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 = 3.6150004 3.6150004 3.6150004 Created orthogonal box = (0.0000000 -71.573356 0.0000000) to (43.829550 71.573356 8.8549063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0687235 5.1123825 5.9032709 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.573356 0.0000000) to (43.829550 71.573356 8.8549063) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0687235 5.1123825 5.9032709 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.573356 0.0000000) to (43.829550 71.573356 8.8549063) create_atoms CPU = 0.003 seconds 2358 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 14 45 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 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 4698 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_762798677854_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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 14 45 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 6.645 | 6.645 | 6.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15785.367 0 -15785.367 61579.2 67 0 -16476.362 0 -16476.362 4456.8226 Loop time of 2.33984 on 1 procs for 67 steps with 4698 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 = -15785.3671237829 -16476.3504817025 -16476.3623951421 Force two-norm initial, final = 2175.9197 0.26657853 Force max component initial, final = 362.05805 0.023376977 Final line search alpha, max atom move = 1.0000000 0.023376977 Iterations, force evaluations = 67 121 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2431 | 2.2431 | 2.2431 | 0.0 | 95.87 Neigh | 0.060101 | 0.060101 | 0.060101 | 0.0 | 2.57 Comm | 0.013711 | 0.013711 | 0.013711 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02289 | | | 0.98 Nlocal: 4698.00 ave 4698 max 4698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11260.0 ave 11260 max 11260 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: 403296.0 ave 403296 max 403296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403296 Ave neighs/atom = 85.844189 Neighbor list builds = 2 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 14 45 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.645 | 6.645 | 6.645 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -16476.362 0 -16476.362 4456.8226 55556.178 72 0 -16476.862 0 -16476.862 -34.909075 55726.875 Loop time of 0.139884 on 1 procs for 5 steps with 4698 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 = -16476.3623951422 -16476.8585961733 -16476.8620813276 Force two-norm initial, final = 302.71130 6.7361729 Force max component initial, final = 267.85473 5.4440105 Final line search alpha, max atom move = 3.1984376e-05 0.00017412328 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13467 | 0.13467 | 0.13467 | 0.0 | 96.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069471 | 0.00069471 | 0.00069471 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004518 | | | 3.23 Nlocal: 4698.00 ave 4698 max 4698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11244.0 ave 11244 max 11244 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: 403392.0 ave 403392 max 403392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403392 Ave neighs/atom = 85.864623 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 14 45 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 6.783 | 6.783 | 6.783 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16476.862 0 -16476.862 -34.909075 Loop time of 1.965e-06 on 1 procs for 0 steps with 4698 atoms 152.7% 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 | | 1.965e-06 | | |100.00 Nlocal: 4698.00 ave 4698 max 4698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11244.0 ave 11244 max 11244 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: 403164.0 ave 403164 max 403164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403164 Ave neighs/atom = 85.816092 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 14 45 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 6.783 | 6.783 | 6.783 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 -16476.862 -16476.862 43.809162 143.75346 8.84874 -34.909075 -34.909075 -156.44531 -50.15907 101.87716 2.1507289 1535.9414 Loop time of 2.286e-06 on 1 procs for 0 steps with 4698 atoms 218.7% 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 | | 2.286e-06 | | |100.00 Nlocal: 4698.00 ave 4698 max 4698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11244.0 ave 11244 max 11244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 201582.0 ave 201582 max 201582 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 403164.0 ave 403164 max 403164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403164 Ave neighs/atom = 85.816092 Neighbor list builds = 0 Dangerous builds = 0 4698 -16476.8620813276 eV 2.15072891011366 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03