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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -47.812887 0.0000000) to (58.558588 47.812887 9.8982079) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6924100 6.1473712 6.5988053 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -47.812887 0.0000000) to (58.558588 47.812887 9.8982079) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6924100 6.1473712 6.5988053 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -47.812887 0.0000000) to (58.558588 47.812887 9.8982079) create_atoms CPU = 0.003 seconds 1687 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 3319 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_338600200739_000#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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 8.280 | 8.280 | 8.280 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12848.105 0 -12848.105 2602.6421 197 0 -12924.808 0 -12924.808 -3854.0159 Loop time of 17.8078 on 1 procs for 197 steps with 3319 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 = -12848.1049979114 -12924.7969632785 -12924.8078636156 Force two-norm initial, final = 48.876708 0.24204432 Force max component initial, final = 5.0785074 0.073793665 Final line search alpha, max atom move = 0.34896449 0.025751369 Iterations, force evaluations = 197 358 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.26 | 17.26 | 17.26 | 0.0 | 96.93 Neigh | 0.42188 | 0.42188 | 0.42188 | 0.0 | 2.37 Comm | 0.059034 | 0.059034 | 0.059034 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06645 | | | 0.37 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13108.0 ave 13108 max 13108 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: 816130.0 ave 816130 max 816130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816130 Ave neighs/atom = 245.89635 Neighbor list builds = 8 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 197 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.03 | 12.03 | 12.03 Mbytes Step Temp E_pair E_mol TotEng Press Volume 197 0 -12924.808 0 -12924.808 -3854.0159 55427.097 200 0 -12925.153 0 -12925.153 122.36364 55153.346 Loop time of 0.228399 on 1 procs for 3 steps with 3319 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 = -12924.8078636156 -12925.1428424834 -12925.1530442025 Force two-norm initial, final = 233.31674 7.4893911 Force max component initial, final = 159.10601 5.3576739 Final line search alpha, max atom move = 5.0364700e-05 0.00026983764 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22526 | 0.22526 | 0.22526 | 0.0 | 98.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051185 | 0.00051185 | 0.00051185 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002629 | | | 1.15 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13110.0 ave 13110 max 13110 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: 816128.0 ave 816128 max 816128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816128 Ave neighs/atom = 245.89575 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.55 | 11.55 | 11.55 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12925.153 0 -12925.153 122.36364 Loop time of 2.586e-06 on 1 procs for 0 steps with 3319 atoms 193.3% 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 | | 2.586e-06 | | |100.00 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13161.0 ave 13161 max 13161 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: 816782.0 ave 816782 max 816782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816782 Ave neighs/atom = 246.09280 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 11.55 | 11.55 | 11.55 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 -12925.153 -12925.153 58.511241 95.360708 9.8846908 122.36364 122.36364 122.76815 88.897625 155.42515 2.5750865 2247.5914 Loop time of 2.976e-06 on 1 procs for 0 steps with 3319 atoms 235.2% 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 | | 2.976e-06 | | |100.00 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13161.0 ave 13161 max 13161 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 408391.0 ave 408391 max 408391 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 816782.0 ave 816782 max 816782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 816782 Ave neighs/atom = 246.09280 Neighbor list builds = 0 Dangerous builds = 0 3319 -12925.1530442025 eV 2.57508647740015 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19