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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -47.958396 0.0000000) to (16.955853 47.958396 5.1123821) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1657649 5.4498177 5.1123821 Created 349 atoms using lattice units in orthogonal box = (0.0000000 -47.958396 0.0000000) to (16.955853 47.958396 5.1123821) create_atoms CPU = 0.003 seconds 349 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1657649 5.4498177 5.1123821 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -47.958396 0.0000000) to (16.955853 47.958396 5.1123821) create_atoms CPU = 0.002 seconds 357 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 6 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 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 704 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_179025990738_005#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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2465.7342 0 -2465.7342 6893.8223 35 0 -2473.3238 0 -2473.3238 5058.7286 Loop time of 0.526531 on 1 procs for 35 steps with 704 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 = -2465.73416633073 -2473.32287012354 -2473.32379242361 Force two-norm initial, final = 12.547040 0.054102177 Force max component initial, final = 2.0951454 0.0048060027 Final line search alpha, max atom move = 1.0000000 0.0048060027 Iterations, force evaluations = 35 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.51208 | 0.51208 | 0.51208 | 0.0 | 97.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0076388 | 0.0076388 | 0.0076388 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006815 | | | 1.29 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4208.00 ave 4208 max 4208 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: 60822.0 ave 60822 max 60822 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60822 Ave neighs/atom = 86.394886 Neighbor list builds = 0 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.546 | 4.546 | 4.546 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -2473.3238 0 -2473.3238 5058.7286 8314.5281 43 0 -2473.5303 0 -2473.5303 103.7043 8340.6601 Loop time of 0.0730627 on 1 procs for 8 steps with 704 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 = -2473.3237924236 -2473.53003835733 -2473.53025902439 Force two-norm initial, final = 63.515018 1.0015538 Force max component initial, final = 61.589225 0.65050306 Final line search alpha, max atom move = 0.00091557552 0.00059558468 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068569 | 0.068569 | 0.068569 | 0.0 | 93.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097031 | 0.00097031 | 0.00097031 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003523 | | | 4.82 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4489.00 ave 4489 max 4489 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: 60576.0 ave 60576 max 60576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60576 Ave neighs/atom = 86.045455 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.684 | 4.684 | 4.684 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2473.5303 0 -2473.5303 103.7043 Loop time of 6.235e-06 on 1 procs for 0 steps with 704 atoms 128.3% 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 | | 6.235e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4489.00 ave 4489 max 4489 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: 60448.0 ave 60448 max 60448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60448 Ave neighs/atom = 85.863636 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.684 | 4.684 | 4.684 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 -2473.5303 -2473.5303 16.940885 96.605473 5.0963893 103.7043 103.7043 99.587715 125.85381 85.671369 2.4732861 214.12515 Loop time of 7.217e-06 on 1 procs for 0 steps with 704 atoms 235.6% 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 | | 7.217e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4489.00 ave 4489 max 4489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30224.0 ave 30224 max 30224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 60448.0 ave 60448 max 60448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60448 Ave neighs/atom = 85.863636 Neighbor list builds = 0 Dangerous builds = 0 704 -2473.53025902439 eV 2.47328609111925 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01