LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -51.123999 0.0000000) to (25.562000 51.123999 3.6150127) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0899200 4.0899200 3.6150127 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -51.123999 0.0000000) to (25.562000 51.123999 3.6150127) create_atoms CPU = 0.003 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0899200 4.0899200 3.6150127 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -51.123999 0.0000000) to (25.562000 51.123999 3.6150127) create_atoms CPU = 0.002 seconds 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 8 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 796 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_028979335952_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.939 | 4.939 | 4.939 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2601.7483 0 -2601.7483 41845.046 72 0 -2805.2252 0 -2805.2252 -1213.3706 Loop time of 15.6282 on 1 procs for 72 steps with 796 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2601.74827647813 -2805.22242462645 -2805.22518364529 Force two-norm initial, final = 411.86754 0.16303970 Force max component initial, final = 139.89121 0.019530317 Final line search alpha, max atom move = 1.0000000 0.019530317 Iterations, force evaluations = 72 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.585 | 15.585 | 15.585 | 0.0 | 99.72 Neigh | 0.012463 | 0.012463 | 0.012463 | 0.0 | 0.08 Comm | 0.016724 | 0.016724 | 0.016724 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01442 | | | 0.09 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5505.00 ave 5505 max 5505 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105348.0 ave 105348 max 105348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105348 Ave neighs/atom = 132.34673 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.941 | 4.941 | 4.941 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -2805.2252 0 -2805.2252 -1213.3706 9448.426 77 0 -2805.2802 0 -2805.2802 122.28057 9439.3346 Loop time of 0.860156 on 1 procs for 5 steps with 796 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2805.2251836453 -2805.28001683596 -2805.28015517143 Force two-norm initial, final = 24.480587 1.5466241 Force max component initial, final = 24.329245 1.2406323 Final line search alpha, max atom move = 0.00058383691 0.00072432694 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85658 | 0.85658 | 0.85658 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079772 | 0.00079772 | 0.00079772 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002779 | | | 0.32 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5501.00 ave 5501 max 5501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105384.0 ave 105384 max 105384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105384 Ave neighs/atom = 132.39196 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 ghost atom cutoff = 7 binsize = 3.5, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.079 | 5.079 | 5.079 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2805.2802 0 -2805.2802 122.28057 Loop time of 6.475e-06 on 1 procs for 0 steps with 796 atoms 185.3% 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 | | 6.475e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5501.00 ave 5501 max 5501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105508.0 ave 105508 max 105508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105508 Ave neighs/atom = 132.54774 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 ghost atom cutoff = 7 binsize = 3.5, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.079 | 5.079 | 5.079 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 -2805.2802 -2805.2802 25.593271 101.8236 3.6221558 122.28057 122.28057 151.07708 4.7709973 210.99364 2.2939099 195.08921 Loop time of 6.846e-06 on 1 procs for 0 steps with 796 atoms 248.3% 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 | | 6.846e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5501.00 ave 5501 max 5501 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52754.0 ave 52754 max 52754 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105508.0 ave 105508 max 105508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105508 Ave neighs/atom = 132.54774 Neighbor list builds = 0 Dangerous builds = 0 796 -2805.28015517143 eV 2.29390986258934 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17