 -9222.9318 59.442994 98.151781 9.9141589 -1058.1093 -1058.1093 -1.7507534 -3174.4834 1.9062402 2.6403657 2285.1408 Loop time of 2.14577e-06 on 1 procs for 0 steps with 3432 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 3432 ave 3432 max 3432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12689 ave 12689 max 12689 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 384758 ave 384758 max 384758 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 769516 ave 769516 max 769516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 769516 Ave neighs/atom = 224.218 Neighbor list builds = 0 Dangerous builds = 0 3432 -9222.93176956357 eV 2.64036569477836 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04