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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -34.564504 0.0000000) to (42.329196 34.564504 7.0063784) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0589640 4.2610246 4.6709189 Created 879 atoms using lattice units in orthogonal box = (0.0000000 -34.564504 0.0000000) to (42.329196 34.564504 7.0063784) create_atoms CPU = 0.001 seconds 879 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0589640 4.2610246 4.6709189 Created 879 atoms using lattice units in orthogonal box = (0.0000000 -34.564504 0.0000000) to (42.329196 34.564504 7.0063784) create_atoms CPU = 0.001 seconds 879 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 18 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 33 atoms, new total = 1725 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.564 | 5.564 | 5.564 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7280.3455 0 -7280.3455 -9596.7864 287 0 -7504.5588 0 -7504.5588 -30117.307 Loop time of 6.98511 on 1 procs for 287 steps with 1725 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 = -7280.3454724675 -7504.55205137479 -7504.55876303471 Force two-norm initial, final = 58.615404 0.39443733 Force max component initial, final = 7.6425361 0.10747392 Final line search alpha, max atom move = 0.25664186 0.027582305 Iterations, force evaluations = 287 534 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7213 | 6.7213 | 6.7213 | 0.0 | 96.22 Neigh | 0.19333 | 0.19333 | 0.19333 | 0.0 | 2.77 Comm | 0.034897 | 0.034897 | 0.034897 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03555 | | | 0.51 Nlocal: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7620.00 ave 7620 max 7620 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: 278948.0 ave 278948 max 278948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278948 Ave neighs/atom = 161.70899 Neighbor list builds = 11 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 287 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.566 | 5.566 | 5.566 Mbytes Step Temp E_pair E_mol TotEng Press Volume 287 0 -7504.5588 0 -7504.5588 -30117.307 20501.892 304 0 -7509.434 0 -7509.434 690.95394 20226.032 Loop time of 0.257485 on 1 procs for 17 steps with 1725 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 = -7504.55876303471 -7509.43263208841 -7509.43395270282 Force two-norm initial, final = 691.37163 12.985124 Force max component initial, final = 639.22149 9.0007235 Final line search alpha, max atom move = 0.0013699688 0.012330710 Iterations, force evaluations = 17 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25037 | 0.25037 | 0.25037 | 0.0 | 97.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010904 | 0.0010904 | 0.0010904 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006023 | | | 2.34 Nlocal: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7572.00 ave 7572 max 7572 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: 279022.0 ave 279022 max 279022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279022 Ave neighs/atom = 161.75188 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.704 | 5.704 | 5.704 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7509.434 0 -7509.434 690.95394 Loop time of 2.106e-06 on 1 procs for 0 steps with 1725 atoms 142.5% 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 | | 2.106e-06 | | |100.00 Nlocal: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7659.00 ave 7659 max 7659 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: 280918.0 ave 280918 max 280918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280918 Ave neighs/atom = 162.85101 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 11 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.704 | 5.704 | 5.704 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 -7509.434 -7509.434 42.411836 69.129008 6.8986368 690.95394 690.95394 -714.37155 3466.8253 -679.59191 2.2929283 9132.8012 Loop time of 1.871e-06 on 1 procs for 0 steps with 1725 atoms 160.3% 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 | | 1.871e-06 | | |100.00 Nlocal: 1725.00 ave 1725 max 1725 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7659.00 ave 7659 max 7659 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140459.0 ave 140459 max 140459 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 280918.0 ave 280918 max 280918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280918 Ave neighs/atom = 162.85101 Neighbor list builds = 0 Dangerous builds = 0 1725 -7509.43395270282 eV 2.29292828758986 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07